Bacterial genome

As of 2014, there are over 30,000 sequenced bacterial genomes publicly available and thousands of metagenome projects. Projects such as the Genomic Encyclopedia of Bacteria and Archaea (GEBA) intend to add more genomes. The single gene comparison is now being supplanted by more general methods. These methods have resulted in novel perspectives on genetic relationships that previously have only been estimated. A significant achievement in the second decade of bacterial genome sequencing was the production of metagenomic data, which covers all DNA present in a sample. Previously, there were only two metagenomic projects published. ==Bacterial genomes==

of the total number of annotated proteins in genomes submitted to GenBank as a function of genome size. Based on data from NCBI genome reports. Bacteria possess a compact genome architecture distinct from eukaryotes in two important ways: bacteria show a strong correlation between genome size and number of functional genes in a genome, and those genes are structured into operons. The main reason for the relative density of bacterial genomes compared to eukaryotic genomes (especially multicellular eukaryotes) is the presence of noncoding DNA in the form of intergenic regions and introns. The general trends of bacterial evolution indicate that bacteria started as free-living organisms. Evolutionary paths led some bacteria to become pathogens and symbionts. The lifestyles of bacteria play an integral role in their respective genome sizes. Free-living bacteria have the largest genomes out of the three types of bacteria; however, they have fewer pseudogenes than bacteria that have recently acquired pathogenicity. Facultative and recently evolved pathogenic bacteria exhibit a smaller genome size than free-living bacteria, yet they have more pseudogenes than any other form of bacteria. Obligate bacterial symbionts or pathogens have the smallest genomes and the fewest pseudogenes of the three groups. The relationship between life-styles of bacteria and genome size raises questions as to the mechanisms of bacterial genome evolution. Researchers have developed several theories to explain the patterns of genome size evolution amongst bacteria. Genome comparisons As single-gene comparisons have largely given way to genome comparisons, phylogeny of bacterial genomes have improved in accuracy. The Average Nucleotide Identity (ANI) method quantifies genetic distance between entire genomes by taking advantage of regions of about 10,000 bp. With enough data from genomes of one genus, algorithms are executed to categorize species. This has been done for the Pseudomonas avellanae species in 2013 Observed ANI values among sequences appear to have an "ANI gap" at 85–95%, suggesting that a genetic boundary suitable for defining a species concept is present. To extract information about bacterial genomes, core- and pan-genome sizes have been assessed for several strains of bacteria. In 2012, the number of core gene families was about 3000. However, by 2015, with an over tenfold increased in available genomes, the pan-genome has increased as well. There is roughly a positive correlation between the number of genomes added and the growth of the pan-genome. On the other hand, the core genome has remain static since 2012. Currently, the E. coli pan-genome is composed of about 90,000 gene families. About one-third of these exist only in a single genome. Many of these, however, are merely gene fragments and the result of calling errors. Still, there are probably over 60,000 unique gene families in E. coli. ==Theories of bacterial genome evolution==

Bacteria lose a large amount of genes as they transition from free-living or facultatively parasitic life cycles to permanent host-dependent life. Towards the lower end of the scale of bacterial genome size are the mycoplasmas and related bacteria. Early molecular phylogenetic studies revealed that mycoplasmas represented an evolutionary derived state, contrary to prior hypotheses. Furthermore, it is now known that mycoplasmas are just one instance of many of genome shrinkage in obligately host-associated bacteria. Other examples are Rickettsia, Buchnera aphidicola, and Borrelia burgdorferi. Small genome size in such species is associated with certain particularities, such as rapid evolution of polypeptide sequences and low GC content in the genome. The convergent evolution of these qualities in unrelated bacteria suggests that an obligate association with a host promotes genome reduction. In addition, small genomes have fewer tRNAs, utilizing one for several amino acids. So, a single codon pairs with multiple codons, which likely yields less-than-optimal translation machinery. It is unknown why obligate intracellular pathogens would benefit by retaining fewer tRNAs and fewer DNA repair enzymes. The data indicates that selection is not a suitable explanation for the small sizes of bacterial genomes. Still, many researchers believe there is some selective pressure on bacteria to maintain small genome size. Deletional bias Selection is but one process involved in evolution. Two other major processes (mutation and genetic drift) can account for the genome sizes of various types of bacteria. A study done by Mira et al. examined the size of insertions and deletions in bacterial pseudogenes. Results indicated that mutational deletions tend to be larger than insertions in bacteria in the absence of gene transfer or gene duplication. At 160 kbp, the genome of Carsonella is one of the most streamlined examples of a genome examined to date. ==Genomic reduction==

Molecular phylogenetics has revealed that every clade of bacteria with genome sizes under 2 Mb was derived from ancestors with much larger genomes, thus refuting the hypothesis that bacteria evolved by the successive doubling of small-genomed ancestors. Recent studies performed by Nilsson et al. examined the rates of bacterial genome reduction of obligate bacteria. Bacteria were cultured introducing frequent bottlenecks and growing cells in serial passage to reduce gene transfer so as to mimic conditions of endosymbiotic bacteria. The data predicted that bacteria exhibiting a one-day generation time lose as many as 1,000 kbp in as few as 50,000 years (a relatively short evolutionary time period). Furthermore, after deleting genes essential to the methyl-directed DNA mismatch repair (MMR) system, it was shown that bacterial genome size reduction increased in rate by as much as 50 times. These results indicate that genome size reduction can occur relatively rapidly, and loss of certain genes can speed up the process of bacterial genome compaction. This is not to suggest that all bacterial genomes are reducing in size and complexity. While many types of bacteria have reduced in genome size from an ancestral state, there are still a huge number of bacteria that maintained or increased genome size over ancestral states. Free-living bacteria experience huge population sizes, fast generation times and a relatively high potential for gene transfer. While deletional bias tends to remove unnecessary sequences, selection can operate significantly amongst free-living bacteria resulting in evolution of new genes and processes. ==Horizontal gene transfer==

Unlike eukaryotes, which evolve mainly through the modification of existing genetic information, bacteria have acquired a large percentage of their genetic diversity by the horizontal transfer of genes. This creates quite dynamic genomes, in which DNA can be introduced into and removed from the chromosome. Bacteria have more variation in their metabolic properties, cellular structures, and lifestyles than can be accounted for by point mutations alone. For example, none of the phenotypic traits that distinguish E. coli from Salmonella enterica can be attributed to point mutation. On the contrary, evidence suggests that horizontal gene transfer has bolstered the diversification and speciation of many bacteria. In order for a bacterium to bind, take up and recombine exogenous DNA into its chromosome, it must enter a special physiological state referred to as "competence". Competence development in the bacterium Bacillus subtilis requires expression of about 40 genes. In general, the DNA integrated into the host chromosome is (with rare exceptions) derived from another bacterium of the same species, and is therefore homologous to the resident chromosome. In B. subtilis the length of the transferred DNA is more than 1 million bases, is likely double stranded DNA, and is often more than a third of the total chromosome length of 4215 kb. Approximately 7-9% of the recipient cells take up an entire chromosome. The capacity for natural transformation appears to be common among prokaryotes, and thus far 67 prokaryotic species (in seven different phyla) are known to undergo this process. Competence for transformation is typically induced by high cell density and/or nutritional limitation, conditions associated with the stationary phase of bacterial growth. Competence is also specifically induced by conditions that damage DNA. For example, transformation is induced in Streptococcus pneumoniae by the DNA damaging agents mitomycin C (a DNA cross-linking agent) and fluoroquinolone (a topoisomerase inhibitor that causes double-strand breaks). In Bacillus subtilis, transformation is stimulated by exposure to UV light, a DNA damaging agent. In Helicobacter pylori, ciprofloxacin, an agent that interacts with DNA gyrase and causes double-strand breaks, induces expression of competence genes, thus increasing the frequency of transformation Using Legionella pneumophila, Charpentier et al. examined 64 toxic molecules to find out which of these induce competence. Of these toxic compounds, only six, all DNA damaging agents, caused strong induction. Bacteria that are growing logarithmically differ from stationary phase bacteria with regard to the number of genome copies present in the cell, and this has implications for the ability to carry out an important DNA repair process. During logarithmic growth, two or more copies of any particular region of the chromosome are ordinarily present in a bacterial cell, as cell division is not precisely matched with chromosome replication. Homologous recombinational repair is an important DNA repair process that is particularly effective for repairing double-strand damages, such as double-strand breaks. This DNA repair process depends on a second homologous chromosome in addition to the damaged chromosome. During logarithmic growth, a DNA damage in one chromosome may be removed by homologous recombinational repair using sequence information from the other homologous chromosome. However, when cells approach stationary phase they typically have just one copy of the chromosome, and homologous recombinational repair then requires input of an homologous template from outside the cell by transformation. To determine whether the adaptive function of transformation is repair of DNA damages, a series of experiments were performed using B. subtilis irradiated by UV light as the damaging agent (reviewed by Michod et al. and Bernstein et al.) These experiments produced results indicating that transforming DNA acts to repair potentially lethal DNA damages caused by UV light in the recipient DNA. The particular process likely responsible for repair was homologous recombinational repair. Thus transformation in bacteria can be regarded as a primitive sexual process, in the sense that it involves interaction of homologous DNA from two individuals to form recombinant DNA that is then passed on to succeeding generations. Bacterial transformation in prokaryotes may have been the ancestral process that evolved into meiotic sexual reproduction in eukaryotes (see Evolution of sexual reproduction; Meiosis.) Traits introduced through lateral gene transfer Antimicrobial resistance genes grant an organism the ability to grow its ecological niche, since it can now survive in the presence of previously lethal compounds. As the benefit to a bacterium earned from receiving such genes are time- and space-independent, those sequences that are highly mobile are selected for. Plasmids are quite mobilizable between taxa and are the most frequent way by which bacteria acquire antibiotic resistance genes. Adoption of a pathogenic lifestyle often yields a fundamental shift in an organism's ecological niche. The erratic phylogenetic distribution of pathogenic organisms implies that bacterial virulence is a consequence of the presence, or obtainment of, genes that are missing in avirulent forms. Evidence of this includes the discovery of large 'virulence' plasmids in pathogenic Shigella and Yersinia, as well as the ability to bestow pathogenic properties onto E. coli via experimental exposure to genes from other species. ==Computer-made form==

In April 2019, scientists at ETH Zurich reported the creation of the world's first bacterial genome, named Caulobacter ethensis-2.0, made entirely by a computer, although a related viable form of C. ethensis-2.0 does not yet exist. ==See also==