Bacterial genome

Bacterial genomes are generally smaller and less variant in size between species when compared with genomes of animals and single cell eukaryotes. Bacterial genomes can range in size anywhere from about 130 kbp[1][2] to over 14 Mbp.[3] Recent advances in sequencing technology led to the discovery of a high correlation between the number of genes and the genome size of bacteria, suggesting that bacteria have relatively small amounts of noncoding DNA.[4] A striking discovery by Cole et al. described massive amounts of gene decay when comparing Leprosy bacillus to ancestral bacteria.[5] Studies have since shown that a large number of bacterial species have undergone genomic degradation resulting in a decrease in genome size from their ancestral state.[6] Over the years, researchers have proposed several theories to explain the general trend of bacterial genome decay and the relatively small size of bacterial genomes. Compelling evidence indicates that the apparent degradation of bacterial genomes is owed to a deletional bias.

Bacterial genomes

Log-log plot 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.[7]

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.[8][9] 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.[9] Some notable exceptions include recently formed pathogenic bacteria. 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.[5]

Furthermore, amongst species of bacteria, there is relatively little variation in genome size when compared with the genome sizes of other major groups of life.[4] Genome size is of little relevance when considering the number of functional genes in eukaryotic species. In bacteria however, the strong correlation between the number of genes and the genome size makes the size of bacterial genomes an interesting topic for research and discussion.[10]

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.[11] 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.

Theories of bacterial genome evolution

Doubling time

One theory predicts that bacteria have smaller genomes due to a selective pressure on genome size to ensure faster replication. The theory is based upon the logical premise that smaller bacterial genomes will take less time to replicate. Subsequently, smaller genomes will be selected preferentially due to enhanced fitness. A study done by Mira et al. indicated little to no correlation between genome size and doubling time.[12] 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 be used to explain 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.[12] Insertions caused by horizontal or lateral gene transfer and gene duplication tend to involve transfer of large amounts of genetic material. Assuming a lack of these processes, genomes will tend to reduce in size in the absence of selective constraint. Evidence of a deletional bias is present in the respective genome sizes of free-living bacteria, facultative and recently derived parasites and obligate parasites and symbionts.

Free-living bacteria tend to have large population sizes and are subject to more opportunity for gene transfer. As such, selection can effectively operate on free-living bacteria to remove deleterious sequences resulting in a relatively small number of pseudogenes. Continually, further selective pressure is evident as free-living bacteria must produce all gene-products independent of a host. Given that there is sufficient opportunity for gene transfer to occur and there are selective pressures against even slightly deleterious deletions, it is intuitive that free-living bacteria should have the largest bacterial genomes of all bacteria types.

Recently formed parasites undergo severe bottlenecks and can rely on host environments to provide gene products. 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. Parasites which have evolved to occupy specific niches are not exposed to much selective pressure. As such, genetic drift dominates the evolution of niche specific bacteria. Extended exposure to deletional bias ensures the removal of most superfluous sequences. Symbionts occur in drastically lower numbers and undergo the most severe bottlenecks of any bacterial type. There is almost no opportunity for gene transfer for endosymbiotic bacteria and as such, genome compaction can be extreme. One of the smallest bacterial genomes ever to be sequenced is that of the endosymbiont Carsonella rudii.[13] At 160 kbp, the genome of Carsonella is one of the most streamlined examples of a genome examined to date.

Genomic degradation

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. [14] 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.[6] 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.

See also

References

  1. ↑ McCutcheon, J. P.; Von Dohlen, C. D. (2011). "An Interdependent Metabolic Patchwork in the Nested Symbiosis of Mealybugs". Current Biology. 21 (16): 1366–1372. doi:10.1016/j.cub.2011.06.051. PMC 3169327Freely accessible. PMID 21835622.
  2. ↑ Van Leuven, JT; Meister, RC; Simon, C; McCutcheon, JP (11 September 2014). "Sympatric speciation in a bacterial endosymbiont results in two genomes with the functionality of one.". Cell. 158 (6): 1270–80. doi:10.1016/j.cell.2014.07.047. PMID 25175626.
  3. ↑ Han, K; Li, ZF; Peng, R; Zhu, LP; Zhou, T; Wang, LG; Li, SG; Zhang, XB; Hu, W; Wu, ZH; Qin, N; Li, YZ (2013). "Extraordinary expansion of a Sorangium cellulosum genome from an alkaline milieu.". Scientific Reports. 3: 2101. doi:10.1038/srep02101. PMID 23812535.
  4. 1 2 Gregory, T. R. (2005). "Synergy between sequence and size in Large-scale genomics". Nature Reviews Genetics. 6 (9): 699–708. doi:10.1038/nrg1674. PMID 16151375.
  5. 1 2 Cole, S. T.; Eiglmeier, K.; Parkhill, J.; James, K. D.; Thomson, N. R.; Wheeler, P. R.; Honoré, N.; Garnier, T.; Churcher, C.; Harris, D.; Mungall, K.; Basham, D.; Brown, D.; Chillingworth, T.; Connor, R.; Davies, R. M.; Devlin, K.; Duthoy, S.; Feltwell, T.; Fraser, A.; Hamlin, N.; Holroyd, S.; Hornsby, T.; Jagels, K.; Lacroix, C.; MacLean, J.; Moule, S.; Murphy, L.; Oliver, K.; Quail, M. A. (2001). "Massive gene decay in the leprosy bacillus". Nature. 409 (6823): 1007–1011. doi:10.1038/35059006. PMID 11234002.
  6. 1 2 Ochman, H. (2005). "Genomes on the shrink". Proceedings of the National Academy of Sciences. 102 (34): 11959–11960. doi:10.1073/pnas.0505863102.
  7. ↑ Koonin, Eugene V. (2011). The Logic of Chance: The Nature and Origin of Biological Evolution. FT Press. ISBN 9780132542494.
  8. ↑ Gregory, T. Ryan (2005). The evolution of the genome. Burlington, MA: Elsevier Academic. ISBN 0123014638.
  9. 1 2 Koonin, E. V. (2009). "Evolution of genome architecture". The International Journal of Biochemistry & Cell Biology. 41 (2): 298–306. doi:10.1016/j.biocel.2008.09.015.
  10. ↑ Kuo, C. -H.; Moran, N. A.; Ochman, H. (2009). "The consequences of genetic drift for bacterial genome complexity". Genome Research. 19 (8): 1450–1454. doi:10.1101/gr.091785.109. PMC 2720180Freely accessible. PMID 19502381.
  11. ↑ Ochman, H.; Davalos, L. M. (2006). "The Nature and Dynamics of Bacterial Genomes". Science. 311 (5768): 1730–1733. doi:10.1126/science.1119966. PMID 16556833.
  12. 1 2 Mira, A.; Ochman, H.; Moran, N. A. (2001). "Deletional bias and the evolution of bacterial genomes". Trends in genetics : TIG. 17 (10): 589–596. doi:10.1016/S0168-9525(01)02447-7. PMID 11585665.
  13. ↑ Nakabachi, A.; Yamashita, A.; Toh, H.; Ishikawa, H.; Dunbar, H. E.; Moran, N. A.; Hattori, M. (2006). "The 160-Kilobase Genome of the Bacterial Endosymbiont Carsonella". Science. 314 (5797): 267. doi:10.1126/science.1134196. PMID 17038615.
  14. ↑ Nilsson, A. I.; Koskiniemi, S.; Eriksson, S.; Kugelberg, E.; Hinton, J. C.; Andersson, D. I. (2005). "Bacterial genome size reduction by experimental evolution". Proceedings of the National Academy of Sciences. 102 (34): 12112–12116. doi:10.1073/pnas.0503654102. PMC 1189319Freely accessible. PMID 16099836.
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