Effector bottleneck: microbial reprogramming of parasitized host cell transcription by epigenetic remodeling of chromatin structure

Abstract

Obligate intracellular pathogenic bacteria evolved to manipulate their host cells with a limited range of proteins constrained by their compact genomes. The harsh environment of a phagocytic defense cell is one that challenges the majority of commensal and pathogenic bacteria; yet, these are the obligatory vertebrate homes for important pathogenic species in the Anaplasmataceae family. Survival requires that the parasite fundamentally alter the native functions of the cell to allow its entry, intracellular replication, and transmission to a hematophagous arthropod. The small genomic repertoires encode several eukaryotic-like proteins, including ankyrin A (AnkA) of Anaplasma phagocytophilum and Ank200 and tandem-repeat containing proteins of Ehrlichia chaffeensis that localize to the host cell nucleus and directly bind DNA. As a model, A. phagocytophilum AnkA appears to directly alter host cell gene expression by recruiting chromatin modifying enzymes such as histone deacetylases and methyltransferases or by acting directly on transcription in cis. While cis binding could feasibly alter limited ranges of genes and cellular functions, the complex and dramatic alterations in transcription observed with infection are difficult to explain on the basis of individually targeted genes. We hypothesize that nucleomodulins can act broadly, even genome-wide, to affect entire chromosomal neighborhoods and topologically associating chromatin domains by recruiting chromatin remodeling complexes or by altering the folding patterns of chromatin that bring distant regulatory regions together to coordinate control of transcriptional reprogramming. This review focuses on the A. phagocytophilum nucleomodulin AnkA, how it impacts host cell transcriptional responses, and current investigations that seek to determine how these multifunctional eukaryotic-like proteins facilitate epigenetic alterations and cellular reprogramming at the chromosomal level.

Keywords: Anaplasma phagocytophilum; DNA methylation; chromatin; epigenetics; histone deacetylase; nucleomodulin.

FIGURE 1

AnkA alters chromatin structure at the CYBB promoter. During Anaplasma phagocytophilum infection, AnkA accumulates in the host cell nucleus where it can directly bind DNA and influence the transcription of CYBB, which encodes the gp91^phox component of the NADPH oxidase. (A) In the absence of infection, CYBB is activated by inflammatory signals and is easily transcribed. (B) During infection, AnkA binds the proximal promoter and recruits HDAC which deacetylates nearby histones in order to inhibit transcription. (C) We propose that additional host or bacterial-derived chromatin modifying enzymes, such as DNMT methylation of host CpGs, may also be involved in altering the host epigenome to the bacterium’s advantage.

FIGURE 2

Heat map demonstrations of long linear chromosomal differential transcription of A. phagocytophilum-infected human neutrophils vs. uninfected neutrophils. The human chromosome number is shown at the top. The colors represent estimates of the SD of differential transcription of the window at each position compared to the overall differential transcription> for that chromosome; dark red = -2 SDs; dark green = +2 SDs.

FIGURE 3

Differential gene expression patterns cluster over large linear genomic regions in A. phagocytophilum-infected human peripheral blood neutrophils. The top panel shows human chromosome 17; the bottom panel shows the MPO/EPX/LPO locus on human chromosome 17 and the large genomic region that is upregulated with infection. The chromosome ideogram is shown at the top. Red bars (left axes) represent differential transcription of individual genes, including some replicates; the dark blue zones (left axes) show the sliding window average log₂-fold differential transcription over the contiguous 9–11 genes (or 0.38–1.25 Mb). The light blue zone at the bottom (right axis) shows the sliding window average over the same region for estimated SDs of log₂-fold differential transcription at each gene or gene feature. Data re-analyzed from Borjesson et al. (2005) www.ncbi.nlm.nih.gov/geo, accession no. GSE2405.

FIGURE 4

Differential gene expression patterns comparing A. phagocytophilum-infected vs. non-infected human peripheral blood neutrophils are clustered over large linear genomic regions. The top panel shows human chromosome 6; the bottom panel shows the MHC locus on human chromosome 6 including a large genomic region spanning the TNF and HLAD loci that are upregulated with infection. The chromosome ideogram is shown at the top. Red bars (left axes) represent differential transcription of individual genes, including some replicates, the dark blue zones (left axes) show the sliding window average log₂-fold differential transcription over the contiguous 9–12 genes (or 0.42–3.24 Mb). The light blue zone at the bottom (right axis) shows the sliding window average over the same region for estimated SDs of log₂-fold differential transcription at each gene or gene feature. Data re-analyzed from Borjesson et al. (2005) http://www.ncbi.nlm.nih.gov/geo, accession no. GSE2405.