arXiv subjects
Zhumur Ghosh
Publications and source records attributed to Zhumur Ghosh.
Identity Elements of Archaeal tRNA
Features unique to a transfer-RNA are recognized by the corresponding tRNA-synthetase. Keeping this in view we isolate the discriminating features of all archaeal tRNA. These are our identity elements. Further, we investigate tRNA-characteristics that delineate the different orders of archaea.
tRNA-isoleucine-tryptophan Composite Gene
Transfer-RNA genes in archaea often have introns intervening between exon sequences. The structural motif at the boundary between exon and intron is the bulge-helix-bulge. Computational investigations of these boundary structures in H. marismortui lead us to propose that tRNA-isoleucine and tRNA-tryptophan genes are co-located. Precise insilico identification of the splice-sites on the bulges at the exon-intron boundaries conduce us to infer that a single intron-containing composite tRNA-gene can give rise to more than one gene produc.
Embedded transfer RNA Genes
In euryarchaeal methanogen M.kandleri and in Nanoarchaea N. equitans some of the missing tRNA genes are embedded in others. We argue from bioinformatic evidence that position specific intron splicing is the key behind co-location of these tRNA genes.
Positioning Crenarchaeal tRNA-Introns
We precisely position a noncanonical intron in the odd second copy of tRNAAsp(GTC) gene in the newly sequenced crenarchaea S.acidocaldarius. The uniform assortment of some features from normal aspartate tDNA and some from those corresponding to non-standard amino acids conduce us to conjecture it to be a novel tRNA gene, probably coding for a modified aspartate residue. Further we reposition intron in tRNAHis(GUG) gene in P.aerophilum.The BHB motif at the exon-intron boundaries are re-analyzed and found to support our conjectures.
Weighted-Codon-Usage Based Phylogeny In Ectocarpales
We analyse forty seven chloroplastid genes of the large subunit of RuBisCO, from the Algal order Ectocarpales, sourced from GenBank. Codon-usage weighted by the nucleotide base bias defines our score called the Codon-Impact-Parameter. This score is used to obtain phylogenetic relations amongst the 47 Ectocarpales. We compare our classification with the ones done earlier.
tRNA-alike in Nanoarchaeum equitans ?
The recent algorithm for five split tRNA-genes in N.equitans is new . It locates missing tRNA-trp, tRNA-imet, tRNA-glu and tRNA-his . But the split tRNA-trp(CCA) solution is anomalous ; the tRNA-imet lacks cognition elements for aminoacylation . In view therefore we present here alternate non-split composite solutions for tRNA-trp, tRNA-imet, tRNA-glu and tRNA-his .