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Factors Influencing the Synonymous Codon and amino acid usage Bias in AT-rich Pseudomonas aeruginosa Phage PhiKZ

Acta Biochimica et Biophysica Sinica 2005年第9期37卷 625-633页

作者： K.SAU~3 S.SAU~2 S.C.MANDAL~(3*) T.C.GHOSH~(1*) 1 Bioinformatics Centre,2 Department of Biochemistry,Bose Institute,P1/12-CIT Scheme ⅦM,Calcutta 700054,India 3 Department of Mathematics,Jadavpur University,Calcutta 700032,India Department of Mathematics Jadavpur University Calcutta 700 032 India.

To reveal how the AT-rich genome of bacteriophage PhiKZ has been shaped in order to carryout its growth in the GC-rich host Pseudomonas aeruginosa,synonymous codon and amino acid usage bias ofPhiKZ was investigated and the data were compared with that of *** was found that synonymouscodon and amino acid usage of PhiKZ was distinct from that of *** contrast to ***,the third codon position of the synonymous codons of PhiKZ carries mostly A or T base;codon usage biasin PhiKZ is dictated mainly by mutational bias and,to a lesser extent,by translational selection.A clusteranalysis of the relative synonymous codon usage values of 16 myoviruses including PhiKZ shows that PhiKZis evolutionary much closer to Escherickia coli phage *** analysis reveals that the three factors ofmean molecular weight,aromaticity and cysteine content are mostly responsible for the variation of aminoacid usage in PhiKZ proteins,whereas amino acid usage of *** proteins is mainly governed bygrand average of hydropathicity,aromaticity and cysteine *** on these observations,we suggestthat codons of the phage-like PhiKZ have evolved to preferentially incorporate the smaller amino acid residuesinto their proteins during translation,thereby economizing the cost of its development in GC-rich ***.

关键词： relative synonymous codon usage (RSCU) correspondence analysis amino acid usage bacteriophage PhiKZ

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Convergent usage of amino acids in Human Cancers as A Reversed Process of Tissue Development

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Genomics, Proteomics & Bioinformatics 2022年第1期20卷 147-162页

作者： Yikai Luo Han Liang Graduate Program in Quantitative and Computational Biosciences Baylor College of MedicineHoustonTX 77030USA Department of Bioinformatics and Computational Biology The University of Texas MD Anderson Cancer CenterHoustonTX 77030USA Department of Systems Biology The University of Texas MD Anderson Cancer CenterHoustonTX 77030USA

Genome-and transcriptome-wide amino acid usage preference across different species is a well-studied phenomenon in molecular evolution,but its characteristics and implication in cancer evolution and therapy remain largely ***,we analyzed large-scale transcriptome/proteome profiles,such as The Cancer Genome Atlas(TCGA),the Genotype-Tissue Expression(GTEx),and the Clinical Proteomic Tumor Analysis Consortium(CPTAC),and found that compared to normal tissues,different cancer types showed a convergent pattern toward using biosynthetically low-cost amino *** a pattern can be accurately captured by a single index based on the average biosynthetic energy cost of amino acids,termed energy cost per amino acid(ECPA).With this index,we further compared the trends of amino acid usage and the contributing genes in cancer and tissue development,and revealed their reversed ***,focusing on the liver,a tissue with a dramatic increase in ECPA during development,we found that ECPA represents a powerful biomarker that could distinguish liver tumors from normal liver samples consistently across 11 independent patient cohorts and outperforms any index based on single *** study reveals an important principle underlying cancer evolution and suggests the global amino acid usage as a system-level biomarker for cancer diagnosis.

关键词： amino acid usage Tissue development Biosynthetic energy Diagnostic biomarker

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