Moonlighting activity of the epigenetic machinery restrains infection

Abstract

Intracellular bacterial pathogens have evolved a range of mechanisms, including manipulation of the host cell epigenetic machinery and host cell gene expression rewiring, to parasitize and thrive inside host phagocytes. A new study in The EMBO Journal (Yaseen et al, 2018) reports that, conversely, host macrophages can use epigenetic modulators to modify the cell surface of invading pathogens and counteract infection. This study opens new avenues to better understand host–pathogen interactions and to develop novel, more effective antimicrobial strategies.

With over 10 million new cases and 1.7 million deaths, tuberculosis (TB) remains the top infectious killer in 2016 according to the World Health Organization. The development of novel therapeutics to combat TB, including new drugs, host‐directed therapies, and a vaccine better than BCG—which protects infants against disseminated TB but poorly protects adults from pulmonary transmissible form of the disease—requires a better understanding of the very complex interplay between the TB bacillus, Mycobacterium tuberculosis (Mtb), and its human host (Wallis et al, 2016). TB transmission occurs through inhalation of Mtb‐containing aerosol droplets expelled by coughing patients. These droplets reach the lung alveoli where the bacilli are recognized and phagocytized by alveolar macrophage. After phagocytosis, bacteria are usually degraded within acidic and hydrolytic phagolysosomes, which arise from the fusion of the bacteria‐containing vacuoles, or phagosomes, with the host cell lysosomes. Mtb is able to counteract this phenomenon and uses infected macrophages as a niche in which it survives and multiplies (Weiss & Schaible, 2015).

One of the mechanisms used by pathogenic microorganisms to survive inside phagocytic cells involves host cell gene expression rewiring by the so‐called nucleomodulins, proteins secreted by the pathogens and targeted to the host cell nucleus where they can either act as bona fide transcription factors, or as modulators of the host cell transcription or epigenetic machineries (Bierne & Cossart, 2012). Recently, several nucleomodulins or putative nucleomodulins were identified in Mtb (Sharma et al, 2015; Yaseen et al, 2015; Jose et al, 2016; Bhat et al, 2017; Wang et al, 2017). In this issue of The EMBO Journal, Yaseen et al (2018) report the unsuspected finding that, conversely, host macrophages can use epigenetic modulators to modify bacterial proteins and reduce Mtb intracellular survival.

In order to investigate the epigenetic response of host macrophages to mycobacterial infection, Yaseen et al (2018) analyzed the expression of several histone methyltransferases and demethylases in human macrophages infected with various Mycobacteria species. They observed that the histone H3K9 methyltransferase SUV39H1 was more abundant after infection of macrophages with mycobacteria, but not with other microorganisms, namely Escherichia coli and Candida glabrata. Surprisingly, immunostaining and fluorescence microscopy examination of infected cells demonstrated that whereas SUV39H1 localized inside the nucleus in uninfected macrophages, its overexpression upon mycobacterial infection was accompanied with relocalization of the protein to the macrophage cytoplasmic space and plasma membrane. These observations were confirmed by cell fractionation and Western blot experiments demonstrating that SUV39H1 associated with the infecting bacilli within the phagosomes and was present in the membrane fraction of the infected cells. In vitro binding assays demonstrated that SUV39H1 was able to readily bind to mycobacteria.

Mtb encodes a histone‐like protein, HupB (Cohavy et al, 1999), also known as laminin binding protein (LBP), previously shown to be localized both in the cytoplasm and at the cell surface of Mtb, and to be involved in mycobacterial binding to the macrophage surface through its interaction with laminin (Lefrancois et al, 2011). In their study, Yaseen et al (2018) identified HupB as a target for the SUV39H1 methyltransferase. Western blotting experiments using mono‐/di‐ or trimethylated lysine‐specific antibodies showed that whereas HupB is mono‐ or dimethylated by an endogenous bacterial methyltransferase, a trimethylated form of the protein is detected upon treatment of mycobacterial extracts with SUV39H1. HupB harbors a Lys¹³⁸‐centered motif similar to the region around Lys⁹ of histone H3. Methylation experiments using mutant forms of HupB demonstrated that Lys¹³⁸ is the trimethylated site in HupB upon SUV39H1 treatment.

In order to explore the functional consequences of SUV39H1 induction and relocalization in mycobacteria‐infected macrophages, Yaseen et al (2018) used the histone methyltransferase inhibitor chaetocin and generated stable THP1 macrophage‐like cell lines expressing either an shRNA directed against SUV39H1 or a control, scrambled, shRNA. Using these tools, the authors compared the behavior of recombinant Mycobacterium smegmatis, a fast‐growing distant cousin of Mtb, or Mtb‐expressing wild‐type or modified forms of HupB altered in Lys¹³⁸. SUV39H1 silencing resulted in an increase in intracellular multiplication of bacteria over‐expressing wild‐type HupB. In contrast, SUV39H1 silencing had no effect on the intracellular bacterial loads when bacteria expressed HupB‐K138A, a mutant form of HupB that cannot be trimethylated. These data indicated that macrophages were able to restrain mycobacterial intracellular survival through SUV39H1‐dependent trimethylation of HupB. In agreement with this finding, infection of mice with recombinant M. smegmatis yielded a higher amount of bacteria in lungs, liver, and spleen when the bacteria expressed HupB‐K138A, compared to bacteria expressing wild‐type HupB. Finally, Yaseen et al (2018) report that treatment of Mtb with SUV39H1 markedly reduces biofilm formation in vitro and mycobacterial aggregation within phagosomes, demonstrating that trimethylation of HupB present in the Mtb envelope alters bacterial adherence.

Altogether, the observations reported by Yaseen et al (2018) bring novel knowledge in host–pathogen interactions (Fig 1). They also raise several important questions. The mechanisms, including receptors, signal transduction pathways, and intracellular partners, leading to the increased expression and subcellular relocalization of SUV39H1 in infected cells, will need to be deciphered. In addition, HupB is known to play an important role as a nucleoid‐associated protein binding to DNA in the bacterial cytoplasm (Holowka et al, 2017) and as a bacterial envelope‐associated protein during adhesion to host cells (Lefrancois et al, 2011). In this context, the mechanisms involved in restriction of infection through HupB trimethylation remain to be fully understood. Finally, it will be most interesting to investigate whether countering infection by SUV39H1 and possibly other host cell epigenetic modulators is a more general response to infection by mycobacteria and other intracellular pathogens.

Figure 1. The role of SUV39H1 in restricting Mycobacterium tuberculosis in macrophages.

Mycobacterium tuberculosis infection of macrophages induces the expression of nuclear SUV39H1 and relocalization of the protein to the host cell surface. At the plasma membrane, SUV39H1 trimethylates the mycobacterial surface protein HupB, which reduces mycobacterial adhesion. After phagocytosis, SUV39H1 localizes in the mycobacterial vacuole. This restricts intracellular survival and/or multiplication of M. tuberculosis. The signaling pathway linking mycobacterial encountering and SUV39H1 upregulation and trafficking outside the nucleus will need to be deciphered. Similarly, the mechanism by which SUV39H1‐mediated trimethylation of HupB restricts mycobacteria inside the host cells will require further investigation.

See also: I Yaseen et al (January 2018)