Horizontal gene transfer in prokaryotes

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For more information, see: Horizontal gene transfer.


Horizontal gene transfer (also lateral gene transfer) is movement of genes between different species, or across broad taxonomic categories.

Horizontal gene transfer is common among bacteria, even very distantly-related ones.

Studies of bacterial genomes have reveal many genomes have "islands" of DNA which change due to loss and gain of foreign DNA and that horizontal gene transfer between distant taxa mediated by bacteriophages and other agents is a major feature of microbial evolution.

Horizontal transfer is thought to be a significant contributer to bacterial antibiotic resistance; when one bacterial cell acquires resistance, it can quickly transfer the resistance genes to many species by plasmid transfer. Enteric bacteria for instance appear to exchange genetic material with each other within the gut in which they live. Virulence genes can be transferred by horizontal gene transfer [1].

There are three common mechanisms for horizontal gene transfer:

Current illustration of the role of horizontal gene transfer in bacterial evolution

Joshua Lederberg in the 1960s (NLM)

When Joshua Lederberg discovered gene transmission among laboratory mutants of the gut bacterium Escherichia coli strain K-12 in 1948 he initiated the modern (and some say Golden) era of bacterial genetics to which he was to contribute many remarkable discoveries and insights. Today, our appreciation of the natural evolution of pathogenic strains of the gut bacterium he investigated in 1948 provides a satisfying vignette of current general understanding of bacterial evolution and of the importance of horizontal gene transfer in bacterial biology. To quote directly from a 2001 review article about pathogenic gut bacteria that cause disease [2]:

It is a mistake to think of E. coli as a homogenous species. Most genes, even those encoding conserved metabolic functions, are polymorphic, with multiple alleles found among different isolates [3]. The composition of the genome of E. coli is also highly dynamic. The fully sequenced genome of the laboratory K-12 strain [used by Lederberg in 1948] , whose derivatives have served an indispensable role in the laboratories of countless scientists, shows evidence of tremendous plasticity [4]. It has been estimated that the K-12 lineage has experienced more than 200 lateral (horizontal) transfer events since it diverged from Salmonella about 100 million years ago and that 18% of its contemporary genes were obtained horizontally from other species [5]. Such fluid gain and loss of genetic material are also seen in the recent comparison of the genomic sequence of a pathogenic E. coli O157:H7 with the K-12 genome. Approximately 4.1 million base pairs of "backbone" sequences are conserved between the genomes, but these stretches are punctuated by hundreds of sequences present in one strain but not in the other. The pathogenic strain contains 1.34 million base pairs of lineage-specific DNA that includes 1,387 new genes; some of these have been implicated in virulence, but many have no known function [6].

The virulence factors that distinguish the various E. coli pathotypes were acquired from numerous sources, including plasmids, bacteriophages, and the genomes of other bacteria. Pathogenicity islands, relatively large (>10 kb) genetic elements that encode virulence factors and are found specifically in the genomes of pathogenic strains, frequently have base compositions that differ drastically from that of the content of the rest of the E. coli genome, indicating that they were acquired from another species.

To get a full appreciation of how the above quoted statement could be deduced from clinical and loboratory investigations, it would be necessary to take a long (and intellectually fruitful ) trip along the history of bacterial genetics.

Major discoveries on horizontal gene transfer in prokaryotes

1928. Discovery of gene transfer in bacteria started in 1928 when Frederick Griffith found Diplococcus pneumoniae bacteria could inherit characteristics (namely the "Smooth" phenotype affecting the bacterial cell coat (capsule)) from non-living extracts of other bacteria, and this change was termed transformation. Oswald T. Avery at the Rockefeller Institute in 1944 showed that the transforming material of Diplococcus was DNA.

1946. Joshua Lederberg and Edward Tatum in a series of very carefully designed experiments managed very low-frequency of genetic transfer between Escherichia coli K-12 bacteria when they were in contact with one-another [7], and this process was later found out by the recognized plasmid, fertility factor F.

1951 Joshua and Ester Lederberg , together with Zinder and Lively reported another case of gene transfer that did not need cell-to-cell contact. In this case the bacteria were Salmonella and it was later that a bacterial virus (bacteriophage) was carring the genes transduction.

Transmissible plasmids in microorganisms

1950-1958. Conjugation in E. coli is shown to be a one way (F+ donor to F- recipient), process, and not two-way cell fusion, encoded by a DNA containing factor F 250,000 base pairs in size that converts recipients to the donor state, and which can move infectiously through a recipient bacterial population[8]. F factor was found to be able to move by conjugation to different species such as Salmonella.

1958. The existence of several genetic structures that can insert within bacterial chomosomes, based on observation of the bacteriophage lambda and fertility factor in 1958 F lead F. Jacob and E. L. Wollman [9] to coin the term episome for DNA elements that have alternate modes of existence within the cell, either in the chromosome, or as autonomously replicating stuctures. Subsequent study of these phenomenon revealed numerous occurences of mobile DNA in a wide range of organisms [10](such as the presence of insertion sequence (IS) "jumping genes" (discussed further below) that allow F plasmid insertion in the chromosome) and widespread horizontal gene transfer involving by bacteriophage, plasmids and mobile DNA in general.

1959. Tomoichiro Akiba and Kunitaro Ochia discover mobile antibiotic resistance genes in bacteria [11], and the horizontal transfer is later shown to mediated by plasmids that inject DNA promiscuously into other cells [12].

1964. Brinton establishes that F factor containing bacteria have pili (fimbrae) fiber-like appendages that are involved making contact with recipients to they can transfer DNA. Similar pili are specified by some R-plasmids.

1960s. R-plasmids are established to be promiscuously transferred among different enteric bacteria. Typically plasmids can be transferred easily among the different species of common gut Gram negative bacteria. Transmissible plasmids are common in stool bacteria, and typically 10-20% of gut E. coli of healthy people (1960-1970) have R-plamids and are antibiotic resistant[13]. Bacteria are discovered to produce colicins, lethal compounds that kill other bacteria which are specified by transmissable plasmids similar to F. Examples are ColE, ColV plasmids.

It is also fully realised that F-factor is not unique, but a special case of a very general phenomenon in bacteria of transmissible and mobile DNA, including R-plasmids, colicin determining (Col) plasmids, and prophages. Interactions between them were discovered, for instance R-plasmids were found which interfered with F-fertility. Plasmids were also discovered that carried bacterial virulence genes, Hemolysin (Hly), and surface antigens (K88). Plasmids are shown to be closed circular DNA molecules which are much smaller than the circular bacterial genome.

Insertion sequences (IS), transposons (Tn) and Mu

1968. James Shapiro discovers that spontaneously occuring insertions of large inserts of extra DNA can causes mutationss in the galactose genes of the bacterium Escherichia coli [14]. This discovery ultimately led to the discovery of mobile insertion sequences (IS). Their similarity to Barbara McClintock's maize transposons was immedidiately relised when IS were found through DNA heteroduplex electron microscopy and DNA hybridization methods to be natural residents of the E. coli chromosome, and frequently components of natural plamids [15]. F-factor carries more than one IS element, and they (as Tn1000) are implicated in enabling bacterial chromosomes to take part in F-mediated conjugation.

1963-1995. Mutator phage Mu of E. coli which inserts at numerous different sites in the E. coli chromosomes as a prophage, and replicates vegetatively by repeated transposition, provides a convenient tool for elucidation of the mechanisms of transposition in great detail [16] [17]. Transposition is usually a rare event, iand is difficult to analyse biochemically with most transposons and insertion sequences. The more frequent "jumping gene" activity og Mu phage facilitated its elucidation as an understandable chemical reaction.

1974. The first transposition of a gene for ampicillin resistance from one R-plasmid to another plasmid is fully characterised [18]. The ampicillin resistance transposon is named Tn3. Other transposons are Tn5 (kanamycin resistance with IS50 at each termini) , and Tn10 ( tetracyline resistance). R-plasmids are currenly thought of as modular replicons put together with Tns and replication origins (ori sites ) providing plasmid-specific sites for initiation of DNA replication, and transposition of Tns is seen to be part of plasmid natural evolution.

Backbones and islands found in genomes

1990-present. Availability of many genome DNA squences reveals bacteria such as E. coli have genomes which consist of a "backbone" of conserved housekeeping genes interrupted by "islands" of changeable genes that are foreign DNA derived inserts (such as inserted prophages) gained during stepwise evolution by gene addition[19] . Lawrence and Ochman (1998) [20] calculate there is constant turnover of horizontally transferred DNA in these islands in E. coli over evolutionary time at the rate of ~16 thousand base-pairs per million years.

2001. The team of Perna and others who did the E. coli HUS pathogen genome analysis in 2001 found that with this pathogen - enterohaemorrhagic Escherichia coli O157:H7 - lateral gene transfer is far more extensive than ever previously previously expected. In fact, 1,387 new genes encoded in strain-specific clusters of different sizes were found in O157:H7. These include candidate virulence factors, alternative metabolic capacities, and several prophages and other new functions [21].

The genomic islands of bacteria associated with virulence get the special name "Pathogenicity islands" (PAI). Studies of pathogenic bacteria E. coli O157:H7 indicate these have very many genes in islands, including the complex and interesting LEE (locus of enterocyte effacement) pathogenicity island [22]; tRNA genes are frequently found at the junctions of pathogenicity islands, and these are conserved sites recognised by many prophages as insertion targets.

References

  1. ↑ Wick LM, Qi W, Lacher DW, Whittam TS. (2005) J Bacteriol. 2005 Mar;187(5):1783-91. Evolution of genomic content in the stepwise emergence of Escherichia coli O157:H7.
  2. ↑ Donnenberg, M. S., and T. S. Whittam. 2001. Pathogenesis and evolution of virulence in enteropathogenic and enterohemorrhagic Escherichia coli. J. Clin. Investig. 107:539-548. (Bold emphasis added)
  3. ↑ Whittam, T.S. 1996. Genetic variation and evolutionary processes in natural populations of Escherichia coli. In Escherichia coli and Salmonella: cellular and molecular biology. F.C. Neidhardt, editor. ASM Press. Washington, DC, USA. pages 2708–2720.
  4. ↑ Blattner, F.R. et al.1997. The complete genome sequence of Escherichia coli K-12. Science. 277:1453-1462.
  5. ↑ Lawrence, J.G., and Ochman, H. 1998. Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. USA. 95:9413-9417.
  6. ↑ Perna, N.T. et al.2001. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature. 409:529-533.
  7. ↑ Lederberg, J. and Tatum, E. L. (1946). Novel genotypes in mixed cultures of biochemical mutants of bacteria. Cold Spring Habor Symposia of Quantitative Biology. 11, p113.
  8. ↑ Hayes, W. (1970) The Genetics of Bacteria and their Viruses. 2nd Edition, Blackwell.
  9. ↑ Jacob, F. and Wollman, E. L. (1958) Les episomes, elements genetiques ajoutes. C. R. Acad, Sci. Paris, 247, p154.
  10. ↑ Berg, D. E. and Howe, M. M. (Eds.)(1989). Mobile DNA. American Society for Microbiology. Washington, D.C.
  11. ↑ Ochia, K. Yamanaka, T. Kimura, K. and Sawada, O. (1959). Inheritance of drug resistance (and its transfer) between Shigella strains and between Shigella and E. coli strains. Nihon Iji Shimpo 1861: p34 (In Japanese)
  12. ↑ S. Falcow (1975)Infectious Multiple Drug Resistance. Pion Press, London.
  13. ↑ Falcow, S. (1975). Infectious multiple Drug Resistance, Pion.
  14. ↑ Shapiro, J. (1969) Mutations caused by the insertion of genetic material into the galactose operon of Escherichia coli. J. Molec. Biol. 40, p93-109.
  15. ↑ Galas, D. J. and Chandler, M. (1989). Bacterial insertion sequences. In Mobile DNA Berg, D E and Howe, E, eds. (Washington, DC: American Society for Microbiology), pp. 109-162.
  16. ↑ Mizuuchi, K. (1992) Transpositional recombination: mechanistic insights from studies of Mu and other elements. Annu. Rev. Biochem. 61, 1011-1051.
  17. ↑ Pato, M. L. (1989) Bacteriophage Mu. In Mobile DNA Berg, D E and Howe, E, eds. (Washington, DC: American Society for Microbiology), pp. 23-52.
  18. ↑ Hedges, R. W. and Jacob, A. F. Transposition of ampicillin resistance from RP4 to other replicons. Mol. Gen. Genetics 132 pages 31-40.
  19. ↑ Wick LM, Qi W, Lacher DW, Whittam TS. (2005) J Bacteriol. 2005 Mar;187(5):1783-91. Evolution of genomic content in the stepwise emergence of Escherichia coli O157:H7.
  20. ↑ Lawrence, J.G., and Ochman, H. 1998. Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. USA. 95:9413-9417.
  21. ↑ Perna NT, Plunkett G 3rd, Burland V, Mau B, Glasner JD, Rose DJ, Mayhew GF, Evans PS, Gregor J, Kirkpatrick HA, Posfai G, Hackett J, Klink S, Boutin A, Shao Y, Miller L, Grotbeck EJ, Davis NW, Lim A, Dimalanta ET, Potamousis KD, Apodaca J, Anantharaman TS, Lin J, Yen G, Schwartz DC, Welch RA, Blattner FR. (2001) Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature. 2001 Jan 25;409(6819):529-33.
  22. ↑ Ohad Gal-Mor and B. Brett Finlay. (2006) Pathogenicity islands: a molecular toolbox for bacterial virulence. Cellular Microbiology 8:11, 1707-1719

Further reading

  • Snyder, L. and Champness, W. (2003) Molecular Genetics of Bacteria, 2nd Edition, ASM Press Washington DCISBN 1-55581-204-X
  • Hayes, W. (1970) The Genetics of Bacteria and their Viruses. 2nd Edition, Blackwell.

External links

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