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 t...
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.
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.
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제안 방법
Data suggest marked codon usage variations among the genes of KVP40 and factors other than mutational bias might also be relevant to variations in codon usage among the genes. In order to determine the factors that influence variations in codon usage among the genes of KVP40, correspondence analysis was conducted on the RSCU values of its 376 genes. Only the distributions of the genes along the first two major axes were shown, as these accounted for 7.
성능/효과
No corre lation was determined to exist between the positions of the genes along the first major axis and Nc. By way of contrast, the positions of the genes along the second major axis were correlated positively with both A3 (r=0.117, p<0.05) and C3 (r=0.201, p<0.01), and correlated negatively with G3 (r= -0.416, p<0.01), and GC3 (r=-0.142, pvQ.01). Interestingly, the positions of the genes along the second major axis were correlated negatively with Nc (r=-0.
These findings suggest that the G-ending codons are clustered on the negative side, whereas the codons ending in A and C predominate on the positive side of the second major axis. In order to determine the differences between the two gene clusters, the degree of codon usage variation in the 10% of genes located at the extreme positive side of axis 2 was compared with that of the 10% of genes located at the extreme negative side of axis 2. In order to estimate the degree of codon usage variation between these two gene sets, we conducted chi square tests, with a p value of <0.
KVP40 is expected to harbor an AT-rich genome. In order to determine whether there is any variation in codon usage among the genes of KVP40, the effective number of codons used by genes (Nc) and the (G + C) percentages at the third positions of codons (GC3) were calculated. It was noted that Nc in KVP40 ranges from 24.
By way of contrast, KVP40-specific tRNAs can be used to recognize 13 of 24 over-represented codons of the highly-expressed genes, and 20 of 35 over-represented codons in the low-expressed genes (Table 1). The data collected appear to suggest that the abundant tRNAs of V parahaemolyticus are utilized prefer entially in the expression of the putative highly-expressed genes of KVP40, whereas the tRNAs harbored by KVP40 may possibly augment the cellular levels of tRNA population, in order to synthesize all its proteins efficiently in a variety of hosts. Functions similar to those of the KVP40-specific tRNAs were 거so suggested to exist in the tRNAs of the mycobacteriophage, Bxzl (Sahu et al.
had also been conducted. The data indicated that the first and second major axes of CA accounted for 17.03% and 10.46% of the total variations in the amino acid com position of KVP40 proteins, respectively. Further analysis showed that the first axis was correlated significantly with the GRAVY (r=0.
, 2005). The putatively highly- and lowly-expressed genes were considered, respectively, on the basis of the lowest 10% and highest 10% of the genes, as determined by their Nc values. The tRNA genes in the KVP40 and V parahaemolyticus genomes were identified via the 'tRNAscanSE，program (http://www.
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