Codon usages of genes on chromosome, and surprisingly, genes in plasmid are primarily affected by strand-specific mutational biases in Lawsonia intracellularis

Genome evolution of Buchnera aphidicola (Gammaproteobacteria): Insights into strand compositional asymmetry, codon usage bias, and phylogenetic implications

Taxa of Buchnera aphidicola (hereafter "Buchnera") are mutualistic intracellular symbionts of aphids, known for their remarkable biological traits such as genome reduction, strand compositional asymmetry, and symbiont-host coevolution. With the growing availability of genomic data, we performed a comprehensive analysis of 103 genomes of Buchnera strains from 12 host subfamilies, focusing on the genomic characterizations, codon usage patterns, and phylogenetic implications. Our findings revealed consistent features among all genomes, including small genome sizes, low GC contents, and gene losses. We also identified strong strand compositional asymmetries in all strains at the genome level. Further investigation suggested that mutation pressure may have played a crucial role in shaping codon usage of Buchnera. Moreover, the genomic asymmetries were reflected in asymmetric codon usage preferences within chromosomal genes. Notably, the levels of these asymmetries were varied among strains and were significantly influenced by the degrees of genome shrinkages. Lastly, our phylogenetic analyses presented an alternative topology of Aphididae, based on the Buchnera symbionts, providing robust confirmation of the paraphylies of Eriosomatinae, and Macrosiphini. Our objectives are to further understand the strand compositional asymmetry and codon usage bias of Buchnera taxa, and provide new perspectives for phylogenetic studies of Aphididae.

Mitogenomic Codon Usage Patterns of Superfamily Certhioidea (Aves, Passeriformes): Insights into Asymmetrical Bias and Phylogenetic Implications

The superfamily Certhioidea currently comprises five families. Due to the rapid diversification, the phylogeny of Certhioidea is still controversial. The advent of next generation sequencing provides a unique opportunity for a mitogenome-wide study. Here, we first provided six new complete mitogenomes of Certhioidea (Certhia americana, C. familiaris, Salpornis spilonota, Cantorchilus leucotis, Pheugopedius coraya, and Pheugopedius genibarbis). We further paid attention to the genomic characteristics, codon usages, evolutionary rates, and phylogeny of the Certhioidea mitogenomes. All mitogenomes we analyzed displayed typical ancestral avian gene order with 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and one control region (CR). Our study indicated the strand-biased compositional asymmetry might shape codon usage preferences in mitochondrial genes. In addition, natural selection might be the main factor in shaping the codon usages of genes. Additionally, evolutionary rate analyses indicated all mitochondrial genes were under purifying selection. Moreover, MT-ATP8 and MT-CO1 were the most rapidly evolving gene and conserved genes, respectively. According to our mitophylogenetic analyses, the monophylies of Troglodytidae and Sittidae were strongly supported. Importantly, we suggest that Salpornis should be separated from Certhiidae and put into Salpornithidae to maintain the monophyly of Certhiidae. Our findings are useful for further evolutionary studies within Certhioidea.

The Shift in Synonymous Codon Usage Reveals Similar Genomic Variation during Domestication of Asian and African Rice

The domestication of wild rice occurred together with genomic variation, including the synonymous nucleotide substitutions that result in synonymous codon usage bias (SCUB). SCUB mirrors the evolutionary specialization of plants, but its characteristics during domestication were not yet addressed. Here, we found cytosine- and guanidine-ending (NNC and NNG) synonymous codons (SCs) were more pronounced than adenosine- and thymine-ending SCs (NNA and NNT) in both wild and cultivated species of Asian and African rice. The ratios of NNC/G to NNA/T codons gradually decreased following the rise in the number of introns, and the preference for NNA/T codons became more obvious in genes with more introns in cultivated rice when compared with those in wild rice. SCUB frequencies were heterogeneous across the exons, with a higher preference for NNA/T in internal exons than in terminal exons. The preference for NNA/T in internal but not terminal exons was more predominant in cultivated rice than in wild rice, with the difference between wild and cultivated rice becoming more remarkable with the rise in exon numbers. The difference in the ratios of codon combinations representing DNA methylation-mediated conversion from cytosine to thymine between wild and cultivated rice coincided with their difference in SCUB frequencies, suggesting that SCUB reveals the possible association between genetic and epigenetic variation during the domestication of rice. Similar patterns of SCUB shift in Asian and African rice indicate that genomic variation occurs in the same non-random manner. SCUB representing non-neutral synonymous mutations can provide insight into the mechanism of genomic variation in domestication and can be used for the genetic dissection of agricultural traits in rice and other crops.

Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins

The replication of DNA is a complex biological process that is essential for life. Bacterial DNA replication is initiated at genomic loci referred to as replication origins (oriCs). Integrating the Z-curve method, DnaA box distribution, and comparative genomic analysis, we developed a web server to predict bacterial oriCs in 2008 called Ori-Finder, which contributes to clarify the characteristics of bacterial oriCs. The oriCs of hundreds of sequenced bacterial genomes have been annotated in the genome reports using Ori-Finder and the predicted results have been deposited in DoriC, a manually curated database of oriCs. This has facilitated large-scale data mining of functional elements in oriCs and strand-biased analysis. Here, we describe Ori-Finder 2022 with updated prediction framework, interactive visualization module, new analysis module, and user-friendly interface. More species-specific indicator genes and functional elements of oriCs are integrated into the updated framework, which has also been redesigned to predict oriCs in draft genomes. The interactive visualization module displays more genomic information related to oriCs and their functional elements. The analysis module includes regulatory protein annotation, repeat sequence discovery, homologous oriC search, and strand-biased analyses. The redesigned interface provides additional customization options for oriC prediction. Ori-Finder 2022 is freely available at http://tubic.tju.edu.cn/Ori-Finder/ and https://tubic.org/Ori-Finder/.

Alteration of synonymous codon usage bias accompanies polyploidization in wheat

The diploidization of polyploid genomes is accompanied by genomic variation, including synonymous nucleotide substitutions that may lead to synonymous codon usage bias (SCUB). SCUB can mirror the evolutionary specialization of plants, but its effect on the formation of polyploidies is not well documented. We explored this issue here with hexaploid wheat and its progenitors. Synonymous codons (SCs) ending in either cytosine (NNC) or guanidine (NNG) were more frequent than those ending in either adenosine (NNA) or thymine (NNT), and the preference for NNC/G codons followed the increase in genome ploidy. The ratios between NNC/G and NNA/T codons gradually decreased in genes with more introns, and the difference in these ratios between wheat and its progenitors diminished with increasing ploidy. SCUB frequencies were heterogeneous among exons, and the bias preferred to NNA/T in more internal exons, especially for genes with more exons; while the preference did not appear to associate with ploidy. The SCUB alteration of the progenitors was different during the formation of hexaploid wheat, so that SCUB was the homogeneous among A, B and D subgenomes. DNA methylation-mediated conversion from cytosine to thymine weakened following the increase of genome ploidy, coinciding with the stronger bias for NNC/G SCs in the genome as a function of ploidy, suggesting that SCUB contribute to the epigenetic variation in hexaploid wheat. The patterns in SCUB mirrored the formation of hexaploid wheat, which provides new insight into genome shock-induced genetic variation during polyploidization. SCs representing non-neutral synonymous mutations can be used for genetic dissection and improvement of agricultural traits of wheat and other polyploidies.

Consistent Clustering Pattern of Prokaryotic Genes Based on Base Frequency at the Second Codon Position and its Association with Functional Category Preference

In 2002, our research group observed a gene clustering pattern based on the base frequency of A versus T at the second codon position in the genome of Vibrio cholera and found that the functional category distribution of genes in the two clusters was different. With the availability of a large number of sequenced genomes, we performed a systematic investigation of A2–T2 distribution and found that 2694 out of 2764 prokaryotic genomes have an optimal clustering number of two, indicating a consistent pattern. Analysis of the functional categories of the coding genes in each cluster in 1483 prokaryotic genomes indicated, that 99.33% of the genomes exhibited a significant difference (p < 0.01) in function distribution between the two clusters. Specifically, functional category P was overrepresented in the small cluster of 98.65% of genomes, whereas categories J, K, and L were overrepresented in the larger cluster of over 98.52% of genomes. Lineage analysis uncovered that these preferences appear consistently across all phyla. Overall, our work revealed an almost universal clustering pattern based on the relative frequency of A2 versus T2 and its role in functional category preference. These findings will promote the understanding of the rationality of theoretical prediction of functional classes of genes from their nucleotide sequences and how protein function is determined by DNA sequence.

Graphical abstract

Asymmetric Somatic Hybridization Affects Synonymous Codon Usage Bias in Wheat

Asymmetric somatic hybridization is an efficient strategy for crop breeding by introducing exogenous chromatin fragments, which leads to whole genomic shock and local chromosomal shock that induces genome-wide genetic variation including indel (insertion and deletion) and nucleotide substitution. Nucleotide substitution causes synonymous codon usage bias (SCUB), an indicator of genomic mutation and natural selection. However, how asymmetric somatic hybridization affects SCUB has not been addressed. Here, we explored this issue by comparing expressed sequence tags of a common wheat cultivar and its asymmetric somatic hybrid line. Asymmetric somatic hybridization affected SCUB and promoted the bias to A- and T-ending synonymous codon (SCs). SCUB frequencies in chromosomes introgressed with exogenous fragments were comparable to those in chromosomes without exogenous fragments, showing that exogenous fragments had no local chromosomal effect. Asymmetric somatic hybridization affected SCUB frequencies in indel-flanking sequences more strongly than in non-flanking sequences, and this stronger effect was present in both chromosomes with and without exogenous fragments. DNA methylation-driven SCUB shift was more pronounced than other SC pairs. SCUB shift was similar among seven groups of allelic chromosomes as well as three sub-genomes. Our work demonstrates that the SCUB shift induced by asymmetric somatic hybridization is attributed to the whole genomic shock, and DNA methylation is a putative force of SCUB shift during asymmetric somatic hybridization. Asymmetric somatic hybridization provides an available method for deepening the nature of SCUB shift and genetic variation induced by genomic shock.

Polyploidization is accompanied by synonymous codon usage bias in the chloroplast genomes of both cotton and wheat

Synonymous codon usage bias (SCUB) of both nuclear and organellar genes can mirror the evolutionary specialization of plants. The polyploidization process exposes the nucleus to genomic shock, a syndrome which promotes, among other genetic variants, SCUB. Its effect on organellar genes has not, however, been widely addressed. The present analysis targeted the chloroplast genomes of two leading polyploid crop species, namely cotton and bread wheat. The frequency of codons in the chloroplast genomes ending in either adenosine (NNA) or thymine (NNT) proved to be higher than those ending in either guanidine or cytosine (NNG or NNC), and this difference was conserved when comparisons were made between polyploid and diploid forms in both the cotton and wheat taxa. Preference for NNA/T codons was heterogeneous among genes with various numbers of introns and was also differential among the exons. SCUB patterns distinguished tetraploid cotton from its diploid progenitor species, as well as bread wheat from its diploid/tetraploid progenitor species, indicating that SCUB in the chloroplast genome partially mirrors the formation of polyploidies.

Reconsidering plasmid maintenance factors for computational plasmid design

Plasmids are genetic parasites of microorganisms. The genomes of naturally occurring plasmids are expected to be polished via natural selection to achieve long-term persistence in the microbial cell population. However, plasmid genomes are extremely diverse, and the rules governing plasmid genomes are not fully understood. Therefore, computationally designing plasmid genomes optimized for model and nonmodel organisms remains challenging. Here, we summarize current knowledge of the plasmid genome organization and the factors that can affect plasmid persistence, with the aim of constructing synthetic plasmids for use in gram-negative bacteria. Then, we introduce publicly available resources, plasmid data, and bioinformatics tools that are useful for computational plasmid design.

Recent development of Ori-Finder system and DoriC database for microbial replication origins

DNA replication begins at replication origins in all three domains of life. Identification and characterization of replication origins are important not only in providing insights into the structure and function of the replication origins but also in understanding the regulatory mechanisms of the initiation step in DNA replication. The Z-curve method has been used in the identification of replication origins in archaeal genomes successfully since 2002. Furthermore, the Web servers of Ori-Finder and Ori-Finder 2 have been developed to predict replication origins in both bacterial and archaeal genomes based on the Z-curve method, and the replication origins with manual curation have been collected into an online database, DoriC. Ori-Finder system and DoriC database are currently used in the research field of DNA replication origins in prokaryotes, including: (i) identification of oriC regions in bacterial and archaeal genomes; (ii) discovery and analysis of the conserved sequences within oriC regions; and (iii) strand-biased analysis of bacterial genomes.

Up to now, more and more predicted results by Ori-Finder system were supported by subsequent experiments, and Ori-Finder system has been used to identify the replication origins in > 100 newly sequenced prokaryotes in their genome reports. In addition, the data in DoriC database have been widely used in the large-scale analyses of replication origins and strand bias in prokaryotic genomes. Here, we review the development of Ori-Finder system and DoriC database as well as their applications. Some future directions and aspects for extending the application of Ori-Finder and DoriC are also presented.

Mutational Pressure in Zika Virus: Local ADAR-Editing Areas Associated with Pauses in Translation and Replication

Zika virus (ZIKV) spread led to the recent medical health emergency of international concern. Understanding the variations in virus system is of utmost need. Using available complete sequences of ZIKV we estimated directions of mutational pressure along the length of consensus sequences of three lineages of the virus. Results showed that guanine usage is growing in ZIKV RNA plus strand due to adenine to guanine transitions, while adenine usage is growing due to cytosine to adenine transversions. Especially high levels of guanine have been found in two-fold degenerated sites of certain areas of RNA plus strand with high amount of secondary structure. The usage of cytosine in two-fold degenerated sites shows direct dependence on the amount of secondary structure in 52% (consensus sequence of East African ZIKV lineage)—32% (consensus sequence of epidemic strains) of the length of RNA minus strand. These facts are the evidences of ADAR-editing of both strands of ZIKV genome during pauses in replication. RNA plus strand can also be edited by ADAR during pauses in translation caused by the appearance of groups of rare codons. According to our results, RNA minus strand of epidemic ZIKV strain has lower number of points in which polymerase can be stalled (allowing ADAR-editing) compared to other strains. The data on preferable directions of mutational pressure in epidemic ZIKV strain is useful for future vaccine development and understanding the evolution of new strains.

Multiple Evolutionary Selections Involved in Synonymous Codon Usages in the Streptococcus agalactiae Genome

Streptococcus agalactiae is an important human and animal pathogen. To better understand the genetic features and evolution of S. agalactiae, multiple factors influencing synonymous codon usage patterns in S. agalactiae were analyzed in this study. A- and U-ending rich codons were used in S. agalactiae function genes through the overall codon usage analysis, indicating that Adenine (A)/Thymine (T) compositional constraints might contribute an important role to the synonymous codon usage pattern. The GC3% against the effective number of codon (ENC) value suggested that translational selection was the important factor for codon bias in the microorganism. Principal component analysis (PCA) showed that (i) mutational pressure was the most important factor in shaping codon usage of all open reading frames (ORFs) in the S. agalactiae genome; (ii) strand specific mutational bias was not capable of influencing the codon usage bias in the leading and lagging strands; and (iii) gene length was not the important factor in synonymous codon usage pattern in this organism. Additionally, the high correlation between tRNA adaptation index (tAI) value and codon adaptation index (CAI), frequency of optimal codons (Fop) value, reinforced the role of natural selection for efficient translation in S. agalactiae. Comparison of synonymous codon usage pattern between S. agalactiae and susceptible hosts (human and tilapia) showed that synonymous codon usage of S. agalactiae was independent of the synonymous codon usage of susceptible hosts. The study of codon usage in S. agalactiae may provide evidence about the molecular evolution of the bacterium and a greater understanding of evolutionary relationships between S. agalactiae and its hosts.

Multiple Factors Drive Replicating Strand Composition Bias in Bacterial Genomes

Composition bias from Chargaff’s second parity rule (PR2) has long been found in sequenced genomes, and is believed to relate strongly with the replication process in microbial genomes. However, some disagreement on the underlying reason for strand composition bias remains. We performed an integrative analysis of various genomic features that might influence composition bias using a large-scale dataset of 1111 genomes. Our results indicate (1) the bias was stronger in obligate intracellular bacteria than in other free-living species (p-value = 0.0305); (2) Fusobacteria and Firmicutes had the highest average bias among the 24 microbial phyla analyzed; (3) the strength of selected codon usage bias and generation times were not observably related to strand composition bias (p-value = 0.3247); (4) significant negative relationships were found between GC content, genome size, rearrangement frequency, Clusters of Orthologous Groups (COG) functional subcategories A, C, I, Q, and composition bias (p-values < 1.0 × 10⁻⁸); (5) gene density and COG functional subcategories D, F, J, L, and V were positively related with composition bias (p-value < 2.2 × 10⁻¹⁶); and (6) gene density made the most important contribution to composition bias, indicating transcriptional bias was associated strongly with strand composition bias. Therefore, strand composition bias was found to be influenced by multiple factors with varying weights.

Synonymous codon usage bias in plant mitochondrial genes is associated with intron number and mirrors species evolution

Synonymous codon usage bias (SCUB) is a common event that a non-uniform usage of codons often occurs in nearly all organisms. We previously found that SCUB is correlated with both intron number and exon position in the plant nuclear genome but not in the plastid genome; SCUB in both nuclear and plastid genome can mirror the evolutionary specialization. However, how about the rules in the mitochondrial genome has not been addressed. Here, we present an analysis of SCUB in the mitochondrial genome, based on 24 plant species ranging from algae to land plants. The frequencies of NNA and NNT (A- and T-ending codons) are higher than those of NNG and NNC, with the strongest preference in bryophytes and the weakest in land plants, suggesting an association between SCUB and plant evolution. The preference for NNA and NNT is more evident in genes harboring a greater number of introns in land plants, but the bias to NNA and NNT exhibits even among exons. The pattern of SCUB in the mitochondrial genome differs in some respects to that present in both the nuclear and plastid genomes.

Synonymous Codon Usage Bias in the Plastid Genome is Unrelated to Gene Structure and Shows Evolutionary Heterogeneity

Synonymous codon usage bias (SCUB) is the nonuniform usage of codons, occurring often in nearly all organisms. Our previous study found that SCUB is correlated with intron number, is unequal among exons in the plant nuclear genome, and mirrors evolutionary specialization. However, whether this rule exists in the plastid genome has not been addressed. Here, we present an analysis of SCUB in the plastid genomes of 25 species from lower to higher plants (algae, bryophytes, pteridophytes, gymnosperms, and spermatophytes). We found NNA and NNT (A- and T-ending codons) are preferential in the plastid genomes of all plants. Interestingly, this preference is heterogeneous among taxonomies of plants, with the strongest preference in bryophytes and the weakest in pteridophytes, suggesting an association between SCUB and plant evolution. In addition, SCUB frequencies are consistent among genes with varied introns and among exons, indicating that the bias of NNA and NNT is unrelated to either intron number or exon position. Further, SCUB is associated with DNA methylation–induced conversion of cytosine to thymine in the vascular plants but not in algae or bryophytes. These data demonstrate that these SCUB profiles in the plastid genome are distinctly different compared with the nuclear genome.

Analysis of genomic characters reveals that four distinct gene clusters are correlated with different functions in Burkholderia cenocepacia AU 1054

Possessing three circular chromosomes is a distinct genomic characteristic of Burkholderia cenocepacia AU 1054, a clinically important pathogen in cystic fibrosis. In this study, base composition, codon usage and functional role category were analyzed in the B. cenocepacia AU 1054 genome. Although no bias in the base and codon usage was detected between any two chromosomes, function differences did exist in the genes of each chromosome. Similar base composition and differential functional role categories indicated that genes on these three chromosomes were relatively stable and that a proper division of labor was established. Based on variations in the base or codon usage, four small gene clusters were observed in all of the genes. Multivariate analysis revealed that protein hydrophobicity played a predominant role in shaping base usage bias, while horizontal gene transfer and the gene expression level were the two most important factors that affected the codon usage bias. Interestingly, we also found that these gene clusters were correlated with different biological functions: (i) 45 pyrimidine-leading-codon preferred genes were predominantly involved in regulatory function; (ii) most drug resistance-related genes involved in 826 genes that coding for hydrophobic proteins; (iii) most of the 111 horizontal transfer genes were responsible for genomic plasticity; and (iv) 73 highly expressed genes (predicted by their codon adaptation index values) showed environmental adaptation to cystic fibrosis. Our results showed that genes with base or codon usage bias were affected by mutational pressure and natural selection, and their functions could contribute to drug assistance and transmissible activity in B. cenocepacia.

DNA replication and strand asymmetry in prokaryotic and mitochondrial genomes

Different patterns of strand asymmetry have been documented in a variety of prokaryotic genomes as well as mitochondrial genomes. Because different replication mechanisms often lead to different patterns of strand asymmetry, much can be learned of replication mechanisms by examining strand asymmetry. Here I summarize the diverse patterns of strand asymmetry among different taxonomic groups to suggest that (1) the single-origin replication may not be universal among bacterial species as the endosymbionts Wigglesworthia glossinidia, Wolbachia species, cyanobacterium Synechocystis 6803 and Mycoplasma pulmonis genomes all exhibit strand asymmetry patterns consistent with the multiple origins of replication, (2) different replication origins in some archaeal genomes leave quite different patterns of strand asymmetry, suggesting that different replication origins in the same genome may be differentially used, (3) mitochondrial genomes from representative vertebrate species share one strand asymmetry pattern consistent with the strand-displacement replication documented in mammalian mtDNA, suggesting that the mtDNA replication mechanism in mammals may be shared among all vertebrate species, and (4) mitochondrial genomes from primitive forms of metazoans such as the sponge and hydra (representing Porifera and Cnidaria, respectively), as well as those from plants, have strand asymmetry patterns similar to single-origin or multi-origin replications observed in prokaryotes and are drastically different from mitochondrial genomes from other metazoans. This may explain why sponge and hydra mitochondrial genomes, as well as plant mitochondrial genomes, evolves much slower than those from other metazoans.

Coding constraints modulate chemically spontaneous mutational replication gradients in mitochondrial genomes

Distances from heavy and light strand replication origins determine duration mitochondrial DNA remains singlestranded during replication. Hydrolytic deaminations from A->G and C->T occur more on single- than doublestranded DNA. Corresponding replicational nucleotide gradients exist across mitochondrial genomes, most at 3rd, least 2^nd codon positions. DNA singlestrandedness during RNA transcription causes gradients mainly in long-lived species with relatively slow metabolism (high transcription/replication ratios). Third codon nucleotide contents, evolutionary results of mutation cumulation, follow replicational, not transcriptional gradients in Homo; observed human mutations follow transcriptional gradients. Synonymous third codon position transitions potentially alter adaptive off frame information. No mutational gradients occur at synonymous positions forming off frame stops (these adaptively stop early accidental frameshifted protein synthesis), nor in regions coding for putative overlapping genes according to an overlapping genetic code reassigning stop codons to amino acids. Deviation of 3rd codon nucleotide contents from deamination gradients increases with coding importance of main frame 3rd codon positions in overlapping genes (greatest if these are 2^nd position in overlapping genes). Third codon position deamination gradients calculated separately for each codon family are strongest where synonymous transitions are rarely pathogenic; weakest where transitions are frequently pathogenic. Synonymous mutations affect translational accuracy, such as error compensation of misloaded tRNAs by codon-anticodon mismatches (prevents amino acid misinsertion despite tRNA misacylation), a potential cause of pathogenic mutations at synonymous codon positions. Indeed, codon-family-specific gradients are inversely proportional to error compensation associated with gradient-promoted transitions. Deamination gradients reflect spontaneous chemical reactions in singlestranded DNA, but functional coding constraints modulate gradients.

Measures of compositional strand bias related to replication machinery and its applications

The compositional asymmetry of complementary bases in nucleotide sequences implies the existence of a mutational or selectional bias in the two strands of the DNA duplex, which is commonly shaped by strand-specific mechanisms in transcription or replication. Such strand bias in genomes, frequently visualized by GC skew graphs, is used for the computational prediction of transcription start sites and replication origins, as well as for comparative evolutionary genomics studies. The use of measures of compositional strand bias in order to quantify the degree of strand asymmetry is crucial, as it is the basis for determining the applicability of compositional analysis and comparing the strength of the mutational bias in different biological machineries in various species. Here, we review the measures of strand bias that have been proposed to date, including the ∆GC skew, the B₁ index, the predictability score of linear discriminant analysis for gene orientation, the signal-to-noise ratio of the oligonucleotide bias, and the GC skew index. These measures have been predominantly designed for and applied to the analysis of replication-related mutational processes in prokaryotes, but we also give research examples in eukaryotes.

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.

A blueprint for a mutationist theory of replicative strand asymmetries formation

In the present review, we summarized current knowledge on replicative strand asymmetries in prokaryotic genomes. A cornerstone for the creation of a theory of their formation has been overviewed. According to our recent works, the probability of nonsense mutation caused by replication-associated mutational pressure is higher for genes from lagging strands than for genes from leading strands of both bacterial and archaeal genomes. Lower density of open reading frames in lagging strands can be explained by faster rates of nonsense mutations in genes situated on them. According to the asymmetries in nucleotide usage in fourfold and twofold degenerate sites, the direction of replication-associated mutational pressure for genes from lagging strands is usually the same as the direction of transcription-associated mutational pressure. It means that lagging strands should accumulate more 8-oxo-G, uracil and 5-formyl-uracil, respectively. In our opinion, consequences of cytosine deamination (C to T transitions) do not lead to the decrease of cytosine usage in genes from lagging strands because of the consequences of thymine oxidation (T to C transitions), while guanine oxidation (causing G to T transversions) makes the main contribution into the decrease of guanine usage in fourfold degenerate sites of genes from lagging strands. Nucleotide usage asymmetries and bias in density of coding regions can be found in archaeal genomes, although, the percent of "inversed" asymmetries is much higher for them than for bacterial genomes. "Homogenized" and "inversed" replicative strand asymmetries in archaeal genomes can be used as retrospective indexes for detection of OriC translocations and large inversions.

[Strong strand specific composition bias-a genomic character of some obligate parasites or symbionts]

DNA replication includes a set of asymmetric mechanisms, which is a division into lagging and leading strands. The former is synthesized continuously whereas the synthesis for the latter is discontinuous. Such a asymmetric mechanism leads to distinct nucleotide composition of these two strands. Strands specific nucleotide composition bias was originally found in genomes of echinoderm and vertebrate mitochondria and then in several bacterial genomes. With the rapid growth in the number of sequenced genomes, many bacteria and even eukaryotes are found to have the consistent strand composition bias. In some bacteria, the extent of strand specific composition bias was so strong that genes on the two replicating strands could be separated according to their codon usages. Till now, 11 obligate intracellular bacteria have been found to have separate codon usages according to whether genes located on the leading or lagging strands. However, there is still not a well-accepted theory that could interpret the reason for the occurrence of separate codon usages in some special bacterial genomes and not in others. This paper reviews the related works and points out its open problems.

Analysis of codon usage in type 1 and the new genotypes of duck hepatitis virus

In this study, an abundant (A + U)% and low codon bias were revealed in duck hepatitis virus type 1 (DHV-1) and the new serotype strains isolated from Taiwan, South Korea and Mainland China (DHV-N). The general correlation between base composition and codon usage bias suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage bias in these samples. By comparative analysis of the codon usage patterns of 40 ORFs of DHV, we found that all of DHV-1 strains grouped in genotype C; the DHV-N strains isolated in South Korea and China clustered into genotypes B; and the DHV-N strains isolated from Taiwan clustered into genotypes A. The findings revealed that more than one subtype of DHV-1 circulated in East Asia. Furthermore, the results of phylogenetic analyses based on RSCU values and Clustal W method indicated obvious phylogenetic congruities. This suggested that better genome consistency of DHV may exist in nature and phylogenetic analyses based on RSCU values maybe a good method in classifying genotypes of the virus. Our work might give some clues to the features and some evolutionary information of DHV.

Codon Usage Patterns in Corynebacterium glutamicum: Mutational Bias, Natural Selection and Amino Acid Conservation

The alternative synonymous codons in Corynebacterium glutamicum, a well-known bacterium used in industry for the production of amino acid, have been investigated by multivariate analysis. As C. glutamicum is a GC-rich organism, G and C are expected to predominate at the third position of codons. Indeed, overall codon usage analyses have indicated that C and/or G ending codons are predominant in this organism. Through multivariate statistical analysis, apart from mutational selection, we identified three other trends of codon usage variation among the genes. Firstly, the majority of highly expressed genes are scattered towards the positive end of the first axis, whereas the majority of lowly expressed genes are clustered towards the other end of the first axis. Furthermore, the distinct difference in the two sets of genes was that the C ending codons are predominate in putatively highly expressed genes, suggesting that the C ending codons are translationally optimal in this organism. Secondly, the majority of the putatively highly expressed genes have a tendency to locate on the leading strand, which indicates that replicational and transciptional selection might be invoked. Thirdly, highly expressed genes are more conserved than lowly expressed genes by synonymous and nonsynonymous substitutions among orthologous genes fromthe genomes of C. glutamicum and C. diphtheriae. We also analyzed other factors such as the length of genes and hydrophobicity that might influence codon usage and found their contributions to be weak.

Codon usage and gene expression pattern of Stenotrophomonas maltophilia R551-3 for pathogenic mode of living

Stenotrophomonas maltophilia strain R551-3 is a multiple-antibiotic-resistant opportunistic human pathogen involved in nosocomial infections. It has a widely distributed GC-rich (>66%) genome. Analysis of differential expression of the genes of this genome reveals that majority of genes belonging to highly expressed category are mostly present on lagging strand without showing any strand specific codon usage bias. Relatively small number of lowly expressed genes is equally distributed on both leading and lagging strands with a difference in codon usage pattern between them. Among several multi drug resistance genes of S. maltophilia involving lowly expressed category some are predicted as horizontally transferred. It can be inferred that horizontally transferred genes may have been imported into this genome for their pathogenic mode of living. Our study may help to modify the expression level of the target genes of this human pathogen in order to control its infection.