Ehrlichia chaffeensis TRP47 enters the nucleus via a MYND-binding domain-dependent mechanism and predominantly binds enhancers of host genes associated with signal transduction, cytoskeletal organization, and immune response

Abstract

Ehrlichia chaffeensis is an obligately intracellular bacterium that establishes infection in mononuclear phagocytes through largely undefined reprogramming strategies including modulation of host gene transcription. In this study, we demonstrate that the E. chaffeensis effector TRP47 enters the host cell nucleus and binds regulatory regions of host genes relevant to infection. TRP47 was observed in the nucleus of E. chaffeensis-infected host cells, and nuclear localization was dependent on a variant MYND-binding domain. An electrophoretic mobility shift assay (EMSA) demonstrated that TRP47 directly binds host DNA via its tandem repeat domain. Utilizing chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq) with E. chaffeensis-infected cells, TRP47 was found to bind at multiple sites in the human genome (n = 2,051 at p < 10−30). Ontology analysis identified genes involved in functions such as immune response, cytoskeletal organization, and signal transduction. TRP47-bound genes included RNA-coding genes, many of these linked to cell proliferation or apoptosis. Comparison of TRP47 binding sites with those of previously-identified E. chaffeensis nucleomodulins identified multiple genes and gene functional categories in common including intracellular transport, cell signaling, and transcriptional regulation. Further, motif analysis followed by EMSA with synthetic oligonucleotides containing discovered motifs revealed a conserved TRP47 DNA-binding motif. This study reveals that TRP47 is a nucleomodulin that enters the nucleus via a MYND-binding domain and appears to play a role in host cell reprogramming by regulation of transcription.

Bacterial Manipulation of Wnt Signaling: A Host-Pathogen Tug-of-Wnt

“…TRPs also interact with nuclear proteins involved in Wnt target gene epigenetic modification and expression, including the Wnt response element transcriptional repressor TLE4 (102), co-activator DAZAP2 (103), and histone remodeling proteins ARID1B, KDM6B, and IRF2BP2 (104–106). Furthermore, TRP32, TRP47, and TRP120 DNA-binding motifs are within the promoter region of numerous Wnt target genes, indicating the TRPs may directly influence Wnt gene transcription through nucleomodulin activity (33–35). Although these specific interactions have not yet been investigated, it is likely that the nucleomodulin activity of TRP effectors or the recently discovered ubiquitin ligase activity of TRP120, plays a role in manipulation of these target proteins, facilitating Wnt pathway activity and ultimately enhancing E. chaffeensis intracellular survival (107).…”

Bacterial Factors Targeting the Nucleus: The Growing Family of Nucleomodulins

“…These observations support the hypothesis of large-scale transcriptional alteration induced by Ank200 via mechanisms associated with the regulation of Alu-Sx elements. TRP32 and TRP120 bind to host-cell DNA at G-rich and G + C-rich motifs, respectively, as well as chromatin-associated proteins, such as histone methylases and demethylases, polycomb-group (PcG) proteins and other components of chromatin-remodeling complexes [43][44][45][46][47][48]. TRP120 acts as a transcriptional activator for host genes [44], while TRP32 activates or represses expression of its target genes [46,47].…”

“…TRP120 acts as a transcriptional activator for host genes [44], while TRP32 activates or represses expression of its target genes [46,47]. Recently, another TRP effector, TRP47, has been identified as a fourth E. chaffeensis nucleomodulin [48]. TRP47 translocates into the nucleus via a MYND (myeloid, Nervy, and DEAF-1)-binding domain and targets multiple infection-associated genes by binding DNA at G + C-rich motifs.…”

“…TRP47 translocates into the nucleus via a MYND (myeloid, Nervy, and DEAF-1)-binding domain and targets multiple infection-associated genes by binding DNA at G + C-rich motifs. It can be noted that the MYND domain, which is a zinc finger motif that primarily functions as a protein-protein interaction module, is present in several host chromatin-remodeling proteins [48,49].…”

Detection of specific IgM and IgG antibodies in acute canine monocytic ehrlichiosis that recognize recombinant gp36 antigens

“…Previous reports have demonstrated that TRP has various interactions with host proteins in the regulation of biological processes. This major immunoreactive protein of E. chaffeensis interacts with multiple host proteins involved in posttranscriptional modification processes ( Lina et al., 2016 ; Kibler et al., 2018 ).…”