Phase and antigenic variation in bacteria

Abstract

Phase and antigenic variation result in a heterogenic phenotype of a clonal bacterial population, in which individual cells either express the phase-variable protein(s) or not, or express one of multiple antigenic forms of the protein, respectively. This form of regulation has been identified mainly, but by no means exclusively, for a wide variety of surface structures in animal pathogens and is implicated as a virulence strategy. This review provides an overview of the many bacterial proteins and structures that are under the control of phase or antigenic variation. The context is mainly within the role of the proteins and variation for pathogenesis, which reflects the main body of literature. The occurrence of phase variation in expression of genes not readily recognizable as virulence factors is highlighted as well, to illustrate that our current knowledge is incomplete. From recent genome sequence analysis, it has become clear that phase variation may be more widespread than is currently recognized, and a brief discussion is included to show how genome sequence analysis can provide novel information, as well as its limitations. The current state of knowledge of the molecular mechanisms leading to phase variation and antigenic variation are reviewed, and the way in which these mechanisms form part of the general regulatory network of the cell is addressed. Arguments both for and against a role of phase and antigenic variation in immune evasion are presented and put into new perspective by distinguishing between a role in bacterial persistence in a host and a role in facilitating evasion of cross-immunity. Finally, examples are presented to illustrate that phase-variable gene expression should be taken into account in the development of diagnostic assays and in the interpretation of experimental results and epidemiological studies.

FIG. 1.

Phase variation as a result of SSM at short sequence repeats. (A) Schematic of the four positions, relative to a gene, at which short sequence repeats can cause phase variation. Indicated are a coding sequence (open rectangle), promoter (−10, −35) with RNA polymerase (RNA pol), the +1 transcription start site, the Shine-Dalgarno sequence for ribosome binding (SD), and the ATG translation start codon. Repeat sequences at regions 1 through 4 can lead to phase variation by affecting transcription initiation (regions 1 and 2), translation (region 4), and as yet unidentified means (region 3) (see the text). (B) Effect on the translation product of a one-unit insertion due to SSM at the tetranucleotide repeat sequence (AGTC) in the coding sequence of mod of H. influenzae (HI056). Partial nucleotide and amino acid sequences and numbering are indicated for 31 (on) and 32 (off) tetranucleotide repeats. Note that as a result of the insertion, the reading frame changes at amino acid 177, which leads to the formation of a premature stop codon (*) following amino acid 194.

FIG. 2.

Intermediate hybrid model for gene conversion at pilE in N. gonorrhoeae as a result of homologous recombination (142). Open rectangles designate the conserved region of the pil gene, patterns designate the different variable sequences, and the thick bar indicates some of the very short conserved sequences. (A) DNA exchange occurs between a silent pilS locus and the pilE locus of the donor chromosome at a short region of homology. This RecA-independent recombination is indicated by the light cross and results in the formation of an intermediate pilE-pilS hybrid molecule, depicted here as a circular extrachromosomal molecule. The predominant intermediate hybrid molecule may have a different structure (176). (B) The intermediate hybrid structure donates sequence to the pilE locus of the recipient chromosome, involving two crossover events, a RecA-dependent one at a larger region of homology (heavy cross) flanking the pil sequence and one at a short region of homology, depicted here within the pil sequence.

FIG. 3.

Phase variation of type 1 fimbrial expression, encoded by the fim operon, in E. coli as a result of DNA inversion mediated by SSM. The relative positions of the promoters (open arrows), genes (open rectangles), and inverted repeats IRR and IRL (triangles) at fim are shown. The invertible DNA sequence and its orientation are depicted by a shaded bar. IRR an IRL are within the binding sites for the recombinases FimB and FimE. Binding sites for other regulatory proteins (Lrp and integration host factor) are not shown (see the text). The drawing is not to scale and is not meant to convey protein size or other biochemical properties.

FIG. 4.

DNA methylation-dependent phase variation of the pap operon in E. coli. Proteins that are essential for the “on” and “off” phases, and the relative positions of their binding sites, are depicted. Note that the methylation state of the two GATC DNA sequences, depicted by Me, also differ in the two phases as a result of the accessibility of Dam. The drawing is not to scale and is not meant to convey protein size or biochemical properties. See the text for additional information.