The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
tRNomics: Analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features
Open accessAbstract
From 50 genomes of the three domains of life (7 eukarya, 13 archaea, and 30 bacteria), we extracted, analyzed, and compared over 4,000 sequences corresponding to cytoplasmic, nonorganellar tRNAs. For each genome, the complete set of tRNAs required to read the 61 sense codons was identified, which permitted revelation of three major anticodon-sparing strategies. Other features and sequence peculiarities analyzed are the following: (1) fit to the standard cloverleaf structure, (2) characteristic consensus sequences for elongator and initiator tDNAs, (3) frequencies of bases at each sequence position, (4) type and frequencies of conserved 2D and 3D base pairs, (5) anticodon/tDNA usages and anticodon-sparing strategies, (6) identification of the tRNA-Ile with anticodon CAU reading AUA, (7) size of variable arm, (8) occurrence and location of introns, (9) occurrence of 3'-CCA and 5'-extra G encoded at the tDNA level, and (10) distribution of the tRNA genes in genomes and their mode of transcription. Among all tRNA isoacceptors, we found that initiator tDNA-iMet is the most conserved across the three domains, yet domain-specific signatures exist. Also, according to which tRNA feature is considered (5'-extra G encoded in tDNAs-His, AUA codon read by tRNA-Ile with anticodon CAU, presence of intron, absence of "two-out-of-three" reading mode and short V-arm in tDNA-Tyr) Archaea sequester either with Bacteria or Eukarya. No common features between Eukarya and Bacteria not shared with Archaea could be unveiled. Thus, from the tRNomic point of view, Archaea appears as an "intermediate domain" between Eukarya and Bacteria.
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Cites
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The complete genome sequence of the gram-positive bacterium Bacillus subtilis.
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The Complete Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis ssp. lactis IL1403
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tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes
Chan, P. P., Lin, B. Y., Mak, A. J., & Lowe, T. M. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab688 · Cited by 1,925
Dujon, B., Sherman, D., Fischer, G., Durrens, P., Casaregola, S., Lafontaine, I., de Montigny, J., Marck, C., Neuvéglise, C., Talla, E., et al. (2004) · Nature · doi:10.1038/nature02579 · Cited by 1,623
Self-citationGenome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D
Matsuzaki, M., Misumi, O., Shin-i, T., Maruyama, S., Takahara, M., Miyagishima, S.-Y., Mori, T., Nishida, K., Yagisawa, F., Nishida, K., et al. (2004) · Nature · doi:10.1038/nature02398 · Cited by 1,085
The Mechanism of Eukaryotic Translation Initiation: New Insights and Challenges
Hinnebusch, A. G., & Lorsch, J. R. (2012) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a011544 · Cited by 503
The critical role of RNA processing and degradation in the control of gene expression
Arraiano, C. M., Andrade, J. M., Domingues, S., Guinote, I. B., Malecki, M., Matos, R. G., Moreira, R. N., Pobre, V., Reis, F. P., Saramago, M., et al. (2010) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2010.00242.x · Cited by 349
Metadata
- Authors
- MARCK, C., & GROSJEAN, H.
- Venue
- RNA
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2002-10
- Volume
- 8
- Issue
- 10
- Pages
- 1189-1232
- ISSN
- 1355-8382 (ISSN-L)
- OpenAlex
- W2083691392
- Cited by
- 376
- References
- 7
- FWCI
- 6.26
- Type
- journal article
- Language
- en
- Open access
- green
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- MARCK, C., & GROSJEAN, H. (2002). tRNomics: Analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features. RNA. https://doi.org/10.1017/s1355838202022021
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