Jean R. Lobry

Relationships Between Genomic G+C Content, RNA Secondary Structures, and Optimal Growth Temperature in Prokaryotes

Abstract. G:C pairs are more stable than A:T pairs because they have an additional hydrogen bond. This has led to many studies on the correlation between the guanine+cytosine (G+C) content of nucleic acids and temperature over the last 20 years. We collected the optimal growth temperatures (Topt) and the G+C contents of genomic DNA; 23S, 16S, and 5S ribosomal RNAs; and transfer RNAs for 764 prokaryotic species. No correlation was found between genomic G+C content and Topt, but there were striking correlations between the G+C content of ribosomal and transfer RNA stems and Topt. Two explanations have been proposed—neutral evolution and selection pressure—for the approximate equalities of G and C (respectively, A and T) contents within each strand of DNA molecules. Our results do not support the notion that selection pressure induces complementary oligonucleotides in close proximity and therefore numerous secondary structures in prokaryotic DNA, as the genomic G+C content does not behave in the same way as that of folded RNA with respect to optimal growth temperature.

SeqinR 1.0-2: A Contributed Package to the R Project for Statistical Computing Devoted to Biological Sequences Retrieval and Analysis

The seqinR package for the R environment is a library of utilities to retrieve and analyse biological sequences. It provides an interface between i) the R language and environment for statistical computing and graphics and ii) the ACNUC sequence retrieval system for nucleotide and protein sequence databases such as GenBank, EMBL, SWISS-PROT. ACNUC is very efficient in providing direct access to subsequences of biological interest (e.g. protein coding regions, tRNA or rRNA coding regions) present in GenBank and in EMBL. Thanks to a simple query language, it is then easy under R to select sequences of interest and then use all the power of the R environment to analyze them. The ACNUC databases can be locally installed but they are more conveniently accessed through a web server to take advantage of centralized daily updates. The aim of this paper is to provide a handout on basic sequence analyses under seqinR with a special focus on multivariate methods.

Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms

In the absence of bias between the two DNA strands for mutation and selection, the base composition within each strand should be such that A = T and C = G (this state is called Parity Rule type 2, PR2). At a genome scale, i.e. when considering the base composition of a whole genome, PR2 is a good approximation, but there are local and systematic deviations. The question is whether these deviations are a consequence of an underlying bias in mutation or selection. We have tried to review published hypotheses to classify them within the mutational or selective group. This dichotomy is, however, too crude because there is at least one hypothesis based simultaneously upon mutation and selection.

Asymmetric directional mutation pressures in bacteria

BackgroundWhen there are no strand-specific biases in mutation and selection rates (that is, in the substitution rates) between the two strands of DNA, the average nucleotide composition is theoretically expected to be A = T and G = C within each strand. Deviations from these equalities are therefore evidence for an asymmetry in selection and/or mutation between the two strands. By focusing on weakly selected regions that could be oriented with respect to replication in 43 out of 51 completely sequenced bacterial chromosomes, we have been able to detect asymmetric directional mutation pressures.ResultsMost of the 43 chromosomes were found to be relatively enriched in G over C and T over A, and slightly depleted in G+C, in their weakly selected positions (intergenic regions and third codon positions) in the leading strand compared with the lagging strand. Deviations from A = T and G = C were highly correlated between third codon positions and intergenic regions, with a lower degree of deviation in intergenic regions, and were not correlated with overall genomic G+C content.ConclusionsDuring the course of bacterial chromosome evolution, the effects of asymmetric directional mutation pressures are commonly observed in weakly selected positions. The degree of deviation from equality is highly variable among species, and within species is higher in third codon positions than in intergenic regions. The orientation of these effects is almost universal and is compatible in most cases with the hypothesis of an excess of cytosine deamination in the single-stranded state during DNA replication. However, the variation in G+C content between species is influenced by factors other than asymmetric mutation pressure.

Properties of a general model of DNA evolution under no-strand-bias conditions

Under the hypothesis of no-strand-bias conditions, the Watson and Crick base-pairing rule decreases the complexity of models of DNA evolution by reducing to six the maximum number of substitution rates. It was shown that intrastrand equimolarity between A and T (A*T*) and between G and C (G*C*) is a general asymptotic property of this class of models. This statistical prediction was observed on 60 long genomic fragments (>50 kbp) from various kingdoms, even when the effect of the two opposite orientations for coding sequences is removed. The practical consequence of the model for estimating the expected number of substitutions per site between two homologous DNA sequences is discussed.

Influence of genomic G+C content on average amino-acid composition of proteins from 59 bacterial species

The amino-acid composition of 23,490 proteins from 59 bacterial species was analyzed as a function of genomic G+C content. Observed amino-acid frequencies were compared with those expected from a neutral model assuming the absence of selection on average protein composition. Integral membrane proteins and non-integral membrane proteins were analyzed separately. The average deviation from this neutral model shows that there is a selective pressure increasing content in charged amino acids for non-integral membrane proteins, and content in hydrophobic amino acids for integral membrane proteins. Amino-acid frequencies were greatly influenced by genomic G+C content, but the influence was found to be often weaker than predicted. This may be evidence for a selective pressure, maintaining most amino-acid frequencies close to an optimal value. Concordance between the genetic code and protein composition is discussed in the light of this observation.

Origin of Replication of Mycoplasma genitalium

olaris genomic regions (1), whereas linkage blocks lacking H. petiolaris markers were designated H. annuus regions (0), thereby generating the composite distribution of parental genomic regions shown in Fig. 2. Parental markers in H. anomalus either matched (0,0 or 1,1) or did not match (0,1 or 1,0) the corresponding genomic region in the experimental hybrids. 14. E. M. McCarthy, M. A. Amussen, W. W. Anderson, Heredity 74, 502 (1995); V. Grant, Genetics 54, 1189 (1966). 15. Spearmans rank correlation coefficient was calculated for each pairwise combination of the three hybrid lineages. The percentage at which a marker introgressed for a given lineage was scored in the following manner: 0.0% = 0; 1 to 25% = 1; 26 to 50% = 2; 51 to 100% = 3. Lineages x 11, r, = 0.79, P < 0.0001; lineages x ll, r, = 0.74, P < 0.0001; lineages 11 x ll, r, = 0.73, P < 0.0001. 16. N. H. Barton and G. M. Hewitt, Heredity 47, 367 (1981). 17. C.-I. Wu and M. F. Palopoli, Annu. Rev. Genet. 27, 283 (1994). 18. The following equation was used to compute the test statistic (p) for two-way epistatic interactions among unlinked loci (NjO,,,j, number of unlinked loci; Nprogeny, number of progeny tested; and /ocusn,p = 0 if the H. petiolaris marker is absent and 1 if present):

Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes

SUMMARY A program called Oriloc has been developed for the prediction of bacterial replication origins. The method builds on the fact that there are compositional asymmetries between the leading and the lagging strand for replication. The program works with unannotated sequences in fasta format and therefore uses glimmer 2.0 outputs to discriminate between codon positions so as to increase the signal/noise ratio.

Physical mapping of an origin of bidirectional replication at the centre of the Borrelia burgdorferi linear chromosome

The Borrelia burgdorferi chromosome is linear, with telomeres characterized by terminal inverted repeats and covalently closed single‐stranded hairpin loops. The replication mechanism of these unusual molecules is unknown. Previous analyses of bacterial chromosomes for which the complete sequence has been determined, including that of B. burgdorferi, revealed an abrupt switch in polarity of CG skew at known or putative origins of replication. We used nascent DNA strand analysis to physically map the B. burgdorferi origin to within a 2 kb region at the centre of the linear chromosome, and to show that replication proceeds bidirectionally from this origin. The results are consistent with replication models in which termination occurs at the telomeres after bidirectional, symmetrical elongation from the central origin. Sequences typical of origins of other bacterial chromosomes were not found at the origin of this spirochete. The most likely location of the replication origin of the linear chromosome is the 240 bp sequence between dnaA and dnaN where the switch in CG skew occurs.

A simple vectorial representation of DNA sequences for the detection of replication origins in bacteria

A simple adaptation of Ninios vectorial representation of DNA sequences for the detection of replication origins in bacteria is presented. The origins of replication in Escherichia coli, Bacillus subtilis, Haemophilus influenzae and Mycoplasma genitalium are well outlined with this graphical representation.