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:10.1093/plcell/koaa017

Cited by 35 publications

(45 citation statements)

References 120 publications

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“…Gradient profiling by sequencing and mass spectrometry (Grad-Seq) is a hybrid complexome analysis that combines density gradient centrifugation with quantitative protein mass spectrometry with RNA-seq and has the power to quantitatively profile transcripts or non-coding RNA that co-segregate with proteins. [20,58,[67][68][69].…”

Section: Rna-protein Complexesmentioning

confidence: 99%

Complexome Profiling: Assembly and Remodeling of Protein Complexes

Wittig

Malacarne

2021

IJMS

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Many proteins have been found to operate in a complex with various biomolecules such as proteins, nucleic acids, carbohydrates, or lipids. Protein complexes can be transient, stable or dynamic and their association is controlled under variable cellular conditions. Complexome profiling is a recently developed mass spectrometry-based method that combines mild separation techniques, native gel electrophoresis, and density gradient centrifugation with quantitative mass spectrometry to generate inventories of protein assemblies within a cell or subcellular fraction. This review summarizes applications of complexome profiling with respect to assembly ranging from single subunits to large macromolecular complexes, as well as their stability, and remodeling in health and disease.

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Section: Rna-protein Complexesmentioning

confidence: 99%

Complexome Profiling: Assembly and Remodeling of Protein Complexes

Wittig

Malacarne

2021

IJMS

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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 pneumoniae (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 KZ transcripts during viral infection in what can be considered the first "dual Gradseq" experiment (Gerovac et al, 2021).…”

Section: Case Study: Comparative Analysis Of Bacterial Stable Rnpsmentioning

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: Class Iib: New Ribosome Assembly Factorsmentioning

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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“…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: Salt Stress Differentially Affects Chromosome Regionsmentioning

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

Cited by 35 publications

References 120 publications

Complexome Profiling: Assembly and Remodeling of Protein Complexes

Complexome Profiling: Assembly and Remodeling of Protein Complexes

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

Integrative analysis of the salt stress response in cyanobacteria

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