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Optimum growth temperature and the base composition of open reading frames in prokaryotes

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Abstract

The purine-loading index (PLI) is the difference between the numbers of purines (A+G) and pyrimidines (T+C) per kilobase of single-stranded nucleic acid. By purine-loading their mRNAs organisms may minimize unnecessary RNA–RNA interactions and prevent inadvertent formation of "self" double-stranded RNA. Since RNA–RNA interactions have a strong entropy-driven component, this need to minimize should increase as temperature increases. Consistent with this, we report for 550 prokaryotic species that optimum growth temperature is related to the average PLI of open reading frames. With increasing temperature prokaryotes tend to acquire base A and lose base C, while keeping bases T and G relatively constant. Accordingly, while the PLI increases, the (G+C)% decreases. The previously observed positive correlation between (G+C)% and optimum growth temperature, which applies to RNA species whose structure is of major importance for their function (ribosomal and transfer RNAs) does not apply to mRNAs, and hence is unlikely to apply generally to genomic DNA.

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Fig. 1a, b.
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Abbreviations

CUTG:

Codon usage tables from GenBank

ΔS:

Chargaff difference for the S bases ("GC skew")

ΔW:

Chargaff difference for the W bases ("AT skew")

ORF:

Open reading frame

PLI:

Purine-loading index

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Acknowledgments

We thank James Gerlach, Christopher Madill, Andrew Schramm, and Scott Smith for advice and assistance. Jean Lobry and Daniel Chessel kindly made their paper available prior to publication. Access to the GCG suite of programs was provided by the Canadian Bioinformatics Resource (Halifax). Academic Press, Cold Spring Harbor Laboratory Press, and Elsevier Science gave permissions for the inclusion of full-text versions of some of the cited papers in Forsdyke's web pages, which may be accessed at http://post.queensu.ca/~forsdyke/bioinfor.htm

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Authors and Affiliations

  1. Department of Biochemistry, Queen's University, Kingston, Ontario, K7L3N6, Canada

    R. J. Lambros, J. R. Mortimer & D. R. Forsdyke

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  1. R. J. Lambros
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  2. J. R. Mortimer
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  3. D. R. Forsdyke
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Correspondence to D. R. Forsdyke.

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Communicated by F. Robb

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Lambros, R.J., Mortimer, J.R. & Forsdyke, D.R. Optimum growth temperature and the base composition of open reading frames in prokaryotes. Extremophiles 7, 443–450 (2003). https://doi.org/10.1007/s00792-003-0353-4

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