The antisense transcriptome of the halophilic archaeon Halobacterium salinarum

• Grant number: 15/21038-1
• Support Opportunities: Regular Research Grants
• Start date: February 01, 2016
• End date: September 30, 2018
• Field of knowledge: Biological Sciences - Biochemistry - Molecular Biology
• Principal Investigator: Tie Koide
• Grantee: Tie Koide
• Host Institution: Faculdade de Medicina de Ribeirão Preto (FMRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
• City of the host institution: Ribeirão Preto
• Associated researchers: Ricardo Zorzetto Nicoliello Vêncio

Abstract

The pervasive transcription hypothesis states that all DNA of an organism is associated with at least one transcript and it has been strenghtened by the acquisison of massive transcriptomic data. An important question that arises in this context is the functionality and regulation of theses transcripts in a global gene regulatory network, specially of transcripts located antisense to annotated genes. In this research project, we will use the halophilic archaeon Halobacterium salinarum NRC-1 as a model organism to study the archaeal antisense transcriptome and its influence in the post-transcriptional regulation. Member of the third domain of life, this microbe with its unique biochemical characteristics has been used as a model in systems biology, with gene regulatory networks already stablished based on coding genes. In this project, we will use experimental approaches associated with bioinformatics tools to precisely identify H. salinarum antisense transcriptome and study its regulation upon environmental stresses and RNAses influence. The integration of highthroughput data using systems approaches will allow the formulation of new hypothesis concerning specific antisense RNAs that will be experimentally validated by overexpression and phenotypic evaluations. This project will contribute to understand the global post-transcriptional gene regulatory network of archaea, consolidating the use of systems approaches to elucidate the still incipient biology from the third domain of life. (AU)

Scientific publications

(6)

(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)

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. (14/04046-8, 16/06378-3, 15/07386-7, 17/02127-9, 15/21038-1, 17/03052-2)

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. (15/12012-9, 15/21038-1, 13/21522-5, 17/03052-2, 11/14455-4)

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. (15/07386-7, 16/06378-3, 15/21038-1, 14/04046-8, 17/03052-2)

LORENZETTI, ALAN P. R.; KUSEBAUCH, ULRIKE; ZARAMELA, LIVIA S.; WU, WEI-JU; DE ALMEIDA, JOAO P. P.; TURKARSLAN, SERDAR; L. G. DE LOMANA, ADRIAN; GOMES-FILHO, JOSE V.; VENCIO, RICARDO Z. N.; MORITZ, ROBERT L.; et al. A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon. MSYSTEMS, v. 8, n. 2, p. 22-pg., 2023-03-13. (17/03052-2, 15/21038-1, 11/07487-7, 19/13440-5, 13/21522-5, 09/09532-0)

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. (11/14455-4, 15/21038-1, 17/03052-2, 11/07487-7, 15/12012-9)

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. (15/21038-1, 17/03052-2)