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Studies on Synonymous Codon and Amino Acid Usage Biases in the Broad-Host Range Bacteriophage KVP40
Sau Keya,Gupta Sanjib Kumar,Sau Subrata,Mandal Subhas Chandra,Ghosh Tapash Chandra The Microbiological Society of Korea 2007 The journal of microbiology Vol.45 No.1
In this study, the relative synonymous codon and amino acid usage biases of the broad-host range phage, KVP40, were investigated in an attempt to understand the structure and function of its proteins/protein-coding genes, as well as the role of its tRNAs. Synonymous codons in KVP40 were determined to be AT-rich at the third codon positions, and their variations are dictated principally by both mutational bias and translational selection. Further analysis revealed that the RSCU of KVP40 is distinct from that of its Vibrio hosts, V. cholerae and V. parahaemolyticus. Interestingly, the expression of the putative highly expressed genes of KVP40 appear to be preferentially influenced by the abundant host tRNA species, whereas the tRNAs expressed by KVP40 may be required for the efficient synthesis of all its proteins in a diverse array of hosts. The data generated in this study also revealed that KVP40 proteins are rich in low molecular weight amino acid residues, and that these variations are influenced primarily by hydropathy, mean molecular weight, aromaticity, and cysteine content.
Studies on Synonymous Codon and Amino Acid Usage Biases in the Broad-Host Range Bacteriophage KVP40
Keya Sau,Sanjib Kumar Gupta,Subrata Sau,Subhas Chandra Mandal,Tapash Chandra Ghosh 한국미생물학회 2007 The journal of microbiology Vol.45 No.1
In this study, the relative synonymous codon and amino acid usage biases of the broad-host range phage, KVP40, were investigated in an attempt to understand the structure and function of its proteins/proteincoding genes, as well as the role of its tRNAs. Synonymous codons in KVP40 were determined to be ATrich at the third codon positions, and their variations are dictated principally by both mutational bias and translational selection. Further analysis revealed that the RSCU of KVP40 is distinct from that of its Vibrio hosts, V. cholerae and V. parahaemolyticus. Interestingly, the expression of the putative highly expressed genes of KVP40 appear to be preferentially influenced by the abundant host tRNA species, whereas the tRNAs expressed by KVP40 may be required for the efficient synthesis of all its proteins in a diverse array of hosts. The data generated in this study also revealed that KVP40 proteins are rich in low molecular weight amino acid residues, and that these variations are influenced primarily by hydropathy, mean molecular weight, aromaticity, and cysteine content.
( Keya Sahu ),( Sanjib Kumar Gupta ),( Tapash Chandra Ghosh ),( Subrata Sau ) 생화학분자생물학회 2004 BMB Reports Vol.37 No.4
The extent of codon usage in the protein coding genes of the mycobacteriophage, Bxzl, and its plating bacteria, M. smegmatis, were determined, and it was observed that the codons ending with either G and / or C were predominant in both the organisms. Multivariate statistical analysis showed that in both organisms, the genes were separated along the first major explanatory axis according to their expression levels and their genomic GC content at the synonymous third positions of the codons. The second major explanatory axis differentiates the genes according to their genome type. A comparison of the relative synonymous codon usage between 20 highly- and 20 lowly expressed genes from Bxzl identified 21 codons, which are statistically over represented in the former group of genes. Further analysis found that the Bxzl- specific tRNA species could recognize 13 out of the 21 over represented synonymous codons, which incorporated 13 amino acid residues preferentially into the highly expressed proteins of Bxzl. In contrast, seven amino acid residues were preferentially incorporated into the lowly expressed proteins by 10 other tRNA species of Bxzl. This analysis predicts for the first time that the Bxzl-specific tRNA species modulates the optimal expression of its proteins during development.
Sahu, Keya,Gupta, Sanjib Kumar,Ghosh, Tapash Chandra,Sau, Subrata Korean Society for Biochemistry and Molecular Biol 2004 Journal of biochemistry and molecular biology Vol.37 No.4
The extent of codon usage in the protein coding genes of the mycobacteriophage, Bxz1, and its plating bacteria, M. smegmatis, were determined, and it was observed that the codons ending with either G and / or C were predominant in both the organisms. Multivariate statistical analysis showed that in both organisms, the genes were separated along the first major explanatory axis according to their expression levels and their genomic GC content at the synonymous third positions of the codons. The second major explanatory axis differentiates the genes according to their genome type. A comparison of the relative synonymous codon usage between 20 highly- and 20 lowly expressed genes from Bxz1 identified 21 codons, which are statistically over represented in the former group of genes. Further analysis found that the Bxz1- specific tRNA species could recognize 13 out of the 21 over represented synonymous codons, which incorporated 13 amino acid residues preferentially into the highly expressed proteins of Bxz1. In contrast, seven amino acid residues were preferentially incorporated into the lowly expressed proteins by 10 other tRNA species of Bxz1. This analysis predicts for the first time that the Bxz1-specific tRNA species modulates the optimal expression of its proteins during development.
Stabilization of the primary sigma factor of Staphylococcus aureus by core RNA polymerase
( Rajkrishna Mondal ),( Tridib Ganguly ),( Palas K Chanda ),( Amitava Bandhu ),( Biswanath Jana ),( Keya Sau ),( Chia Y Lee ),( Subrata Sau ) 생화학분자생물학회 2010 BMB Reports Vol.43 No.3
The primary sigma factor (σA) of Staphylococcus aureus, a potential drug target, was little investigated at the structural level. Using an N-terminal histidine-tagged σA (His-σA), here we have demonstrated that it exits as a monomer in solution, possesses multiple domains, harbors primarily α-helix and efficiently binds to a S. aureus promoter DNA in the presence of core RNA polymerase. While both N- and C-terminal ends of His- σA are flexible in nature, two Trp residues in its DNA binding region are buried. Upon increasing the incubation temperature from 25° to 40℃, ~60% of the input His-σA was cleaved by thermolysin. Aggregation of His-σA was also initiated rapidly at 45℃. From the equilibrium unfolding experiment, the Gibbs free energy of stabilization of His-σA was estimated to be +0.70 kcal mol-1. The data together suggest that primary sigma factor of S. aureus is an unstable protein. Core RNA polymerase however stabilized σA appreciably. [BMB reports 2010; 43(3): 176-181]