Epigenetics and bacterial infections

Abstract

Epigenetic mechanisms regulate expression of the genome to generate various cell types during development or orchestrate cellular responses to external stimuli. Recent studies highlight that bacteria can affect the chromatin structure and transcriptional program of host cells by influencing diverse epigenetic factors (i.e., histone modifications, DNA methylation, chromatin-associated complexes, noncoding RNAs, and RNA splicing factors). In this article, we first review the molecular bases of the epigenetic language and then describe the current state of research regarding how bacteria can alter epigenetic marks and machineries. Bacterial-induced epigenetic deregulations may affect host cell function either to promote host defense or to allow pathogen persistence. Thus, pathogenic bacteria can be considered as potential epimutagens able to reshape the epigenome. Their effects might generate specific, long-lasting imprints on host cells, leading to a memory of infection that influences immunity and might be at the origin of unexplained diseases.

Figure 1.

Chromatin modifications and regulators. Chromatin modifications open or close the chromatin structure, thereby activating or repressing gene expression. Serine phosphorylation on lysine 10 of histone H3 (S10p), acetylation on lysine 14 of H3 (K14ac), and methylation on lysine 4 of H4 (K4me) are examples of activating marks. Conversely, dephosphorylation, deacetylation, and demethylation of the same residues are associated with repression. Methylation of lysine 9 of H3 (K9me) and 5-cytosine methylation of DNA (5mC) are also repressive marks. These modifications are catalyzed or reversed by different enzymes known as “writers” or “erasers,” respectively. An example of writer and eraser for each modification is shown in the color of the modification. Erasure of DNA methylation involves intermediate chemical modifications of 5mC, followed by passive demethylation or DNA repair. 5mC can be hydroxylated by TET dioxygenases (Tahiliani et al. 2009) to form 5hmC, and further oxidized to produce 5fC and 5caC (Wu and Zhang 2011). 5hmC is poorly recognized by DNMT1 and thus can lead to passive demethylation. In addition, 5mC and 5hmC can both be deaminated by AID/APOBEC deaminases to form modified uracyls, 5mU or 5hmU. Excision of modified bases (5mU, 5hmU, 5fC, and 5caC) by DNA glycosylases followed by repair via BER (base excision repair)/NER (nucleotide excision repair) is proposed to regenerate the unmethylated cytosine (Bhutani et al. 2011; Wu and Zhang 2011). Modified residues are recognized and interpreted by different protein modules, known as “readers.” For instance, the bromodomain of HAT p300 binds H3K14ac, the chromodomain of HP1 binds H3K9me, and the methyl-CpG-binding domain (MBD) of MBD1 binds 5meC. Examples of epigenetic cross talks are shown: H3S10p is often associated with H3K14ac and H3K9ac (not shown). H3K9me is often associated with 5mC, on cross-interactions between the H3K9 methyltransferase (G9a/SETDB1), DNMT, HP1, and MBD1. Overall, the chromatin compaction, loss of histone activation marks, and removal of transcription factors accompany gene silencing. HAT, histone acetyltransferase; HDAC, histone deacetylase; HMT, histone methyltransferase; HDM, histone demethyltransferase; DNMT, DNA methyltransferases. Abbreviations are listed in Table 1.

Figure 2.

Three examples of chromatin-modifying complexes and their mode of action. (A) The nucleosome remodeling and histone deacetylase NuRD (or Mi-2) complex contains different subunits involved in nucleosome remodeling (CHD3/CHD4), histone deacetylation (HDAC1/HDAC2), histone demethylation (LSD1), and binding to transcription factors and histones. Additionally, MBD2 recruits NuRD to methylated DNA, whereas MBD3 (whose MBD region is mutated and does not bind methylated DNA) interacts with transcription factors. The function and targeting of the complex to specific loci depends on the combinatorial assembly of the different subunit isoforms. Most often, recruitment of the NuRD complex by a tissue-specific transcription factor to gene promoters mediates transcriptional repression. In the case of the transcription factor c-Jun of the AP1 family, recent studies suggest that its recruitment to the NuRD complex involves MBD3 interaction with unphosphorylated c-Jun. On activation of the JNK pathway, c-Jun phosphorylation mediates MBD3/c-Jun dissociation, resulting in derepression of transcription of target genes (e.g., cell-cycle and cell-differentiation genes) (Aguilera et al. 2011). Abbreviations are listed in Table 1. (B) Mammalian PcG proteins form two multiprotein complexes, polycomb repressive complexes 1 and 2 (PRC1 and PRC2). PRC2 contains a histone-methyltransferase subunit (EZH2, not shown) that generates H3K27me3. PRC1 binds H3K27me3 and catalyzes ubiquitinylation of H2AK119. An early event in chromosome X inactivation in mammalian females is the recruitment of PRC2 by the XIST long coding RNA, inducing H3K27me3 and H2AK119ub along the inactive X chromosome. PRC2 has the ability to recruit DNMTs to some of its target genes, thereby stimulating de novo DNA methylation. (C) The BAHD1-associated chromatin-silencing complex has been discovered by the study of the bacterial protein LntA from L. monocytogenes. Two-hybrid screen, coimmunoprecipitation, and colocalization experiments (Bierne et al. 2009), as well as tandem-affinity purification (Lebreton et al. 2011), identified components associated to BAHD1, i.e., HP1, MBD1, KAP1, histone methyltransferase (SETDB1), and deacetylases (HDAC1/2). Our data suggest that BAHD1 acts as a silencer by tethering chromatin regulators and modifying enzymes to sequence-specific transcription factors (TF), enabling local chromatin compaction. BAHD1-associated heterochromatin sites are enriched in H3K27me3, but the relationship with PRC2 is unknown. Like for NuRD, the function and targeting of the BAHD1 complex to specific genes likely depend on the combinatorial assembly of the different subunits, in response to signals to which cells are submitted. On Listeria infection, the BAHD1 complex assembles at promoters of a set of interferon-stimulated genes (ISGs), as shown in Figure 4.

Figure 3.

Bacterial signaling to histones and downstream effects. Schematic representation of Listeria monocytogenes-, Bacillus anthracis-, Mycobacterium tuberculosis-, Helicobacter pylori-, or Porphyromonas gingivalis-induced signaling pathways leading to histone modifications, as detailed in the text. Bacterial products inducing host cellular signaling are in yellow. Membrane (TNF-α-R, IFN-γ, TLR2, TLR4) or cytosolic (NOD1) receptors are indicated by a red oval. Effects on target genes are indicated by arrows (up for activation and down for repression). Cell types in which studies have been performed are listed below. Abbreviations are listed in Table 1.

Figure 4.

Bacterial nucleomodulins targeting chromatin. Schematic representation of Chlamydia, Anaplasma, Listeria, and Shigella secreted factors involved in the control of gene expression in the nucleus of host cells, as detailed in the text. The bacterial nucleomodulins are in yellow. 1. Chlamydia histone-methyltransferase NUE methylate’s mammalian histones. However, target genes are unknown. 2. Binding to AT-rich sequences and silencing of CYBB expression by Anaplasma Ank effector AnkA. 3. Inhibition of the BAHD1-associated heterochromatic complex and induction of interferon-stimulated genes by Listeria LntA. On Listeria infection, an unknown signaling pathway drives the BAHD1-associated chromatin complex (see Fig. 2C) to repress interferon-stimulated genes. When Listeria produces and secretes LntA, this factor enters the nucleus and interacts with BAHD1, destabilizes the silencing complex, restores histone acetylation (Ac), and enhances the expression of ISGs. 4. Control of a set of NF-κB (p65-p50) regulated genes by Shigella posttranslational modifiers OspF, which eliminylates MAP kinases preventing phosphorylation of histone H3, and IpaH9.8, which ubiquitinylates and promotes degradation of the splicing factor U2AF³⁵. OspF and another effector, OspB, bind the retinoblastoma protein (Rb), which potentially recruits several chromatin-remodeling enzymes (not shown). Ac, Acetylation; Me, methylation; P, phosphorylation; E, eliminylation; UB, ubiquitinylation.