Analysis of amino acid and codon usage in Paramecium bursaria

Hideo Dohra, Masahiro Fujishima, Haruo Suzuki

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

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.

Original languageEnglish
Article number37343
Pages (from-to)3113-3118
Number of pages6
JournalFEBS Letters
Volume589
Issue number20
DOIs
Publication statusPublished - 2015 Oct 7
Externally publishedYes

Fingerprint

Paramecium
Codon
Chlorella
Amino Acids
Transcriptome
Bearings (structural)
Genes
Chlorophyta
Symbiosis
Algae
Ports and harbors
Gene expression
Cysteine
Membrane Proteins
Gene Expression

Keywords

  • Amino acid usage
  • Gene expression
  • Paramecium bursaria
  • Synonymous codon usage
  • Transcriptome

ASJC Scopus subject areas

  • Structural Biology
  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Genetics
  • Cell Biology

Cite this

Analysis of amino acid and codon usage in Paramecium bursaria. / Dohra, Hideo; Fujishima, Masahiro; Suzuki, Haruo.

In: FEBS Letters, Vol. 589, No. 20, 37343, 07.10.2015, p. 3113-3118.

Research output: Contribution to journalArticle

Dohra, Hideo ; Fujishima, Masahiro ; Suzuki, Haruo. / Analysis of amino acid and codon usage in Paramecium bursaria. In: FEBS Letters. 2015 ; Vol. 589, No. 20. pp. 3113-3118.
@article{4086f1796f4b4848aaab565139ddeca2,
title = "Analysis of amino acid and codon usage in Paramecium bursaria",
abstract = "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.",
keywords = "Amino acid usage, Gene expression, Paramecium bursaria, Synonymous codon usage, Transcriptome",
author = "Hideo Dohra and Masahiro Fujishima and Haruo Suzuki",
year = "2015",
month = "10",
day = "7",
doi = "10.1016/j.febslet.2015.08.033",
language = "English",
volume = "589",
pages = "3113--3118",
journal = "FEBS Letters",
issn = "0014-5793",
publisher = "Elsevier",
number = "20",

}

TY - JOUR

T1 - Analysis of amino acid and codon usage in Paramecium bursaria

AU - Dohra, Hideo

AU - Fujishima, Masahiro

AU - Suzuki, Haruo

PY - 2015/10/7

Y1 - 2015/10/7

N2 - 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.

AB - 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.

KW - Amino acid usage

KW - Gene expression

KW - Paramecium bursaria

KW - Synonymous codon usage

KW - Transcriptome

UR - http://www.scopus.com/inward/record.url?scp=84943200770&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84943200770&partnerID=8YFLogxK

U2 - 10.1016/j.febslet.2015.08.033

DO - 10.1016/j.febslet.2015.08.033

M3 - Article

C2 - 26341535

AN - SCOPUS:84943200770

VL - 589

SP - 3113

EP - 3118

JO - FEBS Letters

JF - FEBS Letters

SN - 0014-5793

IS - 20

M1 - 37343

ER -