The use of the rare TTA codon in Streptomyces genes : significance of the codon context?

Silov, Serhii; Zaburannyi, Nestor; Anisimova, Maria; Ostash, Bohdan

doi:10.1007/s12088-020-00902-6

Publication type:	Article in scientific journal
Type of review:	Peer review (publication)
Title:	The use of the rare TTA codon in Streptomyces genes : significance of the codon context?
Authors:	Silov, Serhii Zaburannyi, Nestor Anisimova, Maria Ostash, Bohdan
et. al:	No
DOI:	10.1007/s12088-020-00902-6
Published in:	Indian Journal of Microbiology
Volume(Issue):	61
Issue:	1
Page(s):	24
Pages to:	30
Issue Date:	2020
Publisher / Ed. Institution:	Springer
ISSN:	0046-8991 0973-7715
Language:	English
Subjects:	BldA-regulation; Streptomyces; UUA codon; Morphological differentiation
Subject (DDC):	572: Biochemistry 579: Microbiology
Abstract:	Streptomycetes, Gram-positive bacteria with huge and GC-rich genomes provide an ample example of codon usage bias taken to the extreme. Particularly, in all sequenced to date streptomycete genomes leucyl codon TTA is the rarest one. It is present (usually once or twice) in 70–200 out of 7000–8000 coding sequences that make up a typical streptomycete genome. tRNALeu UAA of streptomycetes, encoded by the bldA gene, has been shown to be present in mature form only after the onset of morphological differentiation and activation of secondary metabolism. Consequently, during the early stages of cell growth, the translation of genes carrying the TTA codon can be interrupted due to the absence of tRNALeu UAA. Several reports show that mutations of TTA to synonymous codons in certain genes indeed relieve their expression from bldA dependence. However, the deletion of bldA does not always arrest the expression of TTA-containing genes. The nucleotides T/C downstream of TTA were suggested, in 2002, to favor TTA mistranslation. We tested this hypothesis using sizable datasets derived from individual Streptomyces genome and a subset of TTA? genes for secondary metabolism known for their active expression. Our results revealed nucleotide biases downstream of NNA codons family, such as the preference for C and the avoidance of A. Yet, none of the observed biases was sufficient to claim a special case for TTA codon. Hence, the issue of codon context and TTA codon mistranslation in Streptomyces deserves further elaboration.
Further description:	Erworben im Rahmen der Schweizer Nationallizenzen (http://www.nationallizenzen.ch)
URI:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7810805/ https://digitalcollection.zhaw.ch/handle/11475/21303
Fulltext version:	Published version
License (according to publishing contract):	Licence according to publishing contract
Departement:	Life Sciences and Facility Management
Organisational Unit:	Institute of Computational Life Sciences (ICLS)
Published as part of the ZHAW project:	The effect of programmed ribosomal frameshifting on codon usage bias
Appears in collections:	Publikationen Life Sciences und Facility Management

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Silov, S., Zaburannyi, N., Anisimova, M., & Ostash, B. (2020). The use of the rare TTA codon in Streptomyces genes : significance of the codon context? Indian Journal of Microbiology, 61(1), 24–30. https://doi.org/10.1007/s12088-020-00902-6

Silov, S. et al. (2020) ‘The use of the rare TTA codon in Streptomyces genes : significance of the codon context?’, Indian Journal of Microbiology, 61(1), pp. 24–30. Available at: https://doi.org/10.1007/s12088-020-00902-6.

S. Silov, N. Zaburannyi, M. Anisimova, and B. Ostash, “The use of the rare TTA codon in Streptomyces genes : significance of the codon context?,” Indian Journal of Microbiology, vol. 61, no. 1, pp. 24–30, 2020, doi: 10.1007/s12088-020-00902-6.

SILOV, Serhii, Nestor ZABURANNYI, Maria ANISIMOVA und Bohdan OSTASH, 2020. The use of the rare TTA codon in Streptomyces genes : significance of the codon context? Indian Journal of Microbiology [online]. 2020. Bd. 61, Nr. 1, S. 24–30. DOI 10.1007/s12088-020-00902-6. Verfügbar unter: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7810805/

Silov, Serhii, Nestor Zaburannyi, Maria Anisimova, and Bohdan Ostash. 2020. “The Use of the Rare TTA Codon in Streptomyces Genes : Significance of the Codon Context?” Indian Journal of Microbiology 61 (1): 24–30. https://doi.org/10.1007/s12088-020-00902-6.

Silov, Serhii, et al. “The Use of the Rare TTA Codon in Streptomyces Genes : Significance of the Codon Context?” Indian Journal of Microbiology, vol. 61, no. 1, 2020, pp. 24–30, https://doi.org/10.1007/s12088-020-00902-6.