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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

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Author(s):
Ten-Caten, Felipe [1] ; Vencio, Ricardo Z. N. [2] ; Lorenzetti, Alan Pericles R. [1] ; Zaramela, Livia Soares [1] ; Santana, Ana Carolina [3] ; Koide, Tie [1]
Total Authors: 6
Affiliation:
[1] Univ Sao Paulo, Ribeirao Preto Med Sch, Dept Biochem & Immunol, Ribeirao Preto - Brazil
[2] Univ Sao Paulo, Fac Filosofia Ciencias & Letras Ribeirao Preto, Dept Computat & Math, Ribeirao Preto - Brazil
[3] Univ Sao Paulo, Ribeirao Preto Med Sch, Dept Cell & Mol Biol & Pathogen Bioagents, Ribeirao Preto - Brazil
Total Affiliations: 3
Document type: Journal article
Source: RNA BIOLOGY; v. 15, n. 8, p. 1119-1132, 2018.
Web of Science Citations: 4
Abstract

Prokaryotic genomes show a high level of information compaction often with different molecules transcribed from the same locus. Although antisense RNAs have been relatively well studied, RNAs in the same strand, internal RNAs (intraRNAs), are still poorly understood. The question of how common is the translation of overlapping reading frames remains open. We address this question in the model archaeon Halobacterium salinarum. In the present work we used differential RNA-seq (dRNA-seq) in H. salinarum NRC-1 to locate intraRNA signals in subsets of internal transcription start sites (iTSS) and establish the open reading frames associated to them (intraORFs). Using C-terminally flagged proteins, we experimentally observed isoforms accurately predicted by intraRNA translation for kef1, acs3 and orc4 genes. We also recovered from the literature and mass spectrometry databases several instances of protein isoforms consistent with intraRNA translation such as the gas vesicle protein gene gvpC1. We found evidence for intraRNAs in horizontally transferred genes such as the chaperone dnaK and the aerobic respiration related cydA in both H. salinarum and Escherichia coli. Also, intraRNA translation evidence in H. salinarum, E. coli and yeast of a universal elongation factor (aEF-2, fusA and eEF-2) suggests that this is an ancient phenomenon present in all domains of life. (AU)

FAPESP's process: 11/14455-4 - RNA-seq: segmentation and modeling of the signal
Grantee:Felipe ten Caten
Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
FAPESP's process: 15/21038-1 - The antisense transcriptome of the halophilic archaeon Halobacterium salinarum
Grantee:Tie Koide
Support Opportunities: Regular Research Grants
FAPESP's process: 17/03052-2 - Non-coding RNAs derived from insertion sequences in the halophilic archaeon Halobacterium salinarum NRC-1
Grantee:Alan Péricles Rodrigues Lorenzetti
Support Opportunities: Scholarships in Brazil - Doctorate
FAPESP's process: 11/07487-7 - Identification and characterization of Lsm-binding non-coding RNAs in the extremophile Halobacterium salinarum
Grantee:Lívia Soares Zaramela
Support Opportunities: Scholarships in Brazil - Doctorate
FAPESP's process: 15/12012-9 - Transcription Start Site (TSS) identification in extremophilic archaeon Halobacterium salinarum NRC-1 and its association with intraRNAs production
Grantee:Felipe ten Caten
Support Opportunities: Scholarships in Brazil - Doctorate (Direct)