Bacterial genome
[6] A striking discovery by Cole et al. described massive amounts of gene decay when comparing Leprosy bacillus to ancestral bacteria.
[5] 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.
This was initially described in a study by Cole et al. in which Mycobacterium leprae was discovered to have a significantly higher percentage of pseudogenes to functional genes (~40%) than its free-living ancestors.
The Average Nucleotide Identity (ANI) method quantifies genetic distance between entire genomes by taking advantage of regions of about 10,000 bp.
[14] To extract information about bacterial genomes, core- and pan-genome sizes have been assessed for several strains of bacteria.
Early molecular phylogenetic studies revealed that mycoplasmas represented an evolutionary derived state, contrary to prior hypotheses.
The convergent evolution of these qualities in unrelated bacteria suggests that an obligate association with a host promotes genome reduction.
For example, many eliminated genes code for products that are involved in universal cellular processes, including replication, transcription, and translation.
However some genes, such as those encoding the RecA protein, were found to be nearly ubiquitous, indicating that a large majority of bacterial genomes are probably capable of homologous recombination.
Such a shift in lifestyle often results in a reduction in the genetic population size of a lineage, since there is a finite number of hosts to occupy.
As such, selection can effectively operate on free-living bacteria to remove deleterious sequences resulting in a relatively small number of pseudogenes.
As such, in recently-formed and facultative parasites, there is an accumulation of pseudogenes and transposable elements due to a lack of selective pressure against deletions.
The population bottlenecks reduce gene transfer and as such, deletional bias ensures the reduction of genome size in parasitic bacteria.
Obligatory parasites and symbionts have the smallest genome sizes due to prolonged effects of deletional bias.
Symbionts occur in drastically lower numbers and undergo the most severe bottlenecks of any bacterial type.
[19] Recent studies performed by Nilsson et al. examined the rates of bacterial genome reduction of obligate bacteria.
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.
[8] 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.
For example, many of the S. enterica genes that are not present in E. coli have base compositions that differ from the overall 52% GC content of the entire chromosome.
Furthermore, the regions adjacent to horizontally obtained genes often have remnants of translocatable elements, transfer origins of plasmids, or known attachment sites of phage integrases.
The hyperthermophilic Eubacteria Aquifex aeolicus and Thermotoga maritima each has many genes that are similar in protein sequence to homologues in thermophilic Archaea.
[21] Conjugation involves physical contact between donor and recipient cells and is able to mediate transfers of genes between domains, such as between bacteria and yeast.
Despite the multitude of mechanisms mediating gene transfer among bacteria, the process's success is not guaranteed unless the received sequence is stably maintained in the recipient.
[22] 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”.
[26] Competence for transformation is typically induced by high cell density and/or nutritional limitation, conditions associated with the stationary phase of bacterial growth.
[28] 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[29] Using Legionella pneumophila, Charpentier et al.[30] examined 64 toxic molecules to find out which of these induce competence.
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.
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.
[21] 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.
