Revisiting the expression signature of pks15/1 unveils regulatory patterns controlling phenolphtiocerol and phenolglycolipid production in pathogenic mycobacteria

Abstract

One of the most important and exclusive characteristics of mycobacteria is their cell wall. Amongst its constituent components are two related families of glycosylated lipids, diphthioceranates and phthiocerol dimycocerosate (PDIM) and its variant phenolic glycolipids (PGL). PGL have been associated with cell wall impermeability, phagocytosis, defence against nitrosative and oxidative stress and, intriguingly, biofilm formation. In bacteria from the Mycobacterium tuberculosis complex (MTBC), the biosynthetic pathway of the phenolphthiocerol moiety of PGL depends upon the expression of several genes encoding type I polyketide synthases (PKS), namely ppsA-E and pks15/1 which constitute the PDIM + PGL locus, and that are highly conserved in PDIM/PGL-producing strains. Consensus has not been achieved regarding the genetic organization of pks15/1 locus and knowledge is lacking on its transcriptional signature. Here we explore publicly available datasets of transcriptome data (RNA-seq) from more than 100 MTBC experiments in 40 growth conditions to outline the transcriptional structure and signature of pks15/1, using a differential expression approach to infer the regulatory patterns involving these and related genes. We show that pks1 expression is highly correlated with fadD22, Rv2949c, lppX, fadD29 and, also, pks6 and pks12, with the first three putatively integrating into a polycistronic structure. We evidence dynamic transcriptional heterogeneity within the genes involved in phenolphtiocerol and phenolic glycolipid production, most exhibiting up-regulation upon acidic pH and antibiotic exposure and down-regulation under hypoxia, dormancy, and low/high iron concentration. We finally propose a model based on transcriptome data in which σ D positively regulates pks1, pks15 and fadD22, while σ B and σ E factors exert negative regulation at an upper level.

Exposure ofMycobacterium tuberculosisto human alveolar lining fluid shows temporal and strain-specific adaptation to the lung environment

“…These glycolipids are major M.tb cell envelope components (Garcia-Vilanova et al 2019), where some of them are described as being significantly reduced in content on the M.tb cell envelope surface after only 15-min of exposure to human ALF (Arcos et al 2011), indicating a potential compensatory upregulation of these cell envelope biosynthetic and transport genes to restore these components on the M.tb cell surface. Indeed, pks1, involved in the synthesis of immunomodulatory phenolic glycolipids (PGLs) produced by some M.tb strains and associated with cell envelope impermeability, phagocytosis, defense against oxidative stress and biofilm formation (Pang et al 2012;Garcia-Vilanova et al 2019;Ramos et al 2020), was upregulated in all M.tb strains in this study, although was only significant in CDC1551 and W-7642 (Figure 7B, Supplemental Table S2). We note here, though, that many clinical isolates (including CDC1551), as well as laboratory strain H37Rv, contain a pks1-15 polymorphism associated with the inability of these strains to synthesize PGL (Constant et al 2002).…”

“…Further, other genes involved in the biosynthesis of the M.tb cell envelope were significantly upregulated in W-7642, such as pks1 and pks15 (PGL synthesis) (Ramos et al 2020), murE and murF (peptidoglycan synthesis) (Maitra et al 2019), aftD (biosynthesis of the arabinogalactan region of the M.tb cell envelope backbone known as mycolyl-arabinogalactan-peptidoglycan complex or mAGP) (Skovierova et al 2009), Rv2974c (hypothetical protein potentially involved in glycerolipid and glycerophospholipid metabolism) (Vargas et al 2021), and several lipid and amino acid metabolic genes ( Supplemental Table S2 ) implicated in cell envelope biomass synthesis (Maitra et al 2019). These results indicate that, even though exposure to functional ALF cleaves components of the cell envelope (Arcos et al 2011), strains HN878 and W-7642 are capable of reprograming their metabolism and upregulating genes involved in the synthesis of cell surface components involved in M.tb survival and pathogenesis (DAT/PAT and SL-1).…”

Psk-1 virulence gene-induced pulmonary and systemic tuberculosis in a young female with normal immune function

“…Based on an in vitro live bacterial transcriptome experiment, pks-1 has been reported to have a greater effect than pks-15 on regulating fadD22, Rv2949c, lppX, fadD29, and other genes, thus promoting PGL synthesis. PGL is known to be related to several cell functions, particularly the impermeability of the cell wall, phagocytosis, the defence mechanism against nitroso compounds, oxidative stress, and the ability of mycobacteria to form bio lms, allowing strains to grow rapidly and invade the host [17].…”

Antimycobacterial Activities of Hydroxamic Acids and Their Iron(II/III), Nickel(II), Copper(II) and Zinc(II) Complexes

“…The phenolphthiocerol (phthiocerol) moiety biosynthesis of PGL (PDIM) requires several type I polyketide synthases (PKS) encoded by ppsA-E and pks15/1, among others, like Pks12, Pks18, TesA, DrrB, Pks6, PpgK, ClpS and Mmpl7 [35][36][37][38][39][40]. The expression of pks1 also correlates with other gene expressions, like the expression of fadD22, Rv2949c, lppX, fadD29, pks6 and pks12 [41]. The largest open-reading frame (pks12) in the genome of M. tuberculosis H37Rv encodes probable polyketide synthase needed to produce fatty acids, probably involved in the synthesis of phthiocerol, the diol required for DIM synthesis [37].…”