Composition strand asymmetries in prokaryotic genomes: mutational bias and biased gene orientation

A novel skew analysis reveals substitution asymmetries linked to genetic code GC-biases and PolIII a-subunit isoforms

Strand biases reflect deviations from a null expectation of DNA evolution that assumes strand-symmetric substitution rates. Here, we present strong evidence that nearest-neighbour preferences are a strand-biased feature of bacterial genomes, indicating neighbour-dependent substitution asymmetries. To detect such asymmetries we introduce an alignment free index (relative abundance skews). The profiles of relative abundance skews along coding sequences can trace the phylogenetic relations of bacteria, suggesting that the patterns of neighbour-dependent substitution strand-biases are not common among different lineages, but are rather species-specific. Analysis of neighbour-dependent and codon-site skews sheds light on the origins of substitution asymmetries. Via a simple model we argue that the structure of the genetic code imposes position-dependent substitution strand-biases along coding sequences, as a response to GC mutation pressure. Thus, the organization of the genetic code per se can lead to an uneven distribution of nucleotides among different codon sites, even when requirements for specific codons and amino-acids are not accounted for. Moreover, our results suggest that strand-biases in replication fidelity of PolIII α-subunit induce substitution asymmetries, both neighbour-dependent and independent, on a genome scale. The role of DNA repair systems, such as transcription-coupled repair, is also considered.

Microbial lifestyle and genome signatures

Microbes are known for their unique ability to adapt to varying lifestyle and environment, even to the extreme or adverse ones. The genomic architecture of a microbe may bear the signatures not only of its phylogenetic position, but also of the kind of lifestyle to which it is adapted. The present review aims to provide an account of the specific genome signatures observed in microbes acclimatized to distinct lifestyles or ecological niches. Niche-specific signatures identified at different levels of microbial genome organization like base composition, GC-skew, purine-pyrimidine ratio, dinucleotide abundance, codon bias, oligonucleotide composition etc. have been discussed. Among the specific cases highlighted in the review are the phenomena of genome shrinkage in obligatory host-restricted microbes, genome expansion in strictly intra-amoebal pathogens, strand-specific codon usage in intracellular species, acquisition of genome islands in pathogenic or symbiotic organisms, discriminatory genomic traits of marine microbes with distinct trophic strategies, and conspicuous sequence features of certain extremophiles like those adapted to high temperature or high salinity.

Nucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomes

Nucleotide compositional asymmetry (NCA) between leading and lagging strands (LeS and LaS) is dynamic and diverse among eubacterial genomes due to different mutation and selection forces. A thorough investigation is needed in order to study the relationship between nucleotide composition dynamics and gene distribution biases. Based on a collection of 364 eubacterial genomes that were grouped according to a DnaE-based scheme (DnaE1-DnaE1, DnaE2-DnaE1, and DnaE3-PolC), we investigated NCA and nucleotide composition gradients at three codon positions and found that there was universal G-enrichment on LeS among all groups. This was due to a strong selection for G-heading (codon position1 or cp1) codons and mutation pressure that led to more G-ending (cp3) codons. Moreover, a slight T-enrichment of LeS due to the mutation of cytosine deamination at cp3 was universal among DnaE1-DnaE1 and DnaE2-DnaE1 genomes, but was not clearly seen among DnaE3-PolC genomes, in which A-enrichment of LeS was proposed to be the effect of selections unique to polC and a mutation bias toward A-richness at cp1 that may be a result of transcription-coupled DNA repair mechanisms. Furthermore, strand-biased gene distribution enhances the purine-richness of LeS for DnaE3-PolC genomes and T-richness of LeS for DnaE1-DnaE1 and DnaE2-dnaE1 genomes.

The organization of the bacterial genome

Many bacterial cellular processes interact intimately with the chromosome. Such interplay is the major driving force of genome structure or organization. Interactions take place at different scales-local for gene expression, global for replication-and lead to the differentiation of the chromosome into organizational units such as operons, replichores, or macrodomains. These processes are intermingled in the cell and create complex higher-level organizational features that are adaptive because they favor the interplay between the processes. The surprising result of selection for genome organization is that gene repertoires change much more quickly than chromosomal structure. Comparative genomics and experimental genomic manipulations are untangling the different cellular and evolutionary mechanisms causing such resilience to change. Since organization results from cellular processes, a better understanding of chromosome organization will help unravel the underlying cellular processes and their diversity.

From GC skews to wavelets: a gentle guide to the analysis of compositional asymmetries in genomic data

Compositional asymmetries are pervasive in DNA sequences. They are the result of the asymmetric interactions between DNA and cellular mechanisms such as replication and transcription. Here, we review many of the methods that have been proposed over the years to analyse compositional asymmetries in DNA sequences. Among these we list GC skews, oligonucleotide skews and wavelets, which among other uses have been extensively employed to delimitate origins and termini of replication in genomes. We also review the use of multivariate methods, such as factorial correspondence analysis, discriminant analysis and analysis of variance, which allow assigning compositional strand asymmetries to the different biological processes shaping sequence composition. Finally, we review methods that have been used to infer substitution matrices and allow understanding the mutational processes underlying strand asymmetry. We focus on replication asymmetries because they have been more thoroughly studied, but the methods may be adapted, and often are, to other problems. Although strand asymmetry has been studied more frequently through compositional skews of nucleotides or oligonucleotides, we recall that, depending on the goal of the analysis, other methods may be more appropriate to answer certain biological questions. We also refer to programs freely available to analyse strand asymmetry.

GraphDNA: a Java program for graphical display of DNA composition analyses

Background

Under conditions of no strand bias the number of Gs is equal to that of Cs for each DNA strand; similarly, the total number of Ts is equal to that of As. However, within each strand there are considerable local deviations from the A = T and G = C equality. These asymmetries in nucleotide composition have been extensively analyzed in prokaryotic and eukaryotic genomes and related to chromosome organization, transcription orientation and other processes in certain organisms. To carry out analysis of intra-strand nucleotide distribution several graphical methods have been developed.

Results

GraphDNA is a new Java application that provides a simple, user-friendly interface for the visualization of DNA nucleotide composition. The program accepts GenBank, EMBL and FASTA files as an input, and it displays multiple DNA nucleotide composition graphs (skews and walks) in a single window to allow direct comparisons between the sequences. We illustrate the use of DNA skews for characterization of poxvirus and coronavirus genomes.

Conclusion

GraphDNA is a platform-independent, Open Source, tool for the analysis of nucleotide trends in DNA sequences. Multiple sequence formats can be read and multiple sequences may be plotted in a single results window.

Similar compositional biases are caused by very different mutational effects

Compositional replication strand bias, commonly referred to as GC skew, is present in many genomes of prokaryotes, eukaryotes, and viruses. Although cytosine deamination in ssDNA (resulting in C-->T changes on the leading strand) is often invoked as its major cause, the precise contributions of this and other substitution types are currently unknown. It is also unclear if the underlying mutational asymmetries are the same among taxa, are stable over time, or how closely the observed biases are to mutational equilibrium. We analyzed nearly neutral sites of seven taxa each with between three and six complete bacterial genomes, and inferred the substitution spectra of fourfold degenerate positions in nonhighly expressed genes. Using a bootstrap procedure, we extracted compositional biases associated with replication and identified the significant asymmetries. Although all taxa showed an overrepresentation of G relative to C on the leading strand (and imbalances between A and T), widely variable substitution asymmetries are noted. Surprisingly, all substitution types show significant asymmetry in at least one taxon, but none were universally biased in all taxa. Notably, in the two most biased genomes, A-->G, rather than C-->T, shapes the compositional bias. Given the variability in these biases, we propose that the process is multifactorial. Finally, we also find that most genomes are not at compositional equilibrium, and suggest that mutational-based heterotachy is deeply imprinted in the history of biological macromolecules. This shows that similar compositional biases associated with the same essential well-conserved process, replication, do not reflect similar mutational processes in different genomes, and that caution is required in inferring the roles of specific mutational biases on the basis of contemporary patterns of sequence composition.

Evolutionary constraints on codon and amino acid usage in two strains of human pathogenic actinobacteria Tropheryma whipplei

The factors governing codon and amino acid usages in the predicted protein-coding sequences of Tropheryma whipplei TW08/27 and Twist genomes have been analyzed. Multivariate analysis identifies the replicational-transcriptional selection coupled with DNA strand-specific asymmetric mutational bias as a major driving force behind the significant interstrand variations in synonymous codon usage patterns in T. whipplei genes, while a residual intrastrand synonymous codon bias is imparted by a selection force operating at the level of translation. The strand-specific mutational pressure has little influence on the amino acid usage, for which the mean hydropathy level and aromaticity are the major sources of variation, both having nearly equal impact. In spite of the intracellular lifestyle, the amino acid usage in highly expressed gene products of T. whipplei follows the cost-minimization hypothesis. The products of the highly expressed genes of these relatively A + T-rich actinobacteria prefer to use the residues encoded by GC-rich codons, probably due to greater conservation of a GC-rich ancestral state in the highly expressed genes, as suggested by the lower values of the rate of nonsynonymous divergences between orthologous sequences of highly expressed genes from the two strains of T. whipplei. Both the genomes under study are characterized by the presence of two distinct groups of membrane-associated genes, products of which exhibit significant differences in primary and potential secondary structures as well as in the propensity of protein disorder.

A study on the correlation of nucleotide skews and the positioning of the origin of replication: different modes of replication in bacterial species

Deviations from Chargaff's 2nd parity rule, according to which A approximately T and G approximately C in single stranded DNA, have been associated with replication as well as with transcription in prokaryotes. Based on observations regarding mainly the transcription-replication co-linearity in a large number of prokaryotic species, we formulate the hypothesis that the replication procedure may follow different modes between genomes throughout which the skews clearly follow different patterns. We draw the conclusion that multiple functional sites of origin of replication may exist in the genomes of most archaea and in some exceptional cases of eubacteria, while in the majority of eubacteria, replication occurs through a single fixed origin.

The replication-related organization of bacterial genomes

The replication of the chromosome is among the most essential functions of the bacterial cell and influences many other cellular mechanisms, from gene expression to cell division. Yet the way it impacts on the bacterial chromosome was not fully acknowledged until the availability of complete genomes allowed one to look upon genomes as more than bags of genes. Chromosomal replication includes a set of asymmetric mechanisms, among which are a division in a lagging and a leading strand and a gradient between early and late replicating regions. These differences are the causes of many of the organizational features observed in bacterial genomes, in terms of both gene distribution and sequence composition along the chromosome. When asymmetries or gradients increase in some genomes, e.g. due to a different composition of the DNA polymerase or to a higher growth rate, so do the corresponding biases. As some of the features of the chromosome structure seem to be under strong selection, understanding such biases is important for the understanding of chromosome organization and adaptation. Inversely, understanding chromosome organization may shed further light on questions relating to replication and cell division. Ultimately, the understanding of the interplay between these different elements will allow a better understanding of bacterial genetics and evolution.

Temporal and spatial regulation in prokaryotic cell cycle progression and development

Bacteria exhibit a high degree of intracellular organization, both in the timing of essential processes and in the placement of the chromosome, the division site, and individual structural and regulatory proteins. We examine the temporal and spatial regulation of the Caulobacter cell cycle, bacterial chromosome segregation and cytokinesis, and Bacillus subtilis sporulation. Mechanisms that control timing of cell cycle and developmental events include transcriptional cascades, regulated phosphorylation and proteolysis of signal transduction proteins, transient genetic asymmetry, and intercellular communication. Surprisingly, many signal transduction proteins are dynamically localized to specific subcellular addresses during the cell division cycle and sporulation, and proper localization is essential for their function. The Min proteins that govern division site selection in Escherichia coli may be the first example of a system that generates positional information de novo.

From genes to genomes: universal scale-invariant properties of microbial chromosome organisation

The availability of complete genome sequences for a large variety of organisms is a major advance in understanding genome structure and function. One attribute of genome structure is chromosome organisation in terms of gene localisation and orientation. For example, bacterial operons, i.e. clusters of co-oriented genes that form transcription units, enable functionally related genes to be expressed simultaneously. The description of genome organisation was pioneered with the study of the distribution of genes of the Escherichia coli partial genetic map before the full genome sequence was known. Deploying powerful techniques from circular statistics and signal processing, we revisit the issue of gene localisation and orientation using 89 complete microbial chromosomes from the eubacterial and archaeal domains. We demonstrate that there is no characteristic size pertinent to the description of chromosome structure, e.g. there does not exist any single length appropriate to describe gene clustering. Our results show that, for all 89 chromosomes, gene positions and gene orientations share a common form of scale-invariant correlations known as "long-range correlations" that we can reveal for distances from the gene length, up to the chromosome size. This observation indicates that genes tend to assemble and to co-orient over any scale of observation greater than a few kilobases. This unexpected property of chromosome structure can be portrayed as an operon-like organisation at all scales and implies that a complete scale range extending over more than three orders of magnitudes of chromosome segment lengths is necessary to properly describe prokaryotic genome organisation. We propose that this pattern results from the effects of the superhelical context on gene expression coupled with the structure and dynamics of the nucleoid, possibly accommodating the diverse gene expression profiles needed during the different stages of cellular life.

The genome of Campylobacter jejuni: codon and amino acid usage

The genes from the genome of the AT-rich bacterium Campylobacter jejuni were analysed and characterised with respect to usage and amino acid usage. Codon usage is generally biased for all amino acids having synonymous codons, so that AT-rich synonyms are most frequently used. Markov chain analysis showed that codon bias and over- or underrepresentation of the corresponding tri-letter words are not related. Predicted secondary structure, lipophilicity, codon position within the gene, strand, and position on the (+)-strand were all shown to be determinants of codon usage, and these effects were in part directly explained by compositional phenomena. Codon context and the GC-content at the wobble position of the fourfold degenerate sites exert indirect effects on codon usage. The factors that affect codon usage seem to affect all amino acids, rather than selected amino acids. The usage of amino acids correlates well with the GC-content of genes, i.e. usage of amino acids encoded by GC-rich codons increases with GC-content and vice versa.

Does RNA polymerase help drive chromosome segregation in bacteria?

In contrast to eukaryotic cells, bacteria segregate their chromosomes without a conspicuous mitotic apparatus. Replication of bacterial chromosomes initiates bidirectionally from a single site (oriC), and visualization of the region of the chromosome containing oriC in living cells reveals that origins rapidly move apart toward opposite poles of the cell during the cell cycle. The motor that drives this poleward movement is unknown. An attractive candidate is RNA polymerase, which is a powerful and abundant molecular motor. If, as has been suggested for other macromolecular complexes, the movement of RNA polymerase is restricted in the cell, then transcription would translocate the DNA template, thereby providing the motive force to separate replicating chromosomes. A coordinated effect of many transcribing RNA polymerases could result from the widely conserved global bias of gene orientation away from oriC. By using fluorescence microscopy of living Bacillus subtilis cells, we demonstrate that an inhibitor of RNA polymerase acts to inhibit separation of newly duplicated DNAs near the origin of replication. We propose that the force exerted by RNA polymerase contributes to chromosome movement in bacteria, and that this force, coupled with the biased orientation of transcription units, helps to drive chromosome segregation.

Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes?

Replication generates bacterial chromosomes with strands that differ in the number of genes and base composition. It has been suggested that in bacteria such as Bacillus subtilis, PolC is responsible for the synthesis of the leading strand and DnaE for the lagging strand, whereas in many other bacteria DnaE is responsible for the synthesis of both strands. Here, I show that the possession of PolC correlates with leading strands that contain an average of 78% of genes compared with 58% for genomes that do not contain PolC. This suggests that asymmetrical replication forks could have a major role in defining and constraining the structure of the bacterial chromosome. The presence of PolC is not correlated with compositional strand bias, suggesting that the two biases result from different types of structural asymmetry.

Pyrococcus genome comparison evidences chromosome shuffling-driven evolution

The genomes of three Pyrococcus species, P.abyssi, P.furiosus and P.horikoshii, were compared at the DNA level, taking advantage of our identification of their replication origins. Three types of rearrangements have been identified: (i) inversion and translation across the replication axis (origin/terminus), (ii) inversion and translocation restricted to a replichore (the half chromosome divided by the replication axis) and (iii) apparent mobility of long clusters of repeated sequences. Rearrangements restricted within a replichore were more common between P.furiosus and the two other Pyrococcus species than between P.horikoshii and P.abyssi. A strong correlation was found between 23 homologous insertion sequence elements, present only in P.furiosus, and recombined segment boundaries, suggesting that transposition events have been a major cause of genomic disruption in this species. Moreover, gene orientation bias was much more disrupted than strand composition biases in fragments that switched their orientation within a replichore upon recombination. This allowed us to conclude that one reversion and one translation occurred in P.abyssi after its divergence from P.horikoshii, and that a smaller segment has specifically recombined in P.furiosus. Whereas a majority of genes are transcribed in the same direction as DNA replication in P.horikoshii and P.abyssi, the colinearity of transcription and replication is only maintained for highly transcribed genes in P.furiosus. We discuss the implications of genomic rearrangements on gene orientation and composition biases, and their consequences on sequence evolution.