López et al. 2017 (PRJNA413990)

General Details

Title Context-specific Regulation of Coupled Transcription-Translation Modules Predicts Pervasive Ribosome Specialization
Organism
Number of Samples 12
Release Date 2017/10/11 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP119792
ENA SRP119792
GEO
BioProject PRJNA413990

Publication

Title
Authors López García de Lomana A,Kusebauch U,Raman AV,Pan M,Turkarslan S,Lorenzetti APR,Moritz RL,Baliga NS
Journal mSystems
Publication Date 2020 Jul 28
Abstract When organisms encounter an unfavorable environment, they transition to a physiologically distinct, quiescent state wherein abundant transcripts from the previous active growth state continue to persist, albeit their active transcription is downregulated. In order to generate proteins for the new quiescent physiological state, we hypothesized that the translation machinery must selectively translate upregulated transcripts in an intracellular milieu crowded with considerably higher abundance transcripts from the previous active growth state. Here, we have analyzed genome-wide changes in the transcriptome (RNA sequencing [RNA-seq]), changes in translational regulation and efficiency by ribosome profiling across all transcripts (ribosome profiling [Ribo-seq]), and protein level changes in assembled ribosomal proteins (sequential window acquisition of all theoretical mass spectra [SWATH-MS]) to investigate the interplay of transcriptional and translational regulation in Halobacterium salinarum as it transitions from active growth to quiescence. We have discovered that interplay of regulatory processes at different levels of information processing generates condition-specific ribosomal complexes to translate preferentially pools of low abundance and upregulated transcripts. Through analysis of the gene regulatory network architecture of H. salinarum , Escherichia coli , and Saccharomyces cerevisiae , we demonstrate that this conditional, modular organization of regulatory programs governing translational systems is a generalized feature across all domains of life. IMPORTANCE Our findings demonstrate conclusively that low abundance and upregulated transcripts are preferentially translated, potentially by environment-specific translation systems with distinct ribosomal protein composition. We show that a complex interplay of transcriptional and posttranscriptional regulation underlies the conditional and modular regulatory programs that generate ribosomes of distinct protein composition. The modular regulation of ribosomal proteins with other transcription, translation, and metabolic genes is generalizable to bacterial and eukaryotic microbes. These findings are relevant to how microorganisms adapt to unfavorable environments when they transition from active growth to quiescence by generating proteins from upregulated transcripts that are in considerably lower abundance relative to transcripts associated with the previous physiological state. Selective translation of transcripts by distinct ribosomes could form the basis for adaptive evolution to new environments through a modular regulation of the translational systems. Copyright © 2020 López García de Lomana et al.
PMC PMC7394353
PMID 32723790
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR6160960 PRJNA413990 Halobacterium salinarum Ribo-Seq
SRR6160959 PRJNA413990 Halobacterium salinarum Ribo-Seq
SRR6160958 PRJNA413990 Halobacterium salinarum Ribo-Seq
SRR6160957 PRJNA413990 Halobacterium salinarum Ribo-Seq
SRR6160956 PRJNA413990 Halobacterium salinarum Ribo-Seq
SRR6160955 PRJNA413990 Halobacterium salinarum Ribo-Seq
SRR6160952 PRJNA413990 Halobacterium salinarum Ribo-Seq
SRR6160951 PRJNA413990 Halobacterium salinarum Ribo-Seq
SRR6160940 PRJNA413990 Halobacterium salinarum Ribo-Seq
SRR6160939 PRJNA413990 Halobacterium salinarum Ribo-Seq
SRR6160938 PRJNA413990 Halobacterium salinarum Ribo-Seq
SRR6160937 PRJNA413990 Halobacterium salinarum Ribo-Seq
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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