The ‘effective number of codons’ used in a gene

Wright, Frank

doi:10.1016/0378-1119(90)90491-9

Cited by 1,918 publications

(1,945 citation statements)

References 22 publications

Supporting

Mentioning

1,837

Contrasting

Unclassified

Order By: Relevance

“…Codon usage, correspondence analysis (COA) (Greenacre 1984), GC3s (the frequency of codons ending in C or G, excluding Met, Trp, and stop codons), N c [the "effective number of codons" (Wright 1990)], the relative synonymous codon usage (RSCU) (Sharp et al 1986), and the codon adaptation index (CAI) (Sharp and Li 1987) were calculated using the program CodonW 1.3 (written by John Peden and available at ftp://molbiol.ox.ac.uk/Win95.codonW.zip). The CAI was calculated taking as a reference the codon usage of the ribosomal proteins.…”

Section: Methodsmentioning

confidence: 99%

Trends in Codon and Amino Acid Usage in Thermotoga maritima

Zavala

Naya

Romero

et al. 2002

Journal of Molecular Evolution

View full text Add to dashboard Cite

Abstract. The usage of synonymous codons and the frequencies of amino acids were investigated in the complete genome of the bacterium Thermotoga maritima using a multivariate statistical approach. The GC3 content of each gene was the most prominent source of variation of codon usage. Surprisingly the usage of UGU and UGC (synonymous triplets coding for Cys, the least frequent amino acid in this species) was detected as the second most prominent source of variation. However, this result is probably an artifact due to the very low frequency of Cys together with the nonbiased composition of this genome. The third trend was related to the preferential usage of a subset of codons among highly expressed genes, and these triplets are presumed to be translationally optimal. Concerning the amino acid usage, the hydropathy level of each protein (and therefore the frequency of charged residues) was the main trend, while the second factor was related to the frequency of usage of the smaller residues, suggesting that the cell economy strongly influences the architecture of the proteins. The third axis of the analysis discriminated the usage of Phe, Tyr, Trp (aromatic residues) plus Cys, Met, and His. These six residues have in common the property of being the preferential targets of reactive oxygen species, and therefore the anaerobic condition of T. maritima is an important factor for the amino acid frequencies. Finally, the Cys content of each protein was the fourth trend.

show abstract

Section: Methodsmentioning

confidence: 99%

Trends in Codon and Amino Acid Usage in Thermotoga maritima

Zavala

Naya

Romero

et al. 2002

Journal of Molecular Evolution

View full text Add to dashboard Cite

show abstract

“…At the left end of Axis 1, 111 genes (Axis 1<−0.8) were found to have unusually low GC3s values. In most cases, horizontal transfer genes (HTGs) with GC3s-poor content have been noted in ATrich species (Gupta et al 2005;Wright 1990). Nc and GC3s values were employed to identify gene transfer events (Daubin et al 2003;Grocock and Sharp 2002;Guo and Yuan 2009).…”

Section: Resultsmentioning

confidence: 99%

“…In the CodonW system, a value of Nc, the effective number of condons, is used to determine the effective numbers of codons, which fluctuates from 20 to 61. Nc=61 indicates that all sense codons are used randomly, while Nc=20 means that there is a strong bias in codon usage in that only one synonymous codon is used for each amino acid (Guo and Yuan 2009;Wright 1990). The plot of Nc against GC3s, the frequency of G+C at the synonymous third codon position, can be used to detect whether the genes on the genome suffered selective or mutational pressure (Guo and Yuan 2009).…”

Section: Electronic Supplementary Materialsmentioning

confidence: 99%

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

Yuan

Yang

Ren

et al. 2013

Appl Microbiol Biotechnol

View full text Add to dashboard Cite

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-leadingcodon 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.

show abstract

“…The gene was designed based on the amino acid sequence of full-length SGPE by matching the codon preference of B. subtilis (Shields & Sharp, 1987;Wright, 1990). The full-length gene was prepared from 32 oligonucleotides using the overlap PCR technique (Higuchi, 1989).…”

Section: Construction Of a Synthetic Gene And Expression Vector For Sgpementioning

confidence: 99%

“…The DNA sequence was designed to match the codon preference of B. subtilis (Shields & Sharp, 1987;Wright, 1990), i.e., the G/C-content of the gene was altered from 94% G/C on the third position of the codon to 49%. Incorporation of a large number of unique restriction sites allowed easy mutagenesis of the gene (see below).…”

Section: Construction Of a Synthetic Gene For Sgpementioning

confidence: 99%

Characterization of the S₁ binding site of the glutamic acid‐specific protease from Streptomyces griseus

1996

View full text Add to dashboard Cite

The glutamic acid-specific protease from Streptomyces griseus (SGPE) is an 18.4-kDa serine protease with a distinct preference for Glu in the PI position. Other enzymes characterized by a strong preference for negatively charged residues in the PI position, e.g., interleukin-lp converting enzyme (ICE), use Arg or Lys residues as counterions within the SI binding site. However, in SGPE, this function is contributed by a His residue (His 213) and two Ser residues (Ser 192 and S216). It is demonstrated that proSGPE is activated autocatalytically and dependent on the presence of a Glu residue in the -1 position. Based on this observation, the importance of the individual SI residues is evaluated considering that enzymes unable to recognize a Glu in the PI position will not be activated. Among the residues constituting the S , binding site, it is demonstrated that His 213 and Ser 192 are essential for recognition of Glu in the PI position, whereas Ser 216 is less important for catalysis but has an influence on stabilization of the ground state. From the three-dimensional structure, it appears that His 213 is linked to two other His residues (His 199 and His 228). forming a His triad extending from the S I binding site to the back of the enzyme. This hypothesis has been tested by substitution of His 199 and His 228 with other amino acid residues. The catalytic parameters obtained with the mutant enzymes, as well as the pH dependence, do not support this theory; rather, it appears that His 199 is responsible for orienting His 21 3 and that His 228 has no function associated with the recognition of Glu in P I .

show abstract

The ‘effective number of codons’ used in a gene

Cited by 1,918 publications

References 22 publications

Trends in Codon and Amino Acid Usage in Thermotoga maritima

Trends in Codon and Amino Acid Usage in Thermotoga maritima

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

Characterization of the S₁ binding site of the glutamic acid‐specific protease from Streptomyces griseus

Contact Info

Product

Resources

About

The ‘effective number of codons’ used in a gene

Cited by 1,918 publications

References 22 publications

Trends in Codon and Amino Acid Usage in Thermotoga maritima

Trends in Codon and Amino Acid Usage in Thermotoga maritima

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

Characterization of the S1 binding site of the glutamic acid‐specific protease from Streptomyces griseus

Contact Info

Product

Resources

About

Characterization of the S₁ binding site of the glutamic acid‐specific protease from Streptomyces griseus