Salinity Tolerance in Plants -

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About the Special Issue Editor Jose Antonio Hernández Cortés is a Senior Researcher at the Spanish National Research Council (CSIC) in Murcia (CEBAS, Spain). He has worked in CEBAS-CSIC since 1988, and received a permanent position in 2000. During the years 1992–1995 he made a stay at the ENSAT (Toulouse, France) under the supervision of Dr. Claudine Balagué, and he worked in the isolation and characterization of genes encoding for ACC oxidase in melon plants. Later, in 1997, he worked in John Innes Centre (Norwich, England) under the supervision of Prof. Phil Mullineaux on the effect of high light stress in antioxidant metabolism in peas plants. He works in the fields of Plant Physiology and Biochemistry in different subjects, such as salinity, seed biology, antioxidant metabolism, and redox signaling. Since 2008, Dr. Hernandez has been part of the Fruit Biotechnology Group of the Plant Breeding Department at CEBAS-CSIC. In this group, he has studied the response of fruit trees to abiotic (salinity and drought) and biotic stresses (plum pox virus infection) in fruit trees. In the past 2–3 years, Dr. Hernandez has been working in the physiological and biochemical characterization of peach bud dormancy, studying the evolution of sugar and starch contents, hormonal profiles, and antioxidant metabolism. ix International Journal of Molecular Sciences Editorial Salinity Tolerance in Plants: Trends and Perspectives Jose Antonio Hernández Group of Fruit Trees Biotechnology, Dept. Plant Breeding, CEBAS-CSIC, Campus Universitario de Espinardo, 25, 30100 Murcia, Spain; [email protected]; Tel.: +34-968-396-200 Received: 30 April 2019; Accepted: 14 May 2019; Published: 15 May 2019 Salinity stress is one of the more prevailing abiotic stresses which results in significant losses in agricultural crop production, particularly in arid and semi-arid areas. According to FAO, around 800 million hectares of land are affected by salinity worldwide. Therefore, it is of vital importance to know the mechanisms of salinity tolerance in order to obtain plants with a better response to this abiotic stress. At the same time, it is necessary to achieve these objectives with sustainable agricultural practices that allow obtaining more productive crops under a future scenario of climate change. The first symptoms from the early hours until a few days later associated with saline stress are displayed in the roots by suffering an osmotic stress associated with the accumulation of phytotoxic ions. In the long term, salinity induces ion toxicity due to a nutrient imbalance in the cytosol. In addition, salt stress is also manifested as an oxidative stress at the subcellular level, mediated by reactive oxygen species (ROS) [1]. All these responses to salinity contribute to deleterious effects on plants, although there are tolerant plants to NaCl that can implement a series of adaptations to acclimate to salinity that can help their survival. These adaptation mechanisms include morphological, physiological, biochemical, and molecular changes [1]. The majority of research on salt tolerance in plants in this Special Issue is focused on determining which genes are involved in the molecular mechanisms of tolerance. Likewise, there are also an important number of works using transgenic plants in order to get a better response to salinity. 1. Transcriptomic and Genomic Approaches Transcriptome sequencing may provide a functional view of the plant resistance mechanisms to salt stress. Wang et al. [2] performed a transcriptome analysis of short-term acclimation (for 24 h) in the algae Chlamydomonas reinhardtii to salt stress (200 mM NaCl) [2]. The authors identified 10,635 unigenes as differentially expressed in C. reinhardtii under salt stress by RNA-seq, including 5920 that were up-regulated and 4715 that were down-regulated. Using GO (gene onthology) terms, MapMan, and KEGG (Kyoto Encyclopedia of Genes and Genomes) functional enrichment analyses, the potential mechanisms for responses to salt stress were identified [2]. These analyses reported that lipid homeostasis and the regulation of phosphatidic acid acetate levels had a key role in improving tolerance to salt stress, and use as an alternative source of energy for solving the impairment of photosynthesis and the enhancement of glycolysis metabolism [2]. By using also C. reinhardtii as an experimental organism, [3] evaluated the role of the basic leucine-region zipper (bZIP) transcription factors (TFs) in response to salt stress [3]. They identified, using a genome-wide analysis, 17 C. reinhardtii bZIP (CrebZIP) TFs containing typical bZIP structure, as well as the CrebZIP gene structures and their chromosomal assignment were also analysed [3]. The expression profiling of CrebZIP genes by qRT-PCR indicated that six CrebZIPs might be involved in stress response and lipid accumulation. The authors also concluded that CrebZIPs TFs may play important roles in mediating photosynthesis, as suggested by the reported reduced chlorophyll content and Fv/Fm, and the increased NPQ, carotenoid, and oil contents which could be interpreted as adaptive mechanisms to salt stress [3]. Int. J. Mol. Sci. 2019, 20, 2408; doi:10.3390/ijms20102408 1 www.mdpi.com/journal/ijms Int. J. Mol. Sci. 2019, 20, 2408 Wu et al. [4] sequenced the flax (Linum usitatissimum L.) transcriptome to identify differentially-expressed unigenes (DEUs) under NaCl stress [4]. After the results of the flax transcriptome were confirmed using qRT-PCR, a large-scale analysis of expressed sequence tag-derived simple sequence repeat (EST-SSRs) markers was conducted using public resources in order to understand the functions of the identified genes. The authors identified 33,774 significant DEUs (18,040 up-regulated and 15,734 down-regulated) [4]. The functional categories of the DEUs were mostly assigned as signal transduction of plant hormones, photosynthesis-antenna proteins, and biosynthesis of amino acids, which are important in flax responses to NaCl exposure [4]. They also identified a number of DEUs homologous to known plant transcription factors that regulate abiotic stress responses, such as bZIP, HD-ZIP, NAC, MYB, GATA, CAMTA, and B3. The authors also suggested an important role of the bZIP TFs in the response to salinity [4]. Grapevine (Vitis vinifera) is an economically important fruit crop. This fact makes the search for salt-tolerant genotypes a relevant issue. Recently, next-generation sequencing (NGS) technology based on high throughput RNA-Seq technology has been extensively used to unveil and compare the transcriptome profile under abiotic stresses [5], which provides large-scale data to identify and characterize the differentially-expressed genes DEGs. Guan et al. [6] carried out the transcriptomic sequencing of cDNA generated from both control and salt-treated grapevine leaf samples [6]. The GO and KEGG analyses of DEGs in response to salt stress suggested that many genes were involved in various defense-related biological pathways, including ROS scavenging, ion transport, heat shock proteins (HSPs), pathogenesis-related proteins (PRs), and hormone signaling. Furthermore, many DEGs encoded for TFs and essential regulatory proteins involved in signal transduction by regulating genes associated with salinity in grapevine [6]. The authors also observed that salinity negatively affected all gas exchange parameters. The analysis of antioxidant enzymes showed that at short-term (up to 60 h) salinity significantly increased the superoxide dismutase, peroxidase, catalase, and glutathione S-transferase activities in grapevine leaves, suggesting that salt stress induced an oxidative stress. Regarding the ion contents, they showed that Cl- accumulated in the roots more than in the leaves [6], and this response can be considered as an adaptive mechanism limiting the accumulation of these ions in the canopy [1]. Finally, the authors proposed four genes as candidates as potential markers of salt stress (nonspecific lipid-transfer protein, LTP; proline-rich cell wall protein-like, PRPs; glutathione transferase-like, GST; photosystem II reaction center protein, with the aim of explore new approaches to applying the gene information in genetic engineering and breeding purposes [6]. Yu et al. [7] performed a genome-wide association study (GWAS) of salt-tolerance-related phenotypes in rice during the germination stage, in order to identify candidate genes related to salt tolerance [7]. In that regard, they characterized 17 genes that may contribute to salt tolerance during the seed germination stage, which contained highly associated SNPs (single-nucleotide polymorphisms)/indels whiting the coding region. Among these genes, OSMADS31 is involved in floral organ specification as well as in plant growth and development. OSHAK11 coded for a high-affinity K+ uptake transporter, significantly induced by salt-stress and K+ starvation. AGOs play important roles in the regulation of development and stress responses. OsPIN is encoded for an auxin efflux carrier protein, and is involved in the root elongation growth and lateral root formation. Germin family proteins, is involved in plant cell defense and diseases. Finally, SAP (A20/AN1 zinc finger containing proteins) and zinc-induced facilitator-like (ZIFL) family genes are involved in the regulation of stress signaling in plants [7]. Using the same approach (GWAS mapping), Dilnur et al. [8] revealed nine SNP-rich regions significantly associated with plant performance parameters [the relative fresh weight (RFW), the relative stem length (RSL), the relative water content (RWC)] and the comprehensive index of salt tolerance (CIST) in 215 accessions of Asiatic cotton (Gossypium arboretum L.) grown in the absence or the presence of 150 mM NaCl [8]. The analysis showed that most of SNPs which related positively to salt tolerance indicators (RFW, RSL, and RWC) were on chromosome 7. Moreover, most of SNPs related negatively to salt tolerance indicators (relative electric conductivity and relative methylene 2 Int. J. Mol. Sci. 2019, 20, 2408 dioxyamphetamine content,) were on chromosome 3 [8]. In the mentioned SNP-rich region, the authors identified candidate genes possibly associated with salt tolerance in G. arboreum, suggesting that this information could provide essential knowledge which would be very useful to the breeder in order to produce new salt tolerant cotton cultivars [8]. 2. Transgenic Strategy The use of transgenic plants to study the response to salinity is a strategy widely addressed in numerous research groups for many years. The homolog of More Axillary Branches 2 (MAX2) encodes for a key component in the strigolactones (SL) signalling pathway. The overexpression of MAX2 from Sapium sebiferum (SsMAX2) in Arabidopsis plants significantly promoted resistance to different abiotic stresses (drought, osmotic, and salinity) [9]. The authors showed that the protein MAX2 potentially influences chlorophyll metabolism, anthocyanin biosynthesis, soluble sugars, and proline accumulation. The physiological and biochemical analyses demonstrated that SsMAX2 plays a pivotal role in the regulation of redox homeostasis via the regulation of antioxidative enzymes. In this sense, a potential interaction between SL and abscisic acid (ABA) in the adaptation to abiotic was suggested [9]. Rice nucleolin protein (OsNUC1), consisting of two isoforms, OsNUC1-L and OsNUC1-S, is a multifunctional protein involved in salt-stress tolerance. The overexpression of OsNUC1-S gene improved rice productivity under saline conditions, which correlated with a better behaviour of gas exchange parameters (net photosynthesis, stomatal conductance, and transpiration rate) and higher carotenoids contents [10]. Rho-like GTPases (ROPs) from plants are a subfamily of small GTP-binding proteins crucial for plant survival when subjected to abiotic stress. Miao et al. [11] described a novel ROP gene from banana (MaROP5g) whose overexpression increased the tolerance to salt stress in transgenic Arabidopsis thaliana plants. This response was related to minor injury in the plasmatic membrane, as has been shown by reduced lipid peroxidation and electrolyte leakage values. It was also related to an increase in the cytosolic K+ /Na+ ratio and the Ca2+ concentration. In addition, the MaROP5g overexpression up-regulated the salt overly sensitive (SOS)-pathway genes and several genes encoding calcium-signalling pathway proteins, including calcineurin B-like (CBL) proteins, CBL-interacting protein kinases (CIPKs), and calcium-dependent protein kinases (CDPKs) [12]. Bernal-Vicente et al. [13] studied the response to salt stress of a transgenic plum line (J8-1) harbouring four copies of the cytosolic ascorbate peroxidase gene (cytapx) from pea. The authors reported that this plum line was more tolerant to salinity stress in terms of plant growth, chlorophyll contents, chlorophyll fluorescence parameters, and root water contents. In addition, they proposed a connection between the salicylic acid and cyanogenic glucoside (CNglcs) biosynthetic pathways under salt-stress conditions [13]. The overexpression of the cucumber TGase (transglutaminase) gene from Cucumis sativus L. (CsTGase) in tobacco effectively ameliorated salt-induced photoinhibition by increasing the levels of polyamines (PAs) in the chloroplast as well as gas exchange and chlorophyll fluorescence parameters, along with greater abundance of D1 and D2 proteins under saline conditions [14]. In addition, TGase overexpression resulted in chloroplasts that showed more quantity and size of grana compared with wild type plants, suggesting a role of TGase in the chloroplast development. Thus, overexpression of TGase may be an effective strategy for enhancing resistance to salt stress in crops especially sensitive for agronomic production [14]. 3. Physiological and Biochemical Mechanisms Zhang et al. [15] presented a review about the physiological and molecular responses of Populus sp. to salinity. Poplars are used as a model species to study physiological and molecular responses of trees to NaCl stress, taken into account that salinity is one of the limiting factors of afforestation programs. The authors compared the response of salt-tolerant and salt-sensitive Populus species in terms of salinity injury (plant growth, photosynthesis) and primary salt-tolerance mechanisms (ion 3 Int. J. Mol. Sci. 2019, 20, 2408 homeostasis, accumulation of soluble osmolytes), with reactive oxygen species (ROS) and reactive nitrogen species (RNS) metabolism and signaling networks induced by salinity, and they identified candidate genes for improving salt tolerance in the Populus sp. 4. Biostimulants and Salt-Stress Response 4.1. Biostimulants The use of biostimulants is another strategy addressed to overcome the negative effects of salinity. Zhan et al. [16] presented an excellent review about the effect of melatonin in the plant response to salinity. They described the effects of exogenous melatonin in the modulation of the expression of genes involved in melatonin metabolism, the increase of the transcript levels of different stress-responsive genes, and transcription factors involved in the ROS scavenging and of the genes responsible for the maintenance of ion homeostasis. Melatonin also regulates hormone metabolism by up-regulation of gibberellic acid (GA) biosynthesis and abscisic acid (ABA) catabolism genes [16]. Finally, the authors described the identification of a plant melatonin receptor in Arabidopsis [17]. These finding opens new perspectives of research on the role of melatonin in response to abiotic stresses in general, and to salinity in particular. Related to the previous revision, Zhao et al. [18] described that the treatment of Brassica napus L. seedlings with melatonin and NO-releasing compounds such as sodium nitroprusside (SNP), diethylamine NONOate (NONOate), and S-nitrosoglutathione (GSNO) produced synergistic effects that counteracted the seedling growth inhibition induced by NaCl exposure. At the same time, such treatments re-established the redox and ion homeostasis, by decreasing the ROS and lipid peroxidation accumulation as well as the Na+ /K+ ratio. The addition of PTIO (a NO-scavenger) impaired the coupled response of melatonin and SNP, suggesting that NO is required to potentiate the effects of melatonin in protecting plants from salt stress [18]. Chen et al. (2018) [19] studied the salt-stress response of Apocynum venetum L plants, used in traditional Chinese medicine. The authors studied the changes in photosynthetic pigments, osmolytes, lipid peroxidation, some antioxidant enzymes, and ascorbic acid. By using UFLC-QTRAP-MS/MS technology a total of 43 bioactive constituents, including amino acids, nucleosides, organic acids, and flavonoids were successfully identified to change in response to salt stress. They applied a multivariate statistical analysis to evaluate the quality of Apocynum venetum L plants grown under saline conditions [19]. 4.2. Plant Hormones The role of root ABA (including ABA translocation from root to leaf) in the protection of photosystems and photosynthesis against salt stress was studied in Jerusalem artichoke [20]. In this study, the pretreatment of Jerusalem artichoke plants with sodium tungstate (a specific ABA synthesis inhibitor) followed by exposure to salt stress (150 mM NaCl) induced a drastic overaccumulation of Na+ in leaves. Moreover, a decline in net photosynthesis, ØPSII (actual photochemical efficiency of photosystem II) and Fv/Fm (the maximal photosystem II (PSII) quantum yield) was produced, indicating photoinhibition of PSII, along with the establishment of an oxidative stress due to an increase in H2 O2 and lipid peroxidation levels. These results suggest that root ABA can participate in protecting PSII against photoinhibition in Jerusalem artichoke under salt stress, likely via a reduction of Na+ toxicity. In that regard, it has been reported that Na+ can irreversibly inactivate PSII and PSI by inducing secondary oxidative injury or through direct damage on photosynthetic proteins [21,22]. This finding was corroborated by immunoblotting analysis, where a decline in the PSII reaction center protein (PsbA) abundance was observed [20]. 4.3. Protein Kinases, ROS, and Ion Homeostasis Szymanska et al. [23] and Zhang et al. [24] described the involvement of different protein kinases families in the regulation of plant adaptation to salt stress [23,24]. Specifically, Szymanska et al. [23] 4 Int. J. Mol. Sci. 2019, 20, 2408 showed that the SNF1-related protein kinases (SnRK2.4 and SnRK2.10) have a role in the modulation of ROS homeostasis in response to salinity by regulating the expression of several genes related to ROS generation and scavenging in Arabidopsis. Zhang et al. [24] described the importance of CDPKs (Ca2+ -dependent protein kinases) in the adaptation of Arabidopsis to salt stress. In that regard, they reported that the CPK12-RNA interference (RNAi) mutant was more sensitive to salinity than the wild-type plants in terms of seedling growth. This response seemed to be related to the accumulation of phytotoxic ions in the roots as well as the overgeneration of H2 O2 in the CPK12-RNAi mutants [24]. Regarding the effect of salt stress in ion homeostasis, Ali et al. [25] provided a brief overview of the role of the high-affinity potassium-type transporter 1 (HKT1) and their importance in different plant species under salt stress. HKT1-type transporters play a crucial role in Na+ homeostasis, being of pivotal importance to maintain an optimal K+ /Na+ balance in the cytoplasm in response to salt stress for plant survival. The authors described the role of HKT1-type transporters and their functional differences in glycophytes and halophytes [25]. Luo et al. [26] showed that Arabidopsis plants overexpressing a SKn-type dehydrin from Capsicum annuum L. (CaDHN5) resulted an increased tolerance to salt and osmotic stress, suggesting an important role for CaDHN5 in response to the mentioned abiotic stresses [26]. In addition, using VIGS (virus-induced gene silencing) technique, the authors reported that knockdown of the CaDHN5 gen suppressed the expression of manganese superoxide dismutase (MnSOD) and peroxidase (POD) genes in transformed pepper plants [26]. These changes caused a higher oxidative stress in the VIGS lines than in control pepper plants under NaCl or osmotic stress conditions, as observed by the data of some stress-oxidative parameters (superoxide accumulation, lipid peroxidation, and electrolyte leakage), chlorophyll levels, and the rate of water loss. The results demonstrated an important role for the CaDHN5 gene in the tolerance of plants to salt and osmotic stresses as well as in the salt and osmotic stress signalling pathways [26]. The results also indicated that CaDHN5 positively regulates the expression of the MnSOD and POD genes, but also other stress-related genes, including AtSOD1 (encoding a H+ /Na+ plasma membrane antiporter), AtDREB2A (a transcription factor in the ABA signalling pathway), and AtRSA1 and AtRITF1 genes that regulate the transcription of several ROS scavenging-related genes and the AtSOS1 gene [26]. 5. Proteomic Approach The isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic technique was used to identify the differentially-expressed proteins in leaves of two rice genotypes that differ in their tolerance to salt stress [27]. The iTRAQ protein profiling identified in both rice genotypes revealed that the differentially-expressed proteins were mainly involved in the regulation of salt-stress responses, in oxidation-reduction responses, in photosynthesis, and in carbohydrate metabolism. Regarding their subcellular localization, most of them were predicted to localize in cytoplasm and chloroplasts (67.2% of the total up-regulated proteins) [27]. 6. Conclusions and Outlook Salinity is one of the major factors that limits geographical distribution of plants and adversely affects crop productivity and quality worldwide. Salinization affects about 30% of the irrigated land of the world, increasing this area approximately 1–2% per year due to salt-affected land surfaces (FAO, 2014). In Europe, about 3 million hectares of the land are affected by salinization. Unfortunately, this situation will worsen in a context of climate change, where there will be an overall increase in temperature and a decrease in average annual rainfall worldwide. Although an important part of the studies on response to salinity are carried out with Arabidopsis plants, nowadays the use of other species with agronomic interest is also remarkable, including woody plants. 5 Int. J. Mol. Sci. 2019, 20, 2408 Studies on salinity tolerance have focused on different points of view: agronomic, physiological, biochemical, and molecular. However, in recent years, the number of works that address tolerance to salinity from a molecular point of view has increased considerably, in order to search for candidate genes that may be useful to the search for resistant genotypes. The identification of the candidate genes would provide valuable information about the molecular and genetic mechanisms involved in the salt tolerance response, and it would also supply important resources to the breeding programs in order to look for salt tolerance in crop plants. Therefore, obtaining salt-tolerant species is one of the goals for breeders, and probably, the use of transformed plants could improve the salt response in crop plants. In this way, transformed plants with enhanced antioxidant defenses have been obtained in different laboratories, and, in most cases, these plants displayed an improved salt-tolerance response. The overexpression of certain proteins can afford protection against salt stress in plants. In this Special Issue, the author shows that the overexpression of certain transgenes improved the response to salinity in plants in terms of photosynthesis rate, improved the gas exchange parameters, and increased photosynthetic pigments, antioxidant mechanisms, and accumulation of anthocyanins, as well as improved ion homeostasis responses, up-regulation of ABA biosynthesis genes, and plant hormone signaling. However, the use of transgenic plants for agricultural purposes still has a high level of rejection by consumers, for example in the European Union, motivated by its agricultural policy. Another feasible strategy to mitigate salinity impacts on crop production would be breeding salt tolerant cultivars for the production of new varieties which can thrive in more extreme environmental conditions. In this sense, crop wild relatives may contain genes of potential value for plant salinity tolerance. Despite the vast pool of resources that exists, much of the crop germplasm richness found in gene banks is underutilized. In addition, cultivation of halophytic plants at the same time or prior to the cultivation of crop plants (intercropping) would allow the desalination of the soil favoring crop yield and/or, alternatively, the use of saline irrigation water. Complementarily, the use of biostimulants, such as antioxidant compounds, melatonin, plant hormones or NO-releasing compounds can improve the response of plants to salinity. The proteomic approach to study the response to salt stress can provide relevant information in order to know the physiological and biochemical processes affected by salinity. This information can also support the breeding programs to attempt selection of salt-tolerant plants. Finally, the development of plant metabolomics techniques can supply relevant information about the effect of salt stress on cell metabolism. In addition, these techniques may allow for the identification of new metabolites that can be used as markers to better understand the salt tolerance response and help breeders select new tolerant species. Conflicts of Interest: The authors declare no conflict of interest. References 1. Acosta-Motos, J.; Ortuño, M.; Bernal-Vicente, A.; Diaz-Vivancos, P.; Sanchez-Blanco, M.; Hernandez, J. Plant Responses to Salt Stress: Adaptive Mechanisms. Agronomy 2017, 7, 18. [CrossRef] 2. Wang, N.; Qian, Z.; Luo, M.; Fan, S.; Zhang, X.; Zhang, L. Identification of salt stress responding genes using transcriptome analysis in green alga Chlamydomonas reinhardtii. Int. J. Mol. Sci. 2018, 19, 3359. [CrossRef] [PubMed] 3. Ji, C.; Mao, X.; Hao, J.; Wang, X.; Xue, J.; Cui, H.; Li, R. Analysis of bZIP transcription factor family and their expressions under salt stress in Chlamydomonas reinhardtii. Int. J. Mol. Sci. 2018, 19, 2800. [CrossRef] [PubMed] 4. Wu, J.; Zhao, Q.; Wu, G.; Yuan, H.; Ma, Y.; Lin, H.; Pan, L.; Li, S.; Sun, D. Comprehensive analysis of differentially expressed unigenes under nacl stress in flax (Linum usitatissimum L.) using RNA-Seq. Int. J. Mol. Sci. 2019, 20, 369. [CrossRef] 6 Int. J. Mol. Sci. 2019, 20, 2408 5. Haider, M.S.; Kurjogi, M.M.; Khalil-Ur-Rehman, M.; Fiaz, M.; Pervaiz, T.; Jiu, S.; Haifeng, J.; Chen, W.; Fang, J. Grapevine immune signaling network in response to drought stress as revealed by transcriptomic analysis. Plant Physiol. Biochem. 2017, 121, 187–195. [CrossRef] [PubMed] 6. Guan, L.; Haider, M.S.; Khan, N.; Nasim, M.; Jiu, S.; Fiaz, M.; Zhu, X.; Zhang, K.; Fang, J. Transcriptome sequence analysis elaborates a complex defensive mechanism of grapevine (Vitis vinifera L.) in response to salt stress. Int. J. Mol. Sci. 2018, 19, 4019. [CrossRef] 7. Yu, J.; Zhao, W.; Tong, W.; He, Q.; Yoon, M.Y.; Li, F.P.; Choi, B.; Heo, E.B.; Kim, K.W.; Park, Y.J. A Genome-wide association study reveals candidate genes related to salt tolerance in rice (Oryza sativa) at the germination stage. Int. J. Mol. Sci. 2018, 19, 3145. [CrossRef] 8. Dilnur, T.; Peng, Z.; Pan, Z.; Palanga, K.K.; Jia, Y.; Gong, W.; Du, X. Association analysis of salt tolerance in Asiatic cotton (Gossypium arboretum) with SNP markers. Int. J. Mol. Sci. 2019, 20, 2168. [CrossRef] 9. Wang, Q.; Ni, J.; Shah, F.; Liu, W.; Wang, D.; Yao, Y.; Hu, H.; Huang, S.; Hou, J.; Fu, S.; et al. Overexpression of the Stress-Inducible SsMAX2 Promotes Drought and Salt Resistance via the Regulation of Redox Homeostasis in Arabidopsis. Int. J. Mol. Sci. 2019, 20, 837. [CrossRef] 10. Boonchai, C.; Udomchalothorn, T.; Sripinyowanich, S.; Comai, L.; Buaboocha, T.; Chadchawan, S. Rice overexpressing OsNUC1-S reveals differential gene expression leading to yield loss reduction after salt stress at the booting stage. Int. J. Mol. Sci. 2018, 19, 3936. [CrossRef] 11. Miao, H.; Sun, P.; Liu, J.; Wang, J.; Xu, B.; Jin, Z. Overexpression of a novel ROP gene from the banana (MaROP5g) confers increased salt stress tolerance. Int. J. Mol. Sci. 2018, 19, 3108. [CrossRef] [PubMed] 12. Miranda, R.S.; Alvarez-Pizarro, J.C.; Costa, J.H.; Paula, S.O.; Pirsco, J.T.; Gomes-Filho, E. Putative role of glutamine in the activation of CBL/CIPK signaling pathways during salt stress in sorghum. Plant Signal. Behav. 2017, 12, e1361075. [CrossRef] 13. Bernal-Vicente, A.; Cantabella, D.; Petri, C.; Hernández, J.A.; Diaz-Vivancos, P. The Salt-Stress Response of the Transgenic Plum Line J8-1 and Its Interaction with the Salicylic Acid Biosynthetic Pathway from Mandelonitrile. Int. J. Mol. Sci. 2018, 19, 3519. [CrossRef] 14. Zhong, M.; Wang, Y.; Zhang, Y.; Shu, S.; Sun, J.; Guo, S. Overexpression of transglutaminase from cucumber in tobacco increases salt tolerance through regulation of photosynthesis. Int. J. Mol. Sci. 2019, 20, 894. [CrossRef] [PubMed] 15. Zhang, Y.; Liu, L.; Chen, B.; Qin, Z.; Xiao, Y.; Zhang, Y.; Yao, R.; Liu, H.; Yang, H. Progress in understanding the physiological and molecular responses of Populus to salt stress. Int. J. Mol. Sci. 2019, 20, 1312. [CrossRef] 16. Zhan, H.; Nie, X.; Zhang, T.; Li, S.; Wang, X.; Du, X.; Tong, W.; Song, W. Melatonin: A small molecule but important for salt stress tolerance in plants. Int. J. Mol. Sci. 2019, 20, 709. [CrossRef] 17. Wei, J.; Li, D.-X.; Zhang, J.-R.; Shan, C.; Rengel, Z.; Song, Z.-B.; Chen, Q. Phytomelatonin receptor PMTR1-mediated signaling regulates stomatal closure in Arabidopsis thaliana. J. Pineal Res. 2018, 65, e12500. [CrossRef] 18. Zhao, G.; Zhao, Y.; Yu, X.; Kiprotich, F.; Han, H.; Guan, R.; Wang, R.; Shen, W. Nitric oxide is required for melatonin-enhanced tolerance against salinity stress in rapeseed (Brassica napus L.) seedlings. Int. J. Mol. Sci. 2018, 19, 1912. [CrossRef] 19. Chen, C.; Wang, C.; Liu, Z.; Liu, X.; Zou, L.; Shi, J.; Chen, S.; Chen, J.; Tan, M. Variations in physiology and multiple bioactive constituents under salt stress provide insight into the quality evaluation of Apocyni Veneti Folium. Int. J. Mol. Sci. 2018, 19, 3042. [CrossRef] 20. Yan, K.; Bian, T.; He, W.; Han, G.; Lv, M.; Guo, M.; Lu, M. Root abscisic acid contributes to defending photoinibition in jerusalem artichoke (Helianthus tuberosus L.) under salt stress. Int. J. Mol. Sci. 2018, 19, 3934. [CrossRef] [PubMed] 21. Murata, N.; Takahashi, S.; Nishiyama, Y.; Allakhverdiev, S.I. Photoinhibition of photosystem II under environmental stress. Biochim. Biophys. Acta 2007, 1767, 414–421. [CrossRef] [PubMed] 22. Yang, C.; Zhang, Z.S.; Gao, H.Y.; Fan, X.L.; Liu, M.J.; Li, X.D. The mechanism by which NaCl treatment alleviates PSI photoinhibition under chilling-light treatment. J. Photochem. Photobiol. B Biol. 2014, 140, 286–291. [CrossRef] 23. Szymanska, K.P.; Polkowska-Kowalczyk, L.; Lichocka, M.; Maszkowska, J.; Dobrowolska, G. SNF1-related protein kinases SnRK2.4 and SnRK2.10 modulate ROS homeostasis in plant response to salt stress. Int. J. Mol. Sci. 2019, 20, 143. [CrossRef] [PubMed] 7 Int. J. Mol. Sci. 2019, 20, 2408 24. Zhang, H.; Zhang, Y.; Deng, C.; Deng, S.; Li, N.; Zhao, C.; Zhao, R.; Liang, S.; Chen, S. The Arabidopsis Ca2+-dependent protein kinase CPK12 is involved in plant response to salt stress. Int. J. Mol. Sci. 2018, 19, 4062. [CrossRef] 25. Ali, A.; Maggio, A.; Bressan, R.A.; Yun, D.J. Role and functional differences of HKT1-type transporters in plants under salt stress. Int. J. Mol. Sci. 2019, 20, 1059. [CrossRef] 26. Luo, D.; Hou, X.; Zhang, Y.; Meng, Y.; Zhang, H.; Liu, S.; Wang, X.; Chen, R. CaDHN5, a dehydrin gene from pepper, plays an important role in salt and osmotic stress responses. Int. J. Mol. Sci. 2019, 20, 1989. [CrossRef] 27. Hussain, S.; Zhu, C.; Bai, Z.; Huang, J.; Zhu, L.; Cao, X.; Nanda, S.; Hussain, S.; Riaz, A.; Liang, Q.; et al. iTRAQ-based protein profiling and biochemical analysis of two contrasting rice genotypes revealed their differential responses to salt stress. Int. J. Mol. Sci. 2019, 20, 547. [CrossRef] © 2019 by the author. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). 8 International Journal of Molecular Sciences Article Identification of Salt Stress Responding Genes Using Transcriptome Analysis in Green Alga Chlamydomonas reinhardtii Ning Wang † , Zhixin Qian † , Manwei Luo, Shoujin Fan, Xuejie Zhang and Luoyan Zhang * Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University, No. 88 Wenhuadong Road, Jinan 250014, China; [email protected] (N.W.); [email protected] (Z.Q.); [email protected] (M.L.); [email protected] (S.F.); [email protected] (X.Z.) * Correspondence: [email protected]; Tel.: +86-531-86180718 † These authors contributed equally to this work. Received: 16 September 2018; Accepted: 24 October 2018; Published: 26 October 2018 Abstract: Salinity is one of the most important abiotic stresses threatening plant growth and agricultural productivity worldwide. In green alga Chlamydomonas reinhardtii, physiological evidence indicates that saline stress increases intracellular peroxide levels and inhibits photosynthetic-electron flow. However, understanding the genetic underpinnings of salt-responding traits in plantae remains a daunting challenge. In this study, the transcriptome analysis of short-term acclimation to salt stress (200 mM NaCl for 24 h) was performed in C. reinhardtii. A total of 10,635 unigenes were identified as being differently expressed by RNA-seq, including 5920 up- and 4715 down-regulated unigenes. A series of molecular cues were screened for salt stress response, including maintaining the lipid homeostasis by regulating phosphatidic acid, acetate being used as an alternative source of energy for solving impairment of photosynthesis, and enhancement of glycolysis metabolism to decrease the carbohydrate accumulation in cells. Our results may help understand the molecular and genetic underpinnings of salt stress responses in green alga C. reinhardtii. Keywords: Chlamydomonas reinhardtii; salt stress; transcriptome analysis; impairment of photosynthesis; underpinnings of salt stress responses 1. Introduction Salinity is one of the most important abiotic stresses threatening agricultural productivity worldwide. Although plants have gradually evolved a series of adaptive molecular, physiology and biochemistry processes to respond to salinity stress, it could threaten 30% of cultivable soils by 2050 [1,2]. Understanding the molecular machineries of salt stress response in model plants of basal taxa, such as green algae, may contribute to finding the evolutionary cues of abiotic stress response in plants and developing salt-resistant crops with additional salt-responding traits [2–9]. Salt stress causes diverse impacts on plant growth by disturbing the osmotic/ionic balance and eliciting Na+ toxicity [9,10]. Under aquatic saline stress, a series of physical and biochemical processes are recruited by algae to respond to the damage caused by osmotic and ionic stresses, such as photosynthesis inhibition, macromolecular compound synthesis and homeostasis adjustment [6,10–14]. It has been reported that salt stress leads to decreased photosynthetic efficiency [15,16] which influences chlorophyll content in plant leaves [17,18]. In green algae, salt stress remarkably influences the structure and functions of the photosynthetic apparatus in Scenedesmus obliquus [19] and reduces the maximum quantum yield of photosystem II (PSII) in Dunaliella salina [20]. In alga Botryococcus braunii, metabolism of lutein was significantly enhanced under stress conditions [12]. Int. J. Mol. Sci. 2018, 19, 3359; doi:10.3390/ijms19113359 9 www.mdpi.com/journal/ijms Int. J. Mol. Sci. 2018, 19, 3359 Chlamydomonas reinhardtii is a free-living freshwater alga with unicellular vegetative cell. Previous studies exposed the C. reinhardtii strain 21 gr and CC-503 to salt stress and demonstrated the physiological and metabolic processes impacted by ionic toxicity and osmotic stress caused by salt damage [6–8,16,21]. Vega [22] demonstrated that 200 mM NaCl in the culture medium was highly toxic for C. reinhardtii productivity. The addition of NaCl immediately blocked the photosynthetic activity of the alga which partially recovered, after 1 h of treatment, remaining high during the following 24 h. However, after 24 h treatment with NaCl 200 mM, the intracellular catalase activity of the alga reached a 20-fold higher level than in the control cells. The physiological data indicate that saline stress induces in C. reinhardtii an increase of intracellular peroxide, which parallels a significant inhibition of the photosynthetic-electron flow. However, the related machineries of up-stream regulating and the triggering of appropriate cellular and physiological responses to cope with stress circumstances are still largely unknown. Transcriptome sequencing is an effective strategy for detecting potential participants of stress response on a genome-wide scale. Hundreds of studies about salt stress responses in model plant Arabidopsis thaliana [23–26], crops Oryza sativa [23,27] and Glycine max [28], and in some halophytes (plants able to complete their life cycles under saline environments) have been widely conducted using sequencing technologies [7,29–41]. The integrations of genes’ spatio-temporal expression patterns and responding traits have helped to identify a large number of salt stress-related differentially expressed genes (DEGs) and mechanisms. Keeping this in mind, the work presented here was carried out to explore the saline stress-responding mechanisms of C. reinhardtii by transcriptome sequencing of strains GY-D55 wild type. The aim of this study was to identify dys-regulated genes in C. reinhardtii cells under salt stress by RNA-seq, screen physiological and biochemical cues by gene ontology (GO) terms and MapMan functional enrichment analyses, and investigate the physiological adaptions and cellular regulatory networks for salt stress responding. 2. Results 2.1. Transcriptome Profiling of C. reinhardtii After sequencing with the Illumina HiSeq X platform, a total of 56,438,218, 72,853,712, 47,551,786, 56,962,722, 52,926,804 and 55,998,748 high-quality pair-end reads were obtained from three control and three salt stress treated samples of C. reinhardtii (Table 1), respectively. De novo transcriptome assembly generated 91,242 unigenes, with an average length of 2691 nt and N50 of 4554. On average, 90.66% of the reads from six samples were mapped to the reference genome (Table 1). The assembled transcriptome information of C. reinhardtii is shown in Supplementary Figure S1. Table 1. Summary of mapping transcriptome reads to reference sequence. Sample Name Sample Description Total Reads Total Mapped Ratio of Mapped Reads C_0_1 Control replication 1 56,438,218 51,454,456 91.17% C_0_2 Control replication 2 72,853,712 66,008,290 90.60% C_0_3 Control replication 3 47,551,786 43,268,544 90.99% S_200_1 Salt stress replication 1 56,962,722 51,633,614 90.64% S_200_2 Salt stress replication 2 52,926,804 47,815,814 90.34% S_200_3 Salt stress replication 3 55,998,748 50,507,824 90.19% 2.2. Functional Annotations of Unigenes Similarity searches were performed to annotate unigenes against different databases using BLASTX. For C. reinhardtii, 65,679 (71.98%) unigenes were annotated in at least one database (Figure 1C and Supplementary Figure S1). A total of 52,884 (57.96%) and 58,062 (63.63%) unigenes showed similarity to sequences in NR and PFAM databases with an E-value threshold of 1 × 10−5 . 10 Int. J. Mol. Sci. 2018, 19, 3359 About 58,651 (64.28%) unigenes were annotated in the GO database by Blast2GO v2.5 with an E-value cutoff of 1 × 10−6 (Figure 1C and Supplementary Figure S1). Unigenes of the C. reinhardtii were assigned to C. reinhardtii and A. thaliana gene IDs for GO annotation mapping and TFs/PKs perdition. By sequence alignment, a total of 48,158 unigenes were aligned to C. reinhardtii PLAZA genome genes. A total of 54,509 unigenes were assigned to TAIR10 locus IDs by BLASTP with an E-value cutoff of 1 × 10−5 and classified into GO categories for GO analysis (Supplementary Table S1). Figure 1. (A) The morphology of C. reinhardtii cells without addition of NaCl. (B) The morphology of C. reinhardtii cells under 200 mM NaCl treatment. (C) Venn diagram of functional annotations of unigenes in nt (NCBI non-redundant protein sequences), nr (NCBI non-redundant protein sequences), kog (Clusters of Orthologous Groups of proteins), go (Gene Ontology) and pfam (Protein family) databases. (D) Expression patterns of differentially expressed genes (DEGs) identified between 200 mM NaCl treated and control. S_200 indicated cells under 200 mM NaCl stressed condition for 24 h; C_0 indicated cells cultured under control condition. Red and green dots represent DEGs, blue dots indicate genes that were not differentially expressed. In total, 10,635 unigenes were identified as DEGs (padj < 0.05) between S_200 and C_0, including 5920 upregulated genes and 4715 downregulated genes. 2.3. Differently Expressed Genes (DEGs) Calculation To evaluate the relative level of gene expression in C. reinhardtii under control or salt stress treatment, the FPKM values were calculated based on the uniquely mapped reads. The FPKM distributions of unigenes in six samples are shown in Supplementary Figure S2. The FPKM value for genes detected in six samples ranged from 0 to 40,486.05, with mean value of 7.08. By comparative analysis, a part of the genes was observed to be differently expressed in 200 Mm NaCl treated 11 Int. J. Mol. Sci. 2018, 19, 3359 samples: 5920 unigenes were calculated as up-regulated in salt treated samples and 4715 filtered as down-regulated genes with the cutoff of padj < 0.05 and |log2(foldchange)| > 1 (Supplementary Table S2). The most significantly dysregulated 30 genes are recorded in Table 2. The most significantly upregulated unigenes included RNA recognition motif containing gene Cluster-2749.47186 (log2FoldChange [L2 fc] = 3.894), “transcription, DNA-templated” participating gene Cluster-2749.64181 (L2 fc = 5.573) and “potassium ion transport” gene Cluster-2749.61362 (L2 fc = 8.112) (Table 2 and Supplementary Table S2). Downregulated unigenes, included “chlorophyll metabolic process” related gene Cluster-2749.44503 (L2 fc = −8.623) with the lowest p-value, “proteolysis” related gene Cluster-2749.61923 (L2 fc = −6.748) and “regulation of transcription, DNA-templated” participating gene Cluster-2749.45379 (L2 fc = −3.663). Table 2. Top30 dysregulated genes in C. reinhardtii under 200 mM NaCl treated and control conditions. Gene_ID L2 fc pval BP Description Up-regulated Cluster-2749.47186 3.894 3.77 × 10−75 Cluster-2749.64181 5.573 1.55 × 10−69 transcription, DNA-templated Cluster-2749.61362 8.112 1.95 × 10−62 potassium ion transport Cluster-2749.33332 4.129 1.19 × 10−58 signal transduction Cluster-2749.48242 3.610 1.64 × 10−58 Cluster-2749.21356 3.975 4.34 × 10−56 Cluster-2749.37168 3.413 1.00 × 10−52 Cluster-2749.23874 7.849 5.01 × 10−50 lipid metabolic process Cluster-2749.57700 9.756 9.76 × 10−49 iron-sulfur cluster assembly Cluster-2749.59287 3.459 1.42 × 10−43 cell adhesion Cluster-2749.53252 3.877 2.36 × 10−43 pathogenesis Cluster-2749.49912 5.957 1.07 × 10−41 lipoprotein metabolic process Cluster-2749.84953 6.468 2.29 × 10−41 Cluster-2749.82821 2.504 5.20 × 10−41 regulation of protein kinase activity Cluster-2749.3203 7.706 1.83 × 10−38 Down-regulated Cluster-2749.44503 −8.623 4.01 × 10−178 chlorophyll metabolic process Cluster-2749.61923 −6.748 6.07 × 10−81 proteolysis Cluster-2749.38883 −3.906 7.54 × 10−76 Cluster-2749.44595 −2.699 3.50 × 10−74 metabolic process Cluster-2749.45379 −3.663 6.53 × 10−71 regulation of transcription, DNA-templated Cluster-2749.49076 −4.268 2.29 × 10−70 chlorophyll biosynthetic process Cluster-2749.44117 −4.239 1.30 × 10−66 oxidation-reduction process Cluster-2749.42573 −5.023 3.04 × 10−66 protein glycosylation Cluster-2749.32226 −4.043 2.67 × 10−65 proteolysis Cluster-2749.45636 −7.283 1.98 × 10−61 Cluster-2749.44732 −6.934 2.08 × 10−61 Cluster-2749.49721 −7.951 3.18 × 10−58 Cluster-2749.65261 −3.524 1.91 × 10−57 Cluster-2749.36258 −2.996 5.32 × 10−57 Cluster-2749.43872 −4.589 1.10 × 10−55 cell adhesion Note: Top30 dysregulated genes with the lowest p-value (pval) are represented; L2 fc indicates the log2FoldChange of genes differently expressed in 200 mM NaCl treated samples and control samples; BP Description means descriptions of genes’ potential participating biological process predicted by sequence similarity search. 2.4. GO Enrichment of DEGs For uncovering the differences of molecular mechanisms of C. reinhardtii under salt stress, the DEGs were then characterized with GO databases. A total of 353 biological processes (BP) terms were enriched by the 5920 up-regulated unigenes, like “oxidation-reduction process” (GO:0055114), “response to cadmium ion” (GO:0046686) and “response to salt stress” (GO:0009651) (Table 3; Supplementary Table S3). The 4715 down-regulated genes were calculated enriched in 313 BP terms, 12 Int. J. Mol. Sci. 2018, 19, 3359 as “photosynthesis, light harvesting in photosystem I” (GO:0009768), “chlorophyll biosynthetic process” (GO:0015995) and “isoleucine biosynthetic process” (GO:0009097) (Table 3; Supplementary Table S3). Table 3. Top30 biological processes enriched by the up- and down-regulated genes. Annotated Enriched Gene GO ID GO Term p-Value Gene Number Number Up-Regulated GO:0008150 biological process 33682 2820 1.00 × 10−30 GO:0055114 oxidation-reduction process 3653 385 2.90 × 10−27 GO:0046686 response to cadmium ion 1317 159 3.40 × 10−18 GO:0042542 response to hydrogen peroxide 189 41 1.10 × 10−15 GO:0009408 response to heat 717 122 1.40 × 10−15 GO:0051259 protein oligomerization 109 25 7.50 × 10−12 GO:0010090 trichome morphogenesis 131 26 4.60 × 10−10 GO:0009414 response to water deprivation 668 79 6.70 × 10−10 GO:0009651 response to salt stress 1488 143 3.90 × 10−09 GO:0043335 protein unfolding 39 14 1.80 × 10−08 GO:0016036 cellular response to phosphate starvation 262 40 2.40 × 10−08 GO:0010030 positive regulation of seed germination 85 20 6.50 × 10−08 GO:0030866 cortical actin cytoskeleton organization 31 12 7.20 × 10−08 GO:0016477 cell migration 31 12 7.20 × 10−08 GO:0045010 actin nucleation 31 12 7.20 × 10−08 Down-Regulated GO:0008150 biological process 33682 2018 1.00 × 10−30 GO:0009768 photosynthesis, light harvesting in photosystem I 87 46 1.00 × 10−30 GO:0009645 response to low light intensity stimulus 72 37 1.00 × 10−30 GO:0015995 chlorophyll biosynthetic process 242 54 4.40 × 10−29 GO:0009644 response to high light intensity 393 71 6.70 × 10−22 GO:0006412 translation 1779 179 3.80 × 10−16 GO:0009409 response to cold 978 103 5.30 × 10−16 GO:0009269 response to desiccation 41 18 1.00 × 10−14 GO:0009769 photosynthesis, light harvesting in photosystem II 36 17 1.30 × 10−14 GO:0010218 response to far red light 101 25 8.70 × 10−14 GO:0006364 rRNA processing 742 89 2.10 × 10−12 GO:0010114 response to red light 159 28 5.90 × 10−11 GO:0015979 photosynthesis 853 137 2.40 × 10−10 GO:0009097 isoleucine biosynthetic process 53 16 2.60 × 10−10 GO:0009099 valine biosynthetic process 43 14 1.10 × 10−09 2.5. MapMan Enrichment of DEGs A more specific comparison of metabolic and regulatory pathways was conducted using MapMan. A total of 5920 up- and 4715 down-regulated genes were assigned to 1334 and 1050 homologs in Arabidopsis thaliana, respectively. Consequently, these uniquely expressed genes were mapped to 797 pathways by MapMan, of which, 22 pathways were filtered enriched by the dysregulated genes with the cutoff p-value < 0.05 (Figure 3A; Supplementary Table S4). The expression of genes implicated in “TCA/org. transformation.TCA”, “Tetrapyrrole synthesis”, “Starch” and “Sucrose” were over-expressed in C. reinhardtii, while those genes involved in “PS.lightreaction”, “PS.lightreaction.photosystem I” and “PS.lightreaction.photosystem I.LHC-I” were down-regulated in C. reinhardtii during salt stress responding (Figure 3A). 2.6. KEGG Enrichment of DEGs To gain a deeper insight into the regulation of photosynthesis underlying salt stress response, down-regulated unigenes involved in “photosynthesis” KEGG pathways (ko00195) were mapped and shown in Figure 2B. Orthologs of 44 genes annotated in this pathway were filtered as down-regulated in the NaCl treated samples in the green alga, such as, photosystem II oxygen-evolving enhancer protein PSBO Cluster-2749.35825 (L2 fc = −2.5458) and Cluster-2749.43661 (L2 fc = −2.1558), cytochrome b6-f complex iron-sulfur subunit PETC, Cluster-2749.42943 (L2 fc = −2.7088), and F-type H+-transporting ATPase subunit ATPF0A, Cluster-2966.0 (L2 fc = −3.1245) (Figure 2B; Supplementary Table S2). 13 Int. J. Mol. Sci. 2018, 19, 3359 Figure 2. (A) Global view of differently expressed genes (DEGs) involved in diverse metabolic pathways. DEGs genes were selected for the metabolic pathways analysis using the MapMan software (3.5.1 R2). The colored boxes indicate the Log2 of expression ratio of DEGs genes. The dys-regulated unigenes were assigned to 1334 and 1050 homologs in Arabidopsis, respectively. These genes were mapped to 797 pathways by MapMan, of which, 22 pathways were filtered enriched by the dys-regulated genes with the cutoff p-value < 0.05. (B) The KEGG pathways (ko00195) “photosynthesis” mapped with 44 down-regulated unigenes. The down-regulated genes are marked by a green frame. The black solid line with a black arrow means molecular interaction or relation; the black dash line with a black arrow means indirect link or unknown reaction; the red dash line with a red arrow stands for the light quanta. 14 Int. J. Mol. Sci. 2018, 19, 3359 2.7. The Differentially Expressed TFs and PKs Among the expressed unigenes, 2050 and 1624 sequences were assigned to 45 TF families and 78 PK families, respectively (Supplementary Table S5). Of the TF families, MYB family had the largest number of upregulated genes (16 unigenes), including MYB109 ortholog unigenes Cluster-2749.35807 (L2 fc = 2.5798) and Cluster-2749.70085 (L2 fc = 1.3722). In contrast, SET family had the largest number of downregulated genes (16 unigenes). Of the PKs families, TKL-Cr-3 family was uncovered to contain the largest number of upregulated genes. By comparison, CAMK_CDPK and Group-Cr-2 family contained the largest number of downregulated unigenes (Supplementary Table S5). 2.8. Real-Time Quantitative PCR Validation To verify the RNA-seq results, an alternative strategy was selected for the upregulated unigenes. In total, five over-expressed unigenes were randomly selected for validation by qRT-PCR using the same RNA samples that were used for RNA-seq. Primers were designed to span exon-exon junctions (see Supplementary Table S6 and Figure S3). In most cases, the gene expression trends were similar between these two methods; the result is shown in Figure 3. The ortholog of cytosolic small heat shock protein encoding genes HSP17.6A, Cluster-2749.57700, which was detected by RNA-Seq as up-regulating genes in the salt treated samples (L2 fc = 9.76), was also detected to be significantly over-expressed by qRT-PCR method (Figure 3). Figure 3. Real-time PCR verification of five up-regulated genes in C. reinhardtii. The red bars represent the qPCR results of samples under salt stress condition, while the corresponding blue bars represent the results of control samples. The individual black bars, representing the qPCR data, are the means ± SD of nine measurements (three technical replicates each for three biological samples). 3. Discussion Salinity is one of the major environmental factors threatening crop productivity and plant growth worldwide [2,9,42]. Due to the complexity of abiotic stress-responding processes, although several hundreds of salt-responding genes have been reported in plants, understanding the genetic underpinnings of salt-responding traits in plantae remains a daunting challenge. The model alga C. reinhardtii, which contains one large cup-shaped chloroplast, has the ability to adapt rapidly to changing environmental conditions, such as high salinity, via the generation of novel traits [8,14,43,44]. Given previous results from analysis of salt stress in C. reinhardtii and other plants, we analyzed the Illumina RNA-seq data from this alga grown in BG-11 medium with the addition of 200 mM NaCl and analyzed in triplicate after 24 h of incubation [16,22]. In this study, a total of 5920 and 15 Int. J. Mol. Sci. 2018, 19, 3359 4715 unigenes were identified as up- and down-regulated genes in C. reinhardtii under salt stress by RNA-seq. Our study found some molecular cues for reducing the negative effects due to ionic/osmotic toxicity and photosynthesis impairment under saline conditions in C. reinhardtii. Previous studies discovered that the cell density of C. reinhardtii cells obviously reduced when stressed by NaCl [8,14,16,21,22]. Neelam et al. demonstrated that at the morphological level, 150 or 200 mM NaCl salt stress led to palmelloid morphology, flagellar resorption, reduction in cell size, and slower growth rate in C. reinhardtii [21]. It should be noted that dead and dying cells have dys-regulated mRNA and contribute to transcript levels under saline stress. In our study, programmed cell death (PCD) in the C. reinhardtii cell was found with PCD-regulating proteins being significantly up-regulated, e.g., condensin complex subunit (Cluster-2749.11751: L2 fc = 9.368; Cluster-2749.12889: L2 fc = 7.766), sucrose-phosphatase 1 (Cluster-2749.35394: L2 fc = 4.304) and stress tolerance related fibrillin family member (Cluster-2749.70284: L2 fc = 1.920). Saline stress leads to the overproduction of reactive oxygen species (ROS) in plants which are highly reactive and toxic and cause damage to lipids, carbohydrates, proteins and DNA which ultimately results in oxidative stress [8,9,14,45]. The accumulation of ROS also influences the expression of a number of genes and therefore controls many processes, such as growth, cell cycle, PCD, secondary stress responses and systemic signaling [8,9,14,45]. The excess Na+ and oxidative stress in the intracellular or extracellular environment activates the acytoplasmic Ca2+ signal pathway for regulating an osmotic adjustment or homeostasis regulating of salt stress responses [24,29,39,46–51]. In our study, calcium-related pathway in the C. reinhardtii cell was found with several calcium ion binding proteins being significantly upregulated, e.g., peroxygenase 3 (Cluster-2749.55812: L2 fc = 10.431; Cluster-2749.59997: L2 fc = 7.680) and calreticulin (Cluster-2749.35394: L2 fc = 3.082). The short-term (within 48 h) acclimation to salt stress in C. reinhardtii involves activation of phospholipid signaling, leading to the accumulation of phosphatidic acid (PA), which is a lipid second messenger in plant and animal systems [52–54]. In the case of C. reinhardtii, incubation in 150 mM NaCl leads to a three- to four-fold rise of PA levels within minutes [52,55]. Lysophosphatidic acid (LPA) has also been shown to accumulate in this alga under salt stress, with the dose-dependent response reaching a maximum at 300 mM NaCl [55,56]. In this study, soluble lysophosphatidic acid acyltransferase (Cluster-2749.8269: L2 fc = 9.126; Cluster-2749.9895: L2 fc = 8.720) was found to be significantly up-regulated in salt stress treated samples, which indicated the potential role of this gene in maintaining the lipid homeostasis by regulating PA under saline stress [55]. Further, analysis of glycerophospholipid metabolism pathways showed that the alga cells had significant up-regulation of FAD (flavin adenine dinucleotide)-dependent oxidoreductase family protein (Cluster-2749.52046; L2 fc = 2.695) that involves storing lipid catabolism and glycerol assimilation, and in glycerol-3-phosphate shuttle, which transports reduced power from cytosol to mitochondrion [8]. This suggests that the intracellular glycerol pool in C. reinhardtii cells likely increased as a response to salt stress, similar to what has been shown for the green alga Dunaliella tertiolecta [57,58]. Requirement of energy to maintain ion homeostasis is the major metabolic impact of salt stress. The reduction of oxidative stress and osmotic stress, and the up-regulation of heatshock proteins were speculated to aid protein renaturation and recover homeostasis [59–61]. In this study, the stress response is apparent in the C. reinhardtii cells with significant up-regulation of genes involved in oxidative/osmotic stress reduction process including glyceraldehyde-3-phosphate dehydrogenase C subunit 1 (Cluster-2749.27769: L2 fc = 1.930) and fumarase 1 (Cluster-2749.35832: L2 fc = 8.306). In bacterium Escherichia coli, trehalose is synthesized as a compatible solute and enables cells to exclude toxic cations and to acclimate to high concentrations of salt in the growth medium [62]. For maize, trehalose has helped to reduce the negative effects of saline stress as an osmoprotectant [63]. In our study, enzymes involved in trehalose synthesis significantly up-regulated, e.g., trehalose-6-phosphatase synthase S8 (Cluster-2749.17684: L2 fc = 6.453) and trehalose-6-phosphate synthase (Cluster-2749.61951: L2 fc = 1.123). These results indicated the potential underpinnings for these to maintain homeostasis in C. reinhardtii under saline conditions. 16 Int. J. Mol. Sci. 2018, 19, 3359 In plants, saline stress generally causes ion injury and osmotic stress, which interferes with numerous biochemical and physiological processes, including energy metabolism pathways such as photosynthesis [26,36,64,65] and photorespiration [8]. Previous pigment analyses have demonstrated that photosystem I-light harvesting complexes (LHCs) are damaged by ROS at high salt conditions, and PSII proteins involved in oxygen evolution are impaired [21,45]. In our study, impairment of photosynthesis in the C. reinhardtii cell population was found, with several photosystem I-light harvesting complex (LHC) proteins being significantly down-regulated (Figure 2B), e.g., photosystem I light harvesting complex gene LHCA2 (Cluster-2749.32743: L2 fc = −4.74; Cluster-2749.52511: L2 fc = −3.28), LHCA3 (Cluster-2749.43129: L2 fc = −6.583) and LHCA5 (Cluster-2749.40312: L2fc = −11.375; Cluster-2749.34085: L2 fc = −6.553). Further, we found most of the chloroplast encoded transcripts (e.g., PsaA, B, C, J, M) in photosystem I (PSI) were relatively unchanged in level while the nuclear genes (e.g., PsaD, E, G, F, H) down-regulated under saline conditions (Figure 2B). Existing studies have demonstrated the usage of acetate in the medium as alternative source of energy to compensate for the lowered efficiency in photosynthesis [66]. Consistent with this view, we found that acetyl-CoA synthetase (Cluster-2749.60516: L2 fc = 5.144; Cluster-2749.25511: L2 fc = 2.495), which combines acetate and CoA to form acetyl-CoA, was significantly up-regulated in the alga cells under saline conditions. In this study, a significant down-regulation was found in a key enzyme of the glyoxylate cycle—isocitrate lyase (ICL, [Cluster-2749.51492; L2 fc = −3.119]) [8,45,66,67]—which catalyzes the cleavage of isocitrate to succinate and glyoxylate. Together with malate synthase, ICL bypasses the two decarboxylation steps of the tricarboxylic acid cycle (TCA cycle) [8]. The spatio-temporal expression patterns of genes suggest that in alga cells acetyl-CoA is introduced into energy generation pathways for salt stress responses. Glycolysis is considered to play an important role in plant development and adaptation to multiple abiotic stresses, such as cold, salt, and drought. It is the key respiratory pathway for generating ATP and carbohydrates metabolites [50,68–73]. In our work, salt stress significantly increased the expression of genes participating in the metabolism of main carbohydrates, such as starch, sucrose, soluble sugar and glucose (Figure 2A). For example, 31 genes of “glycolytic process” (GO:0006096) over-expressed during salt stress responding, including plastidic pyruvate kinase PKP-ALPHA (Cluster-2749.14688: L2 fc = 8.53) and PKP-BETA1 (Cluster-2749.26182: L2 fc = 3.68). This is consistent with Zhong et al. [68], who reported salt stress significantly increased the main carbohydrate contents of cucumber leaves [53]. Carbohydrates are involved not only in osmotic adjustment, but also can be used as protective agents for homeostasis regulating during salt stress tolerance [24,30,39,48,69,70,74–77]. Given that salt injury caused the destruction of photosynthesis, which might inhibit transport of carbohydrate and accumulate excess starch or sucrose, we speculate C. reinhardtii enhanced glycolysis metabolism to decrease carbohydrate accumulation in cells, which would promote the respiratory metabolism and mitochondrial electron transport, thus reducing the effects of ionic toxicity and osmotic stress caused by salt damage. 4. Materials and Methods 4.1. Chlamydomonas Material Preparation, Salt Stress Treatment and RNA Extraction The C. reinhardtii strain GY-D55 wild type from LeadingTec (Shanghai, China) were grown in 150 mL of BG11 media, and placed on a shaking table with 120 rpm and maintained at light (16 h)/dark (8 h) at 23 ◦ C, with an illumination of 100 μmol m−2 ·s−1 . The density of cell cultures was determined by using the blood cell counting plate, with each value being the means of 6 repeats. Under this condition, C. reinhardtii cells were grown in BG11 for 14 d. The methods published by Zhao [16] and Vega [22] were referenced for NaCl treatment in this study. A total of 50 mL medium with 800 mM NaCl was added to the 150 mL culture medium on a shaking table for finishing 200 mM NaCl treatment, the added NaCl was rapidly diluted, and then the pH value was adjusted to 7.0. A parallel set of cells that were unexposed to NaCl stress conditions 17 Int. J. Mol. Sci. 2018, 19, 3359 and cultured in medium served as the experimental control. A total of 50 mL medium without NaCl was added into the control group. Each treatment had 3 repeats. For 24 h, 200 mM NaCl treatment significantly affected the cellular physiology of the alga, such as its photosynthetic and intracellular catalase activity; in this study, the culture time for C. reinhardtii under salt stress was 24 h. After 24 h, 100 mL cell culture medium was extracted from the NaCl treated and control culture bottles, respectively. The collected cells were centrifuged at 3000× g for 5 min, and the collected cells were resuspended in 25 mL RNAlater (Ambion, Shanghai, China) solution for RNA extraction. The cells of each repeat were mixed and total RNAs were extracted separately using the TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s procedures. RNA quality was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA) and the NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, NC, USA). 4.2. Illumina Library Construction and Sequencing A total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, San Diego, CA, USA) by following manufacturer’s procedures, and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. The random hexamer primer and M-MuLV Reverse Transcriptase (RNase H− ) were used to synthesize the first strand cDNA and the DNA Polymerase I and RNase H were used for second strand cDNA synthesis. Fragments of 150~200 bp cDNA were purified with the AMPure XP system (Beckman Coulter, Beverly, MA, USA). Then, 3 μL USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 ◦ C for 15 min followed by 5 min at 95 ◦ C. Then, PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. Ten cycles were used for PCR enrichment. Finally, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia, San Diego, CA, USA) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina HiSeq X platform (Illumina, San Diego, CA, USA), according to the manufacturer’s procedures. All genetic data have been submitted to the NCBI Sequence Read Archive (SRA) database (https://www.ncbi.nlm.nih.gov/sra), SRA accession: PRJNA490089. 4.3. De Novo Transcriptome Assembling and Unigene Annotation RNA sequencing and de novo transcriptome assembling were conducted to create reference sequence libraries for C. reinhardtii. The RNA sample of each repeat was sequenced separately. cDNA library construction and Illumina pair-end 150 pb sequencing (PE150) were performed at Novogene Co., Ltd. (Shanghai, China), according to instructions provided by Illumina Inc. Reads containing adapter, ploy-N and low-quality reads were removed from raw data for obtaining clean reads. The filtered high-quality reads were used for transcriptome assembling by the Trinity software with default parameters [78]. Clean datasets of 6 samples were pooled for de novo assembling and comprehensive sequence library construction. The Basic Local Alignment Search Tool (BLAST) searches of de novo assembled sequences against public databases (NR, NT, Swiss-Prot, Pfam, KOG/COG, Swiss-Prot, KEGG Ortholog database and Gene Ontology) with an E-value threshold of 10−10 were used for unigenes’ annotation. 4.4. Calculation and Comparison of Unigene Expression The independent transcripts libraries of 3 repeats under NaCl treatment conditions and 3 under control conditions were generated for C. reinhardtii by a PE150 sequencing analysis. The clean reads were aligned to the de novo assembled transcriptome and estimated by the RSEM [79] method. Gene 18 Int. J. Mol. Sci. 2018, 19, 3359 expression levels were calculated by the fragment per kilobase of exon model per million mapped reads (FPKM) method. DESeq2 [80] was used to compare the expression levels between NaCl treated and control samples with an cutoff of adjusted p-value (padj) < 0.05 and |log2(foldchange)| > 1. 4.5. Gene Ontology (GO), Transcription Factors (TFs) and Protein Kinases (PKs) Prediction The unigenes were transferred to the C. reinhardtii and A. thaliana gene IDs by using sequence similarity searching analysis against the genome of C. reinhardtii (ftp://ftp.psb.ugent.be/pub/plaza/ plaza_public_dicots_04/Fasta/cds.all_transcripts.cre.fasta.gz) and A. thaliana (ftp://ftp.psb.ugent.be/ pub/plaza/plaza_public_dicots_04/Fasta/cds.all_transcripts.ath.fasta.gz) with an E-value cutoff of 10−5 . The classifications of TFs and PKs of C. reinhardtii were downloaded from the iTAK database (http: //bioinfo.bti.cornell.edu/cgi-bin/itak/index.cgi) [81]. The GO functional annotations file of A. thaliana was downloaded from Gene Ontology database (submitted 5 June 2018, http://geneontology.org/ gene-associations/gene_association.tair.gz). The TFs and PKs of C. reinhardtii genes were transferred to their hit unigenes and the GO functional annotations of A. thaliana genes were assigned to their ortholog unigenes in C. reinhardtii. 4.6. GO, KEGG and MapMan Annotation and Enrichment The GO enrichment analysis for DEGs of C. reinhardtii was performed by the topGO package of R. KEGG [82] is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies (http://www.genome.jp/kegg/). We used KOBAS [83] software to test the statistical enrichment of differential expression genes in KEGG pathways. MapMan (version 3.5.1 R2) [84] was also used to annotate the DEGs onto metabolic pathways. The DEGs of C. reinhardtii unigene IDs were transferred to the Arabidopsis Information Resource (TAIR) locus IDs during the MapMan analysis. 4.7. Real-Time Quantitative PCR (qRT-PCR) Verification Real-time quantitative PCR (qRT-PCR) was performed to verify the expression patterns revealed by the RNA-seq analysis. The purified RNA of samples under salt stress and control conditions were treated with DNaseI and converted to cDNA using the PrimeScript RT Reagent Kit with gDNA Eraser (Takara, Dalian, China) according to the manufacturer’s procedures. Five up-regulated unigenes in C. reinhardtii were selected for the qRT–PCR assay, including Cluster-2749.49004 (ortholog of HSP81-2), Cluster-2749.57700 (ortholog of HSP17.6A), Cluster-2749.55812 (ortholog of RD20), Cluster-2749.36436 (ortholog of RGP), and Cluster-2749.35807 (ortholog of MYB109). Gene-specific qRT–PCR primers (18–20 bp) (Table S6) were designed using Premier 5.0 software. qPCR was performed using SYBR Green qPCR Master Mix (DBI, Ludwigshafen, Germany) in ABI7500 Real-Time PCR System (ABI, Waltham, MA, USA). Three replicates were performed, and the amplicons were used for melting curve analysis to evaluate the amplification specificity. Relative gene expression was quantified using the 2−(ΔΔCt) method [85]. Ortholog of the A. thaliana housekeeping GTP binding Elongation factor Tu family member AT5G60390 in C. reinhardtii (Cluster-2749.43263) was used to normalize the amount of template cDNA added in each reaction. 5. Conclusions We performed a transcriptome analysis of short-term acclimation to salt stress (200 mM NaCl for 24 h) in C. reinhardtii. In total, 10,635 unigenes were identified as differentially expressed in C. reinhardtii under salt stress by RNA-seq, including 5920 that were up- and 4715 that were down-regulated. A series of molecular cues were screened by GO terms, MapMan and KEGG functional enrichment analyses, which were identified as potential mechanisms for salt stress responses. These mainly include maintaining the lipid homeostasis by regulating phosphatidic acid, acetate being used as an alternative 19 Int. J. Mol. Sci. 2018, 19, 3359 source of energy for solving impairment of photosynthesis and enhancement of glycolysis metabolism to decrease the carbohydrate accumulation in cells. Our results may help understand the molecular and genetic underpinnings of salt responding traits in green alga C. reinhardtii. Supplementary Materials: The following are available online at http://www.mdpi.com/1422-0067/19/11/3359/s1, Figure S1: The assembled transcriptome information of C. reinhardtii, Figure S2: The FPKM density distribution of C. reinhardtii, Table S1: Unigenes of C. reinhardtii annotated in A. thaliana genome by BLASTX analysis, Table S2: Information of the 5920 up- and 4715 down-regulated unigenes in C. reinhardtii, Table S3: The Gene Ontology (GO) enrichment results of the dys-regulated genes in C. reinhardtii, Table S4: The MapMan pathways enrichment results of the dys-regulated genes in C. reinhardtii, Table S5: Information of the differently expressed transcription factors (TFs) and protein kinases (PKs), Table S6: Information of the qRT–PCR primers. Author Contributions: L.Z. and N.W. conceived and designed the study. L.Z., N.W., Z.Q., M.L., X.Z. performed the data collection and analysis. L.Z. and N.W. wrote the paper. L.Z., S.F. and X.Z. reviewed and edited the manuscript. All authors read and approved the manuscript. Funding: This work was supported by National Natural Science Foundation of China (31800185) and A Project of Shandong Province Higher Educational Science and Technology Program (J18KA147). Conflicts of Interest: The authors declare no conflict of interest. Abbreviations DEGs differentially expressed genes TFs transcriptional factors PKs protein kinases GO gene ontology FPKM fragment per kilobase of exon model per million mapped reads qRT-PCR real-time quantitative PCR BP biological processes PSI photosystem I PSII photosystem II PCD programmed cell death ROS reactive oxygen species PA phosphatidic acid References 1. Munns, R.; Tester, M. Mechanisms of salinity tolerance. Annu. Rev. Plant Boil. 2008, 59, 651–681. [CrossRef] [PubMed] 2. Song, J.; Wang, B.S. Using euhalophytes to understand salt tolerance and to develop saline agriculture: Suaeda salsa as a promising model. Ann. Bot. 2015, 115, 541–553. [CrossRef] [PubMed] 3. Epstein, E. Salt-tolerant crops: Origins, development, and prospects of the concept. Plant Soil 1985, 89, 187–198. [CrossRef] 4. Zhang, L.Y.; Zhang, X.J.; Fan, S.J. Meta-analysis of salt-related gene expression profiles identifies common signatures of salt stress responses in Arabidopsis. Plant Syst. Evol. 2017, 303, 757–774. [CrossRef] 5. Yuan, F.; Leng, B.Y.; Wang, B.S. Progress in Studying Salt Secretion from the Salt Glands in Recretohalophytes: How Do Plants Secrete Salt? Front. Plant Sci. 2016, 7, 977. [CrossRef] [PubMed] 6. Khona, D.K.; Shirolikar, S.M.; Gawde, K.K.; Hom, E.; Deodhar, M.A.; D’Souza, J.S. Characterization of salt stress-induced palmelloids in the green alga, Chlamydomonas Reinhardtii. Algal Res. 2016, 16, 434–448. [CrossRef] 7. Shen, X.Y.; Wang, Z.L.; Song, X.F.; Xu, J.J.; Jiang, C.Y.; Zhao, Y.X.; Ma, C.L.; Zhang, H. Transcriptomic profiling revealed an important role of cell wall remodeling and ethylene signaling pathway during salt acclimation in Arabidopsis. Plant Mol. Boil. 2014, 86, 303–317. [CrossRef] [PubMed] 8. Perrineau, M.M.; Zelzion, E.; Gross, J.; Price, D.C.; Boyd, J.; Bhattacharya, D. Evolution of salt tolerance in a laboratory reared population of Chlamydomonas Reinhardtii. Environ. Microbiol. 2014, 16, 1755–1766. [CrossRef] [PubMed] 9. Zhu, J.K. Plant salt tolerance. Trends Plant Sci. 2001, 6, 66–71. [CrossRef] 20 Int. J. Mol. Sci. 2018, 19, 3359 10. Shabala, S.; Munns, R.; Shabala, S. Salinity stress: Physiological constraints and adaptive mechanisms. In Plant Stress Physiology; CABI: Wallingford, UK, 2012. 11. Young, M.A.; Rancier, D.G.; Roy, J.L.; Lunn, S.R.; Armstrong, S.A.; Headley, J.V. Seeding conditions of the halophyte Atriplex patula for optimal growth on a salt impacted site. Int. J. Phytoremediat. 2011, 13, 674–680. [CrossRef] 12. Rao, A.R.; Sarada, R.; Ravishankar, G.A. Enhancement of carotenoids in green alga Botyrocccus braunii in various autotrophic media under stress conditions. Int. J. Biomed. Pharm. Sci. 2010, 4, 87–92. 13. Stanier, R.Y.; Kunisawa, R.; Mandel, M.; Cohenbazire, G. Purification and properties of unicellular blue-green algae (order Chroococcales). Bacteriol. Rev. 1971, 35, 171–205. [PubMed] 14. Liu, F.; Jin, Z.; Wang, Y.; Bi, Y.; Melton, R.J. Plastid Genome of Dictyopteris divaricata (Dictyotales, Phaeophyceae): Understanding the Evolution of Plastid Genomes in Brown Algae. Mar. Biotechnol. 2017, 19, 1–11. [CrossRef] [PubMed] 15. Sayed, O.H. Chlorophyll Fluorescence as a Tool in Cereal Crop Research. Photosynthetica 2003, 41, 321–330. [CrossRef] 16. Zuo, Z.; Chen, Z.; Zhu, Y.; Bai, Y.; Wang, Y. Effects of NaCl and Na2 CO3 stresses on photosynthetic ability of Chlamydomonas Reinhardtii. Biologia 2014, 69, 1314–1322. [CrossRef] 17. Fedina, I.S.; Georgieva, K.; Grigorova, I. Response of Barley Seedlings to UV-B Radiation as Affected by Proline and NaCl. J. Plant Physiol. 2003, 47, 549–554. [CrossRef] 18. Khan, N.A. NaCl-Inhibited Chlorophyll Synthesis and Associated Changes in Ethylene Evolution and Antioxidative Enzyme Activities in Wheat. Boil. Plant. 2003, 47, 437–440. [CrossRef] 19. Demetriou, G.; Neonaki, C.; Navakoudis, E.; Kotzabasis, K. Salt stress impact on the molecular structure and function of the photosynthetic apparatus—The protective role of polyamines. Biochim. Et Biophys. Acta 2007, 1767, 272–280. [CrossRef] [PubMed] 20. Liu, X.D.; Shen, Y.G. Salt shock induces state II transition of the photosynthetic apparatus in dark-adapted Dunaliella salina cells. Environ. Exp. Bot. 2006, 57, 19–24. [CrossRef] 21. Neelam, S.; Subramanyam, R. Alteration of photochemistry and protein degradation of photosystem II from Chlamydomonas reinhardtii under high salt grown cells. J. Photochem. Photobiol. B Boil. 2013, 124, 63–70. [CrossRef] [PubMed] 22. Vega, J.M.; Garbayo, I.; Domínguez, M.J.; Vigara, J. Effect of abiotic stress on photosynthesis and respiration in: Induction of oxidative stress. Enzym. Microb. Technol. 2007, 40, 163–167. [CrossRef] 23. Atkinson, N.J.; Lilley, C.J.; Urwin, P.E. Identification of genes involved in the response of Arabidopsis to simultaneous biotic and abiotic stresses. Plant Physiol. 2013, 162, 2028–2041. [CrossRef] [PubMed] 24. Han, N.; Lan, W.J.; He, X.; Shao, Q.; Wang, B.S.; Zhao, X.J. Expression of a Suaeda salsa Vacuolar H+ /Ca2+ Transporter Gene in Arabidopsis Contributes to Physiological Changes in Salinity. Plant Mol. Boil. Rep. 2012, 30, 470–477. [CrossRef] 25. Qi, Y.C.; Liu, W.Q.; Qiu, L.Y.; Zhang, S.M.; Ma, L.; Zhang, H. Overexpression of glutathione S-transferase gene increases salt tolerance of arabidopsis. Russ. J. Plant Physiol. 2010, 57, 233–240. [CrossRef] 26. Zhang, S.R.; Song, J.; Wang, H.; Feng, G. Effect of salinity on seed germination, ion content and photosynthesis of cotyledons in halophytes or xerophyte growing in Central Asia. J. Plant Ecol. 2010, 3, 259–267. [CrossRef] 27. Lu, T.; Lu, G.; Fan, D.; Zhu, C.; Wei, L.; Qiang, Z.; Qi, F.; Yan, Z.; Guo, Y.; Li, W. Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq. Genome Res. 2010, 20, 1238–1249. [CrossRef] [PubMed] 28. Liu, A.; Xiao, Z.; Li, M.W.; Wong, F.L.; Yung, W.S.; Ku, Y.S.; Wang, Q.; Wang, X.; Xie, M.; Yim, A.K. Transcriptomic reprogramming in soybean seedlings under salt stress. Plant Cell Environ. 2018. [CrossRef] [PubMed] 29. Cui, F.; Sui, N.; Duan, G.; Liu, Y.; Han, Y.; Liu, S.; Wan, S.; Li, G. Identification of Metabolites and Transcripts Involved in Salt Stress and Recovery in Peanut. Front. Plant Sci. 2018, 9, 217. [CrossRef] [PubMed] 30. Guo, J.; Li, Y.; Han, G.; Song, J.; Wang, B. NaCl markedly improved the reproductive capacity of the euhalophyte Suaeda Salsa. Funct. Plant Boil. 2018, 45, 350. [CrossRef] 31. Cao, S.; Du, X.H.; Li, L.H.; Liu, Y.D.; Zhang, L.; Pan, X.; Li, Y.; Li, H.; Lu, H. Overexpression of Populus tomentosa cytosolic ascorbate peroxidase enhances abiotic stress tolerance in tobacco plants. Russ. J. Plant Physiol. 2017, 64, 224–234. [CrossRef] 21 Int. J. Mol. Sci. 2018, 19, 3359 32. Sui, N.; Tian, S.S.; Wang, W.Q.; Wang, M.J.; Fan, H. Overexpression of Glycerol-3-Phosphate Acyltransferase from Suaeda salsa Improves Salt Tolerance in Arabidopsis. Front. Plant Sci. 2017, 8, 1337. [CrossRef] [PubMed] 33. Wang, J.S.; Zhang, Q.; Cui, F.; Hou, L.; Zhao, S.Z.; Xia, H.; Qiu, J.J.; Li, T.T.; Zhang, Y.; Wang, X.J.; et al. Genome-Wide Analysis of Gene Expression Provides New Insights into Cold Responses in Thellungiella Salsuginea. Front. Plant Sci. 2017, 8, 713. [CrossRef] [PubMed] 34. Yuan, F.; Lyu, M.J.A.; Leng, B.Y.; Zhu, X.G.; Wang, B.S. The transcriptome of NaCl-treated Limonium bicolor leaves reveals the genes controlling salt secretion of salt gland. Plant Mol. Boil. 2016, 91, 241–256. [CrossRef] [PubMed] 35. Yuan, F.; Lyu, M.J.A.; Leng, B.Y.; Zheng, G.Y.; Feng, Z.T.; Li, P.H.; Zhu, X.G.; Wang, B.S. Comparative transcriptome analysis of developmental stages of the Limonium bicolor leaf generates insights into salt gland differentiation. Plant Cell Environ. 2015, 38, 1637–1657. [CrossRef] [PubMed] 36. Feng, Z.T.; Deng, Y.Q.; Fan, H.; Sun, Q.J.; Sui, N.; Wang, B.S. Effects of NaCl stress on the growth and photosynthetic characteristics of Ulmus pumila L. seedlings in sand culture. Photosynthetica 2014, 52, 313–320. [CrossRef] 37. Yuan, F.; Chen, M.; Yang, J.C.; Leng, B.Y.; Wang, B.S. A system for the transformation and regeneration of the recretohalophyte Limonium bicolor. In Vitro Cell. Dev. Boil. Plant 2014, 50, 610–617. [CrossRef] 38. Zhang, Q.; Zhao, C.Z.; Li, M.; Sun, W.; Liu, Y.; Xia, H.; Sun, M.N.; Li, A.Q.; Li, C.S.; Zhao, S.Z.; et al. Genome-wide identification of Thellungiella salsuginea microRNAs with putative roles in the salt stress response. BMC Plant Boil. 2013, 13, 180. [CrossRef] [PubMed] 39. Guo, Y.H.; Jia, W.J.; Song, J.; Wang, D.A.; Chen, M.; Wang, B.S. Thellungilla halophila is more adaptive to salinity than Arabidopsis thaliana at stages of seed germination and seedling establishment. Acta Physiol. Plant. 2012, 34, 1287–1294. [CrossRef] 40. Liu, J.; Zhang, F.; Zhou, J.J.; Chen, F.; Wang, B.S.; Xie, X.Z. Phytochrome B control of total leaf area and stomatal density affects drought tolerance in rice. Plant Mol. Boil. 2012, 78, 289–300. [CrossRef] [PubMed] 41. Zhou, J.C.; Fu, T.T.; Sui, N.; Guo, J.R.; Feng, G.; Fan, J.L.; Song, J. The role of salinity in seed maturation of the euhalophyte Suaeda Salsa. Plant Biosyst. 2016, 150, 83–90. [CrossRef] 42. Waśkiewicz, A.; Muzolf-Panek, M.; Goliński, P. Phenolic Content Changes in Plants under Salt Stress; Springer: New York, NY, USA, 2013; pp. 283–314. 43. Sudhir, P.; Murthy, S.D.S. Effects of salt stress on basic processes of photosynthesis. Photosynthetica 2004, 42, 481–486. [CrossRef] 44. Maršálek, B.; Zahradníčková, H.; Hronková, M. Extracellular Production of Abscisic Acid by Soil Algae under Salt, Acid or Drought Stress. Z. Für Naturforschung C 1992, 47, 701–704. [CrossRef] 45. Pineau, B.; Gérard-Hirne, C.; Selve, C. Carotenoid binding to photosystems I and II of Chlamydomonas reinhardtii, cells grown under weak light or exposed to intense light. Plant Physiol. Bioch. 2001, 39, 73–85. [CrossRef] 46. Ding, F.; Chen, M.; Sui, N.; Wang, B.S. Ca2+ significantly enhanced development and salt-secretion rate of salt glands of Limonium bicolor under NaCl treatment. S. Afr. J. Bot. 2010, 76, 95–101. [CrossRef] 47. Feng, Z.T.; Deng, Y.Q.; Zhang, S.C.; Liang, X.; Yuan, F.; Hao, J.L.; Zhang, J.C.; Sun, S.F.; Wang, B.S. K+ accumulation in the cytoplasm and nucleus of the salt gland cells of Limonium bicolor accompanies increased rates of salt secretion under NaCl treatment using NanoSIMS. Plant Sci. 2015, 238, 286–296. [CrossRef] [PubMed] 48. Han, N.; Shao, Q.; Bao, H.Y.; Wang, B.S. Cloning and Characterization of a Ca2+ /H+ Antiporter from Halophyte Suaeda salsa L. Plant Mol. Boil. Rep. 2011, 29, 449–457. [CrossRef] 49. Yang, S.; Li, L.; Zhang, J.; Geng, Y.; Guo, F.; Wang, J.; Meng, J.; Sui, N.; Wan, S.; Li, X. Transcriptome and Differential Expression Profiling Analysis of the Mechanism of Ca(2+ ) Regulation in Peanut (Arachis hypogaea) Pod Development. Front. Plant Sci. 2017, 8, 1609. [CrossRef] [PubMed] 50. Zheng, Y.; Liao, C.C.; Zhao, S.S.; Wang, C.W.; Guo, Y. The Glycosyltransferase QUA1 Regulates Chloroplast-Associated Calcium Signaling During Salt and Drought Stress in Arabidopsis. Plant Cell Physiol. 2017, 58, 329–341. [CrossRef] [PubMed] 51. Zhang, L.Y.; Zhang, Z.; Zhang, X.J.; Yao, Y.; Wang, R.; Duan, B.Y.; Fan, S.J. Comprehensive meta-analysis and co-expression network analysis identify candidate genes for salt stress response in Arabidopsis. Plant Biosyst. 2018. [CrossRef] 22 Int. J. Mol. Sci. 2018, 19, 3359 52. Arisz, S.A.; Valianpour, F.; van Gennip, A.H.; Munnik, T. Substrate preference of stress-activated phospholipase D in Chlamydomonas and its contribution to PA formation. Plant J. Cell Mol. Boil. 2003, 34, 595–604. [CrossRef] 53. Zhou, J.J.; Liu, Q.Q.; Zhang, F.; Wang, Y.Y.; Zhang, S.Y.; Cheng, H.M.; Yan, L.H.; Li, L.; Chen, F.; Xie, X.Z. Overexpression of OsPIL15, a phytochromeinteracting factor- like protein gene, represses etiolated seedling growth in rice. J. Integr. Plant Boil. 2014, 56, 373–387. [CrossRef] [PubMed] 54. Sui, N.; Li, M.; Li, K.; Song, J.; Wang, B.S. Increase in unsaturated fatty acids in membrane lipids of Suaeda salsa L. enhances protection of photosystem II under high salinity. Photosynthetica 2010, 48, 623–629. [CrossRef] 55. Arisz, S.A.; Munnik, T. The salt stress-induced LPA response in Chlamydomonas is produced via PLA2 hydrolysis of DGK-generated phosphatidic acid. J. Lipid Res. 2011, 52, 2012–2020. [CrossRef] [PubMed] 56. Meijer, H.J.; Arisz, S.A.; Van Himbergen, J.A.; Musgrave, A.; Munnik, T. Hyperosmotic stress rapidly generates lyso-phosphatidic acid in Chlamydomonas. Plant J. 2010, 25, 541–548. [CrossRef] 57. Takagi, M.; Karseno; Yoshida, T. Effect of Salt Concentration on Intracellular Accumulation of Lipids and Triacylglyceride in Marine Microalgae Dunaliella Cells. J. Biosci. Bioeng. 2006, 101, 223–226. [CrossRef] [PubMed] 58. Goyal, A. Osmoregulation in Dunaliella, Part II: Photosynthesis and starch contribute carbon for glycerol synthesis during a salt stress in Dunaliella tertiolecta. Plant Physiol. Biochem. 2007, 45, 705–710. [CrossRef] [PubMed] 59. Yokthongwattana, C.; Mahong, B.; Roytrakul, S.; Phaonaklop, N.; Narangajavana, J.; Yokthongwattana, K. Proteomic analysis of salinity-stressed Chlamydomonas reinhardtii revealed differential suppression and induction of a large number of important housekeeping proteins. Planta 2012, 235, 649–659. [CrossRef] [PubMed] 60. Sun, Z.B.; Qi, X.Y.; Wang, Z.L.; Li, P.H.; Wu, C.X.; Zhang, H.; Zhao, Y.X. Overexpression of TsGOLS2, a galactinol synthase, in Arabidopsis thaliana enhances tolerance to high salinity and osmotic stresses. Plant Physiol. Biochem. 2013, 69, 82–89. [CrossRef] [PubMed] 61. Pang, C.H.; Li, K.; Wang, B.S. Overexpression of SsCHLAPXs confers protection against oxidative stress induced by high light in transgenic Arabidopsis thaliana. Physiol. Plant. 2011, 143, 355–366. [CrossRef] [PubMed] 62. Ferjani, A.; Mustardy, L.; Sulpice, R.; Marin, K.; Suzuki, I.; Hagemann, M.; Murata, N. Glucosylglycerol, a compatible solute, sustains cell division under salt stress. Plant Physiol. 2003, 131, 1628–1637. [CrossRef] [PubMed] 63. Zeid, I.M. Trehalose as osmoprotectant for maize under salinity-induced stress. Res. J. Agric. Boil. Sci. 2009, 5, 613–622. 64. Xu, J.J.; Li, Y.Y.; Ma, X.L.; Ding, J.F.; Wang, K.; Wang, S.S.; Tian, Y.; Zhang, H.; Zhu, X.G. Whole transcriptome analysis using next-generation sequencing of model species Setaria viridis to support C4 photosynthesis research. Plant Mol. Boil. 2013, 83, 77–87. [CrossRef] [PubMed] 65. Sui, N.; Han, G.L. Salt-induced photoinhibition of PSII is alleviated in halophyte Thellungiella halophila by increases of unsaturated fatty acids in membrane lipids. Acta Physiol. Plant. 2014, 36, 983–992. [CrossRef] 66. Heifetz, P.B.; Boynton, J.E. Effects of Acetate on Facultative Autotrophy in Chlamydomonas reinhardtii Assessed by Photosynthetic Measurements and Stable Isotope Analyses. Plant Physiol. 2000, 122, 1439–1445. [CrossRef] [PubMed] 67. Soussi, M.; Ocaña, A.; Lluch, C. Effects of salt stress on growth, photosynthesis and nitrogen fixation in chick-pea (Cicer arietinum L.). J. Exp. Bot. 1998, 49, 1329–1337. [CrossRef] 68. Zhong, M.; Yuan, Y.; Shu, S.; Sun, J.; Guo, S.; Yuan, R.; Tang, Y. Effects of exogenous putrescine on glycolysis and Krebs cycle metabolism in cucumber leaves subjected to salt stress. Plant Growth Regul. 2016, 79, 319–330. [CrossRef] 69. Huang, J.; Li, Z.Y.; Biener, G.; Xiong, E.H.; Malik, S.; Eaton, N.; Zhao, C.Z.; Raicu, V.; Kong, H.Z.; Zhao, D.Z. Carbonic Anhydrases Function in Anther Cell Differentiation Downstream of the Receptor-Like Kinase EMS1. Plant Cell 2017, 29, 1335–1356. [CrossRef] [PubMed] 70. Wang, F.X.; Xu, Y.G.; Wang, S.; Shi, W.W.; Liu, R.R.; Feng, G.; Song, J. Salinity affects production and salt tolerance of dimorphic seeds of Suaeda Salsa. Plant Physiol. Biochem. 2015, 95, 41–48. [CrossRef] [PubMed] 71. Shao, Q.; Han, N.; Ding, T.L.; Zhou, F.; Wang, B.S. SsHKT1;1 is a potassium transporter of the C3 halophyte Suaeda salsa that is involved in salt tolerance. Funct. Plant Boil. 2014, 41, 790–802. [CrossRef] 23 Int. J. Mol. Sci. 2018, 19, 3359 72. Li, K.; Pang, C.H.; Ding, F.; Sui, N.; Feng, Z.T.; Wang, B.S. Overexpression of Suaeda salsa stroma ascorbate peroxidase in Arabidopsis chloroplasts enhances salt tolerance of plants. S. Afr. J. Bot. 2012, 78, 235–245. [CrossRef] 73. Liu, S.S.; Wang, W.Q.; Li, M.; Wan, S.B.; Sui, N. Antioxidants and unsaturated fatty acids are involved in salt tolerance in peanut. Acta Physiol. Plant. 2017, 39, 207. [CrossRef] 74. Chen, M.; Song, J.; Wang, B.S. NaCl increases the activity of the plasma membrane H+ -ATPase in C3 halophyte Suaeda salsa callus. Acta Physiol. Plant. 2010, 32, 27–36. [CrossRef] 75. Song, J.; Shi, G.W.; Gao, B.; Fan, H.; Wang, B.S. Waterlogging and salinity effects on two Suaeda salsa populations. Physiol. Plant. 2011, 141, 343–351. [CrossRef] [PubMed] 76. Meng, X.; Yang, D.Y.; Li, X.D.; Zhao, S.Y.; Sui, N.; Meng, Q.W. Physiological changes in fruit ripening caused by overexpression of tomato SlAN2, an R2R3-MYB factor. Plant Physiol. Biochem. 2015, 89, 24–30. [CrossRef] [PubMed] 77. Li, Y.Y.; Ma, X.L.; Zhao, J.L.; Xu, J.J.; Shi, J.F.; Zhu, X.G.; Zhao, Y.X.; Zhang, H. Developmental Genetic Mechanisms of C4 Syndrome Based on Transcriptome Analysis of C3 Cotyledons and C4 Assimilating Shoots in Haloxylon Ammodendron. PLoS ONE 2015, 10, e0117175. [CrossRef] [PubMed] 78. Grabherr, M.G.; Haas, B.J.; Yassour, M.; Levin, J.Z.; Thompson, D.A.; Amit, I.; Adiconis, X.; Fan, L.; Raychowdhury, R.; Zeng, Q.; et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 2011, 29, 644–652. [CrossRef] [PubMed] 79. Li, B.; Dewey, C.N. RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform. 2011, 12, 323. [CrossRef] [PubMed] 80. Haas, B.J.; Papanicolaou, A.; Yassour, M.; Grabherr, M.; Blood, P.D.; Bowden, J.; Couger, M.B.; Eccles, D.; Li, B.; Lieber, M. De novo transcript sequence reconstruction from RNA-Seq: Reference generation and analysis with Trinity. Nat. Protoc. 2013, 8, 1494–1512. [CrossRef] [PubMed] 81. Zheng, Y.; Jiao, C.; Sun, H.; Rosli, H.G.; Pombo, M.A.; Zhang, P.; Banf, M.; Dai, X.; Martin, G.B.; Giovannoni, J.J.; et al. iTAK: A Program for Genome-wide Prediction and Classification of Plant Transcription Factors, Transcriptional Regulators, and Protein Kinases. Mol. Plant 2016, 9, 1667–1670. [CrossRef] [PubMed] 82. Okuda, S.; Yamada, T.; Hamajima, M.; Itoh, M.; Katayama, T.; Bork, P.; Goto, S.; Kanehisa, M. KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res. 2008, 36, W423–W426. [CrossRef] [PubMed] 83. Wu, J.; Mao, X.; Cai, T.; Luo, J.; Wei, L. KOBAS server: A web-based platform for automated annotation and pathway identification. Nucleic Acids Res. 2006, 34, W720–W724. [CrossRef] [PubMed] 84. Thimm, O.; Blasing, O.; Gibon, Y.; Nagel, A.; Meyer, S.; Kruger, P.; Selbig, J.; Muller, L.A.; Rhee, S.Y.; Stitt, M. MAPMAN: A user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. Cell Mol. Boil. 2004, 37, 914–939. [CrossRef] 85. Livak, K.J.; Schmittgen, T.D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C (T)) Method. Methods 2001, 25, 402–408. [CrossRef] [PubMed] © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). 24 International Journal of Molecular Sciences Article Analysis of bZIP Transcription Factor Family and Their Expressions under Salt Stress in Chlamydomonas reinhardtii Chunli Ji, Xue Mao, Jingyun Hao, Xiaodan Wang, Jinai Xue, Hongli Cui and Runzhi Li * Institute of Molecular Agriculture and Bioenergy, Shanxi Agricultural University, Taigu 030801, China; [email protected] (C.J.); [email protected] (X.M.); [email protected] (J.H.); [email protected] (X.W.); [email protected] (J.X.); [email protected] (H.C.) * Correspondence: [email protected]; Tel.: +86-354-628-8344 Received: 20 July 2018; Accepted: 14 September 2018; Published: 17 September 2018 Abstract: The basic leucine-region zipper (bZIP) transcription factors (TFs) act as crucial regulators in various biological processes and stress responses in plants. Currently, bZIP family members and their functions remain elusive in the green unicellular algae Chlamydomonas reinhardtii, an important model organism for molecular investigation with genetic engineering aimed at increasing lipid yields for better biodiesel production. In this study, a total of 17 C. reinhardtii bZIP (CrebZIP) TFs containing typical bZIP structure were identified by a genome-wide analysis. Analysis of the CrebZIP protein physicochemical properties, phylogenetic tree, conserved domain, and secondary structure were conducted. CrebZIP gene structures and their chromosomal assignment were also analyzed. Physiological and photosynthetic characteristics of C. reinhardtii under salt stress were exhibited as lower cell growth and weaker photosynthesis, but increased lipid accumulation. Meanwhile, the expression profiles of six CrebZIP genes were induced to change significantly during salt stress, indicating that certain CrebZIPs may play important roles in mediating photosynthesis and lipid accumulation of microalgae in response to stresses. The present work provided a valuable foundation for functional dissection of CrebZIPs, benefiting the development of better strategies to engineer the regulatory network in microalgae for enhancing biofuel and biomass production. Keywords: Chlamydomonas reinhardtii; bZIP transcription factors; salt stress; transcriptional regulation; photosynthesis; lipid accumulation 1. Introduction Microalgae are considered to be one of the most promising feedstocks for renewable biofuel production. However, the shortage of inexpensive algal biomass currently hampers microalgae-based biofuel industrialization [1]. Microalgae accumulate high level of lipids, mainly in the form of triacylglycerol (TAG), when subjected to nutrient deprivation and other stresses [2–5]. In parallel, these adverse conditions also limit algal biomass accumulation. Consequently, genetic engineering to achieve an optimized balance between oil accumulation and biomass growth may represent an effective strategy for the improvement of microalgae biofuel yield. Therefore, it is necessary to comprehensively analyze the underlying molecular mechanisms that mediate stress-induced accumulation of oil in microalgae, particularly to identify the key transcription factors (TFs). The unicellular algae Chlamydomonas reinhardtii is the de facto model organism for research in microalgae. Various types of omics data for C. reinhardtii are available, including its full genome [6], the proteomics and metabolomics analysis, and the phenotype transition during N starvation [7–13]. These achievements provide the basis for further investigation into oil metabolism and regulation in C. reinhardtii, Int. J. Mol. Sci. 2018, 19, 2800; doi:10.3390/ijms19092800 25 www.mdpi.com/journal/ijms Int. J. Mol. Sci. 2018, 19, 2800 which would shed light on the development of rational strategies for sustainable production of microalgae biofuel. Transcription factor (TF) encoding genes are considered as contributing to the diversity and evolution in plants. Identification of the transcriptional factors and their cognate transcriptional factor binding-sites is essential in manipulating the regulatory network for desired traits of the target molecules [14]. Moreover, the control of transcription initiation rates by transcription factors is an important means to modulate gene expression, and then regulate the organism growth and development [15]. The basic region-leucine zipper (bZIP) family is one of the most conserved and wildly distributed TFs present in multiple eukaryotes. To date, they have been extensively investigated in many plants including Arabidopsis, rice, tomato, maize, sorghum, carrot, and so forth [16–22]. The bZIP TFs have been found to mediate various biological processes, such as cell elongation [23], organ and tissue differentiation [24–26], energy metabolism [27], embryogenesis and seed maturation [28], and so forth. The bZIP TFs also participate in plant responses to biotic and abiotic stresses, including pathogen defense [29,30], hormone and sugar signaling [31,32], light response [33,34], salt and drought tolerance [20,35], and so forth. Typically, bZIP TFs contain a conserved 40–80 amino acid (aa) domain which has two structure motifs: A DNA-binding basic region and a leucine zipper dimerization domain [15]. The basic region composing of around 20 amino acid residues with an invariant N-X7-R/K-X9 motif is highly conserved, and the main function of this region is for nuclear localization and DNA binding. The leucine zipper containing a heptad repeat of leucine is less conserved, with the property for recognition and dimerization [21]. The diversified leucine zipper region is located exactly 9 aa downstream from the C-terminal of the basic region. Although bZIP family members were intensively reported to mediate diverse stress responses in higher plants, little attention has been paid to studying bZIP TFs and their downstream target genes on a genome-wide scale in microalgae. A total of 147 putative TFs of 29 different protein families have been identified in C. reinhardtii, including 1 WRKY, 4 bHLH, 5 C2H2, 11 MYB, 2 MADS, 7 bZIP TFs, and so forth [36]. However, functions remain unclear for the majority of these TFs. The bZIP family is also one of the four largest TF families in oleaginous microalgae Nannochloropsis [14], showing that some bZIPs were putatively related with the transcriptional regulation of TAG biosynthesis pathways in Nannochloropsis. Therefore, the present study focused on the genome-wide identification of bZIP TFs in C. reinhardtii and their functional analysis, with an objective to elucidate the mechanism underlying the regulation of fatty acid and oil accumulation, and photosynthesis in microalgae, particularly under stresses. In this study, the bZIP sequences of C. reinhardtii were intensively identified using a proteomic database, and a total of 17 CrebZIP TFs were obtained after removing the redundancy. Bioinformatics tools were employed to perform a detailed analysis of their genetic structure, chromosome distribution, classification, protein domain, and motifs, as well as evolutionary relationship. Furthermore, the physiological and photosynthetic characteristics of C. reinhardtii under salt stress were measured, including biomass concentration, lipid and pigment contents, as well as chlorophyll fluorescence variation. Finally, to infer the potential functions of these CrebZIPs, the expression profiles of CrebZIP genes under salt stress were quantitatively examined using quantitative real time (qRT)-PCR. Thus, these integrated data would provide new insights into comprehensive understanding of the stress-adaptive mechanisms and oil accumulation mediated by bZIP TFs in C. reinhardtii and other microalgae. 2. Results and Discussion 2.1. Identification of C. reinhardtii bZIP Family Members To perform genome-wide identification of bZIP proteins in C. reinhardtii, BLAST and the Hidden Markov Model (HMM) profiles of the bZIP domain were used to screen the C. reinhardtii genome and proteome database, with bZIP sequences from Arabidopsis as the query. A total of 17 CrebZIP genes in 26 Int. J. Mol. Sci. 2018, 19, 2800 C. reinhardtii were identified and denominated as CrebZIP1–CrebZIP17 based on their locations in the chromosome (Table 1). The number of CrebZIPs obtained here was not consistent with previous reports. Corrêa et al. and Riano-Pachon et al. identified 7 putative CrebZIP TF coding sequences [15,36]. However, study on the evolution of bZIP family TFs among different plants by Que et al. detected 19 bZIP TFs in C. reinhardtii. They summarized that the number of bZIP TFs in algae (less than 20) and land plants (greater than 25) differed remarkably, and bZIP TFs might thus have expanded many times during plant evolution [22]. Such difference in bZIP numbers in C. reinhardtii might have resulted from different versions of the C. reinhardtii genome and protein database, and criteria used in those reports. Conserved Domain Database (CDD) and Simple Modular Architecture Research Tool (SMART) analysis indicated that the 17 CrebZIP proteins all had typical bZIP conserved domains. Table 1 summarizes their physicochemical properties, including the protein length which ranged from 334 (CrebZIP13) to 2018 (CrebZIP1) amino acids, the corresponding molecular weight which varied from 3,4514.92 to 198,080.64 Da, and theoretical isoelectric point (pI) which varied from 4.96 (CrebZIP13) to 9.55 (CrebZIP12). The great difference in these properties may reflect their functional diversity in C. reinhardtii. The minus hydrophility of all CrebZIP proteins and their higher instability index (>40) showed that they were hydrophilic and unstable. To get the protein structure information of these CrebZIP members, the secondary structure of the proteins was predicted by the PBIL LYON-GERLAND database. The secondary structure information is listed in Table 2, including α-helix, extended strand, and random coil. Of them, random coil accounted for a higher percentage (45.23–72.75%), while extended strand had the lowest proportion (0.42–8.73%). No β-bridge was detected in CrebZIPs. 27 Table 1. Physicochemical properties of CrebZIP gene coding proteins. NCBI Accession Phytozome Chromosome Localization Molecular Instability Gene Number Protein Length (aa) Theoretical pI Hydrophility Number Identifier (bp) Weight (Da) Index CrebZIP1 PNW88934.1 Cre01.g051174 Chr.1: 7078516–7088297 2018 198,080.64 6.00 −0.422 68.82 CrebZIP2 PNW83651.1 Cre05.g238250 Chr.5: 2933060–2936249 524 53,624.16 5.47 −0.045 58.98 CrebZIP3 PNW80451.1 Cre07.g318050 Chr.7: 782941–789359 802 82,929.15 6.16 −0.406 59.38 CrebZIP4 PNW80535.1 Cre07.g321550 Chr.7: 1255642–1260306 393 41,429.96 5.48 −0.510 44.72 CrebZIP5 PNW81157.1 Cre07.g344668 Chr.7: 4675427–4680202 750 72,176.41 6.18 −0.046 65.59 Int. J. Mol. Sci. 2018, 19, 2800 CrebZIP6 PNW79382.1 Cre09.g413050 Chr.9: 7331940–7342521 1053 106,414.13 6.42 −0.401 54.24 CrebZIP7 PNW77489.1 Cre10.g438850 Chr.10: 2769177–2772294 485 49,874.20 6.64 −0.678 58.82 CrebZIP8 PNW77864.1 Cre10.g454850 Chr.10: 4910181–4919296 1363 128,662.31 8.75 −0.249 64.61 CrebZIP9 PNW74780.1 Cre12.g510200 Chr.12: 2010086–2013670 353 35, 933.29 6.36 −0. 398 58.58 CrebZIP10 PNW74984.1 Cre12.g501600 Chr.12: 2939321–2944866 902 89,920.31 6.25 −0.274 56.84 CrebZIP11 PNW75863.1 Cre12.g557300 Chr.12: 7330581–7337724 1526 154,908.24 9.40 −0.719 65.07 CrebZIP12 PNW73681.1 Cre13.g568350 Chr.13: 981891–989596 1150 114,710.75 9.55 −0.563 68.90 CrebZIP13 XP_001693067.1 Cre13.g590350 Chr.13: 3885273–3888238 334 34,514.92 4.96 −0.172 58.83 CrebZIP14 PNW71231.1 Cre16.g692250 Chr.16: 591049–600037 1525 153,084.80 5.30 −0.558 72.50 CrebZIP15 PNW71414.1 Cre16.g653300 Chr.16: 1524635–1531081 867 90,393.04 6.11 −0.374 55.17 CrebZIP16 PNW72253.1 Cre16.g675700 Chr.16: 6123854–6131215 1172 115,285.37 6.48 −0.512 46.46 CrebZIP17 PNW71098.1 Cre17.g746547 Chr.17: 7009739–7013345 767 75,438.72 6.01 −0.379 55.72 28 Int. J. Mol. Sci. 2018, 19, 2800 Table 2. Secondary structure of CrebZIP proteins. Gene Number Alpha Helix (%) Extended Strand (%) Beta Bridge (%) Random Coil (%) CrebZIP1 24.58 2.68 0 72.75 CrebZIP2 53.24 1.53 0 45.23 CrebZIP3 36.41 8.73 0 54.86 CrebZIP4 45.29 1.53 0 53.18 CrebZIP5 41.60 0.80 0 57.60 CrebZIP6 43.49 2.94 0 53.56 CrebZIP7 45.80 0.42 0 53.78 CrebZIP8 30.01 3.67 0 66.32 CrebZIP9 36.54 8.22 0 55.24 CrebZIP10 38.03 3.77 0 58.20 CrebZIP11 26.34 4.59 0 69.07 CrebZIP12 39.57 3.22 0 57.22 CrebZIP13 50.30 3.59 0 46.11 CrebZIP14 39.08 1.70 0 59.21 CrebZIP15 46.25 1.85 0 51.90 CrebZIP16 33.19 1.88 0 64.93 CrebZIP17 27.38 3.00 0 69.62 2.2. Phylogenetic and Motif Analysis of CrebZIP Proteins To explore the evolution and classification of CrebZIP TFs, we performed a phylogenetic analysis (Figure 1) of 17 CrebZIP and 11 AtbZIP protein sequences. AtbZIPs were selected according to the classification of Arabidopsis bZIP proteins. Ten groups of AtbZIP proteins named Group A, B, C, D, E, F, G, H, I, and S were defined according to the sequence similarity of the basic region and other conserved motifs [17]. Those AtbZIP proteins that did not fit into any group mentioned above were classified as Group U (unknown). One AtbZIP protein was selected from each group respectively, including AtbZIP12 (Group A), AtbZIP17 (Group B), AtbZIP9 (Group C), AtbZIP20 (Group D), AtbZIP34 (Group E), AtbZIP19 (Group F), AtbZIP16 (Group G), AtbZIP56 (Group H), AtbZIP18 (Group I), AtbZIP1 (Group S), and AtbZIP60 (Group U). As shown in Figure 1, most bZIP members from the same species tended to cluster together. Only three CrebZIPs (CrebZIP2, 7, and 15) were grouped together with three AtbZIPs (AtbZIP16, 17 and 20), respectively, forming three subfamilies. Analysis on sequence identity and the similarity of bZIP proteins between C. reinhardtii and Arabidopsis grouped in the same subfamilies, showed low levels of amino acid conservation between the two species. CrebZIP2 and AtbZIP16 had 10.8% identity and 14.4% similarity, while CrebZIP7 and AtbZIP17 exhibited 10.5% identity and 16.9% similarity. The third pair of CrebZIP15 and AtbZIP20 only had 6.6% identity and 11.6% similarity. The remaining 14 CrebZIPs were grouped into 8 subfamilies, with each containing two CrebZIP members except for CrebZIP1 and CrebZIP5, which were classified as two single-member subfamilies. It is possible that the 14 CrebZIPs may have independent ancestral origins different from the AtbZIPs, in consideration of the fact that C. reinhardtii is a lower plant, while Arabidopsis is a higher plant. To extend the bZIP analysis to larger lineages of green plants, bZIP members from two bryophytes including Physcomitrella patens and Marchantia polymorpha were also added into the phylogenetic analysis, as bryophytes are considered as one of the earliest diverging distant land-plant lineages. Table S1 shows 43 PpbZIP genes from P. patens and 14 MpbZIP genes from M. polymorpha that were identified. SMART analysis indicated that these bZIP proteins all had the typical bZIP conserved domains. The phylogenetic analysis of bZIP proteins from C. reinhardtii, Arabidopsis, P. patens, and M. polymophra indicated that most CrebZIP proteins were also not highly homologous with P. patens and M. polymorpha bZIPs (Figure S1). Two CrebZIPs (CrebZIP 2 and 6) and two MpbZIPs (MpbZIP4 and 12) clustered together, respectively. However, levels of identity and similarity were very low between the CrebZIPs and MpbZIPs grouped in the same subfamilies. The identity and similarity between CrebZIP2 and MpbZIP4 were 14.5% and 19.8%, respectively, while CrebZIP6 and MpbZIP12 only shared 8.6% identity and 13.4% similarity. 29