tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence

Lowe, Todd M.; Eddy, Sean R.

doi:10.1093/nar/25.5.0955

Cited by 4,563 publications

(3,009 citation statements)

References 26 publications

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“…Hydropathy profiles (Kyte and Doolittle 1982) were constructed using PEPPLOT in the GCG package. Transfer RNA genes were identified using the tRNA scan program (Lowe and Eddy 1997). Alignment of amino acid sequences was achieved using CLUSTALW (Thompson et al 1994).…”

Section: Sequence Analysismentioning

confidence: 99%

Partial Sequence of the Mitochondrial Genome of Littorina saxatilis: Relevance to Gastropod Phylogenetics

1999

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A 8022 base pair fragment from the mitochondrial DNA of the prosobranch gastropod Littorina saxatilis has been sequenced and shown to contain the complete genes for 12 transfer RNAs and five protein genes (CoII, ATPase 6, ATPase 8, ND1, ND6), two partial protein genes (CoI and cyt b), and two ribosomal RNAs (small and large subunits). The order of these constituent genes differs from those of other molluscan mitochondrial gene arrangements. Only a single rearrangement involving a block of protein coding genes and three tRNA translocations are necessary to produce identical gene orders between L. saxatilis and K. tunicata. However, only one gene boundary is shared between the L. saxatilis gene order and that of the pulmonate gastropod Cepaea nemoralis. This extends the observation that there is little conservation of mitochrondrial gene order amongst the Mollusca and suggests that radical mitochondrial DNA gene rearrangement has occurred on the branch leading to the pulmonates.

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Section: Sequence Analysismentioning

confidence: 99%

Partial Sequence of the Mitochondrial Genome of Littorina saxatilis: Relevance to Gastropod Phylogenetics

1999

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“…The DNA size and GC content of the isolated phage were determined. The presence of tRNA was scanned through tRNAscan-SE Search (tRNAscan v1.3) [39]. …”

Section: Methodsmentioning

confidence: 99%

Complete Genome Sequence of <b><i>Proteus mirabilis</i></b> Phage pPM_01 Isolated from Raw Sewage

Wirjon¹,

Lau

Arip³

2016

Intervirology

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Objectives: Phage pPM_01 was previously isolated from a raw sewage treatment facility located in Batu Maung, Penang, Malaysia, and it was highly lytic against Proteus mirabilis, which causes urinary tract infections in humans. In this paper, we characterize the biology and complete genome sequence of the phage. Methods and Results: Transmission electron microscopy revealed phage pPM_01 to be a siphovirus (the first reported virus to infect P. mirabilis), with its complete genome sequence successfully determined. The genome was sequenced using Illumina technology and the reads obtained were assembled using CLC Genomic Workbench v.7.0.3. The whole genome contains a total of 58,546 bp of linear double-stranded DNA with a G+C content of 46.9%. Seventy putative genes were identified and annotated using various bioinformatics tools including RAST, Geneious v.R7, National Center for Biotechnology Information (NCBI) BLAST, and tRNAscan-SE-v1.3 Search. Functional clusters of related potential genes were defined (structural, lytic, packaging, replication, modification, and modulatory). The whole genome sequence showed a low similarity to known phages (i.e., Enterobacter phage Enc34 and Enterobacteria phage Chi). Host range determination and SDS-PAGE analysis were also performed. Conclusions: The inability to lysogenize a host, the absence of endotoxin genes in the annotated genome, and the lytic behavior suggest phage pPM_01 as a possible safe biological candidate to control P. mirabilis infection.

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“…The nucleotide sequence of the leucyl tRNA bearing UAA anticodon and of that bearing CAG anticodon for the three Frankia strains (ACN14a, EAN1pec and CcI3) and S. coelicolor was obtained from Genomic tRNA database (http://lowelab.ucsc.edu/GtRNAdb/) (Lowe and Eddy 1997). The secondary structural information of the respective tRNA was also gathered from the same database.…”

Section: Modeling Trna Structurementioning

confidence: 99%

Identification of TTA codon containing genes in Frankia and exploration of the role of tRNA in regulating these genes

et al. 2011

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The TTA codon, one of the six available codons for the amino acid leucine, is the rarest codon among the high GC genomes of Actinobacteria including Frankia. This codon has been implicated in various regulatory mechanisms involving secondary metabolism and morphological development. TTA-mediated gene regulation is well documented in Streptomyces coelicolor, but that role has not been investigated in other Actinobacteria including Frankia. Among the various Actinomycetes with a GC content of more than 70%, Frankia genomes had the highest percentages of TTA-containing genes ranging from 5.2 to 10.68% of the genome. In contrast, TTA-bearing genes comprised 1.7, 3.4 and 4.1% of the Streptomyces coelicolor, S. avermitilis and Nocardia farcinia genomes, respectively. We analyzed their functional role, evolutionary significance, horizontal acquisition and the codon-anticodon interaction. The TTA-bearing genes were found to be well represented in metabolic genes involved in amino acid transport and secondary metabolism. A reciprocal Blast search reveal that many of the TTA-bearing genes have orthologs in the other Frankia genomes, and some of these orthologous genes also have a TTA codon in them. The gene expression level of TTA-containing genes was estimated by the use of the codon adaption index (CAI), and the CAI values were found to have a positive correlation with the GC3 (GC content at the 3rd codon position). A full-atomic 3D model of the leucine tRNA recognizing the TTA (UUA) codon was generated and utilized for in silico docking to determine binding affinity in codon-anticodon interaction. We found a proficient codon-anticodon interaction for this codon which is perhaps why so many genes hold on to this rare codon without compromising their translational efficiency.

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tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence

Cited by 4,563 publications

References 26 publications

Partial Sequence of the Mitochondrial Genome of Littorina saxatilis: Relevance to Gastropod Phylogenetics

Partial Sequence of the Mitochondrial Genome of Littorina saxatilis: Relevance to Gastropod Phylogenetics

Complete Genome Sequence of <b><i>Proteus mirabilis</i></b> Phage pPM_01 Isolated from Raw Sewage

Identification of TTA codon containing genes in Frankia and exploration of the role of tRNA in regulating these genes

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