Factors Influencing the Synonymous Codon and Amino Acid Usage Bias in AT-rich Pseudomonas aeruginosa Phage PhiKZ

  1. K. SAU3,
  2. S. SAU2,
  3. S. C. MANDAL3,*,
  4. T. C. GHOSH1,*

Article first published online: 27 SEP 2005

DOI: 10.1111/j.1745-7270.2005.00089.x

Issue

Acta Biochimica et Biophysica Sinica

Acta Biochimica et Biophysica Sinica

Volume 37, Issue 9, pages 625–633, September 2005

Additional Information

How to Cite

SAU, K., SAU, S., MANDAL, S. C. and GHOSH, T. C. (2005), Factors Influencing the Synonymous Codon and Amino Acid Usage Bias in AT-rich Pseudomonas aeruginosa Phage PhiKZ. Acta Biochimica et Biophysica Sinica, 37: 625–633. doi: 10.1111/j.1745-7270.2005.00089.x

Author Information

  1. 1

    Bioinformatics Centre, Bose Institute, P1/12-CIT Scheme VII M, Calcutta 700 054, India;

  2. 2

    Department of Biochemistry, Bose Institute, P1/12-CIT Scheme VII M, Calcutta 700 054, India;

  3. 3

    Department of Mathematics, Jadavpur University, Calcutta 700 032, India

* *Corresponding authors: S. C. MANDAL: E-mail, jumscm@yahoo.com T. C. GHOSH: Tel, +91-33-2334 6626; Fax, +91-33-2334 3886; E-mail, tapash@bic.boseinst.ernet.in

Publication History

  1. Issue published online: 27 SEP 2005
  2. Article first published online: 27 SEP 2005
  3. Received: April 28, 2005 Accepted: June 11, 2005

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Keywords:

  • relative synonymous codon usage (RSCU);
  • correspondence analysis;
  • amino acid usage;
  • bacteriophage PhiKZ

Abstract To reveal how the AT-rich genome of bacteriophage PhiKZ has been shaped in order to carry out its growth in the GC-rich host Pseudomonas aeruginosa, synonymous codon and amino acid usage bias of PhiKZ was investigated and the data were compared with that of P. aeruginosa. It was found that synonymous codon and amino acid usage of PhiKZ was distinct from that of P. aeruginosa. In contrast to P. aeruginosa, the third codon position of the synonymous codons of PhiKZ carries mostly A or T base; codon usage bias in PhiKZ is dictated mainly by mutational bias and, to a lesser extent, by translational selection. A cluster analysis of the relative synonymous codon usage values of 16 myoviruses including PhiKZ shows that PhiKZ is evolutionary much closer to Escherichia coli phage T4. Further analysis reveals that the three factors of mean molecular weight, aromaticity and cysteine content are mostly responsible for the variation of amino acid usage in PhiKZ proteins, whereas amino acid usage of P. aeruginosa proteins is mainly governed by grand average of hydropathicity, aromaticity and cysteine content. Based on these observations, we suggest that codons of the phage-like PhiKZ have evolved to preferentially incorporate the smaller amino acid residues into their proteins during translation, thereby economizing the cost of its development in GC-rich P. aeruginosa.

Edited by Zu-Hong LU

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