Review
Playing Dr Jekyll and Mr Hyde: combined mechanisms of phase variation in bacteria

https://doi.org/10.1016/S1369-5274(00)00253-8Get rights and content

Abstract

Phase variation is the adaptive process by which bacteria undergo frequent and reversible phenotypic changes resulting from genetic alterations in specific loci of their genomes. This process is crucial for the survival of pathogens and commensals in hostile and ever-changing host environments. Despite important differences in the molecular mechanisms that mediate and regulate phase variation, related strategies have evolved to generate high levels of genetic diversity through complex and combinatorial reshuffling of genetic information. Recent studies, supported by the emergence of global genomic approaches, have revealed that bacterial pathogens often use a combination of different mechanisms to vary the expression of a variety of biological functions, providing new insights into bacterial adaptation and virulence mechanisms. Recent advances in the understanding of the molecular mechanisms of phase variation are reviewed, and differences in these mechanisms outlined.

Introduction

“If he be Mr Hyde, I shall be Mr Seek!”, (RL Stevenson, The Strange Case of Dr Jekyll and Mr Hyde).

Genetic and functional studies, along with recent data from comparative genomics, demonstrate that microorganisms have evolved different strategies to respond and adapt to their environments. Like other organisms, bacteria use classical sensor–effector regulatory circuits to modulate gene expression in response to external stimuli. However, predetermined gene regulation systems are clearly inadequate for the survival of pathogens and symbionts that have to face unpredictable environmental challenges, owing to polymorphism and the immune systems of their hosts. These organisms have opted for an alternative, multicellular-like adaptive strategy based on the production of genetic diversity followed by selection and clonal expansion of the fittest individuals.

Examination of the genomes of pathogenic bacterial species reveals the existence of multiple mechanisms that allow continuous evolution through the deletion, duplication and lateral acquisition of genetic material (1., 2., 3•., 4., 5., 6.; see also the review by DA Rowe-Magnus and D Mazel in this issue, pp 565–569). In addition to this overall genome plasticity, subpopulations of pathogens and commensals exhibit accelerated rates of spontaneous mutations that may facilitate their rapid adaptation to new environmental conditions. Recent in vivo studies, however, demonstrate that such a mutator phenotype may cause long-term disadvantages, owing to indiscriminate and irreversible accumulation of potentially deleterious mutations ([7•]; see also the review by M Radman and F Taddei in this issue, pp 582–585).

To alleviate this problem, bacteria have evolved the ability to produce reversible and high-frequency genetic changes in specific genomic loci, termed ‘contingency’ loci, without increasing the overall mutability of the rest of the genome 8., 9.. The best-documented of these loci are involved in the biosynthesis of surface-exposed antigenic structures, such as outer lipopolysaccharides (LPSs) and lipoproteins, pili, flagella and other secreted proteins that also play a crucial role in the interactions between the bacteria and their host, by modulating their tissue tropism or their ability to use locally available nutrients. Therefore, varying the expression of these structures allows bacteria to counteract the host immune defences as well as to colonise new ecological niches.

Reversible alteration of gene expression in these different loci is mediated by a variety of molecular mechanisms that modify the sequence and/or the structure of DNA 8., 9., 10., 11., 12•.. Some of these mechanisms primarily function as binary switches to turn individual genes ‘on’ or ‘off’, whereas others are used to express multiphasic phenotypes by promoting complex and combinatorial DNA sequence rearrangements. The genomes of bacteria that use these different mechanisms often contain large multigene families that serve as templates for the production of high levels of genetic diversity.

This review discusses recent advances in the understanding of the molecular mechanisms of phase variation and their biological significance, attempting to outline the differences in these mechanisms as well as several aspects that may be viewed as ‘variations on a theme’.

Section snippets

Turning genes ‘on’ or ‘off’ by universal slipped-strand mispairing mechanisms

Phase variation in many bacterial species is mediated by frequent and reversible changes in the lengths of short DNA sequence repeats (termed microsatellites) that are associated with a subset of specific genes 8., 13.. The gain or loss of repeat units in these homo- or heteropolymeric tracts is thought to involve a mechanism of slipped-strand mispairing (SSM) that can occur during chromosomal replication (Fig. 1a) or in the course of a variety of DNA repair and recombination processes that

Site-specific DNA rearrangements

The genomes of many bacterial species exhibit an unexpected potential to undergo homologous recombination-dependent and -independent DNA rearrangements, owing to the presence of multiple repetitive DNA sequences including a variety of transposable elements 1., 2., 3•.. Some of these recombination events may occur spontaneously with respect to time and space and contribute to the overall genetic diversity of a population, whereas others are targeted to specific genomic loci and provide an

DNA shuffling by gene conversion and allele replacement

Unidirectional gene conversion is the result of DNA recombination reactions that lead to complete or partial replacement of one expressed recipient gene with variable DNA segments from a silent copy located in a different part of the genome. Recombination is unidirectional and apparently non-reciprocal, ensuring that the DNA sequence of the donor locus remains unaltered. By reshuffling DNA information from large reservoirs of variable donor sequences, each containing multiple exchangeable

Regulation and control of phase variation: when and at what rate?

Because of their role in adapting bacteria to unpredictable environmental fluctuations, phase-variation mechanisms are often described as essentially stochastic processes that generate random combinations of phenotypes without anticipating whether or not these will be beneficial. However, this does not rule out the possibility that the rate at which genetic diversity is generated may be influenced by external factors, such as stress conditions or cell density. Altering phase-variation

Old and new phase-variable phenotypes: not just surface antigens

Whole-genome-sequence analyses have largely confirmed the importance of varying surface-exposed antigens for allowing bacterial commensals and pathogens to evade the immune system of their host and to adapt to ever-changing environments. However, these analyses, together with several genetic studies, have shown that not all phase-variable genes are associated with cell-surface functions, thereby unveiling new facets of bacterial adaptive strategies.

An increasing number of novel contingency loci

Conclusions

Many questions about the molecular and genetic mechanisms of bacterial phase variation remain unsolved. An emerging view is that they represent fascinating examples of convergent evolution, in which existing mechanisms allowing local modification of the structure and sequence of DNA have been adapted to produce high levels of reversible genetic diversity in strategic regions of the genome. As a consequence, a single mechanism can be used to mediate phase variation in a variety of functions and,

Update

The complete genome sequence of a virulent isolate of Streptococcus pneumoniae recently reported by Tettelin et al. [104•] supports and extends the view that this important pathogen has evolved a range of mechanisms to undergo adaptive genetic changes [3•]. Up to 5% of the genome is composed of insertion sequences belonging to different families, compared with 0–3% in other bacteria. Together with previously identified dispersed DNA sequences termed the ‘RUP’ and ‘BOX’ elements, this high

Acknowledgements

I thank D Yogev for communicating data prior to publication. Also, M Deghorain, S Kotsonis and R Rezsöhazy for critical reading of the manuscript, and S Burteau for technical assistance. The author is a postdoctoral researcher at the Fonds National pour la Recherche Scientifique.

References and recommended reading

Papers of particular interest, published within the annual period of review,have been highlighted as:

  • • of special interest

  • •• of outstanding interest

References (104)

  • C.S. Carrick et al.

    Neisseria gonorrhoeae contains multiple copies of a gene that may encode a site-specific recombinase and is associated with DNA rearrangements

    Gene

    (1998)
  • J.R. Zhang et al.

    Antigenic variation in Lyme disease borreliae by promiscuous recombination of VMP-like sequence cassettes

    Cell

    (1997)
  • A. Travers et al.

    DNA supercoiling and transcription in Escherichia coli: the FIS connection

    Biochimie

    (2001)
  • B. Hallet et al.

    Reciprocal control of catalysis by the tyrosine recombinase XerC and XerD: an enzymatic switch in site-specific recombination

    Mol Cell

    (1999)
  • C. Bucci et al.

    Hypermutation in pathogenic bacteria: frequent phase variation in meningococci is a phenotypic trait of a specialized mutator biotype

    Mol Cell

    (1999)
  • D. Romero et al.

    Repeated sequences in bacterial chromosomes and plasmids: a glimpse from sequenced genomes

    Res Microbiol

    (1999)
  • J.P. Claverys et al.

    Adaptation to environment: Streptococcus pneumoniae, a paradigm for recombination-mediated genetic plasticity?

    Mol Microbiol

    (2000)
  • B.W. Wren

    Microbial genome analysis: insights into virulence, host adaptation and evolution

    Nat Rev Genet

    (2000)
  • H. Ochman et al.

    Lateral gene transfer and the nature of bacterial innovation

    Nature

    (2000)
  • H. Ochman et al.

    Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis

    Science

    (2001)
  • A. Giraud et al.

    Costs and benefits of high mutation rates: adaptive evolution of bacteria in the mouse gut

    Science

    (2001)
  • E.R. Moxon et al.

    The tinkerer's evolving tool-box

    Nature

    (1997)
  • K. Dybvig

    DNA rearrangements and phenotypic switching in prokaryotes

    Mol Microbiol

    (1993)
  • K.W. Deitsch et al.

    Shared themes of antigenic variation and virulence in bacterial, protozoal, and fungal infections

    Microbiol Mol Biol Rev

    (1997)
  • I.R. Henderson et al.

    Molecular switches — the ON and OFF of bacterial phase variation

    Mol Microbiol

    (1999)
  • A. van Belkum et al.

    Short-sequence DNA repeats in prokaryotic genomes

    Microbiol Mol Biol Rev

    (1998)
  • G.F. Richard et al.

    Mini- and microsatellite expansions: the recombination connection

    EMBO Rep

    (2000)
  • I.V. Kovtun et al.

    Trinucleotide expansion in haploid germ cells by gap repair

    Nature Genet

    (2001)
  • D.W. Hood et al.

    DNA repeats identify novel virulence genes in Haemophilus influenzae

    Proc Natl Acad Sci USA

    (1996)
  • C.D. Bayliss et al.

    The simple sequence contingency loci of Haemophilus influenzae and Neisseria meningitidis

    J Clin Invest

    (2001)
  • J.F. Tomb et al.

    The complete genome sequence of the gastric pathogen Helicobacter pylori

    Nature

    (1997)
  • N.J. Saunders et al.

    Simple sequence repeats in the Helicobacter pylori genome

    Mol Microbiol

    (1998)
  • R.A. Alm et al.

    Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori

    Nature

    (1999)
  • J. Parkhill et al.

    The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences

    Nature

    (2000)
  • J. Parkhill et al.

    Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491

    Nature

    (2000)
  • H. Tettelin et al.

    Complete genome sequence of Neisseria meningitidis serogroup B strain MC58

    Science

    (2000)
  • N.J. Saunders et al.

    Repeat-associated phase variable genes in the complete genome sequence of Neisseria meningitidis strain MC58

    Mol Microbiol

    (2000)
  • A. Lavitola et al.

    Intracistronic transcription termination in polysialyltransferase gene (siaD) affects phase variation in Neisseria meningitidis

    Mol Microbiol

    (1999)
  • M.D. Glew et al.

    Expression of the pMGA genes of Mycoplasma gallisepticum is controlled by variation in the GAA trinucleotide repeat lengths within the 5′ noncoding regions

    Infect Immun

    (1998)
  • M.D. Glew et al.

    pMGA phenotypic variation in Mycoplasma gallisepticum occurs in vivo and is mediated by trinucleotide repeat length variation

    Infect Immun

    (2000)
  • L. Liu et al.

    GAA trinucleotide repeat region regulates M9/pMGA gene expression in Mycoplasma gallisepticum

    Infect Immun

    (2000)
  • E.R. Lafontaine et al.

    Expression of the Moraxella catarrhalis Usp A1 protein undergoes phase variation and is regulated at the transcriptional level

    J Bacteriol

    (2001)
  • S. Dawid et al.

    Variation in expression of the Haemophilus influenzae HMW adhesins: a prokaryotic system reminiscent of eukaryotes

    Proc Natl Acad Sci USA

    (1999)
  • X. Nassif et al.

    Interactions of pathogenic Neisseria with host cells. Is it possible to assemble the puzzle?

    Mol Microbiol

    (1999)
  • G. Wang et al.

    Lewis antigens in Helicobacter pylori: biosynthesis and phase variation

    Mol Microbiol

    (2000)
  • M.J. Blaser et al.

    Helicobacter pylori genetic diversity and risk of human disease

    J Clin Invest

    (2001)
  • D. Linton et al.

    Phase variation of a β-1,3 galactosyltransferase involved in generation of the ganglioside GM1-like lipooligosaccharide of Campylobacter jejuni

    Mol Microbiol

    (2000)
  • H.A. Harvey et al.

    Gonococcal lipooligosaccharide is a ligand for the asialoglycoprotein receptor on human sperm

    Mol Microbiol

    (2000)
  • A.G. Lenich et al.

    Amino acid sequence homology between Piv, an essential protein in site-specific DNA inversion in Moraxella lacunata, and transposases of an unusual family of insertion elements

    J Bacteriol

    (1994)
  • T. Komano

    Shufflons: Multiple inversion systems and integrons

    Annu Rev Genet

    (1999)
  • Cited by (123)

    View all citing articles on Scopus
    View full text