An unusual codon usage pattern in the ciliate family Ophryoscolecidae and its implications for determining the source of cloned DNA

N.R. McEwan*, D. Gatherer, S.C.P. Eschenlauer, F.M. McIntosh, R.E. Calza, R. John Wallace, C. Jamie Newbold

*Corresponding author for this work

Research output: Contribution to journalArticleResearchpeer-review

6 Citations (Scopus)

Abstract

A bias in the codon utilization pattern of members of the ciliate family Ophryoscolecidae is described. A pattern of preferential use of AGA to encode arginine, and a bias against the occurrence of G in position three of codons for lysine, glutamine and glutamic acid, are described. Evidence is provided primarily for species of the Ophryoscolecidae family which are found in the rumen, but the general principle extends to a species found in non-rumen environments. Within those species found in the rumen, it appears to have the potential for use as a discriminatory tool for the identification of sequences against a background of possible contamination. The origin of such sequence contamination may be the host organism, plant material eaten by the host, and fungal material present in the host. Comparisons with other organisms possessing a similarly low GC content suggests that much of this codon bias is not solely attributable to the low GC content, but that a more complex phenomenon, such as strand bias, is in operation.
Original languageEnglish
Pages (from-to)21-28
Number of pages8
JournalAnaerobe
Volume6
Issue number1
DOIs
Publication statusPrint publication - Feb 2000
Externally publishedYes

Fingerprint

Codon
Rumen
Base Composition
DNA
Glutamine
Lysine
Arginine
Glutamic Acid

Bibliographical note

Cited By :6

Export Date: 18 May 2019

Cite this

McEwan, N.R. ; Gatherer, D. ; Eschenlauer, S.C.P. ; McIntosh, F.M. ; Calza, R.E. ; John Wallace, R. ; Jamie Newbold, C. / An unusual codon usage pattern in the ciliate family Ophryoscolecidae and its implications for determining the source of cloned DNA. In: Anaerobe. 2000 ; Vol. 6, No. 1. pp. 21-28.
@article{56f0030d15f34e32bf872c044b7f4c1f,
title = "An unusual codon usage pattern in the ciliate family Ophryoscolecidae and its implications for determining the source of cloned DNA",
abstract = "A bias in the codon utilization pattern of members of the ciliate family Ophryoscolecidae is described. A pattern of preferential use of AGA to encode arginine, and a bias against the occurrence of G in position three of codons for lysine, glutamine and glutamic acid, are described. Evidence is provided primarily for species of the Ophryoscolecidae family which are found in the rumen, but the general principle extends to a species found in non-rumen environments. Within those species found in the rumen, it appears to have the potential for use as a discriminatory tool for the identification of sequences against a background of possible contamination. The origin of such sequence contamination may be the host organism, plant material eaten by the host, and fungal material present in the host. Comparisons with other organisms possessing a similarly low GC content suggests that much of this codon bias is not solely attributable to the low GC content, but that a more complex phenomenon, such as strand bias, is in operation.",
author = "N.R. McEwan and D. Gatherer and S.C.P. Eschenlauer and F.M. McIntosh and R.E. Calza and {John Wallace}, R. and {Jamie Newbold}, C.",
note = "Cited By :6 Export Date: 18 May 2019",
year = "2000",
month = "2",
doi = "10.1006/anae.1999.0310",
language = "English",
volume = "6",
pages = "21--28",
journal = "Anaerobe",
issn = "1075-9964",
publisher = "Academic Press Inc.",
number = "1",

}

An unusual codon usage pattern in the ciliate family Ophryoscolecidae and its implications for determining the source of cloned DNA. / McEwan, N.R.; Gatherer, D.; Eschenlauer, S.C.P.; McIntosh, F.M.; Calza, R.E.; John Wallace, R.; Jamie Newbold, C.

In: Anaerobe, Vol. 6, No. 1, 02.2000, p. 21-28.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - An unusual codon usage pattern in the ciliate family Ophryoscolecidae and its implications for determining the source of cloned DNA

AU - McEwan, N.R.

AU - Gatherer, D.

AU - Eschenlauer, S.C.P.

AU - McIntosh, F.M.

AU - Calza, R.E.

AU - John Wallace, R.

AU - Jamie Newbold, C.

N1 - Cited By :6 Export Date: 18 May 2019

PY - 2000/2

Y1 - 2000/2

N2 - A bias in the codon utilization pattern of members of the ciliate family Ophryoscolecidae is described. A pattern of preferential use of AGA to encode arginine, and a bias against the occurrence of G in position three of codons for lysine, glutamine and glutamic acid, are described. Evidence is provided primarily for species of the Ophryoscolecidae family which are found in the rumen, but the general principle extends to a species found in non-rumen environments. Within those species found in the rumen, it appears to have the potential for use as a discriminatory tool for the identification of sequences against a background of possible contamination. The origin of such sequence contamination may be the host organism, plant material eaten by the host, and fungal material present in the host. Comparisons with other organisms possessing a similarly low GC content suggests that much of this codon bias is not solely attributable to the low GC content, but that a more complex phenomenon, such as strand bias, is in operation.

AB - A bias in the codon utilization pattern of members of the ciliate family Ophryoscolecidae is described. A pattern of preferential use of AGA to encode arginine, and a bias against the occurrence of G in position three of codons for lysine, glutamine and glutamic acid, are described. Evidence is provided primarily for species of the Ophryoscolecidae family which are found in the rumen, but the general principle extends to a species found in non-rumen environments. Within those species found in the rumen, it appears to have the potential for use as a discriminatory tool for the identification of sequences against a background of possible contamination. The origin of such sequence contamination may be the host organism, plant material eaten by the host, and fungal material present in the host. Comparisons with other organisms possessing a similarly low GC content suggests that much of this codon bias is not solely attributable to the low GC content, but that a more complex phenomenon, such as strand bias, is in operation.

U2 - 10.1006/anae.1999.0310

DO - 10.1006/anae.1999.0310

M3 - Article

VL - 6

SP - 21

EP - 28

JO - Anaerobe

JF - Anaerobe

SN - 1075-9964

IS - 1

ER -