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Identification of small proteins and peptides in extremophile Halobacterium salinarum: discriminating of non-coding RNAs and small ORFs

Grant number: 13/23712-6
Support Opportunities:Scholarships in Brazil - Post-Doctoral
Effective date (Start): March 01, 2014
Effective date (End): December 31, 2014
Field of knowledge:Biological Sciences - Biochemistry - Molecular Biology
Principal Investigator:Tie Koide
Grantee:Gilvan Pessoa Furtado
Host Institution: Faculdade de Medicina de Ribeirão Preto (FMRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
Associated research grant:09/09532-0 - Systems biology of the extremophile Halobacterium salinarum: role of the non-coding RNAs in the global gene regulatory network model, AP.JP


The principle of Systems Biology argues that the understanding of the overall functioning of an organism cannot be obtained simply by studying its isolated parts, since the interactions between them give rise to new properties. Global analyzes have been possible due to the constant improvement of techniques for high-throughput analysis in which a large number of data can be analyzed simultaneously in an integrated way. Among the model organisms used to systems studies, the haloarchaea Halobacterium salinarum has received much attention due to interesting biological properties such as their adaptive capacity to live in hypersaline environments and molecular properties very similar to those present in eukaryotes. Previous studies in this model organism suggest that non-coding RNAs (ncRNA) play an important regulatory role and they are differentially expressed in certain cellular conditions. However in recent years, several scientific studies have shown in many organisms that genomic regions previously classified as non-coding are, in fact, small ORFs (smORFs) encoding proteins with important functional properties. In order to verify the existence of unannotated smORFs in H. salinarum, we have used bioinformatics tools to identify all possible start and stop codons in all open reading frames of the genome and compared the location of these codons with RNAseq data. This initial analysis showed that there is a high probability of finding smORFs not yet identified in this organism. We propose to analyze and validate the existence of smORFs in H. salinarum with further analysis in silico, as well as the use of techniques of mass spectrometry and chromosomal tagging.

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Scientific publications
(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)
SILVA-ROCHA, RAFAEL; PONTELLI, MARJORIE CORNEJO; FURTADO, GILVAN PESSOA; ZARAMELA, LIVIA SOARES; KOIDE, TIE. Development of New Modular Genetic Tools for Engineering the Halophilic Archaeon Halobacterium salinarum. PLoS One, v. 10, n. 6, . (13/04125-2, 11/07487-7, 13/23712-6, 09/09532-0)

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