Skip to content
2000
  1. Home
  2. A-Z Publications
  3. Current Genomics
  4. Volume 26, Issue 2
  5. Article
Volume 26, Issue 2
  • ISSN: 1389-2029
  • E-ISSN: 1875-5488

Abstract

Analyzing prokaryotic codon usage trends has become a crucial topic of study with significant ramifications for comprehending microbial genetics, classification, evolution, and the control of gene expression. This review study explores the numerous facets of prokaryotic codon usage patterns, looking at different parameters like habitat and lifestyle across broad groups of prokaryotes by emphasizing the role of codon reprogramming in adaptive strategies and its integration into systems biology. We also explored the numerous variables driving codon usage bias, including natural selection, mutation, horizontal gene transfer, codon-anticodon interaction, and genomic composition in prokaryotes through a thorough study of current literature. Furthermore, a special session on codon usage on pathogenic prokaryotes and the role of codon usage in the phylogeny of prokaryotes has been discussed. We also looked at the various software and indices that have been recently applied to prokaryotic genomes. The promising directions that lay ahead to map the future of codon usage research on prokaryotes have been emphasized. Codon usage variations across prokaryotic communities could be better understood by combining environmental, metagenomic, and system biology approaches.

© 2025 Bentham Science Publishers
Loading

Article metrics loading...

/content/journals/cg/10.2174/0113892029325491240919151045
2024-10-01
2025-04-21

  • From This Site

    /content/journals/cg/10.2174/0113892029325491240919151045
    dcterms_title,dcterms_subject,pub_keyword
    -contentType:Contributor -contentType:Concept -contentType:Institution
    10
    5
Loading full text...

Full text loading...

References

  1. LiuY. A code within the genetic code: codon usage regulates co- translational protein folding.Cell Commun. Signal.202018114510.1186/s12964‑020‑00642‑632907610
     [Google Scholar]
  2. OelschlaegerP. Molecular Mechanisms and the Significance of Synonymous Mutations.Biomolecules202414113210.3390/biom1401013238275761
     [Google Scholar]
  3. ParvathyS.T. UdayasuriyanV. BhadanaV. Codon usage bias.Mol. Biol. Rep.202249153956510.1007/s11033‑021‑06749‑434822069
     [Google Scholar]
  4. RochaE.P.C. Codon usage bias from tRNA’s point of view: Redundancy, specialization, and efficient decoding for translation optimization.Genome Res.200414112279228610.1101/gr.289690415479947
     [Google Scholar]
  5. HiaF. TakeuchiO. The effects of codon bias and optimality on mRNA and protein regulation.Cell. Mol. Life Sci.20217851909192810.1007/s00018‑020‑03685‑733128106
     [Google Scholar]
  6. LópezJ.L. LozanoM.J. FabreM.L. LagaresA. Codon usage optimization in the prokaryotic tree of life: how synonymous codons are differentially selected in sequence domains with different expression levels and degrees of conservation.MBio2020114e00766-2010.1128/mBio.00766‑2032694138
     [Google Scholar]
  7. de la TorreD. ChinJ.W. Reprogramming the genetic code.Nat. Rev. Genet.202122316918410.1038/s41576‑020‑00307‑733318706
     [Google Scholar]
  8. RobertsonW.E. FunkeL.F.H. de la TorreD. FredensJ. ElliottT.S. SpinckM. ChristovaY. CervettiniD. BögeF.L. LiuK.C. BuseS. MaslenS. SalmondG.P.C. ChinJ.W. Sense codon reassignment enables viral resistance and encoded polymer synthesis.Science202137265461057106210.1126/science.abg302934083482
     [Google Scholar]
  9. KacarB. Foundations for reconstructing early microbial life.arXiv202410.48550/arXiv.2406.09354.
     [Google Scholar]
  10. Tonkin-HillG. CoranderJ. ParkhillJ. Challenges in prokaryote pangenomics.Microb. Genom.2023951510.1099/mgen.0.00102137227251
     [Google Scholar]
  11. ZhangZ. WangJ. WangJ. WangJ. LiY. Estimate of the sequenced proportion of the global prokaryotic genome.Microbiome20208113410.1186/s40168‑020‑00903‑z32938501
     [Google Scholar]
  12. ArellaD. DiluccaM. GiansantiA. Codon usage bias and environmental adaptation in microbial organisms.Mol. Genet. Genomics2021296375176210.1007/s00438‑021‑01771‑433818631
     [Google Scholar]
  13. LiuY. YangQ. ZhaoF. Synonymous but not silent: the codon usage code for gene expression and protein folding.Annu. Rev. Biochem.202190137540110.1146/annurev‑biochem‑071320‑11270133441035
     [Google Scholar]
  14. RadványiÁ. KunÁ. The Mutational Robustness of the Genetic Code and Codon Usage in Environmental Context: A Non-Extremophilic Preference?Life (Basel)202111877310.3390/life1108077334440517
     [Google Scholar]
  15. ClarkB.C. KolbV.M. Macrobiont: Cradle for the Origin of Life and Creation of a Biosphere.Life (Basel)2020101127810.3390/life1011027833198206
     [Google Scholar]
  16. ImachiH. NobuM.K. NakaharaN. MoronoY. OgawaraM. TakakiY. TakanoY. UematsuK. IkutaT. ItoM. MatsuiY. MiyazakiM. MurataK. SaitoY. SakaiS. SongC. TasumiE. YamanakaY. YamaguchiT. KamagataY. TamakiH. TakaiK. Isolation of an archaeon at the prokaryote–eukaryote interface.Nature2020577779151952510.1038/s41586‑019‑1916‑631942073
     [Google Scholar]
  17. MoodyE.R.R. MahendrarajahT.A. DombrowskiN. ClarkJ.W. PetitjeanC. OffreP. SzöllősiG.J. SpangA. WilliamsT.A. An estimate of the deepest branches of the tree of life from ancient vertically evolving genes.eLife202211e6669510.7554/eLife.6669535190025
     [Google Scholar]
  18. Du ToitA. The branches of the tree of life.Nat. Rev. Microbiol.202220525425510.1038/s41579‑022‑00719‑835233106
     [Google Scholar]
  19. PavaoA. ZhangE. MonestierA. PeltierJ. DupuyB. ChengL. BryL. HRMAS 13C NMR and genome-scale metabolic modeling identify threonine as a preferred dual redox substrate for Clostridioides difficile. bioRxiv202355816710.1101/2023.09.18.558167
     [Google Scholar]
  20. MeysmanP. Sánchez-RodríguezA. FuQ. MarchalK. EngelenK. Expression divergence between Escherichia coli and Salmonella enterica serovar Typhimurium reflects their lifestyles.Mol. Biol. Evol.20133061302131410.1093/molbev/mst02923427276
     [Google Scholar]
  21. KnöppelA. KnoppM. AlbrechtL.M. LundinE. LustigU. NäsvallJ. AnderssonD.I. Genetic Adaptation to Growth Under Laboratory Conditions in Escherichia coli and Salmonella enterica. Front. Microbiol.2018975676610.3389/fmicb.2018.0075629755424
     [Google Scholar]
  22. MollerA.G. PetitR.A.III ReadT.D. Species-Scale Genomic Analysis of Staphylococcus aureus Genes Influencing Phage Host Range and Their Relationships to Virulence and Antibiotic Resistance Genes.mSystems202271e01083-2110.1128/msystems.01083‑2135040700
     [Google Scholar]
  23. de Crécy-LagardV. RossR. JarochM. MarchandV. EisenhartC. BrégeonD. MotorinY. LimbachP. Survey and Validation of tRNA Modifications and Their Corresponding Genes in Bacillus subtilis sp Subtilis Strain 168.Biomolecules202010797710.3390/biom1007097732629984
     [Google Scholar]
  24. WolffP. VilletteC. ZumstegJ. HeintzD. AntoineL. Chane-Woon-MingB. DroogmansL. GrosjeanH. WesthofE. Comparative patterns of modified nucleotides in individual tRNA species from a mesophilic and two thermophilic archaea.RNA202026121957197510.1261/rna.077537.12032994183
     [Google Scholar]
  25. HuangY. RenQ. HcCUB-Lec, a newly identified C-type lectin that contains a distinct CUB domain and participates in the immune defense of the triangle sail mussel Hyriopsis cumingii. Dev. Comp. Immunol.201993667710.1016/j.dci.2018.12.01230590065
     [Google Scholar]
  26. HuE.Z. LanX.R. LiuZ.L. GaoJ. NiuD.K. A positive correlation between GC content and growth temperature in prokaryotes.BMC Genomics202223111010.1186/s12864‑022‑08353‑735139824
     [Google Scholar]
  27. GranehällL. HuangK.D. TettA. ManghiP. PaladinA. O’SullivanN. Rota-StabelliO. SegataN. ZinkA. MaixnerF. Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter.Microbiome20219119710.1186/s40168‑021‑01132‑834593021
     [Google Scholar]
  28. CuiG. LiJ. GaoZ. WangY. Spatial variations of microbial communities in abyssal and hadal sediments across the Challenger Deep.PeerJ20197e696110.7717/peerj.696131149407
     [Google Scholar]
  29. LópezJ.L. LozanoM.J. LagaresA.Jr FabreM.L. DraghiW.O. Del PapaM.F. PistorioM. BeckerA. WibbergD. SchlüterA. PühlerA. BlomJ. GoesmannA. LagaresA. Codon usage Heterogeneity in the multipartite prokaryote genome: selection-based coding bias associated with gene location, expression level, and ancestry.MBio2019103e00505-1910.1128/mBio.00505‑1931138741
     [Google Scholar]
  30. CarréL. ZaccaiG. DelfosseX. GirardE. FranzettiB. Relevance of earth-bound extremophiles in the search for extraterrestrial life.Astrobiology202222332236710.1089/ast.2021.003335108099
     [Google Scholar]
  31. WuX. WuS. LiD. ZhangJ. HouL. MaJ. LiuW. RenD. ZhuY. HeF. Computational identification of rare codons of Escherichia coli based on codon pairs preference.BMC Bioinformatics2010111616510.1186/1471‑2105‑11‑6120109184
     [Google Scholar]
  32. LauenerF. ImkampF. LehoursP. BuissonnièreA. BenejatL. ZbindenR. KellerP. WagnerK. Genetic Determinants and Prediction of Antibiotic Resistance Phenotypes in Helicobacter pylori. J. Clin. Med.2019815310.3390/jcm801005330621024
     [Google Scholar]
  33. HansonG. CollerJ. Codon optimality, bias and usage in translation and mRNA decay.Nat. Rev. Mol. Cell Biol.2018191203010.1038/nrm.2017.9129018283
     [Google Scholar]
  34. KungV.L. OzerE.A. HauserA.R. The accessory genome of Pseudomonas aeruginosa. Microbiol. Mol. Biol. Rev.201074462164110.1128/MMBR.00027‑1021119020
     [Google Scholar]
  35. LiaoJ. OrsiR.H. CarrollL.M. KovacJ. OuH. ZhangH. WiedmannM. Serotype-specific evolutionary patterns of antimicrobial-resistant Salmonella enterica. BMC Evol. Biol.201919113210.1186/s12862‑019‑1457‑531226931
     [Google Scholar]
  36. PandaA. DrancourtM. TullerT. PontarottiP. Genome-wide analysis of horizontally acquired genes in the genus Mycobacterium.Sci. Rep.2018811481710.1038/s41598‑018‑33261‑w30287860
     [Google Scholar]
  37. DelayeL. VargasC. LatorreA. MoyaA. Inferring Horizontal Gene Transfer with DarkHorse, Phylomizer, and ETE Toolkits.Methods Mol. Biol.2020207535536910.1007/978‑1‑4939‑9877‑7_2531584175
     [Google Scholar]
  38. Perez-ArnaizP. DattaniA. SmithV. AllersT. Haloferax volcanii -A model archaeon for studying DNA replication and repair.Open Biol2020101220029310.1098/rsob.200293
     [Google Scholar]
  39. YeeW.X. BarnesG. LavenderH. TangC.M. Meningococcal factor H-binding protein: implications for disease susceptibility, virulence, and vaccines.Trends Microbiol.202331880581510.1016/j.tim.2023.02.01136941192
     [Google Scholar]
  40. Pérez-CarrascalO.M. TromasN. TerratY. MorenoE. GianiA. Corrêa Braga MarquesL. FortinN. ShapiroB.J. Single- colony sequencing reveals microbe-by-microbiome phylosymbiosis between the cyanobacterium Microcystis and its associated bacteria.Microbiome20219119410.1186/s40168‑021‑01140‑834579777
     [Google Scholar]
  41. Leal ZimmerF.M.A. PaesJ.A. ZahaA. FerreiraH.B. Pathogenicity & virulence of Mycoplasma hyopneumoniae.Virulence20201111600162210.1080/21505594.2020.184265933289597
     [Google Scholar]
  42. RamamurthyT. NandyR.K. MukhopadhyayA.K. DuttaS. MutrejaA. OkamotoK. MiyoshiS.I. NairG.B. GhoshA. Virulence regulation and innate host response in the pathogenicity of Vibrio cholerae.Front. Cell. Infect. Microbiol.20201057209610.3389/fcimb.2020.57209633102256
     [Google Scholar]
  43. HuangR.Y. LeeC.Y. Molecular and functional evidence of phosphatidylserine synthase inVibrio parahaemolyticus.Microbiol. Immunol.2019633-411912910.1111/1348‑0421.1267630854712
     [Google Scholar]
  44. ScottK.A. WilliamsS.A. SantangeloT.J. Thermococcus kodakarensis provides a versatile hyperthermophilic archaeal platform for protein expression.Methods Enzymol.202165924327310.1016/bs.mie.2021.06.01434752288
     [Google Scholar]
  45. MohapatraS.S. FioravantiA. VandameP. SprietC. PiniF. BompardC. BlosseyR. ValetteO. BiondiE.G. Methylation-dependent transcriptional regulation of crescentin gene (creS) by GcrA in Caulobacter crescentus.Mol. Microbiol.2020114112713910.1111/mmi.1450032187735
     [Google Scholar]
  46. de OliveiraJ.L. MoralesA.C. HurstL.D. UrrutiaA.O. ThompsonC.R.L. WolfJ.B. Inferring adaptive codon preference to understand sources of selection shaping codon usage bias.Mol. Biol. Evol.20213883247326610.1093/molbev/msab09933871580
     [Google Scholar]
  47. LeonardoM.R. Review of Polar Microbiology: Life in a Deep Freeze Review of Polar Microbiology: Life in a Deep Freeze; MillerRobert V.WhyteLyle G. (ed); ( 2012). ASM Press, Washington, DC. 312 pages.J. Microbiol. Biol. Educ.201314228328410.1128/jmbe.v14i2.666
     [Google Scholar]
  48. DopsonM. González-RosalesC. HolmesD.S. MykytczukN. Eurypsychrophilic acidophiles: From (meta)genomes to low-temperature biotechnologies.Front. Microbiol.202314114990310.3389/fmicb.2023.114990337007468
     [Google Scholar]
  49. EdbeibM.F. AksoyH.M. KayaY. WahabR.A. HuyopF. Haloadaptation: insights from comparative modeling studies between halotolerant and non-halotolerant dehalogenases.J. Biomol. Struct. Dyn.202038123452346110.1080/07391102.2019.165749831422756
     [Google Scholar]
  50. NguyenK.U. ZhangY. LiuQ. ZhangR. JinX. TaniguchiM. MillerE.S. LindseyJ.S. Tolyporphins–Exotic Tetrapyrrole Pigments in a Cyanobacterium—A Review.Molecules20232816613210.3390/molecules2816613237630384
     [Google Scholar]
  51. HuX. FanG. LiaoH. FuZ. MaC. NiH. LiX. Optimized soluble expression of a novel endoglucanase from Burkholderia pyrrocinia in Escherichia coli .3 Biotech202010938710.1007/s13205‑020‑02327‑w
     [Google Scholar]
  52. SahaJ. SahaB.K. Pal SarkarM. RoyV. MandalP. PalA. Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes.Front. Microbiol.201910289610.3389/fmicb.2019.0289631921071
     [Google Scholar]
  53. InoueK. OguraY. KawanoY. HayashiT. Complete Genome Sequence of Geobacter sulfurreducens Strain YM18, Isolated from River Sediment in Japan.Genome Announc.2018619e00352-1810.1128/genomeA.00352‑1829748402
     [Google Scholar]
  54. DuW. JongbloetsJ.A. GuillaumeM. van de PutteB. BattaglinoB. HellingwerfK.J. Branco dos SantosF. Exploiting Day- and Night-Time Metabolism of Synechocystis sp. PCC 6803 for Fitness-Coupled Fumarate Production around the Clock.ACS Synth. Biol.20198102263226910.1021/acssynbio.9b0028931553573
     [Google Scholar]
  55. SharmaA. GuptaS. PaulK. Codon usage behavior distinguishes pathogenic Clostridium species from the non-pathogenic species.Gene202387314739410.1016/j.gene.2023.14739437137382
     [Google Scholar]
  56. WangQ. ZhangL. ZhangY. ChenH. SongJ. LyuM. ChenR. ZhangL. Comparative genomic analyses reveal genetic characteristics and pathogenic factors of Bacillus pumilus HM-7.Front. Microbiol.202213100864810.3389/fmicb.2022.100864836419435
     [Google Scholar]
  57. CanoA.V. RozhonovaH. StoltzfusA. McCandlishD.M. PayneJ.L. Mutation bias shapes the spectrum of adaptive substitutions.bioRxiv202110.1101/2021.04.14.438663
     [Google Scholar]
  58. BesemerJ. BorodovskyM. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses.Nucleic Acids Res.200533Web ServerW451W45410.1093/nar/gki48715980510
     [Google Scholar]
  59. PuigbòP. BravoI.G. Garcia-VallveS. CAIcal: A combined set of tools to assess codon usage adaptation.Biol. Direct200831383910.1186/1745‑6150‑3‑3818796141
     [Google Scholar]
  60. AtaG. WangH. BaiH. YaoX. TaoS. Edging on mutational bias, induced natural selection from host and natural reservoirs predominates codon usage evolution in hantaan virus.Front. Microbiol.20211269978810.3389/fmicb.2021.69978834276633
     [Google Scholar]
  61. Bahiri-ElitzurS. TullerT. Codon-based indices for modeling gene expression and transcript evolution.Comput. Struct. Biotechnol. J.2021192646266310.1016/j.csbj.2021.04.04234025951
     [Google Scholar]
  62. (a) HuoX. LiuS. LiY. WeiH. GaoJ. YanY. ZhangG. LiuM. Analysis of synonymous codon usage of transcriptome database in Rheum palmatum. PeerJ20219e1045010.7717/peerj.10450 33505783
     [Google Scholar]
  63. (b) SharpP. M. LiW.-H. The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications.Nucl Acids Res19871531281129510.1093/nar/15.3.1281
     [Google Scholar]
  64. (a) XuQ. CaoJ. RaiK.R. ZhuB. LiuD. WanC. Codon usage bias of goose circovirus and its adaptation to host.Poult. Sci2024103710377510.1016/j.psj.2024.10377538713985
     [Google Scholar]
  65. (b) WrightF. The ‘Effective number of codons’ used in a gene.Gene1990871232910.1016/0378‑1119(90)90491‑9
     [Google Scholar]
  66. Sundar PanjaA. The systematic codon usage bias has an important effect on genetic adaption in native species.Gene202492614862710.1016/j.gene.2024.14862738823656
     [Google Scholar]
  67. ChoM. MinX. BeenN. SonH.S. The evolutionary and genetic patterns of African swine fever virus.Infect. Genet. Evol.202412210561210.1016/j.meegid.2024.10561238824981
     [Google Scholar]
  68. WangM. ZhuM. QianJ. YangZ. ShangF. EganA.N. LiP. LiuL. Phylogenomics of mulberries (Morus, Moraceae) inferred from plastomes and single copy nuclear genes.Mol. Phylogenet. Evol.202419710809310.1016/j.ympev.2024.10809338740145
     [Google Scholar]
  69. HuangY. LinT. LuL. CaiF. LinJ. JiangY. LinY. Codon pair optimization (CPO): a software tool for synthetic gene design based on codon pair bias to improve the expression of recombinant proteins in Pichia pastoris. Microb. Cell Fact.202120120921010.1186/s12934‑021‑01696‑y34736476
     [Google Scholar]
  70. CallensM. ScornavaccaC. BedhommeS. Evolutionary responses to codon usage of horizontally transferred genes in Pseudomonas aeruginosa: gene retention, amelioration and compensatory evolution.Microb. Genom.20217621410.1099/mgen.0.00058734165421
     [Google Scholar]
  71. RajkumariJ. ChakrabortyS. PandeyP. Distinctive features gleaned from the comparative genomes analysis of clinical and non-clinical isolates of Klebsiella pneumoniae. Bioinformation202016325626610.6026/9732063001625632308268
     [Google Scholar]
  72. RahbarM.R. ZareiM. JahangiriA. KhaliliS. NezafatN. NegahdaripourM. FattahianY. GhasemiY. Trimeric autotransporter adhesins in Acinetobacter baumannii, coincidental evolution at work.Infect. Genet. Evol.20197111612710.1016/j.meegid.2019.03.02330922803
     [Google Scholar]
  73. LiuH. LuY. LanB. XuJ. Codon usage by chloroplast gene is bias in Hemiptelea davidii. J. Genet.2020991810.1007/s12041‑019‑1167‑132089527
     [Google Scholar]
  74. LiG. ZhangL. XueP. Codon usage divergence of important functional genes in Mycobacterium tuberculosis. Int. J. Biol. Macromol.2022209Pt A1197120410.1016/j.ijbiomac.2022.04.11235460756
     [Google Scholar]
  75. XuQ. ChenH. SunW. ZhuD. ZhangY. ChenJ.L. ChenY. Genome-wide analysis of the synonymous codon usage pattern of Streptococcus suis.Microb. Pathog.202115010473210.1016/j.micpath.2021.10473233429052
     [Google Scholar]
  76. TengW. LiaoB. ChenM. ShuW. Genomic Legacies of Ancient Adaptation Illuminate GC-Content Evolution in Bacteria.Microbiol. Spectr.2023111e02145-2210.1128/spectrum.02145‑2236511682
     [Google Scholar]
  77. Barceló-AntemateD. Fontove-HerreraF. SantosW. MerinoE. The effect of the genomic GC content bias of prokaryotic organisms on the secondary structures of their proteins.PLoS One2023185e028520110.1371/journal.pone.028520137141209
     [Google Scholar]
  78. LucksJ.B. NelsonD.R. KudlaG.R. PlotkinJ.B. Genome landscapes and bacteriophage codon usage.PLOS Comput. Biol.200842e100000110.1371/journal.pcbi.100000118463708
     [Google Scholar]
  79. MarshallC.J. QayyumM.Z. WalkerJ.E. MurakamiK.S. SantangeloT.J. The structure and activities of the archaeal transcription termination factor Eta detail vulnerabilities of the transcription elongation complex.Proc. Natl. Acad. Sci. USA202211932e220758111910.1073/pnas.220758111935917344
     [Google Scholar]
  80. PandaA. TullerT. Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis.NPJ Biofilms Microbiomes2023915610.1038/s41522‑023‑00372‑w36693851
     [Google Scholar]
  81. NguyenT.T. CampC.R. DoanJ.K. TraynelisS.F. SloanS.A. HallR.A. GPR37L1 controls maturation and organization of cortical astrocytes during development.Glia20237181921194610.1002/glia.2437537029775
     [Google Scholar]
  82. BanerjeeS. GuptaP.S.S. IslamR.N.U. BandyopadhyayA.K. Intrinsic basis of thermostability of prolyl oligopeptidase from Pyrococcus furiosus. Sci. Rep.20211111155310.1038/s41598‑021‑90723‑434078944
     [Google Scholar]
  83. BergM.D. BrandlC.J. Transfer RNAs: diversity in form and function.RNA Biol.202118331633910.1080/15476286.2020.180919732900285
     [Google Scholar]
  84. Rodríguez-BeltránJ. León-SampedroR. Ramiro-MartínezP. de la VegaC. BaqueroF. LevinB. R. San MillánÁ. Translational demand is not a major source of plasmid-associated fitness costs.Philos Trans R Soc Lond B Biol Sci202237718422020046310.1098/rstb.2020.0463
     [Google Scholar]
  85. WeiY. SilkeJ.R. XiaX. An improved estimation of tRNA expression to better elucidate the coevolution between tRNA abundance and codon usage in bacteria.Sci. Rep.201991318410.1038/s41598‑019‑39369‑x30816249
     [Google Scholar]
  86. EmamalipourM. SeidiK. Zununi VahedS. Jahanban-EsfahlanA. JaymandM. MajdiH. AmoozgarZ. ChitkushevL.T. JavaheriT. Jahanban-EsfahlanR. ZareP. Horizontal Gene Transfer: From Evolutionary Flexibility to Disease Progression.Front. Cell Dev. Biol.2020822910.3389/fcell.2020.0022932509768
     [Google Scholar]
  87. Garcia-VallvéS. RomeuA. PalauJ. Horizontal gene transfer in bacterial and archaeal complete genomes.Genome Res.200010111719172510.1101/gr.13000011076857
     [Google Scholar]
  88. Acar KiritH. LagatorM. BollbackJ.P. Experimental determination of evolutionary barriers to horizontal gene transfer.BMC Microbiol.202020132610.1186/s12866‑020‑01983‑533115402
     [Google Scholar]
  89. Selleghin-VeigaG. MagpaliL. PicorelliA. SilvaF.A. RamosE. NeryM.F. Breathing Air and Living Underwater: Molecular Evolution of Genes Related to Antioxidant Response in Cetaceans and Pinnipeds.J. Mol. Evol.202492330031610.1007/s00239‑024‑10170‑338735005
     [Google Scholar]
  90. KohC.S. SarinL.P. Transfer RNA modification and infection – Implications for pathogenicity and host responses.Biochim. Biophys. Acta. Gene Regul. Mech.20181861441943210.1016/j.bbagrm.2018.01.01529378328
     [Google Scholar]
  91. XiaP.F. CasiniI. SchulzS. KlaskC.M. AngenentL.T. MolitorB. Reprogramming acetogenic bacteria with CRISPR-targeted base editing via deamination.ACS Synth. Biol.2020982162217110.1021/acssynbio.0c0022632610012
     [Google Scholar]
  92. NowakK. BłażejP. WnetrzakM. MackiewiczD. MackiewiczP. Some theoretical aspects of reprogramming the standard genetic code.Genetics20212181iyab04010.1093/genetics/iyab04033711098
     [Google Scholar]
  93. WalshI.M. BowmanM.A. Soto SantarriagaI.F. RodriguezA. ClarkP.L. Synonymous codon substitutions perturb cotranslational protein folding in vivo and impair cell fitness.Proc. Natl. Acad. Sci. USA202011773528353410.1073/pnas.190712611732015130
     [Google Scholar]
  94. YangQ. LyuX. ZhaoF. LiuY. Effects of codon usage on gene expression are promoter context dependent.Nucleic Acids Res.202149281883110.1093/nar/gkaa125333410890
     [Google Scholar]
  95. MitchenerM.M. BegleyT.J. DedonP.C. Molecular Coping Mechanisms: Reprogramming tRNAs To Regulate Codon-Biased Translation of Stress Response Proteins.Acc. Chem. Res.202356233504351410.1021/acs.accounts.3c0057237992267
     [Google Scholar]
  96. GaydukovaS.A. MoldovanM.A. VallesiA. HeaphyS.M. AtkinsJ.F. GelfandM.S. BaranovP.V. Nontriplet feature of genetic code in Euplotes ciliates is a result of neutral evolution.Proc. Natl. Acad. Sci. USA202312022e222168312010.1073/pnas.222168312037216548
     [Google Scholar]
  97. MekonnenZ.A. Grubor-BaukB. MasavuliM.G. ShresthaA.C. RanasingheC. BullR.A. LloydA.R. GowansE.J. WijesundaraD.K. Toward DNA-Based T-Cell Mediated Vaccines to Target HIV-1 and Hepatitis C Virus: Approaches to Elicit Localized Immunity for Protection.Front. Cell. Infect. Microbiol.20199919210.3389/fcimb.2019.0009131001491
     [Google Scholar]
  98. SomaA. KubotaA. TomoeD. IkeuchiY. KawamuraF. ArimotoH. ShiwaY. KanesakiY. NanamiyaH. YoshikawaH. SuzukiT. SekineY. yaaJ, the tRNA-Specific Adenosine Deaminase, Is Dispensable in Bacillus subtilis. Genes (Basel)2023148151510.3390/genes1408151537628567
     [Google Scholar]
  99. LiuL. WangP. ZhaoD. ZhuL. TangJ. LengW. SuJ. LiuY. BiC. ZhangX. Engineering circularized mRNAs for the production of spider silk proteins.Appl. Environ. Microbiol.2022888e00028-2210.1128/aem.00028‑2235384707
     [Google Scholar]
  100. BłaszczykE. PłocińskiP. LechowiczE. BrzostekA. DziadekB. Korycka-MachałaM. SłomkaM. DziadekJ. Depletion of tRNA CCA-adding enzyme in Mycobacterium tuberculosis leads to polyadenylation of transcripts and precursor tRNAs.Sci. Rep.20231312071710.1038/s41598‑023‑47944‑638001315
     [Google Scholar]
  101. CaoX. SlavoffS.A. Non-AUG start codons: Expanding and regulating the small and alternative ORFeome.Exp. Cell Res.2020391111197310.1016/j.yexcr.2020.11197332209305
     [Google Scholar]
  102. EspinosaR. SørensenM.A. SvenningsenS.L. Escherichia coli protein synthesis is limited by mRNA availability rather than ribosomal capacity during phosphate starvation.Front. Microbiol.20221398981810.3389/fmicb.2022.98981836620012
     [Google Scholar]
  103. O’ConnorD. PintoM.V. SheerinD. TomicA. DruryR.E. Channon-WellsS. GalalU. DoldC. RobinsonH. KerridgeS. PlestedE. HughesH. StockdaleL. SadaranganiM. SnapeM.D. RollierC.S. LevinM. PollardA.J. Gene expression profiling reveals insights into infant immunological and febrile responses to group B meningococcal vaccine.Mol. Syst. Biol.20201611e988810.15252/msb.2020988833210468
     [Google Scholar]
  104. PrendergastA. E. JimK. K. MarnasH. DesbanL. QuanF. B. DjenouneL. LaghiV. HocquemillerA. LunsfordE. T. RousselJ. KeiserL. LejeuneF. X. DhanasekarM. BardetP. L. LevraudJ. P. van de BeekD. Vandenbroucke-GraulsC. M. J. E. WyartC. CSF-contacting neurons respond to Streptococcus pneumoniae and promote host survival during central nervous system infection.Curr Biol2023335940956.e1010.1016/j.cub.2023.01.039
     [Google Scholar]
  105. AntoineL. Bahena-CeronR. Devi BunwareeH. GobryM. LoeglerV. RombyP. MarziS. RNA Modifications in Pathogenic Bacteria: Impact on Host Adaptation and Virulence.Genes (Basel)2021128112510.3390/genes1208112534440299
     [Google Scholar]
  106. de la FuenteR. Díaz-VillanuevaW. ArnauV. MoyaA. Genomic Signature in Evolutionary Biology: A Review.Biology (Basel)202312232210.3390/biology1202032236829597
     [Google Scholar]
  107. DebB. UddinA. ChakrabortyS. Codon usage pattern and its influencing factors in different genomes of hepadnaviruses.Arch. Virol.2020165355757010.1007/s00705‑020‑04533‑632036428
     [Google Scholar]
  108. WrightB.W. MolloyM.P. JaschkeP.R. Overlapping genes in natural and engineered genomes.Nat. Rev. Genet.202223315416810.1038/s41576‑021‑00417‑w34611352
     [Google Scholar]
  109. BardozzoF. LióP. TagliaferriR. A study on multi-omic oscillations in Escherichia coli metabolic networks.BMC Bioinformatics201819S719419510.1186/s12859‑018‑2175‑530066640
     [Google Scholar]
  110. RoodgarM. GoodB.H. GarudN.R. MartisS. AvulaM. ZhouW. LancasterS.M. LeeH. BabveyhA. NesamoneyS. PollardK.S. SnyderM.P. Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment.Genome Res.20213181433144610.1101/gr.265058.12034301627
     [Google Scholar]
/content/journals/cg/10.2174/0113892029325491240919151045
Loading
Unravelling Prokaryotic Codon Usage: Insights from Phylogeny, Influencing Factors and Pathogenicity
Curr. Genomics 26, 81 (2025); https://doi.org/10.2174/0113892029325491240919151045
/content/journals/cg/10.2174/0113892029325491240919151045
/content/journals/cg/10.2174/0113892029325491240919151045
Loading

Data & Media loading...


  • Article Type:     Review Article
Keyword(s): archaea; bacteria; codon usage software; pathogenic prokaryotes; phylogeny; Prokaryotic codon usage

Most Cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error
Please enter a valid_number test