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Synonymous Codon Usages as an Evolutionary Dynamic for Chlamydiaceae. Int J Mol Sci 2018; 19:ijms19124010. [PMID: 30545112 PMCID: PMC6321445 DOI: 10.3390/ijms19124010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/06/2018] [Accepted: 12/10/2018] [Indexed: 01/08/2023] Open
Abstract
The family of Chlamydiaceae contains a group of obligate intracellular bacteria that can infect a wide range of hosts. The evolutionary trend of members in this family is a hot topic, which benefits our understanding of the cross-infection of these pathogens. In this study, 14 whole genomes of 12 Chlamydia species were used to investigate the nucleotide, codon, and amino acid usage bias by synonymous codon usage value and information entropy method. The results showed that all the studied Chlamydia spp. had A/T rich genes with over-represented A or T at the third positions and G or C under-represented at these positions, suggesting that nucleotide usages influenced synonymous codon usages. The overall codon usage trend from synonymous codon usage variations divides the Chlamydia spp. into four separate clusters, while amino acid usage divides the Chlamydia spp. into two clusters with some exceptions, which reflected the genetic diversity of the Chlamydiaceae family members. The overall codon usage pattern represented by the effective number of codons (ENC) was significantly positively correlated to gene GC3 content. A negative correlation exists between ENC and the codon adaptation index for some Chlamydia species. These results suggested that mutation pressure caused by nucleotide composition constraint played an important role in shaping synonymous codon usage patterns. Furthermore, codon usage of T3ss and Pmps gene families adapted to that of the corresponding genome. Taken together, analyses help our understanding of evolutionary interactions between nucleotide, synonymous codon, and amino acid usages in genes of Chlamydiaceae family members.
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Multiple Factors Drive Replicating Strand Composition Bias in Bacterial Genomes. Int J Mol Sci 2015; 16:23111-26. [PMID: 26404268 PMCID: PMC4613354 DOI: 10.3390/ijms160923111] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 08/18/2015] [Accepted: 09/18/2015] [Indexed: 11/18/2022] Open
Abstract
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.
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Roy A, Mukhopadhyay S, Sarkar I, Sen A. Comparative investigation of the various determinants that influence the codon and amino acid usage patterns in the genus Bifidobacterium. World J Microbiol Biotechnol 2015; 31:959-81. [DOI: 10.1007/s11274-015-1850-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 03/31/2015] [Indexed: 12/31/2022]
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Yuan J, Yang M, Ren J, Fu B, Jiang F, Zhang X. Analysis of genomic characters reveals that four distinct gene clusters are correlated with different functions in Burkholderia cenocepacia AU 1054. Appl Microbiol Biotechnol 2013; 98:361-72. [PMID: 24305740 DOI: 10.1007/s00253-013-5415-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 11/11/2013] [Accepted: 11/11/2013] [Indexed: 11/30/2022]
Abstract
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.
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Affiliation(s)
- Jianbo Yuan
- Institute of Oceanology, Chinese Academy of Sciences, No. 7, Nanhai Road, Qingdao, 266071, China
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Xia X. DNA replication and strand asymmetry in prokaryotic and mitochondrial genomes. Curr Genomics 2012; 13:16-27. [PMID: 22942672 PMCID: PMC3269012 DOI: 10.2174/138920212799034776] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 09/26/2011] [Accepted: 10/02/2011] [Indexed: 11/22/2022] Open
Abstract
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.
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Affiliation(s)
- Xuhua Xia
- Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, 30 Marie Curie, P.O. Box 450, Station A, Ottawa, Ontario, Canada
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Seligmann H. Coding constraints modulate chemically spontaneous mutational replication gradients in mitochondrial genomes. Curr Genomics 2012; 13:37-54. [PMID: 22942674 PMCID: PMC3269015 DOI: 10.2174/138920212799034802] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 09/07/2011] [Accepted: 09/20/2011] [Indexed: 11/30/2022] Open
Abstract
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 2nd 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 2nd 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.
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Affiliation(s)
- Hervé Seligmann
- National Collections of Natural History at the Hebrew University of Jerusalem, Jerusalem 91404; Department of Life Sciences, Ben Gurion University, 84105 Beer Sheva, Israel
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Arakawa K, Tomita M. Measures of compositional strand bias related to replication machinery and its applications. Curr Genomics 2012; 13:4-15. [PMID: 22942671 PMCID: PMC3269016 DOI: 10.2174/138920212799034749] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2011] [Revised: 09/10/2011] [Accepted: 09/20/2011] [Indexed: 11/22/2022] Open
Abstract
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.
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Affiliation(s)
- Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Fujisawa 252-8520, Japan
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Dutta C, Paul S. Microbial lifestyle and genome signatures. Curr Genomics 2012; 13:153-62. [PMID: 23024607 PMCID: PMC3308326 DOI: 10.2174/138920212799860698] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 09/13/2011] [Accepted: 09/28/2011] [Indexed: 12/29/2022] Open
Abstract
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.
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Affiliation(s)
- Chitra Dutta
- Structural Biology & Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India
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Guo FB. [Strong strand specific composition bias-a genomic character of some obligate parasites or symbionts]. YI CHUAN = HEREDITAS 2011; 33:1039-1047. [PMID: 21993278 DOI: 10.3724/sp.j.1005.2011.01039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
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.
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Affiliation(s)
- Feng-Biao Guo
- University of Electronic Science and Technology of China, Chengdu, China.
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Seghezzi N, Amar P, Koebmann B, Jensen PR, Virolle MJ. The construction of a library of synthetic promoters revealed some specific features of strong Streptomyces promoters. Appl Microbiol Biotechnol 2011; 90:615-23. [PMID: 21243353 DOI: 10.1007/s00253-010-3018-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 11/12/2010] [Accepted: 11/15/2010] [Indexed: 02/01/2023]
Abstract
Streptomyces are bacteria of industrial interest whose genome contains more than 73% of bases GC. In order to define, in these GC-rich bacteria, specific sequence features of strong promoters, a library of synthetic promoters of various sequence composition was constructed in Streptomyces. To do so, the sequences located upstream, between and downstream of the -35 and -10 consensus promoter sequences were completely randomized and some variability was introduced in the -35 (position 6) and -10 (positions 3, 4 and 5) hexamers recognized by the major vegetative sigma factor HrdB. The synthetic promoters were cloned into the promoter-probe plasmid pIJ487 just upstream of the promoter-less aphII gene that confers resistance to neomycin. This synthetic promoter library was transformed into Streptomyces lividans, and the resulting transformants were screened for their ability to grow in the presence of different concentrations of neomycin (20, 50, and 100 μgml(-1)). Promoter strengths varied up to 12-fold, in small increments of activity increase, as determined by reverse transcriptase-PCR. This collection of promoters of various strengths can be useful for the fine-tuning of gene expression in genetic engineering projects. Thirty-eight promoters were sequenced, and the sequences of the 14 weakest and 14 strongest promoters were compared using the WebLogo software with small sample correction. This comparison revealed that the -10 box, the -10 extended motif as well as the spacer of the strong Streptomyces promoters are more G rich than those of the weak promoters.
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Affiliation(s)
- Nicolas Seghezzi
- Institut de Génétique et Microbiologie, UMR8621 CNRS Université Paris Sud, 91405, Orsay, France
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Guo FB, Yuan JB. Codon usages of genes on chromosome, and surprisingly, genes in plasmid are primarily affected by strand-specific mutational biases in Lawsonia intracellularis. DNA Res 2009; 16:91-104. [PMID: 19221094 PMCID: PMC2671203 DOI: 10.1093/dnares/dsp001] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In this study, the factors driving genome-wide patterns of codon usages in Lawsonia intracellularis genome are determined. For genes on the chromosome of the bacterium, it is found that the most important source of variation results from strand-specific mutational biases. A lesser trend of variation is attributable to genes that are presumed as horizontally transferred. These putative alien genes are unusually GC richer than the other genes, whereas horizontally transferred genes have been observed to be AT rich in bacteria with medium and relatively low G + C contents. Hydropathy of encoded protein and expression level are also found to influence codon usage. Therefore, codon usage in L. intracellularis chromosome is the result of a complex balance among the different mutational and selectional factors. When analyzing genes in the largest plasmid, for the first time it is found that the strand-specific mutational biases are responsible for the primary variation of codon usages in plasmid. Genes, particularly highly expressed genes of this plasmid, are mainly located on the leading strands and this supposed to be the effects exerted by replicational-transcriptional selection. These facts suggest that this plasmid adopts the similar mechanism of replication as the chromosome in L. intracellularis. Common characters among the 10 bacteria in whose genomes the strand-specific mutational biases are the primary source of variation of codon usage are also investigated. For example, it is found that genes dnaT and fis that are involved in DNA replication initiation and re-initiation pathways are absent in all of the 10 bacteria.
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Affiliation(s)
- Feng-Biao Guo
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, People's Republic of China.
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Guo FB, Lin Y. Identify Protein-coding Genes in the Genomes ofAeropyrum pernixK1 andChlorobium tepidumTLS. J Biomol Struct Dyn 2009; 26:413-20. [DOI: 10.1080/07391102.2009.10507256] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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