Functional metagenomics identifies novel genes ABCTPP, TMSRP1 and TLSRP1 among human gut enterotypes

Abstract

Every niche in the biosphere is touched by the seemingly endless capacity of microbes to transform the world around them by adapting swiftly and flexibly to the environmental changes, likewise the gastrointestinal tract is no exception. The ability to cope with rapid changes in external osmolarity is an important aspect of gut microbes for their survival and colonization. Identification of these survival mechanisms is a pivotal step towards understanding genomic suitability of a symbiont for successful human gut colonization. Here we highlight our recent work applying functional metagenomics to study human gut microbiome to identify candidate genes responsible for the salt stress tolerance. A plasmid borne metagenomic library of Bacteroidetes enriched human fecal metagenomic DNA led to identification of unique salt osmotolerance clones SR6 and SR7. Subsequent gene analysis combined with functional studies revealed that TLSRP1 within pSR7 and TMSRP1 and ABCTPP of pSR6 are the active loci responsible for osmotolerance through an energy dependent mechanism. Our study elucidates the novel genetic machinery involved in bestowing osmotolerance in Prevotella and Bacteroidetes, the predominant microbial groups in a North Indian population. This study unravels an alternative method for imparting ionic stress tolerance, which may be prevalent in the human gut microbiome.

Comparative analysis of the alveolar microbiome in COPD, ECOPD, Sarcoidosis, and ILD patients to identify respiratory illnesses specific microbial signatures

“…Moreover, we also observed a significantly higher abundance of Haemophilus in stable COPD groups. These deviations could be seen as a possible outcome of diverse ethnicity, as commonly observed in other human microbiome studies 31 , 32 .…”

Molecular and Biochemical Characterization of Salt-Tolerant Trehalose-6-Phosphate Hydrolases Identified by Screening and Sequencing Salt-Tolerant Clones From the Metagenomic Library of the Gastrointestinal Tract

“…Moreover, the inactivating or denaturizing of proteins and cellular membranes can be prevented even in conditions such as desiccation, hypohydration, torridness, coldness, and oxidation by trehalose ( Elbein et al, 2003 ). As we know, bacteria normally react to osmotic pressure changes in a so-called staged response, to be specific, (1) fast aggregation of K + ; (2) succeeding synthesis or accumulating of osmoprotectant compounds ( Kempf and Bremer, 1998 ; Sleator and Hill, 2002 ; Epstein, 2003 ; Kunte, 2006 ); and (3) an assisting mechanism that may include a broad scope of genes such as htrA gene ( Sleator and Hill, 2005 ), GspM and EchM proteins ( Kapardar et al, 2010a ), ClpS protein ( Kapardar et al, 2010b ), galE , murB , and mazG genes ( Culligan et al, 2012 ), stlA gene ( Culligan et al, 2013 ), sdtR gene ( Culligan et al, 2014a ), brpA gene ( Culligan et al, 2014b ), and TMSRP1 , ABCTPP , and TLSRP1 genes ( Verma et al, 2018 ). As such, further studies on the relations between these genes and enzymes and the microbial salt-tolerance mechanisms might prove much need.…”

“…The brpA gene belongs to the brp/blh family of β-carotene 15,15′-monooxygenase, which encodes a membrane protein. Verma et al (2018) screened salt-tolerant clones, namely, SR6 and SR7, from the human fecal metagenomic library, performed subclone analysis, and found that TMSRP1 , ABCTPP , and TLSRP1 are associated with salt tolerance. Ilmberger et al (2012) obtained salt-tolerant hydrolase from the gastrointestinal microbial metagenome (celA84 in the GH5 family can retain 50% relative activity after 34 days in 4 M NaCl).…”

Overview of the rules of the microbial engagement in the gut microbiome: a step towards microbiome therapeutics

“…Numerous studies have defined the gene clusters responsible for salt tolerance in microbes (Mirete et al 2015). Bacteroidetes enriched faecal samples from the north Indian population possessed ABCTPP and TMSRP1 genes conferring osmotolerance (Verma et al 2018). ABC transport permease protein (ABCTPP) uses an energy-dependent mechanism to reduce the intracellular concentration of stress-causing ions.…”

“…Similarly, TMSRP1 facilitates microbial growth even in the presence of high salt concentration by decreasing the intracellular concentrations of ionic stressors. The TLSRP1 is the Bacteroidetes homologue belonging to TonB linked outer membrane protein sub-family which allows the ligands movement using the proton-motive force but the mechanism by which TLSRP1 decreases osmotic stress remains unidentified (Verma et al 2018). A similar study has identified a salt tolerance gene brpA from the human gut metagenomic library (Culligan et al 2014).…”