Genome Evolution: Prokaryotes PDF

Genome Evolution: Prokaryotes (Lecture 18) NB Read scientific article posted on clickUP: Evolution of small prokaryotic genomes What is a prokaryote? A prokaryote is a Unicellular organism Lacks a nucleus Lacks mitochondria or any...

Genome Evolution: Prokaryotes (Lecture 18) NB Read scientific article posted on clickUP: Evolution of small prokaryotic genomes What is a prokaryote? A prokaryote is a Unicellular organism Lacks a nucleus Lacks mitochondria or any other membrane-bound organelle NOTE: Prokaryotes do have ribosomes: The prokaryotic ribosome is smaller than a eukaryotic ribosome Floats freely in the cytoplasm Ribosomal RNA and proteins are coded for on the circular chromosome Prokaryotes occupy two domains of life: ○ The EUBACTERIA (bacteria) ○ The ARCHAEBACTERIA (archaea) The third domain is occupied by eukaryotes Most of life on Earth is prokaryotic (~ 10:1)  Eukaryotic = “true nucleus” Archaea more closely related to eukaryotes than bacteria Phylogenetics distinguish archaea and bacteria (morphologically similar) Features of prokaryotic genomes Prokaryotic genomes All prokaryotic genomes are haploid Single, circular chromosome containing the house-keeping genes ○ Very small genomes ○ Mostly coding sequence, with very little non-coding sequence ○ Genes organised in operons ○ Genes coded on both strands, often overlapping (“wall to wall”) ○ No introns (but there are exceptions) mtDNA in fungi (introns) → nested genome (= genes with introns) ○ Single origin of replication ○ “Wall-to-wall” coding sequence Often one or more plasmids ○ Smaller than the main chromosome ○ Same features as main chromosome ○ Often contain selectable markers such as resistance genes Carried on plastids → small, can easily move between cells ○ Maintained by selection, lost when selection pressure disappears When plastid not necessary ○ Easily transferred between cells There are exceptions to each one of these general features  Red inner ring = GC content  Genome size in prokaryotes Genome size varies in prokaryotic taxa Large range, variable sizes Core genome, accessory genome, and pangenome Prokaryotes exhibit large intraspecific (within a species) and interspecific (between species) variation in gene content ↑ genes = ↑ genome size Positive correlation between number of protein-coding genes and genome size Core genome All the genes that are common between the individuals/populations of a species Accessory genome All the genes that are present in only a subset of individuals/populations within a species. Pangenome All the genes that are present in all individuals/populations of a species (ie. core genome + accessory genome)  The number of genes in the pangenome, core genome and accessory genome depend on how many organisms were sampled GC content in prokaryotes G≡C - 3 hydrogen bonds ↑ environmental temperature = ↑ GC content (eukaryotes) Mean GC content in prokaryotes varies from 13.5% to 74.7% ○ Distribution of GC content seems to be independent of phylogenetic relationships  ○ Indicates that changes in GC content occur frequently and rapidly Possible explanations: Selectionist view regards GC content as a trait that is determined by selective forces ○ i.e. an adaptation to intrinsic or extrinsic conditions Changes in codon usage due to gene dosage of tRNA genes ○ Illustrated by correlation in GC content in coding regions and in codon positions: ○ tRNA gene determines which codons are preferred Green = highly mutable Blue and red = NB for coding amino acids Black = 1:1 correlation Strand-dependent mutation patterns: certain types of point mutations will occur at different frequencies in the leading and lagging strands → mutational asymmetry, leading to strand-dependent substitution patterns ○ These lead to GC skew, i.e. deviations from equal nucleotide frequencies on a strand  Bottom line = leading strand Endosymbiotic theory or Symbiogenesis Origin of nucleus = Archaea Origin of mitochondria = Proteobacteria (aerobic) Origin of plastids (ie. chloroplasts, etc.) = Cyanobacteria (eubacteria) (photosynthetic) Evolution of genome size in prokaryotes: Mitochondria as an example With some exceptions, animal mitochondrial (mt) genomes contain 12-14 protein coding genes and 24-25 rRNA and tRNA coding genes, have no introns, and very small spacers between genes The most gene-rich mt genomes are found in fungi, plants, and protozoa Compare the # of genes in proteobacteria (the ancestors of mitochondria) with the # of genes in mitochondria ○ Conclude: The bulk of mt genome miniaturisation must have occurred immediately after the endosymbiotic event that gave rise to eukaryotes (1.5 BYA) The gene-rich mt genome of the jakobid protozoan Andalucia godoyi represents a mt genome state that is close to the ancestral state of mt genomes Genome miniaturisation takes place through the loss of genes Genome miniaturisation ○ In prokaryotes, reduction in genome size is invariably associated with loss of function (use it or lose it) ○ Prokaryotic endosymbionts have smaller genomes than obligate parasites, which in turn have smaller genomes than free-living prokaryotes: ○ Endosymbionts < Obligate parasites < Free-living ○ This can be explained by variation in environments that these organisms have adapted to  Obligate endosymbionts: mitochondria, plastids (organelles) ○ Mitochondria entered an ancestral lineage of eukaryotes only once Ancestor of mitochondria was a proteobacterium ○ Plastids entered photosynthetic lineages three times: Glaucophyta, Rhodophyta, Viridiplantae Ancestor of plastids was a photosynthetic cyanobacterium ○ Both have double membranes: one from the ancestral host, one from the ancestral proteobacterium or cyanobacterium ○ Both have their own (reduced) genomes ○ Some genes in obligate endosymbionts have moved to the host nuclear genome, others were lost completely because they were no longer necessary (due to a homogenous environment) ○ Genes that moved to the nuclear genome can be recognized by homology to bacterial genes, and/or different GC content, and/or lack of introns The origins of mitochondria and plastids can be traced back to proteobacteria and cyanobacteria, respectively, based on sequence homology Our mitochondria are more closely related to E. coli than to the nuclei in our cells LUCA