Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea.
Felipe Ten-CatenRicardo Z N VêncioAlan Péricles Rodrigues LorenzettiLivia Soares ZaramelaAna Carolina SantanaTie KoidePublished in: RNA biology (2018)
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.
Keyphrases
- rna seq
- genome wide
- escherichia coli
- single cell
- mass spectrometry
- genome wide identification
- minimally invasive
- systematic review
- dna methylation
- working memory
- acute coronary syndrome
- transcription factor
- genome wide analysis
- copy number
- liquid chromatography
- high resolution
- binding protein
- room temperature
- health information
- staphylococcus aureus
- gene expression
- biofilm formation
- heat shock protein
- oxidative stress
- ms ms
- nucleic acid
- candida albicans
- gas chromatography
- klebsiella pneumoniae
- solid phase extraction
- capillary electrophoresis