R-DeeP/TripepSVM identifies the RNA-binding OB-fold-like protein PatR as regulator of heterocyst patterning DOI Creative Commons
Manuel Brenes‐Álvarez,

Halie R. Ropp,

Dimitrios Papagiannidis

et al.

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 19, 2024

RNA-binding proteins (RBPs) are central components of gene regulatory networks. The differentiation heterocysts in filamentous cyanobacteria is an example cell prokaryotes. Although multiple non-coding transcripts involved this process, no RBPs have been implicated thus far. Here we used quantitative mass spectrometry to analyze the differential fractionation RNA-protein complexes after RNase treatment density gradients yielding 333 RNA-associated proteins, while a bioinformatic prediction yielded 311 RBP candidates Nostoc sp. PCC 7120. We validated vivo capacity six candidates. Some participate essential physiological aspects, such as photosynthesis (Alr2890), thylakoid biogenesis (Vipp1) or heterocyst (PrpA, PatU3), but their association with RNA was unknown. Validated Asl3888 and Alr1700 were not previously characterized. two oligonucleotide/oligosaccharide-binding (OB)-fold-like domains that differentially expressed interacts RNAs. Deletion alr1700 led complete deregulation striking increase number heterocyst-like cells, ultimately lethal absence combined nitrogen. These observations characterize master regulator patterning leading us rename PatR.

Language: Английский

The molecular basis for cellular function of intrinsically disordered protein regions DOI
Alex S. Holehouse, Birthe B. Kragelund

Nature Reviews Molecular Cell Biology, Journal Year: 2023, Volume and Issue: 25(3), P. 187 - 211

Published: Nov. 13, 2023

Language: Английский

Citations

225
Proteomic composition of eukaryotic and bacterial RNA decay condensates suggests convergent evolution DOI

IW Rathnayaka-Mudiyanselage,

Vidhyadhar Nandana,

J O Schrader

et al.

Current Opinion in Microbiology, Journal Year: 2024, Volume and Issue: 79, P. 102467 - 102467

Published: April 3, 2024

Language: Английский

Citations

3
RNA-binding proteins identified by R-DeeP/TripepSVM are involved in heterocyst differentiation DOI Open Access
Manuel Brenes‐Álvarez,

Halie R. Ropp,

Dimitrios Papagiannidis

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 3, 2024

Abstract RNA-binding proteins (RBPs) are central components of gene regulatory networks. The differentiation heterocysts in filamentous cyanobacteria is an example cell prokaryotes. Although multiple non-coding transcripts involved this process, no RBPs have been implicated thus far. Here we used quantitative mass spectrometry to analyze the differential fractionation RNA-protein complexes after RNase treatment density gradients yielding 333 RNA-associated proteins, while a bioinformatic prediction yielded 311 RBP candidates Nostoc sp. PCC 7120. We validated vivo capacity 6 candidates. Some participate essential physiological aspects, such as photosynthesis (Alr2890), thylakoid biogenesis (Vipp1) or heterocyst (PrpA, PatU3), but their association with RNA was unknown. Validated Asl3888 and Alr1700 were not previously characterized. two OB-fold domains that differentially expressed heterocysts. Deletion alr1700 led complete deregulation striking increase number heterocyst-like cells, ultimately lethal absence combined nitrogen. These observations characterize master regulator patterning leading us rename PatR. data can be accessed at https://sunshine.biologie.uni-freiburg.de/R-DeeP-Nostoc/ .

Language: Английский

Citations

2
The contribution of mRNA targeting to spatial protein localization in bacteria DOI Creative Commons
Wenkang Shang, Elisabeth Lichtenberg,

Andreea Mihaela Mlesnita

et al.

FEBS Journal, Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 16, 2024

About 30% of all bacterial proteins execute their function outside the cytosol and must be inserted into or translocated across cytoplasmic membrane. This requires efficient targeting systems that recognize N‐terminal signal sequences in client deliver them to protein transport complexes While importance these machineries for spatial organization cell is well documented multiple studies, contribution mRNA localized translation only beginning emerge. mRNAs can exhibit diverse subcellular localizations accumulate at sites where new required. frequently observed encoding membrane proteins, but physiological enrichment consequences it has insertion encoded have not been explored detail. Here, we briefly highlight some basic concepts sequence‐based describe more detail strategies enable monitoring localization cells potential mechanisms route particular positions within cell. Finally, summarize recent developments demonstrate sustain under stress conditions when protein‐targeting machinery compromised. Thus, likely acts as a back‐up strategy complements canonical targeting.

Language: Английский

Citations

1
Spatial heterogeneity in the photobiology of phototrophs—questions and methods DOI Creative Commons
Radek Kaňa, Meri Eichner, Andrew Gall

et al.

Frontiers in Photobiology, Journal Year: 2024, Volume and Issue: 2

Published: May 7, 2024

Photosynthesis which harvests energy from the Sun, whether it occurs in prokaryotes or eukaryotes, is a key biological process that ultimately nourishes biosphere. The molecular efficiencies of photo-physical and physiological processes are intricately tied not only to photo-physics/enzymatic kinetics proteins involved, but also their spatial co-localization membrane microdomains cell compartments (e.g., membrane-less organelles). Similar heterogeneity function can be found between cells isogenic cultures (phenotypic heterogeneity) filaments phototrophic heterocysts/vegetative nitrogen fixing cyanobacteria). This review paper delves into connection (co)-localization biomolecules (lipids, RNA, DNA, proteins, membranes compartments) functionality situ . We highlight recent methodological advances field super-resolution microscopy, Raman micro-spectroscopy, nanoSIMS, microsensors) showcase applications these methods understanding on single-cell population-scale level. thus aims avenues will help unravel molecular, cellular ecological mechanisms photobiology by combining up-to-date microscopy techniques with more traditional functional approaches.

Language: Английский

Citations

0
R-DeeP/TripepSVM identifies the RNA-binding OB-fold-like protein PatR as regulator of heterocyst patterning DOI Creative Commons
Manuel Brenes‐Álvarez,

Halie R. Ropp,

Dimitrios Papagiannidis

et al.

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 19, 2024

RNA-binding proteins (RBPs) are central components of gene regulatory networks. The differentiation heterocysts in filamentous cyanobacteria is an example cell prokaryotes. Although multiple non-coding transcripts involved this process, no RBPs have been implicated thus far. Here we used quantitative mass spectrometry to analyze the differential fractionation RNA-protein complexes after RNase treatment density gradients yielding 333 RNA-associated proteins, while a bioinformatic prediction yielded 311 RBP candidates Nostoc sp. PCC 7120. We validated vivo capacity six candidates. Some participate essential physiological aspects, such as photosynthesis (Alr2890), thylakoid biogenesis (Vipp1) or heterocyst (PrpA, PatU3), but their association with RNA was unknown. Validated Asl3888 and Alr1700 were not previously characterized. two oligonucleotide/oligosaccharide-binding (OB)-fold-like domains that differentially expressed interacts RNAs. Deletion alr1700 led complete deregulation striking increase number heterocyst-like cells, ultimately lethal absence combined nitrogen. These observations characterize master regulator patterning leading us rename PatR.

Language: Английский

Citations

0