1
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Nandana V, Rathnayaka-Mudiyanselage IW, Muthunayake NS, Hatami A, Mousseau CB, Ortiz-Rodríguez LA, Vaishnav J, Collins M, Gega A, Mallikaarachchi KS, Yassine H, Ghosh A, Biteen JS, Zhu Y, Champion MM, Childers WS, Schrader JM. The BR-body proteome contains a complex network of protein-protein and protein-RNA interactions. Cell Rep 2023; 42:113229. [PMID: 37815915 PMCID: PMC10842194 DOI: 10.1016/j.celrep.2023.113229] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 07/16/2023] [Accepted: 09/22/2023] [Indexed: 10/12/2023] Open
Abstract
Bacterial ribonucleoprotein bodies (BR-bodies) are non-membrane-bound structures that facilitate mRNA decay by concentrating mRNA substrates with RNase E and the associated RNA degradosome machinery. However, the full complement of proteins enriched in BR-bodies has not been defined. Here, we define the protein components of BR-bodies through enrichment of the bodies followed by mass spectrometry-based proteomic analysis. We find 111 BR-body-enriched proteins showing that BR-bodies are more complex than previously assumed. We identify five BR-body-enriched proteins that undergo RNA-dependent phase separation in vitro with a complex network of condensate mixing. We observe that some RNP condensates co-assemble with preferred directionality, suggesting that RNA may be trafficked through RNP condensates in an ordered manner to facilitate mRNA processing/decay, and that some BR-body-associated proteins have the capacity to dissolve the condensate. Altogether, these results suggest that a complex network of protein-protein and protein-RNA interactions controls BR-body phase separation and RNA processing.
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Affiliation(s)
- Vidhyadhar Nandana
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Imalka W Rathnayaka-Mudiyanselage
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA; Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | | | - Ali Hatami
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI 48202, USA
| | - C Bruce Mousseau
- Department of Chemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | | | - Jamuna Vaishnav
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI 48202, USA
| | - Michael Collins
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Alisa Gega
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | | | - Hadi Yassine
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Aishwarya Ghosh
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Julie S Biteen
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yingxi Zhu
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI 48202, USA
| | - Matthew M Champion
- Department of Chemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - W Seth Childers
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Jared M Schrader
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA.
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2
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Ahmed YM, Bowman GR. Phospho-signaling couples polar asymmetry and proteolysis within a membraneless microdomain in C. crescentus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.19.553945. [PMID: 37645878 PMCID: PMC10462113 DOI: 10.1101/2023.08.19.553945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Asymmetric cell division in bacteria is achieved through cell polarization, where regulatory proteins are directed to specific cell poles. Curiously, both poles contain a membraneless microdomain, established by the polar assembly hub PopZ, through most of the cell cycle, yet many PopZ clients are unipolar and transiently localized. We find that PopZ's interaction with the response regulator CpdR is controlled by phosphorylation, via the histidine kinase CckA. Phosphorylated CpdR does not interact with PopZ and is not localized to cell poles. At poles where CckA acts as a phosphatase, de-phosphorylated CpdR binds directly with PopZ and subsequently recruits ClpX, substrates, and other members of a protease complex to the cell pole. We also find that co-recruitment of protease components and substrates to polar microdomains enhances their coordinated activity. This study connects phosphosignaling with polar assembly and the activity of a protease that triggers cell cycle progression and cell differentiation.
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Affiliation(s)
- Yasin M Ahmed
- Department of Molecular Biology, University of Wyoming, Laramie Wyoming 82071
| | - Grant R Bowman
- Department of Molecular Biology, University of Wyoming, Laramie Wyoming 82071
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3
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Nandana V, Rathnayaka-Mudiyanselage IW, Muthunayak NS, Hatami A, Mousseau CB, Ortiz-Rodríguez LA, Vaishnav J, Collins M, Gega A, Mallikaarachchi KS, Yassine H, Ghosh A, Biteen JS, Zhu Y, Champion MM, Childers WS, Schrader JM. The BR-body proteome contains a complex network of protein-protein and protein-RNA interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.18.524314. [PMID: 36712072 PMCID: PMC9882336 DOI: 10.1101/2023.01.18.524314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Bacterial RNP bodies (BR-bodies) are non-membrane-bound structures that facilitate mRNA decay by concentrating mRNA substrates with RNase E and the associated RNA degradosome machinery. However, the full complement of proteins enriched in BR-bodies has not been defined. Here we define the protein components of BR-bodies through enrichment of the bodies followed by mass spectrometry-based proteomic analysis. We found 111 BR-body enriched proteins, including several RNA binding proteins, many of which are also recruited directly to in vitro reconstituted RNase E droplets, showing BR-bodies are more complex than previously assumed. While most BR-body enriched proteins that were tested cannot phase separate, we identified five that undergo RNA-dependent phase separation in vitro, showing other RNP condensates interface with BR-bodies. RNA degradosome protein clients are recruited more strongly to RNase E droplets than droplets of other RNP condensates, implying that client specificity is largely achieved through direct protein-protein interactions. We observe that some RNP condensates assemble with preferred directionally, suggesting that RNA may be trafficked through RNP condensates in an ordered manner to facilitate mRNA processing/decay, and that some BR-body associated proteins have the capacity to dissolve the condensate. Finally, we find that RNA dramatically stimulates the rate of RNase E phase separation in vitro, explaining the dissolution of BR-bodies after cellular mRNA depletion observed previously. Altogether, these results suggest that a complex network of protein-protein and protein-RNA interactions controls BR-body phase separation and RNA processing.
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Affiliation(s)
- V Nandana
- Wayne State University, Department of Biological Sciences, Detroit, MI
| | - I W Rathnayaka-Mudiyanselage
- Wayne State University, Department of Biological Sciences, Detroit, MI
- Wayne State University, Department of Chemistry, Detroit, MI
| | - N S Muthunayak
- Wayne State University, Department of Biological Sciences, Detroit, MI
| | - A Hatami
- Wayne State University, Department of Chemical Engineering and Materials Science, Detroit, MI
| | - C B Mousseau
- University of Notre Dame, Department of Chemistry, Notre Dame, IN
| | | | - J Vaishnav
- Wayne State University, Department of Chemical Engineering and Materials Science, Detroit, MI
| | - M Collins
- University of Pittsburgh, Department of Chemistry, Pittsburgh, PA
| | - A Gega
- Wayne State University, Department of Biological Sciences, Detroit, MI
| | | | - H Yassine
- Wayne State University, Department of Biological Sciences, Detroit, MI
| | - A Ghosh
- Wayne State University, Department of Biological Sciences, Detroit, MI
| | - J S Biteen
- University of Michigan, Department of Chemistry, Ann Arbor, MI
| | - Y Zhu
- Wayne State University, Department of Chemical Engineering and Materials Science, Detroit, MI
| | - M M Champion
- University of Notre Dame, Department of Chemistry, Notre Dame, IN
| | - W S Childers
- University of Pittsburgh, Department of Chemistry, Pittsburgh, PA
| | - J M Schrader
- Wayne State University, Department of Biological Sciences, Detroit, MI
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4
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Tan W, Cheng S, Li Y, Li XY, Lu N, Sun J, Tang G, Yang Y, Cai K, Li X, Ou X, Gao X, Zhao GP, Childers WS, Zhao W. Phase separation modulates the assembly and dynamics of a polarity-related scaffold-signaling hub. Nat Commun 2022; 13:7181. [PMID: 36418326 PMCID: PMC9684454 DOI: 10.1038/s41467-022-35000-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 11/14/2022] [Indexed: 11/26/2022] Open
Abstract
Asymmetric cell division (ACD) produces morphologically and behaviorally distinct cells and is the primary way to generate cell diversity. In the model bacterium Caulobacter crescentus, the polarization of distinct scaffold-signaling hubs at the swarmer and stalked cell poles constitutes the basis of ACD. However, mechanisms involved in the formation of these hubs remain elusive. Here, we show that a swarmer-cell-pole scaffold, PodJ, forms biomolecular condensates both in vitro and in living cells via phase separation. The coiled-coil 4-6 and the intrinsically disordered regions are the primary domains that contribute to biomolecular condensate generation and signaling protein recruitment in PodJ. Moreover, a negative regulation of PodJ phase separation by the stalked-cell-pole scaffold protein SpmX is revealed. SpmX impedes PodJ cell-pole accumulation and affects its recruitment ability. Together, by modulating the assembly and dynamics of scaffold-signaling hubs, phase separation may serve as a general biophysical mechanism that underlies the regulation of ACD in bacteria and other organisms.
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Affiliation(s)
- Wei Tan
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Sihua Cheng
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Yingying Li
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Xiao-Yang Li
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China ,grid.256922.80000 0000 9139 560XDepartment of Pharmacy, School of Life Sciences, Henan University, Kaifeng, 475004 China
| | - Ning Lu
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Jingxian Sun
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Guiyue Tang
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Yujiao Yang
- grid.9227.e0000000119573309CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Kezhu Cai
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China ,grid.263817.90000 0004 1773 1790Department of Materials Science and Engineering, School of Engineering, Southern University of Science and Technology, Shenzhen, 518055 China
| | - Xuefei Li
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Xijun Ou
- grid.263817.90000 0004 1773 1790Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055 China
| | - Xiang Gao
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Guo-Ping Zhao
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China ,grid.9227.e0000000119573309CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443State Key Lab of Genetic Engineering & Institutes of Biomedical Sciences, Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, 200433 China
| | - W. Seth Childers
- grid.21925.3d0000 0004 1936 9000Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Wei Zhao
- grid.458489.c0000 0001 0483 7922CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
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5
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Zhang C, Zhao W, Duvall SW, Kowallis KA, Childers WS. Regulation of the activity of bacterial histidine kinase PleC by the scaffolding protein PodJ. J Biol Chem 2022; 298:101683. [PMID: 35124010 PMCID: PMC8980812 DOI: 10.1016/j.jbc.2022.101683] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 01/31/2022] [Indexed: 12/11/2022] Open
Abstract
Scaffolding proteins can customize the response of signaling networks to support cell development and behaviors. PleC is a bifunctional histidine kinase whose signaling activity coordinates asymmetric cell division to yield a motile swarmer cell and a stalked cell in the gram-negative bacterium Caulobacter crescentus. Past studies have shown that PleC’s switch in activity from kinase to phosphatase correlates with a change in its subcellular localization pattern from diffuse to localized at the new cell pole. Here we investigated how the bacterial scaffolding protein PodJ regulates the subcellular positioning and activity of PleC. We reconstituted the PleC-PodJ signaling complex through both heterologous expressions in Escherichia coli and in vitro studies. In vitro, PodJ phase separates as a biomolecular condensate that recruits PleC and inhibits its kinase activity. We also constructed an in vivo PleC-CcaS chimeric histidine kinase reporter assay and demonstrated using this method that PodJ leverages its intrinsically disordered region to bind to PleC’s PAS sensory domain and regulate PleC-CcaS signaling. Regulation of the PleC-CcaS was most robust when PodJ was concentrated at the cell poles and was dependent on the allosteric coupling between PleC-CcaS’s PAS sensory domain and its downstream histidine kinase domain. In conclusion, our in vitro biochemical studies suggest that PodJ phase separation may be coupled to changes in PleC enzymatic function. We propose that this coupling of phase separation and allosteric regulation may be a generalizable phenomenon among enzymes associated with biomolecular condensates.
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6
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Modeling the temporal dynamics of master regulators and CtrA proteolysis in Caulobacter crescentus cell cycle. PLoS Comput Biol 2022; 18:e1009847. [PMID: 35089921 PMCID: PMC8865702 DOI: 10.1371/journal.pcbi.1009847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 02/23/2022] [Accepted: 01/18/2022] [Indexed: 12/03/2022] Open
Abstract
The cell cycle of Caulobacter crescentus involves the polar morphogenesis and an asymmetric cell division driven by precise interactions and regulations of proteins, which makes Caulobacter an ideal model organism for investigating bacterial cell development and differentiation. The abundance of molecular data accumulated on Caulobacter motivates system biologists to analyze the complex regulatory network of cell cycle via quantitative modeling. In this paper, We propose a comprehensive model to accurately characterize the underlying mechanisms of cell cycle regulation based on the study of: a) chromosome replication and methylation; b) interactive pathways of five master regulatory proteins including DnaA, GcrA, CcrM, CtrA, and SciP, as well as novel consideration of their corresponding mRNAs; c) cell cycle-dependent proteolysis of CtrA through hierarchical protease complexes. The temporal dynamics of our simulation results are able to closely replicate an extensive set of experimental observations and capture the main phenotype of seven mutant strains of Caulobacter crescentus. Collectively, the proposed model can be used to predict phenotypes of other mutant cases, especially for nonviable strains which are hard to cultivate and observe. Moreover, the module of cyclic proteolysis is an efficient tool to study the metabolism of proteins with similar mechanisms. Timed cellular events in both eukaryotes and prokaryotes, such as chromosome replication, transcription, cell differentiation, cytokinesis, and cell division, are controlled by remarkably complex genetic regulations and protein-protein interactions. In this work, we investigate the cell cycle of Caulobacter crescentus, an alphaproteobacterium undergoing asymmetric cell divisions, to understand mechanisms underlying temporal regulations of complex cellular events. The asymmetric lifestyle makes Caulobacter crescentus easily synchronized and tracked, which is the foundation of molecular data accumulation. Here, we utilize the mathematical modeling together with experimental information to systematically integrate the complex gene-protein and protein-protein interactions in cell cycle progression. Using the mathematical model, we capture core features of cell cycle-dependent methylation, transcription, and proteolysis. In mutant cases, we found the complex and redundant regulatory network ensure the robustness of Caulobacter crescentus system because the change of most molecules does not cause immediate mortality, although they influence the time points of cell differentiation and division. The overall model and individual modules such as simulating transcriptional regulations and protease complexes can be further extended to the study of cell development in other bacterial species.
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7
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Felletti M, Romilly C, Wagner EGH, Jonas K. A nascent polypeptide sequence modulates DnaA translation elongation in response to nutrient availability. eLife 2021; 10:71611. [PMID: 34524083 PMCID: PMC8443254 DOI: 10.7554/elife.71611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/15/2021] [Indexed: 01/01/2023] Open
Abstract
The ability to regulate DNA replication initiation in response to changing nutrient conditions is an important feature of most cell types. In bacteria, DNA replication is triggered by the initiator protein DnaA, which has long been suggested to respond to nutritional changes; nevertheless, the underlying mechanisms remain poorly understood. Here, we report a novel mechanism that adjusts DnaA synthesis in response to nutrient availability in Caulobacter crescentus. By performing a detailed biochemical and genetic analysis of the dnaA mRNA, we identified a sequence downstream of the dnaA start codon that inhibits DnaA translation elongation upon carbon exhaustion. Our data show that the corresponding peptide sequence, but not the mRNA secondary structure or the codon choice, is critical for this response, suggesting that specific amino acids in the growing DnaA nascent chain tune translational efficiency. Our study provides new insights into DnaA regulation and highlights the importance of translation elongation as a regulatory target. We propose that translation regulation by nascent chain sequences, like the one described, might constitute a general strategy for modulating the synthesis rate of specific proteins under changing conditions.
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Affiliation(s)
- Michele Felletti
- Science for Life Laboratory and Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Cédric Romilly
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - E Gerhart H Wagner
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Kristina Jonas
- Science for Life Laboratory and Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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8
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Cargo competition for a dimerization interface restricts and stabilizes a bacterial protease adaptor. Proc Natl Acad Sci U S A 2021; 118:2010523118. [PMID: 33875581 DOI: 10.1073/pnas.2010523118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial protein degradation is a regulated process aided by protease adaptors that alter specificity of energy-dependent proteases. In Caulobacter crescentus, cell cycle-dependent protein degradation depends on a hierarchy of adaptors, such as the dimeric RcdA adaptor, which binds multiple cargo and delivers substrates to the ClpXP protease. RcdA itself is degraded in the absence of cargo, and how RcdA recognizes its targets is unknown. Here, we show that RcdA dimerization and cargo binding compete for a common interface. Cargo binding separates RcdA dimers, and a monomeric variant of RcdA fails to be degraded, suggesting that RcdA degradation is a result of self-delivery. Based on HDX-MS studies showing that different cargo rely on different regions of the dimerization interface, we generate RcdA variants that are selective for specific cargo and show cellular defects consistent with changes in selectivity. Finally, we show that masking of cargo binding by dimerization also limits substrate delivery to restrain overly prolific degradation. Using the same interface for dimerization and cargo binding offers an ability to limit excess protease adaptors by self-degradation while providing a capacity for binding a range of substrates.
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9
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Fröhlich KS, Velasco Gomariz M. RNA-controlled regulation in Caulobacter crescentus. Curr Opin Microbiol 2021; 60:1-7. [PMID: 33529919 DOI: 10.1016/j.mib.2021.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 01/10/2023]
Abstract
In the past decades, Caulobacter crescentus has been extensively studied, mostly regarding its dimorphic, asymmetric life cycle. Its distinct mode of reproduction and the need to optimally adapt to ever-changing environmental conditions require tight coordination of gene regulation. Post-transcriptional regulation through non-coding RNAs and RNA-binding proteins constitutes an important layer of expression control in bacteria, but its principles and mechanisms in Caulobacter have only recently been explored. RNA-binding proteins including the RNA chaperone Hfq and ribonuclease RNase E contribute to the activity of regulatory RNAs. Riboswitches and RNA thermometers govern expression of downstream open reading frames, while the small regulatory RNAs CrfA, ChvR and GsrN instead control targets encoded in trans by direct base-pairing interactions.
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Affiliation(s)
- Kathrin S Fröhlich
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany; Microverse Cluster, Friedrich Schiller University, Jena, Germany.
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10
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Sokolovskaya OM, Shelton AN, Taga ME. Sharing vitamins: Cobamides unveil microbial interactions. Science 2020; 369:369/6499/eaba0165. [PMID: 32631870 DOI: 10.1126/science.aba0165] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microbial communities are essential to fundamental processes on Earth. Underlying the compositions and functions of these communities are nutritional interdependencies among individual species. One class of nutrients, cobamides (the family of enzyme cofactors that includes vitamin B12), is widely used for a variety of microbial metabolic functions, but these structurally diverse cofactors are synthesized by only a subset of bacteria and archaea. Advances at different scales of study-from individual isolates, to synthetic consortia, to complex communities-have led to an improved understanding of cobamide sharing. Here, we discuss how cobamides affect microbes at each of these three scales and how integrating different approaches leads to a more complete understanding of microbial interactions.
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Affiliation(s)
- Olga M Sokolovskaya
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Amanda N Shelton
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA.
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