Biology subjects

MUKHERJEE, D.

Publications and source records attributed to MUKHERJEE, D..

3 recordsLinked to original sources

bioRxiv2024

Critical concentration of formate governs the expression of the flagellar and the pathogenicity island-1 genes in Salmonella Typhimurium

Host-derived short-chain fatty acids (SCFAs) are extensively being studied for their role in the virulence and pathogenesis of Salmonella Typhimurium (STM). Formate, an SCFA present in the ileum, functions as a signalling molecule to enhance STM invasion. However, the role of intracellular formate in Salmonella virulence remains poorly understood. To investigate this, we generated knockouts of pflB (pyruvate-formate lyase) and focA (formate transporter). Disruption of formate production through pflB deletion led to reduced flagellation and increased hilA and prgH expression, attributed to elevated intracellular pH and membrane damage. This suppression of flagellar machinery drives a shift from adhesion to invasion, regulated by RpoE via the CsrA/csrB pathway. Additionally, we demonstrate that upon compensation for intracellular deficiency of formate, STM{Delta} pflB starts to utilize formate as a signalling molecule to regulate downstream processes. To the best of our knowledge, this study is the first to establish the critical role of the pflB gene in maintaining intracellular pH and controlling virulence gene expression in STM. Lastly, our findings emphasize the importance of modulating pflB expression across intestinal regions to optimize STM invasion. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/577997v2_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@1fc5ec3org.highwire.dtl.DTLVardef@1b15b61org.highwire.dtl.DTLVardef@e657caorg.highwire.dtl.DTLVardef@8db00f_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2020

Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India

India has recently started sequencing SARS-CoV2 genome from clinical isolates. Currently only few sequences are available from three states in India. Kerala was the first state to deposit complete sequence from two isolates followed by one from Gujarat. On April 27, 2020, the first five sequences from the state of West Bengal (Eastern India) were deposited on a global initiative on sharing avian flu data (GISAID) platform. In this paper we have analysed the spike protein sequences from all these five isolates and also compared for their similarities or differences with other sequences reported in India and with isolates of Wuhan origin. We report one unique mutation at position 723 and the other at 1124 in the S2 domain of spike protein of the isolates from West Bengal only and one mutation downstream of the receptor binding domain at position 614 in S1 domain which was common with the sequence from Gujarat (a state of western part of India). Mutation in the S2 domain showed changes in the secondary structure of the spike protein at region of mutation. We also studied molecular dynamics using normal mode analyses and found that this mutation decreases the flexibility of S2 domain. Since both S1 and S2 are important in receptor binding followed by entry in the host cells, such mutations may define the affinity or avidity of receptor binding.

molecular biology↗

bioRxiv2020

Specific mutations in SARS-CoV2 RNA dependent RNA polymerase and helicase alter protein structure, dynamics and thus function: Effect on viral RNA replication

1.The open reading frame (ORF) 1ab of SARS-CoV2 encodes non-structural proteins involved in viral RNA functions like translation and replication including nsp1-4; 3C like proteinase; nsp6-10; RNA dependent RNA polymerase (RdRp); helicase and 3-5 exonuclease. Sequence analyses of ORF1ab unravelled emergence of mutations especially in the viral RdRp and helicase at specific positions, both of which are important in mediating viral RNA replication. Since proteins are dynamic in nature and their functions are governed by the molecular motions, we performed normal mode analyses of the SARS-CoV2 wild type and mutant RdRp and helicases to understand the effect of mutations on their structure, conformation, dynamics and thus function. Structural analyses revealed that mutation of RdRp (at position 4715 in the context of the polyprotein/ at position 323 of RdRp) leads to rigidification of structure and that mutation in the helicase (at position 5828 of polyprotein/ position 504) leads to destabilization increasing the flexibility of the protein structure. Such structural modifications and protein dynamics alterations might alter unwinding of complex RNA stem loop structures, the affinity/ avidity of polymerase RNA interactions and in turn the viral RNA replication. The mutation analyses of proteins of the SARS-CoV2 RNA replication complex would help targeting RdRp better for therapeutic intervention.

molecular biology↗