Molecular Evolution MBG306 Lecture 6 Dr. Oğuzhan Maraba Darwin’s First Tree of Life • I think case must be that one generation should have as many living as now To do this and to have as many species in same genus (as is) requires extinction Thus between A + B the immense gap of relation C + B the finest gradation B+D rather greater distinction Thus genera would be formed Bearing relation to ancient types with several extinct forms for if each species an ancient is capable of making 13 recent forms, twelve of the contemporaries must have left no offspring at all, so as to keep number of species constant — With respect to extinction we can easy see that variety of ostrich, Petise may not be well adapted, and thus perish out, or on other hand like Orpheus being favourable (page 38 ) many might be produced — This requires principle that the permanent varieties produced by inter confined breeding & changing circumstances are continued & produced according to the adaptation of such circumstances, & therefore that death of species is a consequence (contrary to what would appear from America) Tree of Life • Ernst Haeckel painstakingly drew up a much more comprehensive tree ( pictured ) This represented Earth’s wealth of species in the context of evolution — a concept he dubbed phylogeny ( General Morphology of Organisms ; 1866 ) • The root of the tree symbolizes a common primordial ancestor from which all other forms emerged Haeckel developed his tree over almost 1 , 000 pages, basing it on palaeontological, embryological and systemic data — a precursor to modern biology’s phylogenetic trees • He also coined the term ecology (‘oecologie’), describing it as “the whole science of the relations of the organism to the environment including, in the broad sense, all the ‘conditions of existence’” Hug, L , Baker, B , Anantharaman, K et al A new view of the tree of life Nat Microbiol 1 , 16048 ( 2016 ) https : //doi org/ 10 1038 /nmicrobiol 2016 48 Emergence of Prokaryotes Key steps in the evolution to prokaryotes could be considered as follows ; • Compartmentalization : The formation of a lipid membrane around a collection of biomolecules was crucial This membrane provided protection from the environment and confined biochemical activity, allowing for more efficient and individualized evolution by natural selection • Metabolic Complexity : Early protocells may have developed simple metabolic pathways, enabling them to harness energy and replicate their components The emergence of basic metabolic reactions set the stage for more sophisticated biochemistry • Genetic Information : The encapsulation of self - replicating molecules, such as RNA (as suggested by the RNA World hypothesis), allowed protocells to store and transmit genetic information This was a prerequisite for Darwinian evolution and the eventual development of DNA - based genomes • Selective Advantage : Encapsulation meant that beneficial mutations or catalytic activities would primarily benefit the protocell containing them, rather than diffusing to neighbouring molecules This increased the efficiency of natural selection and promoted the evolution of greater complexity Emergence of Prokaryotes • Over time, protocells that could better maintain their integrity, replicate more reliably, and carry out more efficient metabolic reactions were favoured • Prokaryotic cells, appearing around 3 8 – 3 9 billion years ago, became the first self - sufficient living organisms • Prokaryotes represent the earliest and most fundamental form of cellular life on Earth Their emergence marks a pivotal event in the history of biology, setting the stage for all subsequent evolution • They diversified rapidly, developing mechanisms for : • DNA replication • Transcription • Translation • Variety of metabolic strategies, including photosynthesis and respiration Emergence of Prokaryotes • Early Earth was characterized by a harsh environment : an anoxic (oxygen - free) atmosphere, intense volcanic activity, strong solar radiation, and frequent geological upheaval • The first prokaryotes likely thrived in protected environments such as deep oceans or beneath the Earth's surface, where they were shielded from radiation and temperature extremes Characteristics of Early Prokaryotes Key characteristics of early Prokaryotes are as follows : • Unicellular Structure : Early prokaryotes were single - celled organisms lacking a nucleus or any other membrane - bound organelles Their genetic material was located in a central region called the nucleoid • Simple Cell Organization : The cell structure included a plasma membrane, a rigid cell wall for protection and shape, and sometimes an additional capsule for extra protection and adherence to surfaces • Adaptation to Extreme Environments : Early Earth was characterized by high temperatures, strong radiation, volcanic activity, and an anoxic (oxygen - free) atmosphere Early prokaryotes were adapted to these harsh conditions, often thriving in deep oceans or beneath the surface where they were shielded from radiation Characteristics of Early Prokaryotes • Anaerobic Metabolism : Because the early atmosphere lacked oxygen, the first prokaryotes were anaerobic, meaning they did not require oxygen for survival Many were chemotrophs, obtaining energy from inorganic molecules near hydrothermal vents • Microbial Mats and Biofilms : Fossil evidence shows that early prokaryotes formed microbial mats — multi - layered sheets of bacteria and archaea held together by a sticky extracellular matrix These mats are among the earliest evidence of life and could be found at interfaces between materials, such as on moist surfaces or near hydrothermal vents • Metabolic Diversity : Even among early forms, prokaryotes displayed a range of metabolic pathways Some were phototrophs (using sunlight for energy), and later, cyanobacteria evolved the ability to perform oxygenic photosynthesis, eventually leading to the oxygenation of Earth’s atmosphere • Genetic Exchange and Adaptation : Structures such as pili allowed for genetic exchange between cells, increasing adaptability Flagella provided motility, enabling movement toward favourable environments Early Energy Metabolism • The first prokaryotes likely relied on anaerobic metabolism, breaking down organic molecules in the absence of oxygen through processes akin to glycolysis This anaerobic breakdown of glucose to simpler compounds (e g , lactic acid) generated small amounts of ATP, sufficient for primitive cellular functions but energetically inefficient compared to later pathways • Early energy production was mainly through substrate - level phosphorylation, where phosphate groups are transferred directly to ADP to form ATP without the involvement of oxygen or electron transport chains Early Energy Metabolism Prokaryotes evolved a wide range of metabolic strategies to exploit various energy sources These included : • Chemotrophy : Using inorganic molecules such as hydrogen, sulphur compounds, or iron as electron donors • Phototrophy : Some bacteria developed photosynthesis, initially anoxygenic (not producing oxygen), using light energy to drive metabolism • Oxygenic Photosynthesis : Cyanobacteria evolved the ability to use water as an electron donor, releasing oxygen as a byproduct This innovation dramatically changed Earth's atmosphere during the Great Oxidation Event and enabled aerobic metabolism • The metabolic network of the last bacterial common ancestor (LBCA) included pathways for autotrophic carbon fixation (acetyl - CoA pathway), gluconeogenesis, and energy generation without oxygen, indicating a complex and versatile metabolism early on Regulatory and Network Adaptations • Prokaryotes developed sophisticated regulatory systems to optimize metabolic responses to environmental changes For example, redox - sensing regulators modulate gene expression during shifts between aerobic and anaerobic conditions, adjusting pathways such as nitrate respiration and fermentation to maintain energy production • Horizontal gene transfer played a critical role in metabolic innovation by allowing prokaryotes to acquire entire functional gene modules, including new enzymes and regulatory elements, enabling rapid adaptation to new nutrients and environments • The metabolic toolbox of prokaryotes expanded with genome size, allowing reuse of enzymes and efficient incorporation of new metabolic pathways, which contributed to the quadratic scaling of transcription factors relative to gene number Diversification of Prokaryotes Prokaryotes, encompassing the domains Bacteria and Archaea, represent the most ancient and diverse forms of life on Earth Their diversification is driven by several key factors : • Genetic Diversity : Prokaryotes reproduce rapidly via binary fission, often completing a generation in minutes Although binary fission produces genetically identical clones, prokaryotes have evolved mechanisms for genetic recombination — transformation (uptake of external DNA), transduction (virus - mediated DNA transfer), and conjugation (direct DNA transfer between cells) — which introduce genetic variability This rapid turnover and genetic exchange enable swift adaptation to changing environments and the evolution of new traits, such as antibiotic resistance Diversification of Prokaryotes • Metabolic Versatility : Prokaryotes exhibit extraordinary metabolic diversity They can obtain energy from sunlight (phototrophs) or chemical compounds (chemotrophs), and use a wide range of electron donors and acceptors This versatility allows them to occupy virtually every ecological niche, from deep - sea vents to acidic hot springs and polar ice • Habitat Range : Prokaryotes are ubiquitous, inhabiting every environment on Earth — including extreme conditions such as boiling springs, highly saline lakes, deep ocean trenches, and radioactive sites Archaea are especially noted for thriving in extreme environments, while bacteria are found in more moderate conditions as well as on and inside other living organisms Ecological Impact of Prokaryotes • Nutrient Cycling : Prokaryotes are essential to global nutrient cycles, including the carbon, nitrogen, and sulphur cycles They decompose organic matter, recycle nutrients, and fix atmospheric nitrogen, making it available to plants and other organisms • Formation of Ecosystems : By recycling nutrients and driving chemical transformations, prokaryotes create and sustain ecosystems They were responsible for producing the first oxygen in Earth’s atmosphere through the evolution of cyanobacteria and oxygenic photosynthesis, fundamentally altering the planet’s chemistry and enabling the evolution of aerobic life Summary • By approximately 4 0 – 3 8 billion years ago (Ga), the first prokaryotic cells emerged, characterized by DNA - based genomes and protein - assisted replication These early cells lacked nuclei and organelles but possessed cell walls and metabolic pathways for anaerobic respiration • The divergence of bacteria and archaea occurred during this period, with each domain developing distinct membrane lipids and transcriptional machinery • Cyanobacteria, appearing around 3 5 Ga, revolutionized Earth’s atmosphere through oxygenic photosynthesis, triggering the Great Oxidation Event (GOE) 2 4 billion years ago This metabolic innovation not only altered global biogeochemistry but also imposed selective pressures that drove the evolution of oxygen - tolerant organisms Antibiotic Resistance • 2 types of resistance : • Intrinsic Resistance : Some bacteria naturally possess genes that confer a baseline resistance to certain antibiotics, often through mechanisms like efflux pumps or reduced membrane permeability These intrinsic mechanisms predate clinical antibiotic use and serve ecological roles such as defence against environmental toxins • Acquired Resistance : Bacteria evolve resistance primarily via Darwinian processes, including mutations in existing genes and horizontal gene transfer (HGT) of resistance genes from other bacteria Mobile genetic elements — plasmids, transposons, integrons — play a crucial role in spreading resistance traits rapidly across populations and species • The presence of other microbes influences resistance evolution, as competitive interactions can select for enhanced resistance mechanisms • Resistance genes have been found in ancient DNA samples, indicating that antibiotic resistance is a natural and ancient phenomenon, not solely a modern clinical problem Antibiotic Resistance • Common Resistance Mechanisms : • Antibiotic Modification/Degradation : Enzymes chemically modify (e g , acetylation) or degrade antibiotics (e g , β - lactamases), rendering them ineffective • Efflux Pumps : Transport proteins actively expel antibiotics from the cell, lowering intracellular drug concentrations • Target Modification : Mutations or enzymatic alterations reduce antibiotic binding to targets such as ribosomal RNA or cell wall precursors • Sequestration and Target Bypass : Proteins may sequester antibiotics or produce alternative targets to evade inhibition Engineered Evolution • Experiments with pathogens like Escherichia coli and Pseudomonas aeruginosa show that bacteria can rapidly evolve resistance during a single infection or experimental timeframe by accumulating mutations or acquiring resistance genes Lifestyle Effects on Resistance Evolution : • Bacteria grown in liquid cultures tend to evolve resistance by increasing efflux pump expression and acquiring mutations that block antibiotic binding, often at a fitness cost in drug - free environments • Biofilm - grown bacteria evolve different resistance strategies, sometimes maintaining higher fitness without antibiotics but showing variable cross - resistance or sensitivity to other drugs Synthetic Endosymbiosis and Gene Editing : • Advances in genome engineering (e g , CRISPR - Cas 9 ) allow precise manipulation of bacterial genomes to study resistance mechanisms and potentially develop novel therapeutic strategies