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A Low-Prevalence Single-Nucleotide Polymorphism in the Sensor Kinase Phor in Mycobacterium Tuberculosis Suppresses Its Autophosp

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A Low-Prevalence Single-Nucleotide Polymorphism in the Sensor Kinase Phor in Mycobacterium Tuberculosis Suppresses Its Autophosp fmicb-12-724482 August 19, 2021 Time: 16:39 # 1 ORIGINAL RESEARCH published: 25 August 2021 doi: 10.3389/fmicb.2021.724482 A Low-Prevalence Single-Nucleotide Polymorphism in the Sensor Kinase PhoR in Mycobacterium tuberculosis Suppresses Its Autophosphatase Activity and Reduces Pathogenic Fitness: Implications in Evolutionary Selection Uchenna Watson Waturuocha1,2, M. S. Krishna1, Vandana Malhotra3, Narendra M. Dixit4,5 and Deepak Kumar Saini2,5* 1 Department of Studies in Zoology, University of Mysore, Mysore, India, 2 Department of Molecular Reproduction Development and Genetics, Indian Institute of Science, Bengaluru, India, 3 Sri Venkateswara College, University of Delhi, New Delhi, India, 4 Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India, 5 Center Edited by: for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India George Grant, University of Aberdeen, United Kingdom The genome sequencing of Mycobacterium tuberculosis, the causative organism of Reviewed by: tuberculosis, has significantly improved our understanding of the mechanisms that Amanda Jane Gibson, Aberystwyth University, drive the establishment of infection and disease progression. Several clinical strains United Kingdom of M. tuberculosis exhibit single-nucleotide polymorphisms (SNPs), the implications Roberto Zenteno-Cuevas, of which are only beginning to be understood. Here, we examined the impact of Universidad Veracruzana, Mexico a specific polymorphism in PhoR, the sensor kinase of the PhoPR two-component *Correspondence: Deepak Kumar Saini system. Biochemical analysis revealed reduced autophosphatase/ATPase activity, which [email protected] led to enhanced downstream gene expression. We complemented M. tuberculosis H37Ra with the wild-type and mutant phoPR genes and characterized the strains in Specialty section: This article was submitted to a cell line infection model. We provide an explanation for the low prevalence of the Infectious Diseases, SNP in clinical strains (∼1%), as the mutation causes a survival disadvantage in the a section of the journal Frontiers in Microbiology host cells. The study provides a rare example of selection of a signaling node under Received: 13 June 2021 competing evolutionary forces, wherein a biochemically superior mutation aids bacterial Accepted: 30 July 2021 adaptation within-host but has low fitness for infection and hence is not selected. Our Published: 25 August 2021 study highlights the importance of accounting for such SNPs to test therapeutic and Citation: co-therapeutic methods to combat TB. Waturuocha UW, Krishna MS, Malhotra V, Dixit NM and Saini DK Keywords: single-nucleotide polymorphism, two-component system, histidine kinase, Mycobacterium (2021) A Low-Prevalence tuberculosis, evolutionary fitness, bacterial signal transduction, PhoR Single-Nucleotide Polymorphism in the Sensor Kinase PhoR in Mycobacterium tuberculosis INTRODUCTION Suppresses Its Autophosphatase Activity and Reduces Pathogenic Fitness: Implications in Evolutionary Sequencing of Mycobacterium tuberculosis H37Rv genome, a virulent laboratory strain, has Selection. revolutionized the research done on this pathogen world over (Cole et al., 1998). It revealed Front. Microbiol. 12:724482. the presence of sizeable unknown gene sets, like serine–threonine protein kinases (STPKs) and doi: 10.3389/fmicb.2021.724482 other relatively small groups of typical bacterial signaling systems, the two-component systems Frontiers in Microbiology| www.frontiersin.org 1 August 2021| Volume 12| Article 724482 fmicb-12-724482 August 19, 2021 Time: 16:39 # 2 Waturuocha et al. PhoR Signaling in Clinical Strains of Mycobacterium tuberculosis (TCSs). Over the years, a large number of virulent clinical (Ioerger et al., 2010). This includes the adaptation of H37Rv strains, non-human pathogenic strains, and non-pathogenic to laboratory conditions while remaining virulent in mice mycobacterial strains have been sequenced, aimed at unraveling (Ioerger et al., 2010). It is believed that there are hot spots what makes M. tuberculosis such a successful pathogen (Cole for insertions/duplications, deletions, or substitutions across the et al., 1998; Garnier et al., 2003; Zheng et al., 2008; Ioerger et al., M. tuberculosis genome. Variants have also been observed in 2010; Tekwu et al., 2014; Mohan et al., 2015; Manson et al., 2017; highly conserved TCS regions, such as a SNP in the DNA-binding Borrell et al., 2019). The findings have revealed many differences; domain of the phoP RR that attenuates the H37Ra strain (Wang however, their contribution toward pathogenicity is not clear et al., 2007; Chesne-Seck et al., 2008; Lee et al., 2008) and an (Ioerger et al., 2010). SNP in the SK phoR, which shows functional and phenotypic Given the pathogenic nature of M. tuberculosis, it is expected changes in the clinical strain CDC1551 when compared with to face adverse environments within its host (Chai et al., 2018). To H37Rv (Schreuder et al., 2015), and yet another SNP in the phoR adapt and survive in changing environmental conditions, it uses region of the M. bovis strain, which leads to pleiotropic changes signaling systems called TCSs, which regulate the expression of in the production and secretion of lipids and affects virulence many genes in response to various environmental stimuli (Pang (Gonzalo-Asensio et al., 2014). et al., 2007). TCSs are typically composed of a sensor kinase In the present study, we examined the role of one (SK) as the first component that senses the external stimulus such polymorphism in the PhoR SK and its effect on and undergoes activation by an autophosphorylation event at mycobacterial signaling, virulence, and pathogenicity. Our a specific histidine (His) residue. The second component of findings demonstrate that the mutation enhanced the catalytic a TCS is a response regulator (RR), which the SK activates activity of the SK in both in vitro and in vivo conditions. by a unique phosphotransfer event on a conserved aspartate The presence of the SNP in three of the 242 clinical strains (Asp) residue (Stock et al., 2000; Bourret and Silversmith, 2010). examined suggests a poor evolutionary selection of this variant. The RRs are DNA-binding transcription factors that activate or We hypothesize that the mutant TCS is primed early and repress the transcription of downstream genes and bring about activates higher gene expression upon sensing of stimuli, leading adaptive changes in the bacterium. Among the 12 pairs of TCSs to impaired survival of the mutation carrying bacilli during in M. tuberculosis, the PhoPR TCS is extensively studied and infection. This could explain the poor selection of the SNP in the implicated in regulating various processes, such as virulence wild. Overall, this study presents an example of the evolutionary and growth upon infection (Pérez et al., 2001; Walters et al., benefits of temporally tuned signaling activity and suggests that 2006; Ryndak et al., 2014), lipid biosynthesis (Walters et al., similar competing forces may be at play with other TCSs. 2006), hypoxia (Vashist et al., 2018), pH sensing, and adaptation (Johnson et al., 2015). It is known to regulate the expression of about 2% of the M. tuberculosis genome (Cimino et al., MATERIALS AND METHODS 2012). It is essential for survival and multiplication within macrophages (Ludwiczak et al., 2002), and thus, this operon Chemicals, media, biochemicals, and protein reagents were has been considered to be a master regulator in M. tuberculosis obtained from Merck (Kenilworth, NJ, United States); protein (Ryndak et al., 2008). We analyzed the sequences of several marker was from Abcam (Cambridge, United Kingdom). clinical strains and sought single-nucleotide polymorphisms Restriction enzymes were from Thermo Fisher Scientific (SNPs) primarily in TCS genes to understand the evolutionary (Waltham, MA, United States). Cloning and qRT primers were pressures subjected to TCSs. synthesized by Bioserve (Hyderabad, India); radioactive g32P Comparative sequence analysis of strains from various ATP (>4,000 Ci/mmol) was from BRIT-Jonaki (Hyderabad, lineages of M. tuberculosis sensu stricto (L1–L4 and L7) and India); fetal bovine serum (FBS) from Thermo Fisher Scientific Mycobacterium africanum (L5 and L6), which belong to the (United States); TRIzol from TaKaRa (Seoul, South Korea); 0.1- human-adapted M. tuberculosis complex, that diverged from mm zirconia beads from BioSpec Products Inc., (Bartlesville, strains that infect animals and now cause the disease in humans OK, United States); iScript cDNA synthesis kit from Bio-Rad (Comas et al., 2014), and Mycobacterium bovis, revealed close Laboratories (Hercules, CA, United States); DyNAmo Color to ∼2,000 SNPs. These polymorphisms could be responsible for Flash SYBR Green qPCR Kit from Thermo Fisher Scientific the physiological differences between them. Genomic differences (United States); THP-1 monocyte cell line and H460 epithelial cell among clinical strains have been associated with variations in line from ATCC (Manassas, VA,United States); and H37Ra strain protein and metabolite levels, post-translational modifications of M. tuberculosis from lab collection. (Liu et al., 2014), drug susceptibility (Rouse et al., 1995), transcriptome (Homolka et al., 2010; Rose et al., 2013), and cell In silico Sequence Analysis wall structure (Coscolla and Gagneux, 2014), along with virulence The sequences of 19 clinical isolates from India, reported as and infectivity. It is also observed that strains
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