PICDI, a simple program for codon bias calculation

Rodrı́guez-Belmonte, Esther; Freire-Picos, María Ángeles; Rodríguez-Torres, Ana María; González-Siso, María-Isabel; Cerdán, M. Esperanza; Rodríguez-Seijo, José Manuel

doi:10.1007/bf02900357

Cited by 6 publications

(4 citation statements)

References 8 publications

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“…The complete nucleotide sequence has been entered in the EMBL data library under Accession Number X92944. The sequence was analysed using DNASIS/PROSIS (Hitachi), FASTA (Pearson and Lipman, 1988), CODONS (Lloyd and Sharp, 1992) and PICDI (Rodríguez-Belmonte et al, 1996) software.…”

Section: Sequencingmentioning

confidence: 99%

“…Codon bias analysis, as displayed by calculation of the codon adaptation index (CAI=0·45) using the codon usage data from the CODONS program by Lloyd and Sharp (1992) and the intrinsic codon deviation index (ICDI=0·28) using the PICDI program by Rodríguez-Belmonte et al (1996), revealed that the KlHEM1 gene has a more restricted use of synonymous codons than its homologue from S. cerevisiae (CAI=0·21; ICDI=0·11). This situation is similar to that found when other genes related to respiratory functions are compared in these two yeasts (Luani et al, 1994).…”

Section: Isolation and Sequence Of The Klhem1 Genementioning

confidence: 99%

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Isolation and Characterization of theKlHEM1 Gene inKluyveromyces lactis

González‐Domínguez

Méndez-Carro

Cerdán

1997

Yeast

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The KlHEM1 gene from Kluyveromyces lactis encodes a functional 5‐aminolevulinate synthase (δALA synthase), as confirmed by complementation of a hem1 mutant Saccharomyces cerevisiae strain, homology search, and detection of a 2·3 kb transcript. The gene is highly homologous to the ScHEM1 gene, and the sequence of the promoter region contains a complex combination of putative regulatory signals. Some of them are related to phospholipid biosynthesis, glycolytic metabolism, and regulation by carbon source. Transcription of KlHEM1 increased significantly in response to limited oxygen, and only slightly with the change from repressed (glucose) to derepressed conditions (glycerol). The δALA synthase from K. lactis contains, in the amino‐terminal region, two heme‐responsive elements that are not present in the protein from Saccharomyces cerevisiae. The complete nucleotide sequence has been entered in the EMBL data library under Accession Number X92944. © 1997 John Wiley & Sons, Ltd.

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Section: Sequencingmentioning

confidence: 99%

Section: Isolation and Sequence Of The Klhem1 Genementioning

confidence: 99%

Isolation and Characterization of theKlHEM1 Gene inKluyveromyces lactis

González‐Domínguez

Méndez-Carro

Cerdán

1997

Yeast

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“…Using the PICDI program (Rodriguez-Belmonte et al, 1996), a codon bias index of 0·17 was calculated for the KlHIS4 gene. This represents low bias and compares to values of 0·12 and 0·15 for the P. pastoris and S. cerevisiae genes, respectively (Rodriguez-Belmonte et al, 1996). Thus, KlHIS4 is likely to be expressed at relatively low levels.…”

Section: Resultsmentioning

confidence: 99%

TheHIS4 gene from the yeastKluyveromyces lactis

Freire-Picos

Hampsey

Cerdán

1998

Yeast

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The Kluyveromyces lactis HIS4 gene was cloned by complementation of a Saccharomyces cerevisiae his4 mutant. Sequence analysis revealed a 2388 bp open reading frame encoding a single polypeptide predicted to encompass three distinct enzymatic activities (phosphoribosyl‐AMP cyclohydrolase, phosphoribosyl‐ATP pyrophosphohydrolase and histidinol dehydrogenase). This structural organization is strikingly similar to that of the His4 proteins from S. cerevisiae and Pichia pastoris. Transcript analysis detected a single mRNA species of 2.5 kb. The EMBL accession number of this gene is Y09503. © 1998 John Wiley & Sons, Ltd.

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“…An ICDI estimates codon bias where optimal codons are unknown (Rodríguez-Belmonte et al, 1996). The average ICDI value was 0.182, and vales were well correlated with Nc values.…”

Section: Intrinsic Codon Bias Indexmentioning

confidence: 93%

Strong Selectional Forces Fine-Tune CpG Content in Genes Involved in Neurological Disorders as Revealed by Codon Usage Patterns

et al. 2022

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Neurodegenerative disorders cause irreversible damage to the neurons and adversely affect the quality of life. Protein misfolding and their aggregation in specific parts of the brain, mitochondrial dysfunction, calcium load, proteolytic stress, and oxidative stress are among the causes of neurodegenerative disorders. In addition, altered metabolism has been associated with neurodegeneration as evidenced by reductions in glutamine and alanine in transient global amnesia patients, higher homocysteine-cysteine disulfide, and lower methionine decline in serum urea have been observed in Alzheimer’s disease patients. Neurodegeneration thus appears to be a culmination of altered metabolism. The study’s objective is to analyze various attributes like composition, physical properties of the protein, and factors like selectional and mutational forces, influencing codon usage preferences in a panel of genes involved directly or indirectly in metabolism and contributing to neurodegeneration. Various parameters, including gene composition, dinucleotide analysis, Relative synonymous codon usage (RSCU), Codon adaptation index (CAI), neutrality and parity plots, and different protein indices, were computed and analyzed to determine the codon usage pattern and factors affecting it. The correlation of intrinsic protein properties such as the grand average of hydropathicity index (GRAVY), isoelectric point, hydrophobicity, and acidic, basic, and neutral amino acid content has been found to influence codon usage. In genes up to 800 amino acids long, the GC3 content was highly variable, while GC12 content was relatively constant. An optimum CpG content is present in genes to maintain a high expression level as required for genes involved in metabolism. Also observed was a low codon usage bias with a higher protein expression level. Compositional parameters and nucleotides at the second position of codons played essential roles in explaining the extent of bias. Overall analysis indicated that the dominance of selection pressure and compositional constraints and mutational forces shape codon usage.

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PICDI, a simple program for codon bias calculation

Cited by 6 publications

References 8 publications

Isolation and Characterization of theKlHEM1 Gene inKluyveromyces lactis

Isolation and Characterization of theKlHEM1 Gene inKluyveromyces lactis

TheHIS4 gene from the yeastKluyveromyces lactis

Strong Selectional Forces Fine-Tune CpG Content in Genes Involved in Neurological Disorders as Revealed by Codon Usage Patterns

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