Synonymous codon usage and its potential link with optimal growth temperature in prokaryotes.

The relationship between codon usage in prokaryotes and their ability to grow at extreme temperatures has been given much attention over the past years. Previous studies have suggested that the difference in synonymous codon usage between (hyper)thermophiles and mesophiles is a consequence of a selective pressure linked to growth temperature. Here, we performed an updated analysis of the variation in synonymous codon usage with growth temperature; our study includes a large number of species from a wide taxonomic and growth temperature range. The presence of psychrophilic species in our study allowed us to test whether the same selective pressure acts on synonymous codon usage at very low growth temperature. Our results show that the synonymous codon usage for Arg (through the AGG, AGA and CGT codons) is the most discriminating factor between (hyper)thermophilic and non-thermophilic species, thus confirming previous studies. We report the unusual clustering of an Archaeal psychrophile with the thermophilic and hyperthermophilic species on the synonymous codon usage factorial map; the other psychrophiles in our study cluster with the mesophilic species. Our conclusion is that the difference in synonymous codon usage between (hyper)thermophilic and non-thermophilic species cannot be clearly attributed to a selective pressure linked to growth at high temperatures.

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.

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.

Intra-strand biases in bacteriophage T4 genome.

In bacteriophage T4, a major portion of DNA replication is initiated at random along the map, although several proven and putative origins have been described for early replication. In order to analyze the contribution of transcription and translation as well as DNA replication to intra-strand bias from A = T and G = C, we examined the pattern of the intra-strand biases in the first, second, and third codon positions of the coding regions as well as the intergenic regions of the T4 genome. We found, along the map, characteristic biases both from A = T and G = C for each codon position and the intergenic regions. The bias patterns were closely associated with the location of the sense and anti-sense segments in the genome. The results suggest that: (1) transcription-associated mutation is likely a significant cause of the bias, which is suggested by the pattern of the AT bias (bias from A = T) in the third codon position; (2) DNA replication coupled bias may also exist, which is suggested by the pattern of the GC bias (bias from G = C) in the third codon position and the intergenic regions; and (3) the bias patterns of the first and second codon positions of the sense segments are consistent with universal properties of the coding sequence that G is in excess and T is deficient in the first codon position, and G is deficient in the second codon position.

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

A simple adaptation of Ninio's 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.

Seasonal variations in acute toxoplasmosis in pregnant women in the Rhône-Alpes region (France).

To search for seasonal variations we analysed data on 1998 acute toxoplasmic infections diagnosed between 1988 and 2009 in pregnant women. Two distinctive transmission profiles were observed: one in rural areas, which was strongly influenced by seasons with significantly fewer infections in the first half of the year but maximal risks at the end of summer and end of autumn, and a stable urban distribution with only moderate peaks. Further studies on individual risks and environmental and climatic factors are needed to understand what prevention message should be given to susceptible pregnant women.

One year variability of peak heights, heterozygous balance and inter-locus balance for the DNA positive control of AmpFℓSTR© Identifiler© STR kit.

Multivariate analyses of 205 positive control experiments in an AmpFℓSTR© Identifiler© STR kit were used to analyze the factors affecting peak heights at 16 loci. Peak heights were found to be highly correlated between loci and there was evidence for a difference in sensitivity of the two genetic analyzers in the blue channel. Heterozygous balance response at 10 loci was found to behave as a random variable following a beta-distribution with typical median values of 90%, without locus or genetic analyzer effect. Inter-locus balance at 16 loci was influenced by the blue channel effect and a temporal switch of unexplained origin. The implications of these results for the choice of minimum threshold values in quality control are discussed.

Online synonymous codon usage analyses with the ade4 and seqinR packages.

UNLABELLED: Correspondence analysis of codon usage data is a widely used method in sequence analysis, but the variability in amino acid composition between proteins is a confounding factor when one wants to analyse synonymous codon usage variability. A simple and natural way to cope with this problem is to use within-group correspondence analysis. There is, however, no user-friendly implementation of this method available for genomic studies. Our motivation was to provide to the community a Web facility to easily study synonymous codon usage on a subset of data available in public genomic databases. AVAILABILITY: Availability through the Pole Bioinformatique Lyonnais (PBIL) Web server at http://pbil.univ-lyon1.fr/datasets/charif04/ with a demo allowing us to reproduce the figure in the present application note. All underlying software is distributed under a GPL licence. CONTACT: http://pbil.univ-lyon1.fr/members/lobry.

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*) [corrected] 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.

Asymmetric substitution patterns in the two DNA strands of bacteria.

Analyses of the genomes of three prokaryotes, Escherichia coli, Bacillus subtilis, and Haemophilus influenzae, revealed a new type of genomic compartmentalization of base frequencies. There was a departure from intrastrand equifrequency between A and T or between C and G, showing that the substitution patterns of the two strands of DNA were asymmetric. The positions of the boundaries between these compartments were found to coincide with the origin and terminus of chromosome replication, and there were more A-T and C-G deviations in intergenic regions and third codon positions, suggesting that a mutational bias was responsible for this asymmetry. The strand asymmetry was found to be due to a difference in base compositions of transcripts in the leading and lagging strands. This difference is sufficient to affect codon usage, but it is small compared to the effects of gene expressivity and amino-acid composition.

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.

Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes.

Multivariate analysis of the amino-acid compositions of 999 chromosome-encoded proteins from Escherichia coli showed that three main factors influence the variability of amino-acid composition. The first factor was correlated with the global hydrophobicity of proteins, and it discriminated integral membrane proteins from the others. The second factor was correlated with gene expressivity, showing a bias in highly expressed genes towards amino-acids having abundant major tRNAs. Just as highly expressed genes have reduced codon diversity in protein coding sequences, so do they have a reduced diversity of amino-acid choice. This showed that translational constraints are important enough to affect the global amino-acid composition of proteins. The third factor was correlated with the aromaticity of proteins, showing that aromatic amino-acid content is highly variable.

Co-inertia analysis of amino-acid physico-chemical properties and protein composition with the ADE package.

A multivariate analysis method called co-inertia analysis was used to determine the main relationships between two data tables having identical rows. This method is available in the ADE multivariate analysis package for Macintosh micro-computers. It was applied to two data sets, one containing the amino-acid composition of 999 E. coli proteins, and the other the values of 402 physico-chemical properties for the 20 natural amino-acids. There were strong relationships between amino-acid physico-chemical properties and the composition of proteins. The first common factor was hydrophobicity; it is linked to the biological environment of proteins, either in the cytoplasm (or outside the cell), or in the nonpolar environment of the phospholipid bilayer of biological membranes. The second factor linked the expressivity of protein genes and the propensity of amino-acids to form alpha helix/beta sheets. The third factor showed that heavy, aromatic amino-acids tend to be avoided, except when they are needed for structural or functional reasons. These results are discussed in terms of selective pressure acting on amino-acid composition of proteins.

Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes.

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.

Evolution of DNA base composition under no-strand-bias conditions when the substitution rates are not constant.

The evolution of DNA base composition evolution is simplified to a six-parameter model when there are no strand biases for mutation and selection. We analyzed the dynamics of this model with special attention to the influence of a change in substitution rates. The G + C content of the DNA sequence tends to an equilibrium value that is controlled by four parameters of the model. When the substitution rates are not constant, the G + C equilibrium position is not constant. The DNA sequence base frequencies always tend to a state in which A = T and G = C within a strand, regardless of substitution rates. This is true even when the substitution rates are not constant over time. This provides a simple way of rejecting the model from inspection of present-day DNA base composition.

Analyzing DNA strand compositional asymmetry to identify candidate replication origins of Borrelia burgdorferi linear and circular plasmids.

The Lyme disease agent Borrelia burgdorferi has a genome composed of a linear chromosome and a series of linear and circular plasmids. We previously mapped the oriC of the linear chromosome to the center of the molecule, where a pronounced switch in CG skew occurs. In this study, we analyzed B. burgdorferi plasmid sequences for AT and CG skew in an effort to similarly identify plasmid replication origins. Cumulative skew diagrams of the plasmids suggested that they, like the linear chromosome, replicate bidirectionally from an internal origin. The B. burgdorferi linear chromosome contains homologs to partitioning protein genes soj and spoOJ, which are closely linked to oriC at the minimum cumulative skew point of the 1-Mb molecule. A soj/parA homolog also maps to cumulative skew minima of the B. burgdorferi linear and circular plasmids, further suggesting that these regions contain the replication origin. The heterogeneity in these genes and in the nucleotide sequences of the putative origin regions could account for the mutual compatibility of the multiple DNA elements in B. burgdorferi.

Biphasic kinetics of bacterial killing by quinolones.

The early phases of the bactericidal dynamics of three quinolones against two Escherichia coli strains were studied. Four concentrations of nalidixic acid, pefloxacin and ofloxacin were tested against each strain. In each case biphasic killing of bacteria was observed after a lag phase, and a biexponential model of microbial death could be fitted to the data. A direct relationship existed between the length of the lag phase and the drug concentration. The other parameters of the model appeared to be either strain-dependent, drug-dependent or both, and were characterised by narrow fluctuations. The degree of killing was always higher for ofloxacin. A paradoxical effect seemed to exist for nalidixic acid and pefloxacin in that survival was greater in the presence of 5 x MIC than in the presence of 3 x MIC. It was clear that ofloxacin did not act in the same way as nalidixic acid and pefloxacin. The study illustrated the relevance of mathematical modelling to investigations of the bactericidal effects of antibiotics.

An unexpected correlation between cardinal temperatures of microbial growth highlighted by a new model.

A new model for the prediction of microbial-specific growth rate as a function of temperature is presented. The four parameters of this model are the three cardinal temperatures (Tmax, Tmin and Topt) and the specific growth rate at the optimum temperature (mu opt). A comparison with three other models was made on the basis of several criteria (simplicity and biological significance of parameters, applicability, quality of fit, minimum structural correlations and ease of determination of parameters). A detailed comparison of a 217-point data set, and an extensive comparison of 47 different data sets show that the new model is better than its competitors. The three cardinal temperatures were found to be independent of mu opt. A very strong and unexpected linear correlation between the cardinal temperatures was observed. The consequences of this biological result are discussed, even though causes remain unknown.

Maintenance requirements of Escherichia coli ATCC 25922 in the presence of sub-inhibitory concentrations of various antibiotics.

Escherichia coli ATCC 25922 was grown in minimal medium M63, with glucose 0.1 gL as limiting energy substrate, in the presence of sub-inhibitory concentrations of netilmicin, habekacin, tobramycin, dibekacin, amikacin, kanamycin, amoxycillin, ampicillin, cephalothin, cefoxitin and nalidixic acid. Maintenance requirements were determined with a simple relationship derived from batch growth curves. The apparent relationship between maintenance requirements and antibiotic concentration is an exponential increase, log m(c) = log mo + k.c, where m is maintenance, c antibiotics concentration, mo maintenance without antibiotics, and k a constant. Values for k were found to be in the range 0.5-2.0 mg-1.L.