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Rotter DAO, Heger C, Kühm C, Schmidt N, Schäfer A, Heimerl T, Mack M, Graumann PL. The Acetyltransferase RibT From Bacillus subtilis Affects in vivo Dynamics of the Multimeric Heavy Riboflavin Synthase Complex. Front Microbiol 2022; 13:856820. [PMID: 35495702 PMCID: PMC9048828 DOI: 10.3389/fmicb.2022.856820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/11/2022] [Indexed: 12/02/2022] Open
Abstract
Flavins are ubiquitous molecules in life as they serve as important enzyme cofactors. In the Gram-positive, soil-dwelling bacterium Bacillus subtilis, four well-characterized gene products (the enzymes RibDG, RibE, RibAB, and RibH) catalyze the biosynthesis of riboflavin (RF) from guanosine-triphosphate (GTP) and ribulose-5-phosphate (R5P). The corresponding genes form an operon together with the gene ribT (ribDG-E-AB-H-T), wherein the function of this terminal gene remained enigmatic. RibT has been structurally characterized as a GCN5-like acetyltransferase (GNAT), however, with unidentified target molecules. Bacterial two-hybrid system revealed interactions between RibT, RibH, and RibE, forming the heavy RF synthase complex. Applying single particle tracking (SPT), we found that confined (sub)diffusion of RibT is largely dependent on interacting RibE and, to a lesser degree, on interacting RibH. By induced expression of otherwise low-expressed ribT from an ectopic locus, we observed a decrease in the subpopulation considered to represent capsids of the heavy RF synthase and an increase in the subpopulation thought to represent pentamers of RibH, pointing to a putative role for RibT in capsid disassembly. Complementarily, either deletion of ribT or mutation of a key residue from RibH (K29) suspected to be the substrate of RibT for acetylation leads to increased levels of subpopulations considered as capsids of RibH-mVenus (RibH-mV) in comparison to wild-type (wt)-like cells. Thus, we provide evidence for an indirect involvement of RibT in RF biosynthesis by a putative capsid disassembling mechanism considered to involve acetylation of RibH residue K29 at the three-fold symmetry axis of 60-mer capsids.
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Affiliation(s)
- Daniel Andreas Orlando Rotter
- SYNMIKRO, Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
- BioNTech Manufacturing Marburg GmbH, Marburg, Germany
| | - Christoph Heger
- SYNMIKRO, Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
- BioSpringBiotechnolgie GmbH, Frankfurt am Main, Germany
| | - Christian Kühm
- Institute of Technical Microbiology, University of Applied Sciences Mannheim, Mannheim, Germany
| | - Nina Schmidt
- SYNMIKRO, Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
| | - Antje Schäfer
- SYNMIKRO, Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
| | - Thomas Heimerl
- SYNMIKRO, Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
- Department of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Matthias Mack
- Institute of Technical Microbiology, University of Applied Sciences Mannheim, Mannheim, Germany
| | - Peter L. Graumann
- SYNMIKRO, Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
- Department of Chemistry, Philipps-Universität Marburg, Marburg, Germany
- *Correspondence: Peter L. Graumann
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Oviedo-Bocanegra LM, Hinrichs R, Rotter DAO, Dersch S, Graumann PL. Single molecule/particle tracking analysis program SMTracker 2.0 reveals different dynamics of proteins within the RNA degradosome complex in Bacillus subtilis. Nucleic Acids Res 2021; 49:e112. [PMID: 34417617 PMCID: PMC8565344 DOI: 10.1093/nar/gkab696] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/29/2021] [Indexed: 01/06/2023] Open
Abstract
Single-molecule (particle) tracking is a powerful method to study dynamic processes in cells at highest possible spatial and temporal resolution. We have developed SMTracker, a graphical user interface for automatic quantifying, visualizing and managing of data. Version 2.0 determines distributions of positional displacements in x- and y-direction using multi-state diffusion models, discriminates between Brownian, sub- or superdiffusive behaviour, and locates slow or fast diffusing populations in a standardized cell. Using SMTracker, we show that the Bacillus subtilis RNA degradosome consists of a highly dynamic complex of RNase Y and binding partners. We found similar changes in molecule dynamics for RNase Y, CshA, PNPase and enolase, but not for phosphofructokinase, RNase J1 and J2, to inhibition of transcription. However, the absence of PfkA or of RNase J2 affected molecule dynamics of RNase Y-mVenus, indicating that these two proteins are indeed part of the degradosome. Molecule counting suggests that RNase Y is present as a dimer in cells, at an average copy number of about 500, of which 46% are present in a slow-diffusive state and thus likely engaged within degradosomes. Thus, RNase Y, CshA, PNPase and enolase likely play central roles, and RNase J1, J2 and PfkA more peripheral roles, in degradosome architecture.
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Affiliation(s)
- Luis M Oviedo-Bocanegra
- Centre for Synthetic Microbiology (SYNMIKRO) and Fachbereich Chemie, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Rebecca Hinrichs
- Centre for Synthetic Microbiology (SYNMIKRO) and Fachbereich Chemie, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Daniel Andreas Orlando Rotter
- Centre for Synthetic Microbiology (SYNMIKRO) and Fachbereich Chemie, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Simon Dersch
- Centre for Synthetic Microbiology (SYNMIKRO) and Fachbereich Chemie, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Peter L Graumann
- Centre for Synthetic Microbiology (SYNMIKRO) and Fachbereich Chemie, Philipps-Universität Marburg, 35032 Marburg, Germany
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