Epigenetic gene regulation in the bacterial world

Abstract

Like many eukaryotes, bacteria make widespread use of postreplicative DNA methylation for the epigenetic control of DNA-protein interactions. Unlike eukaryotes, however, bacteria use DNA adenine methylation (rather than DNA cytosine methylation) as an epigenetic signal. DNA adenine methylation plays roles in the virulence of diverse pathogens of humans and livestock animals, including pathogenic Escherichia coli, Salmonella, Vibrio, Yersinia, Haemophilus, and Brucella. In Alphaproteobacteria, methylation of adenine at GANTC sites by the CcrM methylase regulates the cell cycle and couples gene transcription to DNA replication. In Gammaproteobacteria, adenine methylation at GATC sites by the Dam methylase provides signals for DNA replication, chromosome segregation, mismatch repair, packaging of bacteriophage genomes, transposase activity, and regulation of gene expression. Transcriptional repression by Dam methylation appears to be more common than transcriptional activation. Certain promoters are active only during the hemimethylation interval that follows DNA replication; repression is restored when the newly synthesized DNA strand is methylated. In the E. coli genome, however, methylation of specific GATC sites can be blocked by cognate DNA binding proteins. Blockage of GATC methylation beyond cell division permits transmission of DNA methylation patterns to daughter cells and can give rise to distinct epigenetic states, each propagated by a positive feedback loop. Switching between alternative DNA methylation patterns can split clonal bacterial populations into epigenetic lineages in a manner reminiscent of eukaryotic cell differentiation. Inheritance of self-propagating DNA methylation patterns governs phase variation in the E. coli pap operon, the agn43 gene, and other loci encoding virulence-related cell surface functions.

FIG. 1.

Pap phase variation in uropathogenic E. coli. Pap17 pilus phase variation of uropathogenic E. coli strain C1212 was visualized with anti-Pap17 antibodies labeled with 10-nm colloidal gold particles. The bacterium at the left is in the ON-phase state for Pap17 expression, whereas the two bacteria at the right are in the OFF phase. Note that these two bacteria express unmarked Pap21 pili, which are also under phase variation control but are not marked with the anti-Pap17 antiserum. In addition to the Pap pili (diameter of about 7 nm), flagella (diameter of about 20 nm) can also be seen.

FIG. 2.

Generation of hemimethylated and nonmethylated GATC sites. (A) The vast majority of chromosomal GATC sites in E. coli are fully methylated until DNA replication generates two hemimethylated species, one methylated on the top strand and one methylated on the bottom strand. Within a short time after replication (less than 5 min), Dam methylates the nonmethylated GATC site, regenerating a fully methylated GATC site. (B) Two or more helically phased GATC sites (for example, in oriC) can be bound by SeqA when they are in the hemimethylated state. Binding of SeqA inhibits Dam methylation, maintaining the hemimethylated state for a portion of the cell cycle. Dissociation of SeqA allows Dam to methylate the hemimethylated DNAs, generating fully methylated DNA. (C) Certain GATC sites are present within or adjacent to regulatory protein binding sites. In some but not all cases, protein binding blocks DNA methylation over the entire cell cycle, stabilizing the hemimethylated state in the first generation and leading to a nonmethylated state in the second generation (only the second generation for the DNA methylated on the top strand is shown at the right).

FIG. 3.

The Pap OFF- to ON-phase transition mechanism. The regulatory region of the pap operon is shown at the top, with six DNA binding sites for Lrp (gray rectangles) and GATC^prox and GATC^dist within Lrp binding sites 2 and 5, respectively. The divergent papI and papBA promoters are shown with arrows. Lrp (ovals), PapI (triangles), and PapB (diamonds) are shown. The methylation states of the top and bottom DNA strands of a GATC site are depicted by an open circle (nonmethylated) or closed circle (methylated). The OFF-to-ON switch is described in the text.

FIG. 4.

The Pap ON- to OFF-phase transition mechanism. See the legend to Fig. 3 for explanations of symbols. The ON-to-OFF switch mechanism is described in the text.

FIG. 5.

DNA sequence alignment of the GATC box regions from pilus operons under DNA methylation pattern control. DNA base pairs conserved in all pap family regulatory regions are shaded black with light lettering. The distal and proximal regulatory GATC sites (GATC^dist and GATC^prox, respectively) are shown. Arrows show the inverted orientation of the two GATC box regions. The accession numbers for the sequences shown are as follows: pap, X14471; foo, AF109675; sfa, S59541; afa, X76688; daa, M98766; clp, L48184; fae, X77671; pef, L08613.

FIG. 6.

Model for phase variation of the outer membrane protein Ag43. The regulatory region of the agn43 operon is shown at the top (A). The three agn43 regulatory GATC sites, GATC-I (far left), GATC-II (middle), and GATC-III (right) are depicted as gray rectangles (A). The methylation states of the top and bottom DNA strands of a GATC site are depicted by an open circle (nonmethylated) or closed circle (methylated). “Rep” indicates a DNA replication event. The Ag43 switch model is discussed in the text.

FIG. 7.

Epigenetic states of the traJ gene in the Salmonella virulence plasmid. In the donor cell, DNA hemimethylation permits traJ transcription only in the plasmid molecule that carries a methyl group in the noncoding DNA strand. As a consequence, plasmid replication generates two epigenetic states in the traJ gene and permits traJ transcription in only one daughter plasmid molecule. The methylation states of the top and bottom DNA strands of a GATC site are depicted by an open square (nonmethylated) or closed square (methylated). The possibility that the active epigenetic state of traJ can be transferred to the recipient cell is at this stage hypothetical.

FIG. 8.

Multifactorial basis for attenuation in Dam⁻ mutants of Salmonella enterica. The lack of strand discrimination for mismatch repair and altered gene expression patterns may explain some of the pleiotropic defects displayed by Salmonella Dam⁻ mutants in the mouse model (13, 89, 208, 210).