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The Presence of a C− 1/G+ 73 Pair in a tRNA Precursor Influences Processing and Expression In Vivo
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
2008 (English)In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 381, no 5, 1089-1097 p.Article in journal (Refereed) Published
Abstract [en]

To understand whether 5′ and 3′ structural elements of the region corresponding to the mature tRNA affect the expression of the tRNA, we examined several bacterial genomes for tRNA genes where the expression might be potentially affected by structural elements located outside of the mature tRNA. In Pseudomonas aeruginosa, our analysis suggested that the tRNATrp is transcribed together with a putative stem–loop structure followed by a uridine tract immediately downstream of the tRNA region. This structural element, resembling a Rho-independent transcription terminator, might therefore influence the expression and processing of tRNATrp. Moreover, the secondary structure suggested that the discriminator base in the tRNATrp precursor can pair with either the C at position − 1, the 3′ terminal residue in the 5′ leader, or the C immediately 5′ of the uridine tract of the putative Rho-independent transcription terminator. Here, we present in vivo data demonstrating the importance of residue − 1 and the positioning of the putative transcription terminator for the expression of correctly 5′ processed P. aeruginosa tRNATrp in Escherichia coli. Interestingly, we also detected a difference in the appearance of correctly 5′ processed P. aeruginosa tRNATrp in E. coli compared to the situation in P. aeruginosa.

Place, publisher, year, edition, pages
2008. Vol. 381, no 5, 1089-1097 p.
Keyword [en]
RNase P, ribozyme, tRNA precursors, tRNA processing in vivo
National Category
Biochemistry and Molecular Biology
Research subject
Microbiology
Identifiers
URN: urn:nbn:se:uu:diva-100429DOI: 10.1016/j.jmb.2008.06.077ISI: 000259169100001PubMedID: 18625241OAI: oai:DiVA.org:uu-100429DiVA: diva2:210260
Available from: 2009-03-31 Created: 2009-03-31 Last updated: 2017-12-13Bibliographically approved
In thesis
1. tRNA Gene Structures in Bacteria
Open this publication in new window or tab >>tRNA Gene Structures in Bacteria
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

In bacteria, tRNA molecules are produced as precursors with additional nucleotides both upstream and downstream of the tRNA coding sequence. To generate a mature tRNA, the endoribonuclease RNase P removes the upstream sequence, while a number of enzymes can remove the downstream sequence.

In this thesis, the influence of such upstream and downstream sequences on the expression of mature functional tRNA was studied. It was found that in Escherichia coli, the presence of an upstream sequence positively influences tRNA expression. Furthermore, it was shown that the identity of the nucleotide immediatedly 5' of the canonical RNase P cleavage site in a tRNA precursor influenced RNase P cleavage site selection in vivo in E. coli, but not in Pseudomonas aeruginosa. Additionally, a stem-loop in the precursor just downstream of the tRNA increased this "miscleavage". This stem-loop resembled a rho-independent transcription terminator and overlapped the trpT gene in P. aeruginosa, but it only marginally influenced the expression of the downstream secE gene. The trpT and secE genes were found to be cotranscribed. The trpT-secE gene order was also conserved in the majority of bacteria investigated.

The expression of tRNA genes during development in Streptomyces coelicolor was also studied. Here, the expression of most tRNA genes tested increased with time during development. Similarly, the expression of the RNase P RNA increased. The relative increase was quantified and correlated with different criteria related to gene structure and gene organisation, but no significant differences could be found. Moreover, a tRNALeuCAA UUA codon suppressor as well as the cognate bldA tRNA could restore differentiation to a developmentally blocked bldA deletion strain. For both tRNAs, the efficiency of restoration depended on the 5'- and 3'-flanks.

In conclusion, both 5'- and 3'-flanking sequences influence tRNA expression, and bacteria respond differently to changes in their tRNA gene structures.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2009. 67 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 628
National Category
Biochemistry and Molecular Biology
Research subject
Microbiology
Identifiers
urn:nbn:se:uu:diva-100439 (URN)978-91-554-7480-5 (ISBN)
Public defence
2009-05-16, C10:301, Biomedicinskt Centrum, Husargatan 3-5, Uppsala, 10:00 (English)
Opponent
Supervisors
Available from: 2009-04-22 Created: 2009-03-31 Last updated: 2009-04-23Bibliographically approved

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Pettersson, B. M. Fredrik

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