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Kohm K, Jalomo-Khayrova E, Krüger A, Basu S, Steinchen W, Bange G, Frunzke J, Hertel R, Commichau F, Czech L. Structural and functional characterization of MrpR, the master repressor of the Bacillus subtilis prophage SPβ. Nucleic Acids Res 2023; 51:9452-9474. [PMID: 37602373 PMCID: PMC10516654 DOI: 10.1093/nar/gkad675] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 07/11/2023] [Accepted: 08/09/2023] [Indexed: 08/22/2023] Open
Abstract
Prophages control their lifestyle to either be maintained within the host genome or enter the lytic cycle. Bacillus subtilis contains the SPβ prophage whose lysogenic state depends on the MrpR (YopR) protein, a key component of the lysis-lysogeny decision system. Using a historic B. subtilis strain harboring the heat-sensitive SPβ c2 mutant, we demonstrate that the lytic cycle of SPβ c2 can be induced by heat due to a single nucleotide exchange in the mrpR gene, rendering the encoded MrpRG136E protein temperature-sensitive. Structural characterization revealed that MrpR is a DNA-binding protein resembling the overall fold of tyrosine recombinases. MrpR has lost its recombinase function and the G136E exchange impairs its higher-order structure and DNA binding activity. Genome-wide profiling of MrpR binding revealed its association with the previously identified SPbeta repeated element (SPBRE) in the SPβ genome. MrpR functions as a master repressor of SPβ that binds to this conserved element to maintain lysogeny. The heat-inducible excision of the SPβ c2 mutant remains reliant on the serine recombinase SprA. A suppressor mutant analysis identified a previously unknown component of the lysis-lysogeny management system that is crucial for the induction of the lytic cycle of SPβ.
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Affiliation(s)
- Katharina Kohm
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
- FG Molecular Microbiology, Institute for Biology, University of Hohenheim, Stuttgart, Germany
| | - Ekaterina Jalomo-Khayrova
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Phillips-University Marburg, Marburg, Germany
| | - Aileen Krüger
- Institute of Bio- and Geosciences, iBG-1: Biotechnology, FZ Jülich, Germany
| | - Syamantak Basu
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
| | - Wieland Steinchen
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Phillips-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Phillips-University Marburg, Marburg, Germany
- Max-Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Julia Frunzke
- Institute of Bio- and Geosciences, iBG-1: Biotechnology, FZ Jülich, Germany
| | - Robert Hertel
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Göttingen, Germany
| | - Fabian M Commichau
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
- FG Molecular Microbiology, Institute for Biology, University of Hohenheim, Stuttgart, Germany
| | - Laura Czech
- Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Phillips-University Marburg, Marburg, Germany
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2
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Quiroz-Castañeda RE, Aguilar-Díaz H, Amaro-Estrada I. An alternative vaccine target for bovine Anaplasmosis based on enolase, a moonlighting protein. Front Vet Sci 2023; 10:1225873. [PMID: 37808115 PMCID: PMC10556744 DOI: 10.3389/fvets.2023.1225873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 09/11/2023] [Indexed: 10/10/2023] Open
Abstract
The discovery of new targets for preventing bovine anaplasmosis has moved away from focusing on proteins that have already been extensively studied in Anaplasma marginale, including the Major Surface Proteins, Outer Membrane Proteins, and Type IV Secretion System proteins. An alternative is moonlighting or multifunctional proteins, capable of performing various biological functions within various cellular compartments. There are several reports on the role of moonlighting proteins as virulence factors in various microorganisms. Moreover, it is known that about 25% of all moonlighting is involved in the virulence of pathogens. In this work, for the first time, we present the identification of three enolase proteins (AmEno01, AmEno15, and AmEno31) in the genome of Mexican strains of A. marginale. Using bioinformatics tools, we predicted the catalytic domains, enolase signature, and amino acids binding magnesium ion of the catalytic domain and performed a phylogenetic reconstruction. In addition, by molecular docking analysis, we found that AmEno01 would bind to erythrocyte proteins spectrin, ankyrin, and stomatin. This adhesion function has been reported for enolases from other pathogens. It is considered a promising target since blocking this function would impede the fundamental adhesion process that facilitates the infection of erythrocytes. Additionally, molecular docking predicts that AmEno01 could bind to extracellular matrix protein fibronectin, which would be significant if we consider that some proteins with fibronectin domains are localized in tick gut cells and used as an adhesion strategy to gather bacteria before traveling to salivary glands. Derived from the molecular docking analysis of AmEno01, we hypothesized that enolases could be proteins driven by the pathogen and redirected at the expense of the pathogen's needs.
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3
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Dubnau E, DeSantis M, Dubnau D. Formation of a stable RNase Y-RicT (YaaT) complex requires RicA (YmcA) and RicF (YlbF). mBio 2023; 14:e0126923. [PMID: 37555678 PMCID: PMC10470536 DOI: 10.1128/mbio.01269-23] [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: 05/18/2023] [Accepted: 06/28/2023] [Indexed: 08/10/2023] Open
Abstract
In Bacillus subtilis, the RicT (YaaT), RicA (YmcA), and RicF (YlbF) proteins, which form a stable ternary complex, are needed together with RNase Y (Rny) to cleave and thereby stabilize several key transcripts encoding enzymes of intermediary metabolism. We show here that RicT, but not RicA or RicF, forms a stable complex with Rny and that this association requires the presence of RicA and RicF. We propose that RicT is handed off from the ternary complex to Rny. We show further that the two iron-sulfur clusters carried by the ternary Ric complex are required for the formation of the stable RicT-Rny complex. We demonstrate that proteins of the degradosome-like network of B. subtilis, which also interact with Rny, are dispensable for processing of the gapA operon. Thus, Rny participates in distinct RNA-related processes, determined by its binding partners, and a RicT-Rny complex is likely the functional entity for gapA mRNA maturation. IMPORTANCE The action of nucleases on RNA is universal and essential for all forms of life and includes processing steps that lead to the mature and functional forms of certain transcripts. In Bacillus subtilis, it has been shown that key transcripts for energy-producing steps of glycolysis, for nitrogen assimilation, and for oxidative phosphorylation, all of them crucial processes of intermediary metabolism, are cleaved at specific locations, resulting in mRNA stabilization. The proteins required for these cleavages in B. subtilis [Rny (RNase Y), RicA (YmcA), RicF (YlbF), and RicT (YaaT)] are broadly conserved among the firmicutes, including several important pathogens, hinting that regulatory mechanisms they control may also be conserved. Several aspects of these regulatory events have been explored: phenotypes associated with the absence of these proteins have been described, the impact of these absences on the transcriptome has been documented, and there has been significant exploration of the biochemistry and structural biology of Rny and the Ric proteins. The present study further advances our understanding of the association of Ric proteins and Rny and shows that a complex of Rny with RicT is probably the entity that carries out mRNA maturation.
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Affiliation(s)
- Eugenie Dubnau
- Public Health Research Institute, Rutgers University, Newark, New Jersey, USA
| | - Micaela DeSantis
- Public Health Research Institute, Rutgers University, Newark, New Jersey, USA
| | - David Dubnau
- Public Health Research Institute, Rutgers University, Newark, New Jersey, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
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4
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Jeffery CJ. Current successes and remaining challenges in protein function prediction. FRONTIERS IN BIOINFORMATICS 2023; 3:1222182. [PMID: 37576715 PMCID: PMC10415035 DOI: 10.3389/fbinf.2023.1222182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 07/03/2023] [Indexed: 08/15/2023] Open
Abstract
In recent years, improvements in protein function prediction methods have led to increased success in annotating protein sequences. However, the functions of over 30% of protein-coding genes remain unknown for many sequenced genomes. Protein functions vary widely, from catalyzing chemical reactions to binding DNA or RNA or forming structures in the cell, and some types of functions are challenging to predict due to the physical features associated with those functions. Other complications in understanding protein functions arise due to the fact that many proteins have more than one function or very small differences in sequence or structure that correspond to different functions. We will discuss some of the recent developments in predicting protein functions and some of the remaining challenges.
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Affiliation(s)
- Constance J. Jeffery
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
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5
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Dubnau E, DeSantis M, Dubnau D. Formation of a stable RNase Y-RicT (YaaT) complex requires RicA (YmcA) and RicF (YlbF). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541740. [PMID: 37292586 PMCID: PMC10245838 DOI: 10.1101/2023.05.22.541740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In Bacillus subtilis , the RicT (YaaT), RicA (YmcA) and RicF (YlbF) proteins, which form a stable ternary complex, are needed together with RNase Y (Rny), to cleave and thereby stabilize several key transcripts encoding enzymes of intermediary metabolism. We show here that RicT, but not RicA or RicF, forms a stable complex with Rny, and that this association requires the presence of RicA and RicF. We propose that RicT is handed off from the ternary complex to Rny. We show further that the two iron-sulfur clusters carried by the ternary Ric complex are required for the formation of the stable RicT-Rny complex. We demonstrate that proteins of the degradosome-like network of B. subtilis , which also interact with Rny, are dispensable for processing of the gapA operon. Thus, Rny participates in distinct RNA-related processes, determined by its binding partners, and a RicT-Rny complex is likely the functional entity for gapA mRNA maturation. IMPORTANCE The action of nucleases on RNA is universal and essential for all forms of life and includes processing steps that lead to the mature and functional forms of certain transcripts. In B. subtilis it has been shown that key transcripts for energy producing steps of glycolysis, for nitrogen assimilation and for oxidative phosphorylation, all of them crucial processes of intermediary metabolism, are cleaved at specific locations, resulting in mRNA stabilization. The proteins required for these cleavages in B. subtilis (Rny (RNase Y), RicA (YmcA), RicF (YlbF) and RicT (YaaT)) are broadly conserved among the firmicutes, including in several important pathogens, hinting that regulatory mechanisms they control may also be conserved. Several aspects of these regulatory events have been explored: phenotypes associated with the absence of these proteins have been described, the impact of these absences on the transcriptome has been documented, and there has been significant exploration of the biochemistry and structural biology of Rny and the Ric proteins. The present study further advances our understanding of the association of Ric proteins and Rny and shows that a complex of Rny with RicT is probably the entity that carries out mRNA maturation.
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Affiliation(s)
- Eugenie Dubnau
- Public Health Research Institute, Rutgers University, 225 Warren Street, Newark, New Jersey, 07103, USA
| | - Micaela DeSantis
- Public Health Research Institute, Rutgers University, 225 Warren Street, Newark, New Jersey, 07103, USA
| | - David Dubnau
- Public Health Research Institute, Rutgers University, 225 Warren Street, Newark, New Jersey, 07103, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, New Jersey, 07103, USA
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6
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Yadav P, Singh R, Sur S, Bansal S, Chaudhry U, Tandon V. Moonlighting proteins: beacon of hope in era of drug resistance in bacteria. Crit Rev Microbiol 2023; 49:57-81. [PMID: 35220864 DOI: 10.1080/1040841x.2022.2036695] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Moonlighting proteins (MLPs) are ubiquitous and provide a unique advantage to bacteria performing multiple functions using the same genomic content. Targeting MLPs can be considered as a futuristic approach in fighting drug resistance problem. This review follows the MLP trail from its inception to the present-day state, describing a few bacterial MLPs, viz., glyceraldehyde 3'-phosphate dehydrogenase, phosphoglucose isomerase glutamate racemase (GR), and DNA gyrase. Here, we carve out that targeting MLPs are the beacon of hope in an era of increasing drug resistance in bacteria. Evolutionary stability, structure-functional relationships, protein diversity, possible drug targets, and identification of new drugs against bacterial MLP are given due consideration. Before the final curtain calls, we provide a comprehensive list of small molecules that inhibit the biochemical activity of MLPs, which can aid the development of novel molecules to target MLPs for therapeutic applications.
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Affiliation(s)
- Pramod Yadav
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India.,Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, New Delhi, India
| | - Raja Singh
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Souvik Sur
- Research and Development Center, Teerthanker Mahaveer University, Uttar Pradesh, India
| | - Sandhya Bansal
- Norton Thoracic Institute, St. Joseph's Hospital, and Medical Center, Phoenix, AZ, USA
| | - Uma Chaudhry
- Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi, India
| | - Vibha Tandon
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
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Interplay between Sulfur Assimilation and Biodesulfurization Activity in Rhodococcus qingshengii IGTS8: Insights into a Regulatory Role of the Reverse Transsulfuration Pathway. mBio 2022; 13:e0075422. [PMID: 35856606 PMCID: PMC9426449 DOI: 10.1128/mbio.00754-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biodesulfurization is a process that selectively removes sulfur from dibenzothiophene and its derivatives. Several natural biocatalysts harboring the highly conserved desulfurization operon dszABC, which is significantly repressed by methionine, cysteine, and inorganic sulfate, have been isolated. However, the available information on the metabolic regulation of gene expression is still limited. In this study, scarless knockouts of the reverse transsulfuration pathway enzyme genes cbs and metB were constructed in the desulfurizing strain Rhodococcus sp. strain IGTS8. We provide sequence analyses and report the enzymes' involvement in the sulfate- and methionine-dependent repression of biodesulfurization activity. Sulfate addition in the bacterial culture did not repress the desulfurization activity of the Δcbs strain, whereas deletion of metB promoted a significant biodesulfurization activity for sulfate-based growth and an even higher desulfurization activity for methionine-grown cells. In contrast, growth on cysteine completely repressed the desulfurization activity of all strains. Transcript level comparison uncovered a positive effect of cbs and metB gene deletions on dsz gene expression in the presence of sulfate and methionine, but not cysteine, offering insights into a critical role of cystathionine β-synthase (CβS) and MetB in desulfurization activity regulation. IMPORTANCE Precise genome editing of the model biocatalyst Rhodococcus qingshengii IGTS8 was performed for the first time, more than 3 decades after its initial discovery. We thus gained insight into the regulation of dsz gene expression and biocatalyst activity, depending on the presence of two reverse transsulfuration enzymes, CβS and MetB. Moreover, we observed an enhancement of biodesulfurization capability in the presence of otherwise repressive sulfur sources, such as sulfate and l-methionine. The interconnection of cellular sulfur assimilation strategies was revealed and validated.
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8
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Moonlighting in Bacillus subtilis: The Small Proteins SR1P and SR7P Regulate the Moonlighting Activity of Glyceraldehyde 3-Phosphate Dehydrogenase A (GapA) and Enolase in RNA Degradation. Microorganisms 2021; 9:microorganisms9051046. [PMID: 34066298 PMCID: PMC8152036 DOI: 10.3390/microorganisms9051046] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 12/21/2022] Open
Abstract
Moonlighting proteins are proteins with more than one function. During the past 25 years, they have been found to be rather widespread in bacteria. In Bacillus subtilis, moonlighting has been disclosed to occur via DNA, protein or RNA binding or protein phosphorylation. In addition, two metabolic enzymes, enolase and phosphofructokinase, were localized in the degradosome-like network (DLN) where they were thought to be scaffolding components. The DLN comprises the major endoribonuclease RNase Y, 3'-5' exoribonuclease PnpA, endo/5'-3' exoribonucleases J1/J2 and helicase CshA. We have ascertained that the metabolic enzyme GapA is an additional component of the DLN. In addition, we identified two small proteins that bind scaffolding components of the degradosome: SR1P encoded by the dual-function sRNA SR1 binds GapA, promotes the GapA-RNase J1 interaction and increases the RNase J1 activity. SR7P encoded by the dual-function antisense RNA SR7 binds to enolase thereby enhancing the enzymatic activity of enolase bound RNase Y. We discuss the role of small proteins in modulating the activity of two moonlighting proteins.
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9
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Hemmadi V, Biswas M. An overview of moonlighting proteins in Staphylococcus aureus infection. Arch Microbiol 2020; 203:481-498. [PMID: 33048189 PMCID: PMC7551524 DOI: 10.1007/s00203-020-02071-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/29/2020] [Accepted: 10/01/2020] [Indexed: 01/01/2023]
Abstract
Staphylococcus aureus is responsible for numerous instances of superficial, toxin-mediated, and invasive infections. The emergence of methicillin-resistant (MRSA), as well as vancomycin-resistant (VRSA) strains of S. aureus, poses a massive threat to human health. The tenacity of S. aureus to acquire resistance against numerous antibiotics in a very short duration makes the effort towards developing new antibiotics almost futile. S. aureus owes its destructive pathogenicity to the plethora of virulent factors it produces among which a majority of them are moonlighting proteins. Moonlighting proteins are the multifunctional proteins in which a single protein, with different oligomeric conformations, perform multiple independent functions in different cell compartments. Peculiarly, proteins involved in key ancestral functions and metabolic pathways typically exhibit moonlighting functions. Pathogens mainly employ those proteins as virulent factors which exhibit high structural conservation towards their host counterparts. Consequentially, the host immune system counteracts these invading bacterial virulent factors with minimal protective action. Additionally, many moonlighting proteins also play multiple roles in various stages of pathogenicity while augmenting the virulence of the bacterium. This has necessitated elaborative studies to be conducted on moonlighting proteins of S. aureus that can serve as drug targets. This review is a small effort towards understanding the role of various moonlighting proteins in the pathogenicity of S. aureus.
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Affiliation(s)
- Vijay Hemmadi
- Department of Biological Sciences, Birla Institute of Technology and Science, BITS-Pilani, K. K. Birla Goa Campus, NH17B, Zuarinagar, Goa, 403726, India
| | - Malabika Biswas
- Department of Biological Sciences, Birla Institute of Technology and Science, BITS-Pilani, K. K. Birla Goa Campus, NH17B, Zuarinagar, Goa, 403726, India.
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10
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Moonlighting Proteins at the Candidal Cell Surface. Microorganisms 2020; 8:microorganisms8071046. [PMID: 32674422 PMCID: PMC7409194 DOI: 10.3390/microorganisms8071046] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/11/2020] [Accepted: 07/12/2020] [Indexed: 12/31/2022] Open
Abstract
The cell wall in Candida albicans is not only a tight protective envelope but also a point of contact with the human host that provides a dynamic response to the constantly changing environment in infection niches. Particularly important roles are attributed to proteins exposed at the fungal cell surface. These include proteins that are stably and covalently bound to the cell wall or cell membrane and those that are more loosely attached. Interestingly in this regard, numerous loosely attached proteins belong to the class of “moonlighting proteins” that are originally intracellular and that perform essentially different functions in addition to their primary housekeeping roles. These proteins also demonstrate unpredicted interactions with non-canonical partners at an a priori unexpected extracellular location, achieved via non-classical secretion routes. Acting both individually and collectively, the moonlighting proteins contribute to candidal virulence and pathogenicity through their involvement in mechanisms critical for successful host colonization and infection, such as the adhesion to host cells, interactions with plasma homeostatic proteolytic cascades, responses to stress conditions and molecular mimicry. The documented knowledge of the roles of these proteins in C. albicans pathogenicity has utility for assisting the design of new therapeutic, diagnostic and preventive strategies against candidiasis.
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11
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de Alvarenga LV, Hess WR, Hagemann M. AcnSP - A Novel Small Protein Regulator of Aconitase Activity in the Cyanobacterium Synechocystis sp. PCC 6803. Front Microbiol 2020; 11:1445. [PMID: 32695088 PMCID: PMC7336809 DOI: 10.3389/fmicb.2020.01445] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/04/2020] [Indexed: 12/28/2022] Open
Abstract
Synechocystis sp. PCC 6803 is a widely used model cyanobacterium whose genome has been well annotated. However, several additional small protein coding sequences (sORFs) have been recently identified, which might play important roles, for example in the regulation of cellular metabolism. Here, we analyzed the function of a sORF encoding a 44 amino acid peptide showing high similarity to the N-terminal part of aconitase (AcnB). The expression of the gene, which probably originated from a partial gene duplication of chromosomal acnB into the plasmid pSYSA, was verified and it was designated as acnSP. The protein-coding part of acnSP was inactivated by interposon mutagenesis. The obtained mutant displayed slower growth under photoautotrophic conditions with light exceeding 100 μmol photons m–2 s–1 and showed significant changes in the metabolome compared to wild type, including alterations in many metabolites associated to the tricarboxylic acid (TCA) cycle. To analyze a possible direct impact of AcnSP on aconitase, the recombinant Synechocystis enzyme was generated and biochemically characterized. Biochemical analysis revealed that addition of equimolar amounts of AcnSP resulted in an improved substrate affinity (lower Km) and lowered Vmax of aconitase. These results imply that AcnSP can regulate aconitase activity, thereby impacting the carbon flow into the oxidative branch of the cyanobacterial TCA cycle, which is mainly responsible for the synthesis of carbon skeletons needed for ammonia assimilation.
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Affiliation(s)
- Luna V de Alvarenga
- Department of Plant Physiology, Institute of Biosciences, University of Rostock, Rostock, Germany
| | - Wolfgang R Hess
- Genetics & Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg im Breisgau, Germany
| | - Martin Hagemann
- Department of Plant Physiology, Institute of Biosciences, University of Rostock, Rostock, Germany.,Department Life, Light and Matter, University of Rostock, Rostock, Germany
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12
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Bergé M, Pezzatti J, González-Ruiz V, Degeorges L, Mottet-Osman G, Rudaz S, Viollier PH. Bacterial cell cycle control by citrate synthase independent of enzymatic activity. eLife 2020; 9:52272. [PMID: 32149608 PMCID: PMC7083601 DOI: 10.7554/elife.52272] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 03/04/2020] [Indexed: 11/17/2022] Open
Abstract
Proliferating cells must coordinate central metabolism with the cell cycle. How central energy metabolism regulates bacterial cell cycle functions is not well understood. Our forward genetic selection unearthed the Krebs cycle enzyme citrate synthase (CitA) as a checkpoint regulator controlling the G1→S transition in the polarized alpha-proteobacterium Caulobacter crescentus, a model for cell cycle regulation and asymmetric cell division. We find that loss of CitA promotes the accumulation of active CtrA, an essential cell cycle transcriptional regulator that maintains cells in G1-phase, provided that the (p)ppGpp alarmone is present. The enzymatic activity of CitA is dispensable for CtrA control, and functional citrate synthase paralogs cannot replace CitA in promoting S-phase entry. Our evidence suggests that CitA was appropriated specifically to function as a moonlighting enzyme to link central energy metabolism with S-phase entry. Control of the G1-phase by a central metabolic enzyme may be a common mechanism of cellular regulation.
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Affiliation(s)
- Matthieu Bergé
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Julian Pezzatti
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Geneva, Switzerland
| | - Víctor González-Ruiz
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Geneva, Switzerland.,Swiss Centre for Applied Human Toxicology (SCAHT), Basel, Switzerland
| | - Laurence Degeorges
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Geneviève Mottet-Osman
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Serge Rudaz
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Geneva, Switzerland.,Swiss Centre for Applied Human Toxicology (SCAHT), Basel, Switzerland
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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13
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Alvarado A, Behrens W, Josenhans C. Protein Activity Sensing in Bacteria in Regulating Metabolism and Motility. Front Microbiol 2020; 10:3055. [PMID: 32010106 PMCID: PMC6978683 DOI: 10.3389/fmicb.2019.03055] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/18/2019] [Indexed: 01/24/2023] Open
Abstract
Bacteria have evolved complex sensing and signaling systems to react to their changing environments, most of which are present in all domains of life. Canonical bacterial sensing and signaling modules, such as membrane-bound ligand-binding receptors and kinases, are very well described. However, there are distinct sensing mechanisms in bacteria that are less studied. For instance, the sensing of internal or external cues can also be mediated by changes in protein conformation, which can either be implicated in enzymatic reactions, transport channel formation or other important cellular functions. These activities can then feed into pathways of characterized kinases, which translocate the information to the DNA or other response units. This type of bacterial sensory activity has previously been termed protein activity sensing. In this review, we highlight the recent findings about this non-canonical sensory mechanism, as well as its involvement in metabolic functions and bacterial motility. Additionally, we explore some of the specific proteins and protein-protein interactions that mediate protein activity sensing and their downstream effects. The complex sensory activities covered in this review are important for bacterial navigation and gene regulation in their dynamic environment, be it host-associated, in microbial communities or free-living.
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Affiliation(s)
- Alejandra Alvarado
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, Munich, Germany.,German Center for Infection Research (DZIF) Partner Site Munich, Munich, Germany
| | - Wiebke Behrens
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hanover, Germany
| | - Christine Josenhans
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, Munich, Germany.,German Center for Infection Research (DZIF) Partner Site Munich, Munich, Germany.,Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hanover, Germany
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14
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Multitalented actors inside and outside the cell: recent discoveries add to the number of moonlighting proteins. Biochem Soc Trans 2019; 47:1941-1948. [DOI: 10.1042/bst20190798] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/09/2019] [Accepted: 11/11/2019] [Indexed: 01/03/2023]
Abstract
During the past few decades, it's become clear that many enzymes evolved not only to act as specific, finely tuned and carefully regulated catalysts, but also to perform a second, completely different function in the cell. In general, these moonlighting proteins have a single polypeptide chain that performs two or more distinct and physiologically relevant biochemical or biophysical functions. This mini-review describes examples of moonlighting proteins that have been found within the past few years, including some that play key roles in human and animal diseases and in the regulation of biochemical pathways in food crops. Several belong to two of the most common subclasses of moonlighting proteins: trigger enzymes and intracellular/surface moonlighting proteins, but a few represent less often observed combinations of functions. These examples also help illustrate some of the current methods used for identifying proteins with multiple functions. In general, a greater understanding about the functions and molecular mechanisms of moonlighting proteins, their roles in the regulation of cellular processes, and their involvement in health and disease could aid in many areas including developing new antibiotics, predicting the functions of the millions of proteins being identified through genome sequencing projects, designing novel proteins, using biological circuitry analysis to construct bacterial strains that are better producers of materials for industrial use, and developing methods to tweak biochemical pathways for increasing yields of food crops.
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15
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Yus E, Lloréns-Rico V, Martínez S, Gallo C, Eilers H, Blötz C, Stülke J, Lluch-Senar M, Serrano L. Determination of the Gene Regulatory Network of a Genome-Reduced Bacterium Highlights Alternative Regulation Independent of Transcription Factors. Cell Syst 2019; 9:143-158.e13. [PMID: 31445891 PMCID: PMC6721554 DOI: 10.1016/j.cels.2019.07.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 04/14/2019] [Accepted: 06/27/2019] [Indexed: 11/30/2022]
Abstract
Here, we determined the relative importance of different transcriptional mechanisms in the genome-reduced bacterium Mycoplasma pneumoniae, by employing an array of experimental techniques under multiple genetic and environmental perturbations. Of the 143 genes tested (21% of the bacterium’s annotated proteins), only 55% showed an altered phenotype, highlighting the robustness of biological systems. We identified nine transcription factors (TFs) and their targets, representing 43% of the genome, and 16 regulators that indirectly affect transcription. Only 20% of transcriptional regulation is mediated by canonical TFs when responding to perturbations. Using a Random Forest, we quantified the non-redundant contribution of different mechanisms such as supercoiling, metabolic control, RNA degradation, and chromosome topology to transcriptional changes. Model-predicted gene changes correlate well with experimental data in 95% of the tested perturbations, explaining up to 70% of the total variance when also considering noise. This analysis highlights the importance of considering non-TF-mediated regulation when engineering bacteria. Full comprehensive reconstruction of a bacterial gene regulatory network achieved Genome-reduced bacterium Mycoplasma pneumoniae is robust to genetic perturbations Large part of transcription regulation in bacteria is transcription-factor independent Transcription-factor-independent regulation has a smaller dynamic range
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Affiliation(s)
- Eva Yus
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Doctor Aiguader 88, Barcelona 08003, Spain.
| | - Verónica Lloréns-Rico
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Doctor Aiguader 88, Barcelona 08003, Spain.
| | - Sira Martínez
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Doctor Aiguader 88, Barcelona 08003, Spain
| | - Carolina Gallo
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Doctor Aiguader 88, Barcelona 08003, Spain
| | - Hinnerk Eilers
- Department for General Microbiology, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Cedric Blötz
- Department for General Microbiology, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Jörg Stülke
- Department for General Microbiology, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Maria Lluch-Senar
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Doctor Aiguader 88, Barcelona 08003, Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Doctor Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, Barcelona 08010, Spain.
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16
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Jeffery CJ. An enzyme in the test tube, and a transcription factor in the cell: Moonlighting proteins and cellular factors that affect their behavior. Protein Sci 2019; 28:1233-1238. [PMID: 31087733 PMCID: PMC6566513 DOI: 10.1002/pro.3645] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 05/10/2019] [Indexed: 01/05/2023]
Abstract
In the cell, expression levels, allosteric modulators, post-translational modifications, sequestration, and other factors can affect the level of protein function. For moonlighting proteins, cellular factors like these can also affect the kind of protein function. This minireview discusses examples of moonlighting proteins that illustrate how a single protein can have different functions in different cell types, in different intracellular locations, or under varying cellular conditions. This variability in the kind of protein activity, added to the variability in the amount of protein activity, contributes to the difficulty in predicting the behavior of proteins in the cell.
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Affiliation(s)
- Constance J. Jeffery
- Department of Biological SciencesUniversity of Illinois at ChicagoChicagoIllinois60607
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17
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The demise of catalysis, but new functions arise: pseudoenzymes as the phoenixes of the protein world. Biochem Soc Trans 2019; 47:371-379. [PMID: 30710059 DOI: 10.1042/bst20180473] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/21/2018] [Accepted: 01/02/2019] [Indexed: 01/06/2023]
Abstract
Pseudoenzymes are noncatalytic homologues of enzymes and are found in most enzyme families. Although lacking catalytic activity and sometimes referred to as 'dead' enzymes, they instead resemble phoenixes because the loss of a catalytic function during evolution was associated with the development of vital new functions. They are important in regulating the activity and location of catalytically active homologues, scaffolding the assembly of signaling complexes, and regulating transcription or translation. They are key actors in cell proliferation and differentiation, proteostasis, and many other biochemical pathways and processes. They perform their functions in diverse ways, but many retain some aspects of the function of their catalytically active homologues. In some pseudoenzymes, their functions are very different from other members of their protein families, suggesting some arose from ancient moonlighting proteins during evolution. Much less is known about pseudoenzymes than their catalytically active counterparts, but a growing appreciation of their key roles in many important biochemical processes and signaling pathways has led to increased investigation in recent years. It is clear that there is still much more to learn about the structures, functions, and cellular roles of these phoenix-like proteins.
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18
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Harnessing Underground Metabolism for Pathway Development. Trends Biotechnol 2019; 37:29-37. [DOI: 10.1016/j.tibtech.2018.08.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/17/2018] [Accepted: 08/06/2018] [Indexed: 01/13/2023]
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19
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Davidi D, Longo LM, Jabłońska J, Milo R, Tawfik DS. A Bird’s-Eye View of Enzyme Evolution: Chemical, Physicochemical, and Physiological Considerations. Chem Rev 2018; 118:8786-8797. [DOI: 10.1021/acs.chemrev.8b00039] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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van der Stel AX, van de Lest CHA, Huynh S, Parker CT, van Putten JPM, Wösten MMSM. Catabolite repression in Campylobacter jejuni correlates with intracellular succinate levels. Environ Microbiol 2018; 20:1374-1388. [PMID: 29318721 DOI: 10.1111/1462-2920.14042] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/06/2018] [Indexed: 12/28/2022]
Abstract
Bacteria have evolved different mechanisms to catabolize carbon sources from nutrient mixtures. They first consume their preferred carbon source, before others are used. Regulatory mechanisms adapt the metabolism accordingly to maximize growth and to outcompete other organisms. The human pathogen Campylobacter jejuni is an asaccharolytic Gram-negative bacterium that catabolizes amino acids and organic acids for growth. It prefers serine and aspartate as carbon sources, however it lacks all regulators known to be involved in regulating carbon source utilization in other organisms. In which manner C. jejuni adapts its metabolism towards the presence or absence of preferred carbon sources is unknown. In this study, we show with transcriptomic analysis and enzyme assays how C. jejuni adapts its metabolism in response to its preferred carbon sources. In the presence of serine as well as lactate and pyruvate C. jejuni inhibits the utilization of other carbon sources, by repressing the expression of a number of central metabolic enzymes. The regulatory proteins RacR, Cj1000 and CsrA play a role in the regulation of these metabolic enzymes. This metabolism dependent transcriptional repression correlates with an accumulation of intracellular succinate. Hence, we propose a demand-based catabolite repression mechanism in C. jejuni, depended on intracellular succinate levels.
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Affiliation(s)
| | - Chris H A van de Lest
- Department of Biochemistry and Cell Biology, Utrecht University, Utrecht, The Netherlands
| | - Steven Huynh
- Agricultural Research Service, U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Albany, CA, USA
| | - Craig T Parker
- Agricultural Research Service, U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Albany, CA, USA
| | - Jos P M van Putten
- Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Marc M S M Wösten
- Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
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21
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Rosenberg J, Yeak KC, Commichau FM. A two-step evolutionary process establishes a non-native vitamin B6 pathway in Bacillus subtilis. Environ Microbiol 2017; 20:156-168. [PMID: 29027347 DOI: 10.1111/1462-2920.13950] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/22/2017] [Accepted: 09/27/2017] [Indexed: 12/11/2022]
Abstract
Pyridoxal 5'-phosphate (PLP), the most important form of vitamin B6 serves as a cofactor for many proteins. Two alternative pathways for de novo PLP biosynthesis are known: the short deoxy-xylulose-5-phosphate (DXP)-independent pathway, which is present in the Gram-positive model bacterium Bacillus subtilis and the longer DXP-dependent pathway, which has been intensively studied in the Gram-negative model bacterium Escherichia coli. Previous studies revealed that bacteria contain many promiscuous enzymes causing a so-called 'underground metabolism', which can be important for the evolution of novel pathways. Here, we evaluated the potential of B. subtilis to use a truncated non-native DXP-dependent PLP pathway from E. coli for PLP synthesis. Adaptive laboratory evolution experiments revealed that two non-native enzymes catalysing the last steps of the DXP-dependent PLP pathway and two genomic alterations are sufficient to allow growth of vitamin B6 auxotrophic bacteria as rapid as the wild type. Thus, the existence of an underground metabolism in B. subtilis facilitates the generation of a pathway for synthesis of PLP using parts of a non-native vitamin B6 pathway. The introduction of non-native enzymes into a metabolic network and rewiring of native metabolism could be helpful to generate pathways that might be optimized for producing valuable substances.
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Affiliation(s)
- Jonathan Rosenberg
- Department of General Microbiology, Institute for Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - KahYen C Yeak
- Department of General Microbiology, Institute for Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Fabian M Commichau
- Department of General Microbiology, Institute for Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
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22
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Dormeyer M, Lübke AL, Müller P, Lentes S, Reuß DR, Thürmer A, Stülke J, Daniel R, Brantl S, Commichau FM. Hierarchical mutational events compensate for glutamate auxotrophy of a Bacillus subtilis gltC mutant. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:279-289. [PMID: 28294562 DOI: 10.1111/1758-2229.12531] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 03/01/2017] [Accepted: 03/05/2017] [Indexed: 06/06/2023]
Abstract
Glutamate is the major donor of nitrogen for anabolic reactions. The Gram-positive soil bacterium Bacillus subtilis either utilizes exogenously provided glutamate or synthesizes it using the gltAB-encoded glutamate synthase (GOGAT). In the absence of glutamate, the transcription factor GltC activates expression of the GOGAT genes for glutamate production. Consequently, a gltC mutant strain is auxotrophic for glutamate. Using a genetic selection and screening system, we could isolate and differentiate between gltC suppressor mutants in one step. All mutants had acquired the ability to synthesize glutamate, independent of GltC. We identified (i) gain-of-function mutations in the gltR gene, encoding the transcription factor GltR, (ii) mutations in the promoter of the gltAB operon and (iii) massive amplification of the genomic locus containing the gltAB operon. The mutants belonging to the first two classes constitutively expressed the gltAB genes and produced sufficient glutamate for growth. By contrast, mutants that belong to the third class appeared most frequently and solved glutamate limitation by increasing the copy number of the poorly expressed gltAB genes. Thus, glutamate auxotrophy of a B. subtilis gltC mutant can be relieved in multiple ways. Moreover, recombination-dependent amplification of the gltAB genes is the predominant mutational event indicating a hierarchy of mutations.
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Affiliation(s)
- Miriam Dormeyer
- Department of General Microbiology, Georg August University Göttingen, Grisebachstr. 8, Göttingen, 37077, Germany
| | - Anastasia L Lübke
- Department of General Microbiology, Georg August University Göttingen, Grisebachstr. 8, Göttingen, 37077, Germany
| | - Peter Müller
- Department of Genetics, Bacterial Genetics, Friedrich Schiller University Jena, Philosophenweg 12, Jena, 07743, Germany
| | - Sabine Lentes
- Department of General Microbiology, Georg August University Göttingen, Grisebachstr. 8, Göttingen, 37077, Germany
| | - Daniel R Reuß
- Department of General Microbiology, Georg August University Göttingen, Grisebachstr. 8, Göttingen, 37077, Germany
| | - Andrea Thürmer
- Department of Genomic and Applied Microbiology, Georg August University Göttingen, Grisebachstr. 8, Göttingen, 37077, Germany
| | - Jörg Stülke
- Department of General Microbiology, Georg August University Göttingen, Grisebachstr. 8, Göttingen, 37077, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Georg August University Göttingen, Grisebachstr. 8, Göttingen, 37077, Germany
| | - Sabine Brantl
- Department of Genetics, Bacterial Genetics, Friedrich Schiller University Jena, Philosophenweg 12, Jena, 07743, Germany
| | - Fabian M Commichau
- Department of General Microbiology, Georg August University Göttingen, Grisebachstr. 8, Göttingen, 37077, Germany
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23
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Differential Proteome Between Patient-Related and Non-related Environmental Isolates of Legionella pneumophila. Curr Microbiol 2017; 74:344-355. [PMID: 28138785 DOI: 10.1007/s00284-017-1198-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 01/11/2017] [Indexed: 10/20/2022]
Abstract
Molecular epidemiologic studies of Legionella have shown different molecular types coexisting in the same environment, with only one having the ability to trigger an outbreak. We therefore studied the proteome of isolates of these different molecular types in search of the proteins responsible for infection. In this study, we performed a differential proteomic analysis between patient-related and non-patient-related environmental isolates using two-dimensional difference gel electrophoresis (2D-DIGE) combined with mass spectrometry. Sixty-three spots were observed as being different between the two groups; 31 spots were identified corresponding to 23 different proteins. Patient-related isolates overexpressed proteins associated with metabolism, with enzymes of the tricarboxylic acid cycle and the degradation pathways being the most abundant proteins identified. However, the largest group of non-patient-related proteins was associated with stress response. Furthermore, the MOMP protein was located in different spots depending on their patient-related or non-patient-related origin, suggesting different post-translational modifications. According to these results, different bacterial adaptation pathways are activated in stress conditions which influence their ability to produce infection.
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24
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Mignolet J, Holden S, Bergé M, Panis G, Eroglu E, Théraulaz L, Manley S, Viollier PH. Functional dichotomy and distinct nanoscale assemblies of a cell cycle-controlled bipolar zinc-finger regulator. eLife 2016; 5. [PMID: 28008851 PMCID: PMC5182063 DOI: 10.7554/elife.18647] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/01/2016] [Indexed: 11/13/2022] Open
Abstract
Protein polarization underlies differentiation in metazoans and in bacteria. How symmetric polarization can instate functional asymmetry remains elusive. Here, we show by super-resolution photo-activated localization microscopy and edgetic mutations that the bitopic zinc-finger protein ZitP implements specialized developmental functions – pilus biogenesis and multifactorial swarming motility – while shaping distinct nanoscale (bi)polar architectures in the asymmetric model bacterium Caulobacter crescentus. Polar assemblage and accumulation of ZitP and its effector protein CpaM are orchestrated in time and space by conserved components of the cell cycle circuitry that coordinate polar morphogenesis with cell cycle progression, and also act on the master cell cycle regulator CtrA. Thus, this novel class of potentially widespread multifunctional polarity regulators is deeply embedded in the cell cycle circuitry. DOI:http://dx.doi.org/10.7554/eLife.18647.001 Living cells become asymmetric for many different reasons and how they do so has been a long-standing question in biology. In some cells, the asymmetry arises because a given protein accumulates at one side of the cell. In particular, this process happens before some cells divide to produce two non-identical daughter cells that then go on to develop in very different ways – which is vital for the development of almost all multicellular organisms. The single-celled bacterium Caulobacter crescentus also undergoes this type of asymmetric division. The polarized Caulobacter cell produces two very different offsprings – a stationary cell and a nomadic cell that swims using a propeller-like structure, called a flagellum, and has projections called pili on its surface. Before it divides asymmetrically, the Caulobacter cell must accumulate specific proteins at its extremities, or poles. Two such proteins are ZitP and CpaM, which appear to have multiple roles and are thought to interact with other factors that regulate cell division. However, little is known about how ZitP and CpaM become organized at the poles at the right time and how they interact with these regulators of cell division. Mignolet et al. explored how ZitP becomes polarized in Caulobacter crescentus using a combination of approaches including biochemical and genetic analyses and very high-resolution microscopy. This revealed that ZitP accumulated via different pathways at the two poles and that it formed distinct structures at each pole. These structures were associated with different roles for ZitP. While ZitP recruited proteins, including CpaM, required for assembly of pili to one of the poles, it acted differently at the opposite pole. By mutating regions of ZitP, Mignolet et al. went on to show that different regions of the protein carry out these roles. Further experiments demonstrated that regulators of the cell division cycle influenced how ZitP and CpaM accumulated and behaved in cells, ensuring that the proteins carry out their roles at the correct time during division. These findings provide more evidence that proteins can have different roles at distinct sites within a cell, in this case at opposite poles of a cell. Future studies will be needed to determine whether this is seen in cells other than Caulobacter including more complex, non-bacterial cells. DOI:http://dx.doi.org/10.7554/eLife.18647.002
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Affiliation(s)
- Johann Mignolet
- Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Seamus Holden
- Laboratory of Experimental Biophysics, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle, United Kingdom
| | - Matthieu Bergé
- Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Gaël Panis
- Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Ezgi Eroglu
- Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Laurence Théraulaz
- Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Suliana Manley
- Laboratory of Experimental Biophysics, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Patrick H Viollier
- Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
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25
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Hernández MA, Lara J, Gago G, Gramajo H, Alvarez HM. The pleiotropic transcriptional regulator NlpR contributes to the modulation of nitrogen metabolism, lipogenesis and triacylglycerol accumulation in oleaginous rhodococci. Mol Microbiol 2016; 103:366-385. [DOI: 10.1111/mmi.13564] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Martín A. Hernández
- INBIOP (Instituto de Biociencias de la Patagonia), Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Naturales; Universidad Nacional de la Patagonia San Juan Bosco; Ruta Provincial N° 1, Km 4-Ciudad Universitaria 9000 Comodoro Rivadavia Chubut Argentina
| | - Julia Lara
- IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario; Ocampo y Esmeralda 2000 Rosario Santa Fe Argentina
| | - Gabriela Gago
- IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario; Ocampo y Esmeralda 2000 Rosario Santa Fe Argentina
| | - Hugo Gramajo
- IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario; Ocampo y Esmeralda 2000 Rosario Santa Fe Argentina
| | - Héctor M. Alvarez
- INBIOP (Instituto de Biociencias de la Patagonia), Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Naturales; Universidad Nacional de la Patagonia San Juan Bosco; Ruta Provincial N° 1, Km 4-Ciudad Universitaria 9000 Comodoro Rivadavia Chubut Argentina
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26
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Distinct Residues Contribute to Motility Repression and Autoregulation in the Proteus mirabilis Fimbria-Associated Transcriptional Regulator AtfJ. J Bacteriol 2016; 198:2100-12. [PMID: 27246571 DOI: 10.1128/jb.00193-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 05/22/2016] [Indexed: 12/19/2022] Open
Abstract
UNLABELLED Proteus mirabilis contributes to a significant number of catheter-associated urinary tract infections, where coordinated regulation of adherence and motility is critical for ascending disease progression. Previously, the mannose-resistant Proteus-like (MR/P) fimbria-associated transcriptional regulator MrpJ has been shown to both repress motility and directly induce the transcription of its own operon; in addition, it affects the expression of a wide range of cellular processes. Interestingly, 14 additional mrpJ paralogs are included in the P. mirabilis genome. Looking at a selection of MrpJ paralogs, we discovered that these proteins, which consistently repress motility, also have nonidentical functions that include cross-regulation of fimbrial operons. A subset of paralogs, including AtfJ (encoded by the ambient temperature fimbrial operon), Fim8J, and MrpJ, are capable of autoinduction. We identified an element of the atf promoter extending from 487 to 655 nucleotides upstream of the transcriptional start site that is responsive to AtfJ, and we found that AtfJ directly binds this fragment. Mutational analysis of AtfJ revealed that its two identified functions, autoregulation and motility repression, are not invariably linked. Residues within the DNA-binding helix-turn-helix domain are required for motility repression but not necessarily autoregulation. Likewise, the C-terminal domain is dispensable for motility repression but is essential for autoregulation. Supported by a three-dimensional (3D) structural model, we hypothesize that the C-terminal domain confers unique regulatory capacities on the AtfJ family of regulators. IMPORTANCE Balancing adherence with motility is essential for uropathogens to successfully establish a foothold in their host. Proteus mirabilis uses a fimbria-associated transcriptional regulator to switch between these antagonistic processes by increasing fimbrial adherence while simultaneously downregulating flagella. The discovery of multiple related proteins, many of which also function as motility repressors, encoded in the P. mirabilis genome has raised considerable interest as to their functionality and potential redundancy in this organism. This study provides an important advance in this field by elucidating the nonidentical effects of these paralogs on a molecular level. Our mechanistic studies of one member of this group, AtfJ, shed light on how these differing functions may be conferred despite the limited sequence variety exhibited by the paralogous proteins.
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27
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Rosenberg J, Müller P, Lentes S, Thiele MJ, Zeigler DR, Tödter D, Paulus H, Brantl S, Stülke J, Commichau FM. ThrR, a DNA‐binding transcription factor involved in controlling threonine biosynthesis in
Bacillus subtilis. Mol Microbiol 2016; 101:879-93. [DOI: 10.1111/mmi.13429] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Jonathan Rosenberg
- Department of General MicrobiologyGeorg August University GöttingenGrisebachstr. 8Göttingen37077 Germany
| | - Peter Müller
- Department of GeneticsBacterial Genetics, Friedrich Schiller University JenaJena Germany
| | - Sabine Lentes
- Department of General MicrobiologyGeorg August University GöttingenGrisebachstr. 8Göttingen37077 Germany
| | - Martin J. Thiele
- Department of General MicrobiologyGeorg August University GöttingenGrisebachstr. 8Göttingen37077 Germany
| | | | - Dominik Tödter
- Department of General MicrobiologyGeorg August University GöttingenGrisebachstr. 8Göttingen37077 Germany
| | - Henry Paulus
- Boston Biomedical Research InstituteBoston MA USA
| | - Sabine Brantl
- Department of GeneticsBacterial Genetics, Friedrich Schiller University JenaJena Germany
| | - Jörg Stülke
- Department of General MicrobiologyGeorg August University GöttingenGrisebachstr. 8Göttingen37077 Germany
| | - Fabian M. Commichau
- Department of General MicrobiologyGeorg August University GöttingenGrisebachstr. 8Göttingen37077 Germany
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