Biology subjects

Deb, S.

Publications and source records attributed to Deb, S..

25 records · Page 2Linked to original sources

bioRxiv2021

Pufferfish (Tetraodon cutcutia) sampled from freshwater river serves an intermediate reservoir of sucrose nonfermenting variant of Vibrio cholerae PS-4.

This study describes the genomic characteristics of Vibrio cholerae strain PS-4, which fails to ferment sucrose on thiosulfate{square}citrate{square}bile salt{square}sucrose (TCBS) agar medium. This bacterium was isolated from skin mucus of a freshwater pufferfish. In order to understand the sucrose nonfermenting phenotype, the genome of the strain PS-4 was sequenced. The gene encoding the sucrose specific phosphotransferase system IIB (sucR) was absent, resulting for the defective sucrose fermenting phenotype. In contrast, genes encoding glucose-specific transport system IIB (ptsG) and fructose specific transport system IIB (fruA) were present and showing acid production while growing with respective sugars. The overall genome relatedness indices (OGRI) such as in silico DDH, average nucleotide identity (ANI) and average amino acid identity (AAI) were above the threshold value, i.e., 70% and 95-96%, respectively. Phylogenomic analysis based on genome wide core genes and the non-recombinant core-genes, strain PS-4 clustered with Vibrio cholerae ATCC 14035T. Further, genes encoding ctx, zot, ace, tcp and rfb were absent. It showed hemolytic activity and reacted strongly to the R antibody. This is the first report on the existence of Vibrio cholerae from the pufferfish adds to our knowledge of the new ecological niche of this bacterium. IMPORTANCEVibrio cholerae, the causative agent of cholera, is a natural inhabitant of aquatic environments. It ferments sucrose, producing characteristic yellow colonies on TCBS agar. Vibrio cholerae strain PS-4 described in this study was a sucrose nonfermenting variant associated with pufferfish skin and did not produce yellow colonies on TCBS agar. Genes encoding sucrose specific phosphotransferase system IIB (sucR) was absent. The observed phenotype in the characteristic metabolic pathway indicates niche specific adaptive evolution for this bacterium. Our study suggested that nonfermenting phenotype on TCBS agar may not be considered always for Vibrio cholerae species delineation.

microbiology↗

bioRxiv2021

A bacterial derived plant- mimicking cytokinin hormone regulates social behaviour in a rice pathogen

Many plant-associated bacteria produce plant- mimicking hormones which are involved in modulating host physiology. However, their function in modulating bacterial physiology has not been reported. Here we show that the XopQ protein, a type-III effector of the rice pathogen, Xanthomonas oryzae pv. oryzae (Xoo), is involved in cytokinin biosynthesis. Xoo produces and secretes an active form of cytokinin which enables the bacterium to maintain a planktonic lifestyle and promotes virulence. RNA-seq analysis indicates that the cytokinin produced by Xoo is required for the regulation of several genes which are involved in biofilm formation. We have also identified the Xoo isopentenyl transferase gene, which is involved in the cytokinin biosynthesis pathway and is required for maintaining planktonic behaviour and virulence. Furthermore, mutations in the predicted cytokinin receptor kinase (PcrK) and the downstream response regulator (PcrR) of Xoo phenocopy the cytokinin biosynthetic mutants, but are not complemented by supplementation with exogenous cytokinin. Cytokinin biosynthetic functions are encoded in a number of diverse bacterial genomes suggesting that cytokinin may be a widespread signalling molecule in the bacterial kingdom.

microbiology↗

bioRxiv2021

Phylogenomic analysis of the genus Pseudomonas and reclassification of P. humi, P. zeshuii, P. psychrotolerans, P. nitritireducens, P. pharmacofabricae and P. panacis are later heterotypic synonym of P. citronellolis Lang 2007, P. luteola, P. oryzihabitans, P. nitroreducens Lang 2007, P. fluvialis and P. marginalis (Brown 1918) Stevens 1925 (Approved Lists 1980), respectively

The present study described the comparative genomic analysis of the validly named species of the genus Pseudomonas to define the taxonomic assignment. Genomic information for 208 type strains was available in the NCBI genome database at the time of conducting this analysis. The ANI, AAI and in silico DNA DNA hybridization (isDDH) data were higher than the threshold values for the twelve strains with their closely related type species. Whole genome comparisons shared 97 - 99 % average nucleotide identity, 97.85 to 99.19 % average amino acid identity and 72.80 to 90.40 % digital DNA DNA hybridization values. Further, the phylogenomic analysis based on the core genome confirmed that P. humi CCA1 and P. citronellolis LMG 18378, P. zeshuii KACC 15471 and P. luteola NBRC 103146, P. oryzihabitans DSM 6835 and P. psychrotolerans DSM 15758, P. nitroreducens DSM 14399 and P. nitritireducens WZBFD3-5A2, P. fluvialis CCM 8778 and P. pharmacofabricae ZYSR67-Z, P. panacis DSM 18529 and P. marginalis DSM 13124 formed a monophyletic clade. Thus, we proposed six type species viz., P. humi CCA1, P. zeshuii KACC 15471, P. psychrotolerans DSM 15758, P. nitritireducens WZBFD3 5A2, P. pharmacofabricae ZYSR67 Z and P. panacis DSM 18529 are the later heterotypic synonym of P. citronellolis Lang 2007, P. luteola, P. oryzihabitans, P. nitroreducens Lang 2007, P. fluvialis and P. marginalis (Brown 1918) Stevens 1925 (Approved Lists 1980), respectively considering the priority date of publication.

microbiology↗

bioRxiv2020

Classification of grain amaranths using chromosome-level genome assembly of ramdana, A. hypochondriacus

In the age of genomics-based crop improvement, a high-quality genome of a local landrace adapted to the local environmental conditions is critically important. Grain amaranths produce highly nutritional grains with a multitude of desirable properties including C4 photosynthesis highly sought-after in other crops. For improving the agronomic traits of grain amaranth and for the transfer of desirable traits to dicot crops, a reference genome of a local landrace is necessary. Towards this end, our lab had initiated sequencing the genome of Amaranthus (A.) hypochondriacus (A.hyp_K_white) and had reported a draft genome in 2014. We selected this landrace because it is well adapted for cultivation in India during the last century and is currently a candidate for TILLING-based crop improvement. More recently, a high-quality chromosome-level assembly of A. hypochondriacus (PI558499, Plainsman) was reported. Here, we report a chromosome-level assembly of A.hyp_K_white (AhKP) using low-coverage PacBio reads, contigs from the reported draft genome of A.hyp_K_white, raw HiC data and reference genome of Plainsman. The placement of A.hyp_K_white on the phylogenetic tree of grain amaranths of known accessions clearly suggests that A.hyp_K_white is genetically distal from Plainsman and is most closely related to the accession PI619259 from Nepal (Ramdana). Furthermore, the classification of another accession, Suvarna, adapted to the local environment and selected for yield and other desirable traits, is clearly A. cruentus. A classification based on hundreds of thousands of SNPs validated taxonomy-based classification for a majority of the accessions providing the opportunity for reclassification of a few.

genomics↗

bioRxiv2020

Interaction of the Xanthomonas effectors XopQ and XopX results in induction of rice immune responses

Xanthomonas oryzae pv. oryzae uses several type III secretion system (T3SS) effectors, namely XopN, XopQ, XopX, and XopZ, to suppress rice immune responses that are induced following treatment with cell wall degrading enzymes. Here we show that the T3SS secreted effector XopX interacts with two of the eight rice 14-3-3 proteins. Mutants of XopX that are defective in 14-3-3 binding are also defective in suppression of immune responses, suggesting that interaction with 14-3-3 proteins is required for suppression of host innate immunity. However, Agrobacterium mediated delivery of both XopX and XopQ into rice cells results in induction of rice immune responses. These immune responses are not observed when either protein is individually delivered into rice cells. XopQ-XopX induced rice immune responses are not observed in a XopX mutant that is defective in 14-3-3 binding. Yeast two-hybrid and BiFC assays indicate that XopQ and XopX interact with each other. In a screen for Xanthomonas effectors which can suppress XopQ-XopX induced rice immune responses, five effectors were identified, namely XopU, XopV, XopP, XopG and AvrBs2, which were able to do so. These results suggest a complex interplay of Xanthomonas T3SS effectors in suppression of pathogen triggered immunity and effector triggered immunity to promote virulence on rice. Significance statementThis work studies the role of the type III effector XopX in the suppression and induction of rice immune responses, by differential interaction with the 14-3-3 proteins, or with the type III effector XopQ respectively. We have also identified a subset of type III effectors which can suppress this form of immune responses.

molecular biology↗

bioRxiv2019

Rational nanotoolbox with theranostic potential for medicated pro-regenerative corneal implants

Cornea diseases are a leading cause of blindness and the disease burden is exacerbated by the increasing shortage around the world for cadaveric donor corneas. Despite the advances in the field of regenerative medicine, successful transplantation of laboratory made artificial corneas has not been fully realised in clinical practice. The causes of failure of such artificial corneal implants are multifactorial and include latent infections from viruses and other micorbes, enzyme over-expression, implant degradation, extrusion or delayed epithelial regeneration. Therefore, there is an urgent unmet need for developing customized corneal implants to suit the host environment, counter the effects of inflammation or infection and that are able to track early signs of implant failure in situ. In the present work, we describe a nano toolbox comprising tools for drug release and in addition capable of being infection responsive, promoting regeneration including non-invasive monitoring of in situ corneal environment. These nano constructs can be incorporated within pro-regenerative biosynthetic implants, transforming them into theranostic devices able to respond to biological changes following implantation.

biochemistry↗

bioRxiv2018

Serotonin regulates mitochondrial biogenesis and function in rodent cortical neurons via the 5-HT2A receptor and SIRT1-PGC-1α axis

Mitochondria in neurons in addition to their primary role in bioenergetics also contribute to specialized functions including regulation of synaptic transmission, Ca2+ homeostasis, neuronal excitability and stress adaptation. However, the factors that influence mitochondrial biogenesis and function in neurons remain poorly elucidated. Here, we identify an important role for serotonin (5-HT) as a regulator of mitochondrial biogenesis and function in rodent cortical neurons, via a 5-HT2A receptor-mediated recruitment of the SIRT1-PGC-1 axis, which is relevant to the neuroprotective action of 5-HT. 5-HT increased mitochondrial biogenesis, reflected through enhanced mtDNA levels, mitotracker staining, and expression of mitochondrial genes. This was accompanied by increased cellular ATP levels, basal and maximal respiration, as well as spare respiratory capacity. Mechanistically the effects of 5-HT were mediated via the 5-HT2A receptor and master modulators of mitochondrial biogenesis, SIRT1 and PGC-1. SIRT1 was required to mediate the effects of 5-HT on mitochondrial biogenesis and function in cortical neurons. In vivo studies revealed that 5-HT2A receptor stimulation increased cortical mtDNA and ATP levels, in a SIRT1 dependent manner. In cortical neurons, 5-HT enhanced expression of anti-oxidant enzymes, decreased cellular reactive oxygen species, and exhibited neuroprotection against excitotoxic and oxidative stress, an effect that required SIRT1. These findings identify 5-HT as a novel upstream regulator of mitochondrial biogenesis and function in cortical neurons, and implicate the mitochondrial effects of 5-HT in its neuroprotective action.

neuroscience↗