Codon usage analysis in selected virulence genes of Staphylococcal species

Andargie M, Congyi Z (2022) Genome-wide analysis of codon usage in sesame (Sesamum indicum L.). Heliyon 8(1):e08687

Article  CAS  PubMed  Google Scholar 

Arora P, Mukhopadhyay CS, Kaur S (2024) Comparative genome wise analysis of codon usage of Staphylococcus Genus. Curr Genet 70:10. https://doi.org/10.1007/s00294-024-01297-3

Article  CAS  PubMed  Google Scholar 

Baba T, Takeuchi F, Kuroda M, Yuzawa H, Aoki K, Oguchi A, Hiramatsu K (2008) Genome and virulence determinants of high virulence community-acquired MRSA. Lancet 372(9634):874–885

Google Scholar 

Baran RH, Ko H (2008) Detecting horizontally transferred and essential genes based on dinucleotide relative abundance. DNA Res 15(5):267–276

Article  CAS  PubMed  PubMed Central  Google Scholar 

Becker K, Heilmann C, Peters G (2014) Coagulase-negative staphylococci. Clin Microbiol Rev 27(4):870–926

Article  PubMed  PubMed Central  Google Scholar 

Behura SK, Severson DW (2013) Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes. Biol Rev 88(1):49–61

Article  PubMed  Google Scholar 

Benson MA, Ohneck EA, Ryan C, Alonzo F, Smith H, Narechania A, Torres VJ (2014) Evolution of hypervirulence by a MRSA clone through acquisition of a transposable element. Mol Microbiol 93(4):664–681

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bishal AK, Saha S, Sau K (2012) Synonymous codon usage in forty staphylococcal phages identifies the factors controlling codon usage variation and the phages suitable for phage therapy. Bioinformation 8(24):1187

Article  PubMed  PubMed Central  Google Scholar 

Cadieux B, Vijayakumara D, Bernards MA, McGavin MJ, Heinrichs DE, Harvey BJ (2014) Role of lipase from community-associated methicillin-resistant Staphylococcus aureus in hydrolysis of triglyceride and phospholipid, leading to growth in extracellular matrix. Infect Immun 82(8):3284–3295

Google Scholar 

Carbone A, Zinovyev A, Képes F (2003) Codon adaptation index as a measure of dominating codon bias. Bioinformatics 19(16):2005–2015

Article  CAS  PubMed  Google Scholar 

Chakraborty S, Deb B, Barbhuiya PA, Uddin A (2019) Analysis of codon usage patterns and influencing factors in Nipah virus. Virus Res 263:129–138

Article  CAS  PubMed  Google Scholar 

Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y, Jin Q (2005) VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res 33((Database issue)):D325–D328

CAS  PubMed  Google Scholar 

Chen Y (2013) A comparison of synonymous codon usage bias patterns in DNA and RNA virus genomes: quantifying the relative importance of mutational pressure and natural selection. Biomed Res Int. https://doi.org/10.1155/2013/406342

Article  PubMed  PubMed Central  Google Scholar 

Chen Y, Xu Q, Tan C, Li X, Chi X, Cai B, Yu Z, Ma Y, Chen J-L (2017) Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Senecavirus A evolution. Microb Pathog 112:313–319

Article  CAS  PubMed  PubMed Central  Google Scholar 

Coulter SN, Schwan WR, Ng EY, Langhorne MH, Ritchie HD, Westbrock-Wadman S, Stover CK (1998) Staphylococcus aureus genetic loci impacting growth and survival in multiple infection environments. Mol Microbiol 30(2):393–404

Article  CAS  PubMed  Google Scholar 

Deb B, Uddin A, Mazumder GA, Chakraborty S (2018) Analysis of codon usage pattern of mitochondrial protein-coding genes in different hookworms. Mol Biochem Parasitol 219:24–32

Article  CAS  PubMed  Google Scholar 

Foster TJ (2005) Immune evasion by Staphylococci. Nat Rev Microbiol 3(12):948–958

Article  CAS  PubMed  Google Scholar 

Fu Y, Liang F, Li C, Warren A, Shin MK, Li L (2023) Codon usage bias analysis in macronuclear genomes of ciliated protozoa. Microorganisms 11(7):1833

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gill SR, Fouts DE, Archer GL, Mongodin EF, Deboy RT, Ravel J, Fraser CM (2005) Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain. J Bacteriol 187(7):2426–2438

Article  CAS  PubMed  PubMed Central  Google Scholar 

Greenbaum BD, Levine AJ, Bhanot G, Rabadan R (2008) Patterns of evolution and host gene mimicry in influenza and other RNA viruses. PLoS Pathog 4(6):e1000079

Article  PubMed  PubMed Central  Google Scholar 

Guan D-L, Ma L-B, Khan MS, Zhang X-X, Xu S-Q, Xie J-Y (2018) Analysis of codon usage patterns in Hirudinaria manillensis reveals a preference for GC-ending codons caused by dominant selection constraints. BMC Genomics 19:1–14

Article  Google Scholar 

Gupta S, Paul K, Roy A (2021) Codon usage signatures in the genus Cryptococcus: a complex interplay of gene expression, translational selection and compositional bias. Genomics 113(1):821–830

Article  CAS  PubMed  Google Scholar 

Hacker J, Kaper JB (2000) Pathogenicity islands and the evolution of microbes. Annu Rev Microbiol 54(1):641–679

Article  CAS  PubMed  Google Scholar 

Hanson G, Coller J (2018) Codon optimality, bias and usage in translation and mRNA decay. Nat Rev Mol Cell Biol 19(1):20–30

Article  CAS  PubMed  Google Scholar 

Heilmann C, Thumm G, Chhatwal GS, Hartleib J, Uekötter A, Peters G (1997) Identification and characterization of a novel autolysin (Aaa) with adhesive properties from Staphylococcus aureus. Microbiology 143(3):967–973

Google Scholar 

Hershberg R, Petrov DA (2009) General rules for optimal codon choice. PLoS Genet 5(7):e1000556

Article  PubMed  PubMed Central  Google Scholar 

Hershberg R, Petrov DA (2010) Evidence that mutation is universally biased towards AT in bacteria. PLoS Genet 6(9):e1001115

Article  PubMed  PubMed Central  Google Scholar 

Jenul C, Horswill AR (2018) Regulation of Staphylococcus aureus virulence. Microbiol Spectr. https://doi.org/10.1128/microbiolspec.gpp3-0031-2018

Article  Google Scholar 

Karlin S, Campbell AM, Mrázek J (1997) Comparative DNA analysis across diverse genomes. Annu Rev Genet 31(1):337–359

Google Scholar 

Karlin S, Campbell AM, Mrazek J (1998) Comparative DNA analysis across diverse genomes. Annu Rev Genet 32(1):185–225

Article  CAS  PubMed  Google Scholar 

Khandia R, Alqahtani T, Alqahtani AM (2021) Genes common in primary immunodeficiencies and cancer display overrepresentation of codon CTG and dominant role of selection pressure in shaping codon usage. Biomedicines 9(8):1001

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kiedrowski MR, Paharik AE, Ackermann L, Shelton JG, Das S, Ton-That H, Horswill AR (2011) Staphylococcus aureus nuclease is an escape factor for neutrophil extracellular traps and is a virulence determinant in skin infection. Cell Host Microbe 10(5):496–503

Google Scholar 

Kobayashi SD, Malachowa N, DeLeo FR (2013) Pathogenesis of Staphylococcus aureus abscesses. Am J Pathol 183(2):343–352

Google Scholar 

Kudla G, Murray AW, Tollervey D, Plotkin JB (2009) Coding-sequence determinants of gene expression in Escherichia coli. Science 324(5924):255–258

Article  CAS  PubMed 

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