ACUA: A software tool for automated codon usage analysis

Vetrivel, Umashankar; Arunkumar, Vijayakumar; Dorairaj, Sudarsanam

doi:10.6026/97320630002062

Cited by 56 publications

(26 citation statements)

References 3 publications

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“…On average, we calculated 145 mRNA molecules per cell, which is comparable to the mean 257 mRNA molecules per cell for the group of ‘Highly expressed ORFs’ (open reading frames) [42]. We further calculated the codon usage for these subset of S. pombe genes using the ACUA software [43], and found it similar to the mean of total fission yeast genes (Table 1). This indicates that there has not been an evolutionary adaptation to change the codon usage of the stress genes, which are only highly expressed under some stress conditions.…”

Section: Resultsmentioning

confidence: 90%

“…N.P: Not provided.a4932 S. pombe ORFs are described in [42].b30 ORFs with highest expression levels, obtained from [42].c50 genes most up-regulated after treatment with 0.5 mM of H 2 O 2 during 30 minutes [4].dThe number of mRNA molecules per cell at basal levels was obtained from [42].The number of mRNA molecules per cell at induced levels was calculated using the fold induction ratios upon 0.5 mM of H 2 O 2 during 30 minutes from microarray experiments reported at [4].eCodon usage values of ‘Total S. pombe ORFs’ and ‘Highly expressed ORFs’ were obtained from [42].The other codon usage values were calculated using free software ACUA v1.0 [43].ftRNA gene copy number was extracted from PomBase [61].…”

Section: Resultsmentioning

confidence: 99%

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Modification of tRNALysUUU by Elongator Is Essential for Efficient Translation of Stress mRNAs

et al. 2013

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The Elongator complex, including the histone acetyl transferase Sin3/Elp3, was isolated as an RNA polymerase II-interacting complex, and cells deficient in Elongator subunits display transcriptional defects. However, it has also been shown that Elongator mediates the modification of some tRNAs, modulating translation efficiency. We show here that the fission yeast Sin3/Elp3 is important for oxidative stress survival. The stress transcriptional program, governed by the Sty1-Atf1-Pcr1 pathway, is affected in mutant cells, but not severely. On the contrary, cells lacking Sin3/Elp3 cannot modify the uridine wobble nucleoside of certain tRNAs, and other tRNA modifying activities such as Ctu1-Ctu2 are also essential for normal tolerance to H2O2. In particular, a plasmid over-expressing the tRNALys UUU complements the stress-related phenotypes of Sin3/Elp3 mutant cells. We have determined that the main H2O2-dependent genes, including those coding for the transcription factors Atf1 and Pcr1, are highly expressed mRNAs containing a biased number of lysine-coding codons AAA versus AAG. Thus, their mRNAs are poorly translated after stress in cells lacking Sin3/Elp3 or Ctu2, whereas a mutated atf1 transcript with AAA-to-AAG lysine codons is efficiently translated in all strain backgrounds. Our study demonstrates that the lack of a functional Elongator complex results in stress phenotypes due to its contribution to tRNA modification and subsequent translation inefficiency of certain stress-induced, highly expressed mRNAs. These results suggest that the transcriptional defects of these strain backgrounds may be a secondary consequence of the deficient expression of a transcription factor, Atf1-Pcr1, and other components of the transcriptional machinery.

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Section: Resultsmentioning

confidence: 90%

Section: Resultsmentioning

confidence: 99%

Modification of tRNALysUUU by Elongator Is Essential for Efficient Translation of Stress mRNAs

et al. 2013

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“…We used Ori-Finder [25] to check the replication origin- and replication termini-based determination of strand-bias and the localization of the identified target genes in leading or lagging strands. CAI values are reported as one of the measures to evaluate essential genes, with a CAI >0.5 indicative of significant essentiality [26]. We used ACUA software [26] to calculate the CAI values of our identified targets.…”

Section: Methodsmentioning

confidence: 99%

“…CAI values are reported as one of the measures to evaluate essential genes, with a CAI >0.5 indicative of significant essentiality [26]. We used ACUA software [26] to calculate the CAI values of our identified targets. The distribution of enzyme classes of the targets was determined with BRENDA [27] and UniProtKB [28].…”

Section: Methodsmentioning

confidence: 99%

Exoproteome and Secretome Derived Broad Spectrum Novel Drug and Vaccine Candidates in Vibrio cholerae Targeted by Piper betel Derived Compounds

et al. 2013

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Vibrio cholerae is the causal organism of the cholera epidemic, which is mostly prevalent in developing and underdeveloped countries. However, incidences of cholera in developed countries are also alarming. Because of the emergence of new drug-resistant strains, even though several generic drugs and vaccines have been developed over time, Vibrio infections remain a global health problem that appeals for the development of novel drugs and vaccines against the pathogen. Here, applying comparative proteomic and reverse vaccinology approaches to the exoproteome and secretome of the pathogen, we have identified three candidate targets (ompU, uppP and yajC) for most of the pathogenic Vibrio strains. Two targets (uppP and yajC) are novel to Vibrio, and two targets (uppP and ompU) can be used to develop both drugs and vaccines (dual targets) against broad spectrum Vibrio serotypes. Using our novel computational approach, we have identified three peptide vaccine candidates that have high potential to induce both B- and T-cell-mediated immune responses from our identified two dual targets. These two targets were modeled and subjected to virtual screening against natural compounds derived from Piper betel. Seven compounds were identified first time from Piper betel to be highly effective to render the function of these targets to identify them as emerging potential drugs against Vibrio. Our preliminary validation suggests that these identified peptide vaccines and betel compounds are highly effective against Vibrio cholerae. Currently we are exhaustively validating these targets, candidate peptide vaccines, and betel derived lead compounds against a number of Vibrio species.

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“…The RSCU is independent of amino acid composition and is thus useful for comparing different sets of genes [18]. The RSCU and GC-content of each ORF were calculated by ACUA [19]. A synonymous codon was inferred as ''optimal'' when its RSCU was significantly higher in genes expressed at a high level (defined as contigs) than those expressed at a low level (defined as singletons).…”

Section: Codon Usage Biasmentioning

confidence: 99%

Characterization of expressed sequence tag-derived single-nucleotide polymorphisms in the bay scallop Argopecten irradians irradians

Kong

2009

Fish Sci

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We describe herein the discovery of 3905 putative single-nucleotide polymorphisms (SNPs) from the alignment of 4968 sequences in a bay scallop Argopecten irradians irradians expressed sequenced tag (EST) database. The observed frequency of SNPs was estimated at one every 118.2 bp of contig sequences. Thirty of the SNPs were chosen for validation by tetra-primer amplification refractory mutation system-polymerase chain reaction procedure, and 17 of them were polymorphic with minor allele frequency ranging from 0.016 to 0.484. BLASTX gave significant hits for all but one of the 17 genotyped SNP-containing contigs, 11 of which were located in coding regions and all resulted in a synonymous substitution. Parentage simulation demonstrated that SNP markers were more sensitive to the number of parents compared with microsatellites, thus more SNPs were needed to counteract low polymorphism. A table of optimal codons was deduced from the analysis of the A. i. irradians EST dataset to explain the frequency difference for a specific SNP. It seems that the selection of codon usage may be partly responsible for the frequency difference between the two alleles of the coding SNPs. These are the first SNPs developed for the bay scallop and will provide a useful complement to currently available genetic markers.

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ACUA: A software tool for automated codon usage analysis

Cited by 56 publications

References 3 publications

Modification of tRNALysUUU by Elongator Is Essential for Efficient Translation of Stress mRNAs

Modification of tRNALysUUU by Elongator Is Essential for Efficient Translation of Stress mRNAs

Exoproteome and Secretome Derived Broad Spectrum Novel Drug and Vaccine Candidates in Vibrio cholerae Targeted by Piper betel Derived Compounds

Characterization of expressed sequence tag-derived single-nucleotide polymorphisms in the bay scallop Argopecten irradians irradians

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