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Non-coding RNAs derived from insertion sequences in the halophilic archaeon Halobacterium salinarum NRC-1

Grant number: 17/03052-2
Support type:Scholarships in Brazil - Doctorate
Effective date (Start): June 01, 2017
Effective date (End): March 07, 2021
Field of knowledge:Biological Sciences - Biochemistry - Molecular Biology
Cooperation agreement: Coordination of Improvement of Higher Education Personnel (CAPES)
Principal researcher:Tie Koide
Grantee:Alan Péricles Rodrigues Lorenzetti
Home Institution: Faculdade de Medicina de Ribeirão Preto (FMRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
Associated scholarship(s):19/13440-5 - Detection of Insertion Sequence-encoded transposases using proteome data, BE.EP.DR

Abstract

Insertion sequences (IS) are ubiquitous mobile genetic elements in prokaryotes that promote great impact on host genomes. They can provide fitness to organisms by enhancing the genetic diversity and also by modulating gene expression. On the other hand, mobilization events that damage the host are also common, specially when an essential gene is disrupted and compromises the organism viability. Several regulatory mechanisms act to keep low transposition levels, avoiding the deleterious effects of random insertions. In bacteria, antisense RNAs and Hfq protein bind to transposase-encoding messenger RNAs (mRNAs) of IS200/IS605 family elements, preventing the translation and therefore, maintaining low levels of transposase in the cell. In archaea, LSm protein - Hfq's homologue - apparently plays a similar role, although little is known in the third domain of life. Our research team have been studying non-coding RNAs (ncRNAs) in Halobacterium salinarum NRC-1, some of them in the IS context. We analyzed LSm-RNA coimunoprecitation sequencing data from a pilot experiment in H. salinarum, and preliminary results point out that about 85% of intact IS produce transcripts that interact with this protein. In this doctoral research project, we propose the following goals: (i) identify IS-derived sense and antisense RNAs; (ii) characterize their interaction with LSm protein; (iii) identify putative targets of regulation; and (iv) elucidate their secondary structure computationally and experimentally. All these tasks will be performed for H. salinarum NRC-1, our model organism. The prevalence, conservation and specificity of LSm/Hfq-ncRNA interaction across prokaryotes will be analyzed, adding to the comprehension of transposon regulation at the post-transcriptional level. (AU)

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Scientific publications (7)
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
DE ARAUJO, HUGO L.; MARTINS, BIANCA P.; VICENTE, ALEXANDRE M.; LORENZETTI, ALAN P. R.; KOIDE, TIE; MARQUES, V, MARILIS. Cold Regulation of Genes Encoding Ion Transport Systems in the Oligotrophic Bacterium Caulobacter crescentus. MICROBIOLOGY SPECTRUM, v. 9, n. 1 SEP 2021. Web of Science Citations: 0.
IBRAHIM, AMR GALAL ABD EL-RAHEEM; VENCIO, RICARDO Z. N.; LORENZETTI, ALAN P. R.; KOIDE, TIE. Halobacterium salinarum and Haloferax volcanii Comparative Transcriptomics Reveals Conserved Transcriptional Processing Sites. GENES, v. 12, n. 7 JUL 2021. Web of Science Citations: 0.
SILVA, LARISSA G.; LORENZETTI, ALAN P. R.; RIBEIRO, RODOLFO A.; ALVES, INGRID R.; LEADEN, LAURA; GALHARDO, RODRIGO S.; KOIDE, TIE; MARQUES, MARILIS V. OxyR and the hydrogen peroxide stress response in Caulobacter crescentus. Gene, v. 700, p. 70-84, JUN 5 2019. Web of Science Citations: 0.
PEREIRA DE ALMEIDA, JOAO PAULO; VENCIO, RICARDO Z. N.; LORENZETTI, ALAN P. R.; TEN-CATEN, FELIPE; GOMES-FILHO, JOSE VICENTE; KOIDE, TIE. The Primary Antisense Transcriptome of Halobacterium salinarum NRC-1. GENES, v. 10, n. 4 APR 2019. Web of Science Citations: 0.
FERNANDES PEDRO, DANIEL LONGHI; RODRIGUES LORENZETTI, ALAN PERICLES; DOMINGUES, DOUGLAS SILVA; PASCHOAL, ALEXANDRE ROSSI. PlaNC-TE: a comprehensive knowledgebase non-coding RNAs and transposable elements in plants. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, SEP 13 2018. Web of Science Citations: 1.
LEADEN, LAURA; SILVA, LARISSA G.; RIBEIRO, RODOLFO A.; DOS SANTOS, NAARA M.; LORENZETTI, ALAN P. R.; ALEGRIA, THIAGO G. P.; SCHULZ, MARIANE L.; MEDEIROS, MARISA H. G.; KOIDE, TIE; MARQUES, V, MARILIS. Iron Deficiency Generates Oxidative Stress and Activation of the SOS Response in Caulobacter crescentus. FRONTIERS IN MICROBIOLOGY, v. 9, AUG 28 2018. Web of Science Citations: 5.
TEN-CATEN, FELIPE; VENCIO, RICARDO Z. N.; LORENZETTI, ALAN PERICLES R.; ZARAMELA, LIVIA SOARES; SANTANA, ANA CAROLINA; KOIDE, TIE. Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea. RNA BIOLOGY, v. 15, n. 8, p. 1119-1132, 2018. Web of Science Citations: 4.

Please report errors in scientific publications list by writing to: cdi@fapesp.br.