http://192.168.1.40:8080/xmlui/handle/123456789/2402 2026-05-31T13:43:52Z 2026-05-31T13:43:52Z Bagchi, A. Roy, D. Roy, Pradosh http://192.168.1.40:8080/xmlui/handle/123456789/2454 2013-04-02T12:53:49Z 2005-04-01T00:00:00Z

Homology modeling of a transcriptional regulator SoxR of the lithotrophic sulfur oxidation (Sox) operon in alpha-proteobacteria Bagchi, A.; Roy, D.; Roy, Pradosh Microbial oxidation of reduced inorganic sulfur compounds in the environment is one of the major reactions of the global sulfur cycle mediated by phylogenetically diverse prokaryotes. The sulfur oxidizing gene cluster (sox) of alpha-Proteobacteria comprises of at least 15 genes, which form two transcriptional units, viz soxSRT and soxVWXYZABCDEFGH. Sequence analysis reveals that SoxR belongs to the ArsR family of helix-turn-helix DNA binding proteins. Although SoxR proteins do not contain the conserved metal-binding box, ELCVCDL, but there are a number of well conserved residues present throughout the sequence that are previously identified in the known ArsR family proteins. We employed homology modeling to construct the three-dimensional structure of the SoxR from chemolithotrophic alpha-Proteobacteria Pseudaminobacter salicylatoxidans KCT001. The predicted homology model of SoxR shows an overall structural similarity with winged helix-turn-helix family proteins. Since dimerization is essential for DNA binding and repression by the ArsR family proteins we have generated the dimeric model of SoxR that enables us to predict the DNA binding residues of the protein as well as the interaction of SoxR with the predicted promoter region of sox gene cluster.

2005-04-01T00:00:00Z Deb, C. Stackebrandt, E. Pradella, S. Saha, Anupama Roy, P. http://192.168.1.40:8080/xmlui/handle/123456789/2452 2013-04-02T12:42:01Z 2004-06-01T00:00:00Z

Phylogenetically diverse new sulfur chemolithotrophs of alpha-proteobacteria isolated from Indian soils Deb, C.; Stackebrandt, E.; Pradella, S.; Saha, Anupama; Roy, P. Five facultative sulfur chemolithotrophs were isolated from soils to study the diversity of sulfur lithotrophy. Phenotypic characteristics, including sulfur lithotrophic properties and chemotaxonomic features of the isolates, were similar to those of the members of the colorless sulfur bacteria. 16S rDNA sequence analyses rendered placing the isolates to three distinct phylogenetic clusters of alpha-proteobacteria. Three isolates, AS001, AS002, and KCT002, were identified as members of the genus Paracoccus. The strains AS001 and AS002, having identical 16S-rDNA sequence, showed significant 16S rDNA sequence similarity (99.1%) to Paracoccus versutus. The strain KCT002 showed highest (98%) 16S rDNA sequence similarity to P. alcaliphilus and 96% similarity to the pair AS001 and AS002. Isolate KCT001 appeared to be closely related to Pseudaminobacter salicylatoxidans, although sulfur lithotrophy of P. salicylotoxidans is not known. The other isolate, TCK, showed almost identical 16S rDNA (99.9%) sequence with two recently described unclassified chemolithoautotrophic arsenite oxidizing strains. Physiological and chemotaxonomic characteristics and phylogenetic analyses of the five new strains emphasize the need of polyphasic bacterial taxonomy of sulfur lithotrophs. DOI: 10.1007/s00284-003-4250-y

2004-06-01T00:00:00Z Bagchi, Angshuman Roy, Pradosh http://192.168.1.40:8080/xmlui/handle/123456789/2403 2013-04-01T09:08:32Z 2005-06-17T00:00:00Z

Structural insight into SoxC and SoxD interaction and their role in electron transport process in the novel global sulfur cycle in Paracoccus pantotrophus Bagchi, Angshuman; Roy, Pradosh Microbial oxidation of reduced inorganic sulfur compounds mainly sulfur anions in the environment is one of the major reactions of the global sulfur cycle mediated by phylogenetically diverse prokaryotes. The sulfur oxidizing gene cluster (sox) of alpha-Proteobacteria comprises of at least 16 genes, which form two transcriptional units, viz., soxSRT and soxVWXYZABCDEFGH. Sequence analysis reveals that soxD gene product (SoxD) belongs to the di-heme cytochrome c family of electron transport proteins whereas soxC gene product (SoxC) is a sulfur dehydrogenase. We employed homology modeling to construct the three-dimensional structures of the SoxC and SoxD from Paracoccus pantotrophus. SoxD protein is known to interact with SoxC. With the help of docking studies we have identified the residues involved in the interaction of SoxC and SoxD. The putative active site geometries of these two proteins as well as the structural basis of the involvements of these proteins in electron transport process during the oxidation of sulfur anions are also investigated. DOI: 10.1016/j.bbrc.2005.04.028

2005-06-17T00:00:00Z