Analysis of amino acid and codon usage in Paramecium bursaria.
The ciliate Paramecium bursaria harbors the green-alga Chlorella symbionts. We reassembled the P. bursaria transcriptome to minimize falsely fused transcripts, and investigated amino acid and codon usage using the transcriptome data. Surface proteins preferentially use smaller amino acid residues like cysteine. Unusual synonymous codon and amino acid usage in highly expressed genes can reflect a balance between translational selection and other factors. A correlation of gene expression level with synonymous codon or amino acid usage is emphasized in genes down-regulated in symbiont-bearing cells compared to symbiont-free cells. Our results imply that the selection is associated with P. bursaria-Chlorella symbiosis.
Instrumental Research Support Office, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan; Department of Biological Science, Graduate School of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan.
Hideo
H
Dohra
Department of Environmental Science and Engineering, Graduate School of Science and Engineering, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8512, Japan; National Bio-Resource Project of Japan Agency for Medical Research and Development, Japan.
Masahiro
M
Fujishima
Department of Environmental Science and Engineering, Graduate School of Science and Engineering, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8512, Japan. Electronic address: haruo@yamaguchi-u.ac.jp.
Haruo
H
Suzuki
D000596:Amino Acids / Q000235:genetics* / Q000378:metabolism; D002708:Chlorella / Q000502:physiology; D003062:Codon / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods; D054884:Host-Pathogen Interactions; D010247:Paramecium / Q000235:genetics* / Q000378:metabolism / Q000382:microbiology; D014176:Protein Biosynthesis; D015800:Protozoan Proteins / Q000235:genetics / Q000378:metabolism; D013559:Symbiosis; D059467:Transcriptome
D000596:Amino Acids; D003062:Codon; D015800:Protozoan Proteins
Amino acid usage; Gene expression; Paramecium bursaria; Synonymous codon usage; Transcriptome