Biology subjects

Datta, P. P.

Publications and source records attributed to Datta, P. P..

3 recordsLinked to original sources

bioRxiv2026

Comparative cryo-EM structures of CGMMV and ToMMV reveal divergent coat protein packing and electrostatics indicating Tobamovirus host specificity

Tobamoviruses are a group of economically important plant viruses exhibiting extreme stability and persistence. Despite high morphological similarity, they show extensive host-family specificity, cause a range of symptoms, and cause significant global yield loss in fruit and vegetable plants. Composed of a rod-shaped helical assembly of identical coat proteins encasing a single-stranded RNA, Tobamoviruses have long served as fundamental models for understanding helical assemblies. Here we report the cryo-EM structures of two viruses from this genus, CGMMV and ToMMV, at 2.86 [A] and 2.71 [A] resolution, respectively. The structures reveal divergent packing strategies within the virion assembly. While ToMMV is genetically similar to the canonical Tobamovirus TMV and displays a structure closely resembling TMV, CGMMV employs a more hydrophobic packing strategy, particularly in the solvent-exposed inner loop region of the coat protein. Comparative biophysical and molecular dynamics analyses from the reconstructed structures reveal more stable and compact protein packing for CGMMV at both the subunit and assembly levels. Furthermore, this study reports a newly identified electrostatic patch existing at the lower alpha-helix region of the coat protein that serves as an additional RNA-stabilizing region, with host family-specific amino acid substitutions among Tobamoviruses. Our study elucidates the structural mechanics and evolutionary strategies driving virion stability and host diversity while maintaining a conserved helical assembly. These findings reveal how subtle electrostatic tuning and divergent packing strategies drive viral stability and host adaptation within a strictly conserved quaternary scaffold.

biophysics↗

bioRxiv2021

Domain dependent orchestrated regulation of bacterial growth, persistence and chemotaxis by an essential GTPase, CgtA, in Vibrio cholerae

CgtA, an evolutionarily conserved GTPase, associated with the 50S ribosome controls a broad spectrum of physiological processes in bacteria. It has three structural domains, viz., N-terminal domain (NTD), GTPase domain and C-terminal domain (CTD). CgtA regulates expression of several of genes during nutritional stress in Vibrio cholerae. The mechanism of transcriptional regulation by CgtA is unknown, though the NTD concomitantly with the GTPase domain participates in the process. Here, we show that the in vivo deletion of the 57 amino acids long CTD of CgtA GTPase of V. cholerae is dispensable for viability, contrary to the complete knockdown of cgtA gene. Slower growth was observed in cgtA knockdown strain with intermittent diauxic lags in minimal media than the CTD deleted strain. Irreversible defect in colony morphology was observed in the cells with CTD deletion. Resuscitation of persister cells occurred when nutritionally deprived complete cgtA knockdown cells after growing for longer periods were transferred to nutritionally enriched media. The motility of the cgtA knockdown strain was significantly reduced than the wild type cells. Furthermore, CTD deleted cells were also found to be defective in motility, but comparatively lower than cgtA knockdown cells. Elongated and slender V. cholerae cells were observed by SEM imaging upon cgtA depletion, whereas, upon CTD deletion cellular elongation did not occur. Based on our study here, we propose that the CTD of CgtA perceives the nutritional stress response, to which the NTD and GTPase responds.

molecular biology↗

bioRxiv2021

An unusually long 5'UTR of ATP dependent cold shock DEAD-box RNA helicase gene csdA negatively regulates its own expression in Escherichia coli

Cold-shock DEAD-box protein A (CsdA) is an ATP dependant cold shock DEAD-box RNA helicase. It is a major cold shock protein needed for the cold adaptation in Escherichia coli. Although the CsdA has been studied at the protein level, further studies are necessary to understand its mechanisms of gene regulations. In this regard, we have constructed a promoter less vector with the ORF of a GFP reporter and found that the promoter of the csdA gene resides far upstream (more than 800 bases) of its coding region. Furthermore, our in vivo deletion experiment has confirmed the existence of this extraordinarily long 5UTR. Our results show that it represses its own expression. In addition, the short peptide encoding (26 aa) yrbN gene resides within this 5UTR as an operon with 8 overlapping nucleotides with the csdA coding region. Besides, we observed that the csdA gene expression may also occur along with immediate upstream (180 nucleotides) nlpI gene both at 37{degrees}C and 15{degrees}C and from the pnp gene (1173 nucleotides upstream) only during cold. In conclusion, csdA gene has operon feature like prokaryotes, in contrast, it also contains an extraordinarily long 5UTR, found in eukaryotes.

molecular biology↗