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

Version 2 2018-09-20, 01:20
Version 1 2018-09-03, 06:06
posted on 2018-09-20, 01:20 authored by Felipe Ten-Caten, Ricardo Z. N. Vêncio, Alan Péricles R. Lorenzetti, Livia Soares Zaramela, Ana Carolina Santana, Tie Koide

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.


This work was supported by the Fundação de Amparo à Pesquisa do Estado de São Paulo [2015/21038-1]; [2011/07487-7]; [2017/03052-2]; [2011/14455-4]; [2015/12012-9]; Fundação de Apoio ao Ensino, Pesquisa e Assistência do Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo [415/2018]; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) [Finance Code 001]; Conselho Nacional de Desenvolvimento Científico e Tecnológico [166166/2014].