Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq)

Riediger, Matthias; Spät, Philipp; Bilger, R.; Voigt, Karsten; Maček, Boris; Hess, Wolfgang R.

doi:10.1101/2020.07.02.184192

Cited by 7 publications

(11 citation statements)

References 126 publications

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“…In addition, upon temperature upshift to non-permissive conditions, CrhR undergoes rapid repression via conditional proteolysis at the post-translational level through an unknown mechanism (Tarassova et al ., 2014). In localization studies, CrhR localized to the thylakoid membranes and co-sedimented with degradosome and polysome complexes (Rosana et al ., 2016), consistent with the recent co-fractionation analysis using Grad-seq (Riediger et al ., 2021).…”

Section: Introductionsupporting

confidence: 89%

“…Indeed, a role in translation regulation is supported by the observation that CrhR interacts with the rps1a/slr1356 transcript encoding Rps1a. In previous analyses, Rps1a sedimented away from the majority of ribosomal proteins (Riediger et al, 2021) and was reported to perform a role in the Shine-Dalgarno-independent initiation of translation (Mutsuda and Sugiura, 2006;Nakagawa et al, 2010), another process which may hence be related to CrhR helicase activity.…”

Section: The Crhr Interactome In Vivomentioning

confidence: 93%

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The temperature-regulated DEAD-box RNA helicase CrhR interactome: Autoregulation and photosynthesis-related transcripts

Migur

Heyl

Fuß³

et al. 2021

Preprint

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RNA helicases play crucial functions in RNA biology. In plants, RNA helicases are encoded by large gene families, performing roles in abiotic stress responses, development, the post-transcriptional regulation of gene expression as well as house-keeping functions. Several of these RNA helicases are targeted to the organelles, mitochondria and chloroplasts. Cyanobacteria are the direct evolutionary ancestors of plant chloroplasts. The cyanobacterium Synechocystis 6803 encodes a single DEAD-box RNA helicase, CrhR, that is induced by a range of abiotic stresses, including low temperature. Though the ΔcrhR mutant exhibits a severe cold-sensitive phenotype, the physiological function(s) performed by CrhR have not been described. To identify transcripts interacting with CrhR, we performed RNA co-immunoprecipitation with extracts from a Synechocystis crhR deletion mutant expressing the FLAG-tagged native CrhR or a K57A mutated version with an anticipated enhanced RNA binding. The composition of the interactome was strikingly biased towards photosynthesis-associated and redox-controlled transcripts. A transcript highly enriched in all experiments was the crhR mRNA, suggesting an auto-regulatory molecular mechanism. The identified interactome explains the described physiological role of CrhR in response to the redox poise of the photosynthetic electron transport chain and characterizes CrhR as an enzyme with a diverse range of transcripts as molecular targets.

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Section: Introductionsupporting

confidence: 89%

Section: The Crhr Interactome In Vivomentioning

confidence: 93%

The temperature-regulated DEAD-box RNA helicase CrhR interactome: Autoregulation and photosynthesis-related transcripts

Migur

Heyl

Fuß³

et al. 2021

Preprint

Self Cite

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“…In contrast, the CRISPR3 system ( sll7085-sll7090 ) on the same plasmid was consistently down-regulated at RNA and protein level. Recently, it has been shown that these proteins form a stable protein complex together with their cognate crRNAs (Riediger et al, 2021).…”

Section: Resultsmentioning

confidence: 99%

Integrative analysis of the salt stress response in cyanobacteria

Klaehn

Mikkat

Riediger

et al. 2021

Preprint

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Microorganisms evolved specific acclimation strategies to thrive in environments of high or fluctuating salinities. Here, salt acclimation in the model cyanobacterium Synechocystis sp. PCC 6803 was analyzed by integrating transcriptomic, proteomic and metabolomic data. A dynamic reorganization of the transcriptome and proteome occurred during the first hours after salt shock, e.g. involving the upregulation of genes to activate compatible solute biochemistry balancing osmotic pressure. The massive accumulation of glucosylglycerol then had a measurable impact on the overall carbon and nitrogen metabolism. In addition, we observed the coordinated induction of putative regulatory RNAs and of several proteins known for their involvement in other stress responses. Overall, salt-induced changes in the proteome and transcriptome showed good correlations, especially among the stably up-regulated proteins and their transcripts. We define an extended salt stimulon comprising proteins directly or indirectly related to compatible solute metabolism, ion and water movements, and a distinct set of regulatory RNAs involved in post-transcriptional regulation. Our comprehensive data set provides the basis for engineering cyanobacterial salt tolerance and to further understand its regulation.

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“…To date, Grad-seq has been used to profile stable RNPs in several model bacteria, such as the γ-proteobacteria S. Typhimurium ( Smirnov et al, 2016 ; Gerovac et al, 2020 ; Venturini et al, 2020 ), Escherichia coli ( Hör et al, 2020a ), and Pseudomonas aeruginosa ( Gerovac et al, 2021 ), the firmicute Streptococcus pneumonia e ( Hör et al, 2020b ), the cyanobacterium Synechocystis sp. ( Riediger et al, 2020 ), and even in human cells ( Aznaourova et al, 2020 ). Additionally, the RNPs formed by P. aeruginosa RNAs have been analyzed along with phage ΦKZ transcripts during viral infection in what can be considered the first “dual Grad-seq” experiment ( Gerovac et al, 2021 ).…”

Section: Profiling Stable Rnps With Grad-seqmentioning

confidence: 99%

“…Given that yggL is mostly expressed in the exponential phase, and its deletion has a strong effect on the 50S levels, the protein likely functions in late LSU assembly ( Chen and Williamson, 2013 ; Smirnov et al, 2016 ; Hör et al, 2020a ). This specific example provides a modus operandi to study other candidate ribosome biogenesis factors spotted by Grad-seq, especially in less studied species ( Hör et al, 2020b ; Riediger et al, 2020 ).…”

Section: Profiling Stable Rnps With Grad-seqmentioning

confidence: 99%

The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches

Gerovac

Vogel

Smirnov

2021

Front. Mol. Biosci.

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Macromolecular complexes of proteins and RNAs are essential building blocks of cells. These stable supramolecular particles can be viewed as minimal biochemical units whose structural organization, i.e., the way the RNA and the protein interact with each other, is directly linked to their biological function. Whether those are dynamic regulatory ribonucleoproteins (RNPs) or integrated molecular machines involved in gene expression, the comprehensive knowledge of these units is critical to our understanding of key molecular mechanisms and cell physiology phenomena. Such is the goal of diverse complexomic approaches and in particular of the recently developed gradient profiling by sequencing (Grad-seq). By separating cellular protein and RNA complexes on a density gradient and quantifying their distributions genome-wide by mass spectrometry and deep sequencing, Grad-seq charts global landscapes of native macromolecular assemblies. In this review, we propose a function-based ontology of stable RNPs and discuss how Grad-seq and related approaches transformed our perspective of bacterial and eukaryotic ribonucleoproteins by guiding the discovery of new RNA-binding proteins and unusual classes of noncoding RNAs. We highlight some methodological aspects and developments that permit to further boost the power of this technique and to look for exciting new biology in understudied and challenging biological models.

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Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq)

Cited by 7 publications

References 126 publications

The temperature-regulated DEAD-box RNA helicase CrhR interactome: Autoregulation and photosynthesis-related transcripts

The temperature-regulated DEAD-box RNA helicase CrhR interactome: Autoregulation and photosynthesis-related transcripts

Integrative analysis of the salt stress response in cyanobacteria

The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches

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