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Whole Genome Sequencing and Tn 5-Insertion Mutagenesis of Pseudomonas taiwanensis CMS to Probe Its Antagonistic Activity Against Rice Bacterial Blight Disease. Int J Mol Sci 2020; 21:ijms21228639. [PMID: 33207795 PMCID: PMC7696974 DOI: 10.3390/ijms21228639] [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: 09/23/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 01/07/2023] Open
Abstract
The Gram-negative bacterium Pseudomonas taiwanensis is a novel bacterium that uses shrimp shell waste as its sole sources of carbon and nitrogen. It is a versatile bacterium with potential for use in biological control, with activities including toxicity toward insects, fungi, and the rice pathogen Xanthomonas oryzae pv.oryzae (Xoo). In this study, the complete 5.08-Mb genome sequence of P. taiwanensis CMS was determined by a combination of NGS/Sanger sequencing and optical mapping. Comparison of optical maps of seven Pseudomonas species showed that P. taiwanensis is most closely related to P. putida KT 2400. We screened a total of 11,646 individual Tn5-transponson tagged strains to identify genes that are involved in the production and regulation of the iron-chelator pyoverdine in P. taiwanensis, which is a key anti-Xoo factor. Our results indicated that the two-component system (TCS) EnvZ/OmpR plays a positive regulatory role in the production of pyoverdine, whereas the sigma factor RpoS functions as a repressor. The knowledge of the molecular basis of the regulation of pyoverdine by P. taiwanensis provided herein will be useful for its development for use in biological control, including as an anti-Xoo agent.
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Arya G, Pal M, Sharma M, Singh B, Singh S, Agrawal V, Chaba R. Molecular insights into effector binding by DgoR, a GntR/FadR family transcriptional repressor of D-galactonate metabolism in Escherichia coli. Mol Microbiol 2020; 115:591-609. [PMID: 33068046 DOI: 10.1111/mmi.14625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 10/06/2020] [Accepted: 10/09/2020] [Indexed: 01/23/2023]
Abstract
Several GntR/FadR transcriptional regulators govern sugar acid metabolism in bacteria. Although effectors have been identified for a few sugar acid regulators, the mode of effector binding is unknown. Even in the overall FadR subfamily, there are limited details on effector-regulator interactions. Here, we identified the effector-binding cavity in Escherichia coli DgoR, a FadR subfamily transcriptional repressor of D-galactonate metabolism that employs D-galactonate as its effector. Using a genetic screen, we isolated several dgoR superrepressor alleles. Blind docking suggested eight amino acids corresponding to these alleles to form a part of the effector-binding cavity. In vivo and in vitro assays showed that these mutations compromise the inducibility of DgoR without affecting its oligomeric status or affinity for target DNA. Taking Bacillus subtilis GntR as a representative, we demonstrated that the effector-binding cavity is similar among FadR subfamily sugar acid regulators. Finally, a comparison of sugar acid regulators with other FadR members suggested conserved features of effector-regulator recognition within the FadR subfamily. Sugar acid metabolism is widely implicated in bacterial colonization and virulence. The present study sets the basis to investigate the influence of natural genetic variations in FadR subfamily regulators on their sensitivity to sugar acids and ultimately on host-bacterial interactions.
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Affiliation(s)
- Garima Arya
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Mohinder Pal
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Monika Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, India
| | - Bhupinder Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Swati Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
| | - Vishal Agrawal
- Department of Biochemistry, Panjab University, Chandigarh, India
| | - Rachna Chaba
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab, India
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Graf von Armansperg B, Koller F, Gericke N, Hellwig M, Jagtap PKA, Heermann R, Hennig J, Henle T, Lassak J. Transcriptional regulation of the N ε -fructoselysine metabolism in Escherichia coli by global and substrate-specific cues. Mol Microbiol 2020; 115:175-190. [PMID: 32979851 DOI: 10.1111/mmi.14608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 12/19/2022]
Abstract
Thermally processed food is an important part of the human diet. Heat-treatment, however, promotes the formation of so-called Amadori rearrangement products, such as fructoselysine. The gut microbiota including Escherichia coli can utilize these compounds as a nutrient source. While the degradation route for fructoselysine is well described, regulation of the corresponding pathway genes frlABCD remained poorly understood. Here, we used bioinformatics combined with molecular and biochemical analyses and show that fructoselysine metabolism in E. coli is tightly controlled at the transcriptional level. The global regulator CRP (CAP) as well as the alternative sigma factor σ32 (RpoH) contribute to promoter activation at high cAMP-levels and inside warm-blooded hosts, respectively. In addition, we identified and characterized a transcriptional regulator FrlR, encoded adjacent to frlABCD, as fructoselysine-6-phosphate specific repressor. Our study provides profound evidence that the interplay of global and substrate-specific regulation is a perfect adaptation strategy to efficiently utilize unusual substrates within the human gut environment.
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Affiliation(s)
| | - Franziska Koller
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nicola Gericke
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael Hellwig
- Chair of Food Chemistry, Technische Universität Dresden, Dresden, Germany
| | | | - Ralf Heermann
- Institute of Molecular Physiology, Microbiology and Wine Research, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Thomas Henle
- Chair of Food Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Jürgen Lassak
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
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54
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Dudek M, Dieudonné A, Jouanneau D, Rochat T, Michel G, Sarels B, Thomas F. Regulation of alginate catabolism involves a GntR family repressor in the marine flavobacterium Zobellia galactanivorans DsijT. Nucleic Acids Res 2020; 48:7786-7800. [PMID: 32585009 PMCID: PMC7641319 DOI: 10.1093/nar/gkaa533] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/02/2020] [Accepted: 06/10/2020] [Indexed: 12/19/2022] Open
Abstract
Marine flavobacteria possess dedicated Polysaccharide Utilization Loci (PULs) enabling efficient degradation of a variety of algal polysaccharides. The expression of these PULs is tightly controlled by the presence of the substrate, yet details on the regulatory mechanisms are still lacking. The marine flavobacterium Zobellia galactanivorans DsijT digests many algal polysaccharides, including alginate from brown algae. Its complex Alginate Utilization System (AUS) comprises a PUL and several other loci. Here, we showed that the expression of the AUS is strongly and rapidly (<30 min) induced upon addition of alginate, leading to biphasic substrate utilization. Polymeric alginate is first degraded into smaller oligosaccharides that accumulate in the extracellular medium before being assimilated. We found that AusR, a GntR family protein encoded within the PUL, regulates alginate catabolism by repressing the transcription of most AUS genes. Based on our genetic, genomic, transcriptomic and biochemical results, we propose the first model of regulation for a PUL in marine bacteria. AusR binds to promoters of AUS genes via single, double or triple copies of operator. Upon addition of alginate, secreted enzymes expressed at a basal level catalyze the initial breakdown of the polymer. Metabolic intermediates produced during degradation act as effectors of AusR and inhibit the formation of AusR/DNA complexes, thus lifting transcriptional repression.
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Affiliation(s)
- Magda Dudek
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Anissa Dieudonné
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Diane Jouanneau
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Tatiana Rochat
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
| | - Gurvan Michel
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Benoit Sarels
- Sorbonne Université, CNRS, Laboratoire Jacques-Louis Lions, Université de Paris, 75252 Paris, France
| | - François Thomas
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
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Wang T, Qi Y, Wang Z, Zhao J, Ji L, Li J, Cai Z, Yang L, Wu M, Liang H. Coordinated regulation of anthranilate metabolism and bacterial virulence by the GntR family regulator MpaR inPseudomonas aeruginosa. Mol Microbiol 2020; 114:857-869. [PMID: 32748556 DOI: 10.1111/mmi.14584] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 07/23/2020] [Accepted: 07/27/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Tietao Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China Ministry of Education College of Life Sciences Northwest University Xi'an China
| | - Yihang Qi
- Key Laboratory of Resources Biology and Biotechnology in Western China Ministry of Education College of Life Sciences Northwest University Xi'an China
| | - Zhihan Wang
- West China School of Basic Medical Science & Forensic Medicine Sichuan University ChengDu China
| | - Jingru Zhao
- Key Laboratory of Resources Biology and Biotechnology in Western China Ministry of Education College of Life Sciences Northwest University Xi'an China
| | - Linxuan Ji
- Key Laboratory of Resources Biology and Biotechnology in Western China Ministry of Education College of Life Sciences Northwest University Xi'an China
| | - Jun Li
- College of Bioengineering and Biotechnology Zhejiang University of Technology Hangzhou China
| | - Zhao Cai
- School of Medicine Southern University of Science and Technology ShenZhen China
| | - Liang Yang
- School of Medicine Southern University of Science and Technology ShenZhen China
| | - Min Wu
- Department of Basic Science School of Medicine and Health Science University of North Dakota Grand Forks ND USA
| | - Haihua Liang
- Key Laboratory of Resources Biology and Biotechnology in Western China Ministry of Education College of Life Sciences Northwest University Xi'an China
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Frezzini M, Narzi D, Sciolari AM, Guidoni L, Pascarella S. Molecular dynamics of an asymmetric form of GabR, a bacterial transcriptional regulator. Biophys Chem 2020; 262:106380. [PMID: 32413777 DOI: 10.1016/j.bpc.2020.106380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 01/20/2023]
Abstract
GabR is a bacterial transcription regulator with a dimeric structure in which each subunit includes a wHTH (winged Helix-Turn-Helix) domain connected through a peptide linker to a large C-terminal domain folded as the enzyme aspartate aminotransferase (AAT). In Bacillus subtilis, GabR activates the genes involved in the metabolism of γ-amino butyric acid (GABA) upon formation of a PLP-GABA adduct. Recently, the crystallographic structure of an asymmetric form of GabR has been solved. This form (semi-holo) has one active site binding PLP as internal aldimine and the other the PLP-GABA complex. This work reports a molecular dynamics (MD) study aimed at understanding the characteristics of the asymmetric GabR form and compare them to the dynamics properties of previously studied symmetric holo (internal PLP aldimine at both active sites) and holo-GABA (containing PLP-GABA adducts) GabRs. Standard molecular dynamics and data analysis techniques have been used. The results indicate a remarkable asymmetry in the mobility and interactions of the different structural portions of the semi-holo GabR and of a few residues at the active site. The pattern is different from that observed in the other symmetrical GabR forms. The asymmetric perturbation of the active site residues may suggest the existence of a form of allosteric interference between the two active sites.
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Affiliation(s)
- Mario Frezzini
- Department of Information Engineering, Computer Science and Mathematics, University of L'Aquila, 67100 L'Aquila, Italy.
| | - Daniele Narzi
- Department of Physics and Chemistry Sciences, University of L'Aquila, 67100 L'Aquila, Italy.
| | | | - Leonardo Guidoni
- Department of Physics and Chemistry Sciences, University of L'Aquila, 67100 L'Aquila, Italy.
| | - Stefano Pascarella
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, 00185 Rome, Italy.
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57
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Transcriptional regulation of a gonococcal gene encoding a virulence factor (L-lactate permease). PLoS Pathog 2019; 15:e1008233. [PMID: 31860664 PMCID: PMC6957213 DOI: 10.1371/journal.ppat.1008233] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 01/13/2020] [Accepted: 11/22/2019] [Indexed: 12/16/2022] Open
Abstract
GdhR is a GntR-type regulator of Neisseria gonorrhoeae encoded by a gene (gdhR) belonging to the MtrR regulon, which comprises multiple genes required for antibiotic resistance such as the mtrCDE efflux pump genes. In previous work we showed that loss of gdhR results in enhanced gonococcal fitness in a female mouse model of lower genital tract infection. Here, we used RNA-Seq to perform a transcriptional profiling study to determine the GdhR regulon. GdhR was found to regulate the expression of 2.3% of all the genes in gonococcal strain FA19, of which 39 were activated and 11 were repressed. Within the GdhR regulon we found that lctP, which encodes a unique L-lactate transporter and has been associated with gonococcal pathogenesis, was the highest of GdhR-repressed genes. By using in vitro transcription and DNase I footpriting assays we mapped the lctP transcriptional start site (TSS) and determined that GdhR directly inhibits transcription by binding to an inverted repeat sequence located 9 bases downstream of the lctP TSS. Epistasis analysis revealed that, while loss of lctP increased susceptibility of gonococci to hydrogen peroxide (H2O2) the loss of gdhR enhanced resistance; however, this GdhR-endowed property was reversed in a double gdhR lctP null mutant. We assessed the effect of different carbon sources on lctP expression and found that D-glucose, but not L-lactate or pyruvate, repressed lctP expression within a physiological concentration range but in a GdhR-independent manner. Moreover, we found that adding glucose to the medium enhanced susceptibility of gonococci to hydrogen peroxide. We propose a model for the role of lctP regulation via GdhR and glucose in the pathogenesis of N. gonorrhoeae.
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58
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Frezzini M, Guidoni L, Pascarella S. Conformational transitions induced by γ-amino butyrate binding in GabR, a bacterial transcriptional regulator. Sci Rep 2019; 9:19319. [PMID: 31848410 PMCID: PMC6917764 DOI: 10.1038/s41598-019-55581-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 11/20/2019] [Indexed: 11/09/2022] Open
Abstract
GabR from Bacillus subtilis is a transcriptional regulator of the MocR subfamily of GntR regulators. The MocR architecture is characterized by the presence of an N-terminal winged-Helix-Turn-Helix domain and a C-terminal domain folded as the pyridoxal 5′-phosphate (PLP) dependent aspartate aminotransferase (AAT). The two domains are linked by a peptide bridge. GabR activates transcription of genes involved in γ-amino butyrate (GABA) degradation upon binding of PLP and GABA. This work is aimed at contributing to the understanding of the molecular mechanism underlying the GabR transcription activation upon GABA binding. To this purpose, the structure of the entire GabR dimer with GABA external aldimine (holo-GABA) has been reconstructed using available crystallographic data. The structure of the apo (without any ligand) and holo (with PLP) GabR forms have been derived from the holo-GABA. An extensive 1 μs comparative molecular dynamics (MD) has been applied to the three forms. Results showed that the presence of GABA external aldimine stiffens the GabR, stabilizes the AAT domain in the closed form and couples the AAT and HTH domains dynamics. Apo and holo GabR appear more flexible especially at the level of the HTH and linker portions and small AAT subdomain.
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Affiliation(s)
- Mario Frezzini
- Department of Information Engineering, Computer Science and Mathematics, University of L'Aquila, 67100, L'Aquila, Italy
| | - Leonardo Guidoni
- Department of Physics and Chemistry Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Stefano Pascarella
- Department of Biochemical Sciences "A Rossi Fanelli", Sapienza, University of Rome, 00185, Rome, Italy.
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59
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Bouillaut L, Newton W, Sonenshein AL, Belitsky BR. DdlR, an essential transcriptional regulator of peptidoglycan biosynthesis in Clostridioides difficile. Mol Microbiol 2019; 112:1453-1470. [PMID: 31483905 DOI: 10.1111/mmi.14371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2019] [Indexed: 12/11/2022]
Abstract
D-Ala-D-Ala ligase, encoded by ddl genes, is responsible for the synthesis of a dipeptide, D-Ala-D-Ala, an essential precursor of bacterial peptidoglycan. In Clostridioides difficile, the single ddl gene is located upstream of the ddlR gene, which encodes a putative transcriptional regulator. Using mutational and transcriptional analysis and DNA-binding assays, DdlR was found to be a direct activator of the ddl ddlR operon. DdlR is a member of the MocR/GabR-type proteins that have aminotransferase-like, pyridoxal 5'-phosphate-binding domains. A DdlR mutation that prevented covalent binding of pyridoxal 5'-phosphate abolished the ability of DdlR to activate transcription. Addition of D-Ala-D-Ala to the medium inactivated DdlR, reducing dipeptide biosynthesis. In contrast, D-Ala-D-Ala limitation caused a dramatic increase in expression from the ddl promoter. Though uncommon for transcription regulators, C. difficile DdlR is essential, as the ddlR null mutant cells could not grow even in complex laboratory media in the absence of D-Ala-D-Ala. A dyad symmetry sequence, which is located immediately upstream of the -35 region of the ddl promoter, serves as an important element of the DdlR-binding site. This sequence is conserved upstream of putative DdlR targets in other bacteria of classes Clostridia and Bacilli, indicating a similar mode of regulation of these genes.
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Affiliation(s)
- Laurent Bouillaut
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - William Newton
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Abraham L Sonenshein
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Boris R Belitsky
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
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Wang C, Wang J, Yuan J, Jiang L, Jiang X, Yang B, Zhao G, Liu B, Huang D. Generation of
Streptomyces hygroscopicus
cell factories with enhanced ascomycin production by combined elicitation and pathway‐engineering strategies. Biotechnol Bioeng 2019; 116:3382-3395. [DOI: 10.1002/bit.27158] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/26/2019] [Accepted: 08/28/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Cheng Wang
- Department of Forestry Engineering, College of ForestryNorthwest A&F UniversityYangling Shaanxi China
| | - Junhua Wang
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin China
| | - Jian Yuan
- Key Laboratory of Molecular Microbiology and TechnologyMinistry of EducationTianjin China
- TEDA Institute of Biological Sciences and BiotechnologyNankai UniversityTianjin China
| | - Lingyan Jiang
- Key Laboratory of Molecular Microbiology and TechnologyMinistry of EducationTianjin China
- TEDA Institute of Biological Sciences and BiotechnologyNankai UniversityTianjin China
| | - Xiaolong Jiang
- Key Laboratory of Molecular Microbiology and TechnologyMinistry of EducationTianjin China
- TEDA Institute of Biological Sciences and BiotechnologyNankai UniversityTianjin China
| | - Bin Yang
- Key Laboratory of Molecular Microbiology and TechnologyMinistry of EducationTianjin China
- TEDA Institute of Biological Sciences and BiotechnologyNankai UniversityTianjin China
| | - Guang Zhao
- Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao Shandong China
| | - Bin Liu
- Key Laboratory of Molecular Microbiology and TechnologyMinistry of EducationTianjin China
- TEDA Institute of Biological Sciences and BiotechnologyNankai UniversityTianjin China
- Tianjin Key Laboratory of Microbial Functional GenomicsNankai UniversityTianjin China
| | - Di Huang
- Key Laboratory of Molecular Microbiology and TechnologyMinistry of EducationTianjin China
- TEDA Institute of Biological Sciences and BiotechnologyNankai UniversityTianjin China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and EngineeringNankai UniversityTianjin China
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Lemmens L, Tilleman L, De Koning E, Valegård K, Lindås AC, Van Nieuwerburgh F, Maes D, Peeters E. YtrA Sa, a GntR-Family Transcription Factor, Represses Two Genetic Loci Encoding Membrane Proteins in Sulfolobus acidocaldarius. Front Microbiol 2019; 10:2084. [PMID: 31552000 PMCID: PMC6746942 DOI: 10.3389/fmicb.2019.02084] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/23/2019] [Indexed: 11/25/2022] Open
Abstract
In bacteria, the GntR family is a widespread family of transcription factors responsible for the regulation of a myriad of biological processes. In contrast, despite their occurrence in archaea only a little information is available on the function of GntR-like transcription factors in this domain of life. The thermoacidophilic crenarchaeon Sulfolobus acidocaldarius harbors a GntR-like regulator belonging to the YtrA subfamily, encoded as the first gene in an operon with a second gene encoding a putative membrane protein. Here, we present a detailed characterization of this regulator, named YtrASa, with a focus on regulon determination and mechanistic analysis with regards to DNA binding. Genome-wide chromatin immunoprecipitation and transcriptome experiments, the latter employing a ytrASa overexpression strain, demonstrate that the regulator acts as a repressor on a very restricted regulon, consisting of only two targets including the operon encoding its own gene and a distinct genetic locus encoding another putative membrane protein. For both targets, a conserved 14-bp semi-palindromic binding motif was delineated that covers the transcriptional start site and that is surrounded by additional half-site motifs. The crystallographic structure of YtrASa was determined, revealing a compact dimeric structure in which the DNA-binding motifs are oriented ideally to enable a specific high-affinity interaction with the core binding motif. This study provides new insights into the functioning of a YtrA-like regulator in the archaeal domain of life.
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Affiliation(s)
- Liesbeth Lemmens
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Laurentijn Tilleman
- Laboratory for Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Ezra De Koning
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Karin Valegård
- Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Ann-Christin Lindås
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Filip Van Nieuwerburgh
- Laboratory for Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Dominique Maes
- Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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Elucidating the Role and Regulation of a Lactate Permease as Lactate Transporter in Bacillus coagulans DSM1. Appl Environ Microbiol 2019; 85:AEM.00672-19. [PMID: 31101607 DOI: 10.1128/aem.00672-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/07/2019] [Indexed: 01/17/2023] Open
Abstract
A key feature of Bacillus coagulans is its ability to produce l-lactate via homofermentative metabolism. A putative lactate permease-encoding gene (lutP) and the gene encoding its regulator (lutR) were identified in one operon in B. coagulans strains. LutP orthologs are highly conserved and located adjacent to the gene cluster related to lactate utilization in most lactate-utilizing microorganisms. However, no lactate utilization genes were found adjacent to lutP in all sequenced B. coagulans strains. The stand-alone presence of lutP in l-lactate producers indicates that it may have functions in lactate production. In this study, B. coagulans DSM1 was used as a representative strain, and the critical roles of LutP and its regulation were described. Transport property assays showed that LutP was essential for lactate uptake. Its regulator LutR directly interacted with the lutP-lutR intergenic region, and lutP transcription was activated by l-lactate via regulation by LutR. A biolayer interferometry assay further confirmed that LutR bound to an 11-bp inverted repeat in the intergenic region, and lutP transcription began when the binding of LutR to the lutP upstream sequence was inhibited. We conclusively showed that lutP encodes a functional lactate permease in B. coagulans IMPORTANCE Lactate-utilizing strains require lactate permease (LutP) to transport lactate into cells. Bacillus coagulans LutP is a previously uncharacterized lactate permease with no lactate utilization genes situated either adjacent to or remotely from it. In this study, an active lactate permease in an l-lactate producer, B. coagulans DSM1, was identified. Lactate supplementation regulated the expression of lactate permease. This study presents physiological evidence of the presence of a lactate transporter in B. coagulans Our findings indicate a potential target for the engineering of strains in order to improve their fermentation characteristics.
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63
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El Shazely B, Urbański A, Johnston PR, Rolff J. In vivo exposure of insect AMP resistant Staphylococcus aureus to an insect immune system. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 110:60-68. [PMID: 31051236 DOI: 10.1016/j.ibmb.2019.04.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 04/04/2019] [Accepted: 04/29/2019] [Indexed: 06/09/2023]
Abstract
Antimicrobial peptides (AMPs) are important immune effectors in insects. Bacteria have a limited number of ways to resist AMPs, and AMP-resistance is often costly. Recently, it has become clear that AMP activities in vitro and in vivo differ. Although some studies have followed the in vivo survival of AMP resistant pathogens, studying a pathogen resistant to the AMPs of that particular host has never been reported. Here, we infected the mealworm beetle Tenebrio molitor with Staphylococcus aureus strains that were evolved in vitro in the presence of one or two antimicrobial peptides from T. molitor. We found that the Tenebrio immune system could clear mutant Tenecin resistant strains at least as efficiently as sensitive controls. The bacterial load of Tenecin resistant S. aureus segregated by mutation. Strains with mutations in both the pmt and rpo operons showed the highest in vivo survival and therefore showed the lowest fitness cost amongst the evolved resistance mutations. In contrast, Tenecin resistant strains with mutations in the nsa and rpo operons showed much lower survival within the hosts. Our study shows that Tenecin resistant strains are phagocytosed at a lower rate. The nsa/rpo mutants were phagocytosed at a higher rate than other Tenecin resistant S. aureus strains. The differences in resistance against AMPs and phagocytosis did not translate into changes in virulence. AMP resistance, while a prerequisite for an infection in vertebrates, does not provide a survival advantage to S. aureus in a host environment that is dominated by AMPs.
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Affiliation(s)
- Baydaa El Shazely
- Evolutionary Biology, Institute for Biology, Free University of Berlin, Berlin, Germany; Zoology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Arkadiusz Urbański
- Department of Animal Physiology and Development, Faculty of Biology, Adam Mickiewicz University in Poznań, Poland
| | - Paul R Johnston
- Evolutionary Biology, Institute for Biology, Free University of Berlin, Berlin, Germany; Berlin Center for Genomics in Biodiversity Research, Berlin, Germany; Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Jens Rolff
- Evolutionary Biology, Institute for Biology, Free University of Berlin, Berlin, Germany; Berlin Center for Genomics in Biodiversity Research, Berlin, Germany; Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany.
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64
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Newman J, Caron K, Nebl T, Peat TS. Structures of the transcriptional regulator BgaR, a lactose sensor. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:639-646. [PMID: 31282473 DOI: 10.1107/s2059798319008131] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/06/2019] [Indexed: 11/10/2022]
Abstract
The structure of BgaR, a transcriptional regulator of the lactose operon in Clostridium perfringens, has been solved by SAD phasing using a mercury derivative. BgaR is an exquisite sensor of lactose, with a binding affinity in the low-micromolar range. This sensor and regulator has been captured bound to lactose and to lactulose as well as in a nominal apo form, and was compared with AraC, another saccharide-binding transcriptional regulator. It is shown that the saccharides bind in the N-terminal region of a jelly-roll fold, but that part of the saccharide is exposed to bulk solvent. This differs from the classical AraC saccharide-binding site, which is mostly sequestered from the bulk solvent. The structures of BgaR bound to lactose and to lactulose highlight how specific and nonspecific interactions lead to a higher binding affinity of BgaR for lactose compared with lactulose. Moreover, solving multiple structures of BgaR in different space groups, both bound to saccharides and unbound, verified that the dimer interface along a C-terminal helix is similar to the dimer interface observed in AraC.
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Affiliation(s)
- Janet Newman
- Biomedical Program, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Karine Caron
- Health and Biosecurity, CSIRO, Clunies Ross Street, Black Mountain, ACT 2601, Australia
| | - Tom Nebl
- Biomedical Program, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Thomas S Peat
- Biomedical Program, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
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Purtov YA, Tutukina MN, Nikulin AD, Ozoline ON. The Topology of the Contacts of Potential Ligands for the UxuR Transcription Factor of Escherichia coli as Revealed by Flexible Molecular Docking. Biophysics (Nagoya-shi) 2019. [DOI: 10.1134/s0006350919010160] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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66
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Identification of a GntR family regulator BusR Tha and its regulatory mechanism in the glycine betaine ABC transport system of Tetragenococcus halophilus. Extremophiles 2019; 23:451-460. [PMID: 31053934 DOI: 10.1007/s00792-019-01096-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/25/2019] [Indexed: 10/26/2022]
Abstract
Glycine betaine is one of the most effective compatible solutes of the halophilic lactic acid bacterium Tetragenococcus halophilus, the transportation of which is essential for its survival under salinity stress condition. In the current study, we attempted to define a glycine betaine ABC transporter system of T. halophilus, busATha, which plays an important role in adapting to salinity condition. The expression of busATha enhanced the growth of the recombinant strain under high salinity. BusRTha, a transcription regulator that represses the expression of busATha, was characterized, and the repression was abrogated under high salinity. The binding of the regulator was demonstrated through electrophoretic mobility shift assays, and the binding sites were characterized as 5'-AAA(T/G)TGAC(C/A)(G/A)T(C/A)C-3'. This is the first studied transcription regulator of T. halophilus, and our findings provide insights into the molecular mechanism of halophilic life and tools for further application of halophiles as chassis in industrial biotechnology.
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Pascarella S. Computational classification of MocR transcriptional regulators into subgroups as a support for experimental and functional characterization. Bioinformation 2019; 15:151-159. [PMID: 31435161 PMCID: PMC6677901 DOI: 10.6026/97320630015151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/03/2019] [Indexed: 11/23/2022] Open
Abstract
MocR bacterial transcriptional regulators are a subfamily within the GntR family. The MocR proteins possess an N-terminal domain containing the winged Helix-Turn-Helix (wHTH) motif and a C-terminal domain whose architecture is homologous to the fold type-I pyridoxal 5'-phosphate (PLP) dependent enzymes and whose archetypical protein is aspartate aminotransferase (AAT). The ancestor of the fold type-I PLP dependent super-family is considered one of the earliest enzymes. The members of this super-family are the product of evolution which resulted in a diversified protein population able to catalyze a set of reactions on substrates often containing amino groups. The MocR regulators are activators or repressors of gene control within many metabolic pathways often involving PLP enzymes. This diversity implies that MocR specifically responds to different classes of effector molecules. Therefore, it is of interest to compare the AAT domains of MocR from six bacteria phyla. Multi dimensional scaling and cluster analyses suggested that at least three subgroups exist within the population that reflects functional specialization rather than taxonomic origin. The AAT-domains of the three clusters display variable degree of similarity to different fold type-I PLP enzyme families. The results support the hypothesis that independent fusion events generated at least three different MocR subgroups.
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Affiliation(s)
- Stefano Pascarella
- Structural bioinformatics and Molecular modelling Lab;Dipartimento di Scienze biochimiche;Sapienza Universita di Roma;00185 Roma,Italy
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Molecular and Functional Insights into the Regulation of d-Galactonate Metabolism by the Transcriptional Regulator DgoR in Escherichia coli. J Bacteriol 2019; 201:JB.00281-18. [PMID: 30455279 DOI: 10.1128/jb.00281-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 11/07/2018] [Indexed: 12/11/2022] Open
Abstract
d-Galactonate, an aldonic sugar acid, is used as a carbon source by Escherichia coli, and the structural dgo genes involved in its metabolism have previously been investigated. Here, using genetic, biochemical and bioinformatics approaches, we present the first detailed molecular and functional insights into the regulation of d-galactonate metabolism in E. coli K-12 by the transcriptional regulator DgoR. We found that dgoR deletion accelerates the growth of E. coli in d-galactonate concomitant with the strong constitutive expression of dgo genes. In the dgo locus, sequence upstream of dgoR alone harbors the d-galactonate-inducible promoter that likely drives the expression of all dgo genes. DgoR exerts repression on the dgo operon by binding two inverted repeats overlapping the dgo promoter. Binding of d-galactonate induces a conformational change in DgoR to derepress the dgo operon. The findings from our work firmly place DgoR in the GntR family of transcriptional regulators: DgoR binds an operator sequence [5'-TTGTA(G/C)TACA(A/T)-3'] matching the signature of GntR family members that recognize inverted repeats [5'-(N) y GT(N) x AC(N) y -3', where x and y indicate the number of nucleotides, which varies], and it shares critical protein-DNA contacts. We also identified features in DgoR that are otherwise less conserved in the GntR family. Recently, missense mutations in dgoR were recovered in a natural E. coli isolate adapted to the mammalian gut. Our results show these mutants to be DNA binding defective, emphasizing that mutations in the dgo-regulatory elements are selected in the host to allow simultaneous induction of dgo genes. The present study sets the basis to explore the regulation of dgo genes in additional enterobacterial strains where they have been implicated in host-bacterium interactions.IMPORTANCE d-Galactonate is a widely prevalent aldonic sugar acid. Despite the proposed significance of the d-galactonate metabolic pathway in the interaction of enteric bacteria with their hosts, there are no details on its regulation even in Escherichia coli, which has been known to utilize d-galactonate since the 1970s. Here, using multiple methodologies, we identified the promoter, operator, and effector of DgoR, the transcriptional repressor of d-galactonate metabolism in E. coli We establish DgoR as a GntR family transcriptional regulator. Recently, a human urinary tract isolate of E. coli introduced in the mouse gut was found to accumulate missense mutations in dgoR Our results show these mutants to be DNA binding defective, hence emphasizing the role of the d-galactonate metabolic pathway in bacterial colonization of the mammalian gut.
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Lambrecht SJ, Wahlig JML, Steglich C. The GntR family transcriptional regulator PMM1637 regulates the highly conserved cyanobacterial sRNA Yfr2 in marine picocyanobacteria. DNA Res 2019; 25:489-497. [PMID: 29901694 PMCID: PMC6191309 DOI: 10.1093/dnares/dsy019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/14/2018] [Indexed: 11/21/2022] Open
Abstract
Prochlorococcus is a marine picocyanobacterium with a streamlined genome that is adapted to different ecological niches in the oligotrophic oceans. There are currently >20 regulatory small RNAs (sRNAs) that have been identified in the model strain Prochlorococcus MED4. While most of these sRNAs are ecotype-specific, sRNA homologs of Yfr1 and of the Yfr2 family are widely found throughout the cyanobacterial phylum. Although they were identified 13 yrs ago, the functions of Yfr1 and Yfr2 have remained unknown. We observed a strong induction of two Yfr2 sRNA homologs of Prochlorococcus MED4 during high light stress and nitrogen starvation. Several Prochlorococcus and marine Synechococcus yfr2 promoter regions contain a conserved motif we named CGRE1 (cyanobacterial GntR family transcriptional regulator responsive element 1). Using the conserved promoter region as bait in a DNA affinity pull-down assay we identified the GntR family transcriptional regulator PMM1637 as a binding partner. Similar to Yfr2, homologs of PMM1637 are universally and exclusively found in cyanobacteria. We suggest that PMM1637 governs the induction of gene expression of Yfr2 homologs containing CGRE1 in their promoters under nitrogen-depleted and high-light stress conditions.
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Affiliation(s)
- S Joke Lambrecht
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | - J Mascha L Wahlig
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | - Claudia Steglich
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
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Wetzel ME, Asenstorfer RE, Tate ME, Farrand SK. Quorum-dependent transfer of the opine-catabolic plasmid pAoF64/95 is regulated by a novel mechanism involving inhibition of the TraR antiactivator TraM. Microbiologyopen 2019; 8:e00625. [PMID: 29635848 PMCID: PMC6341043 DOI: 10.1002/mbo3.625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 01/27/2018] [Accepted: 01/30/2018] [Indexed: 11/06/2022] Open
Abstract
We previously described a plasmid of Agrobacterium spp., pAoF64/95, in which the quorum-sensing system that controls conjugative transfer is induced by the opine mannopine. We also showed that the quorum-sensing regulators TraR, TraM, and TraI function similarly to their counterparts in other repABC plasmids. However, traR, unlike its counterpart on Ti plasmids, is monocistronic and not located in an operon that is inducible by the conjugative opine. Here, we report that both traR and traM are expressed constitutively and not regulated by growth with mannopine. We report two additional regulatory genes, mrtR and tmsP, that are involved in a novel mechanism of control of TraR activity. Both genes are located in the distantly linked region of pAoF64/95 encoding mannopine utilization. MrtR, in the absence of mannopine, represses the four-gene mocC operon as well as tmsP, which is the distal gene of the eight-gene motA operon. As judged by a bacterial two-hybrid analysis, TmsP, which shows amino acid sequence relatedness with the TraM-binding domain of TraR, interacts with the antiactivator. We propose a model in which mannopine, acting through the repressor MrtR, induces expression of TmsP which then titrates the levels of TraM thereby freeing TraR to activate the tra regulon.
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Affiliation(s)
- Margaret E. Wetzel
- Department of MicrobiologyThe University of Illinois at Urbana‐ChampaignUrbanaILUSA
| | | | - Max E. Tate
- School of Agriculture, Food and WineThe University of AdelaideOsmondSAAustralia
| | - Stephen K. Farrand
- Department of MicrobiologyThe University of Illinois at Urbana‐ChampaignUrbanaILUSA
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71
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Ordóñez-Robles M, Rodríguez-García A, Martín JF. Genome-wide transcriptome response of Streptomyces tsukubaensis to N-acetylglucosamine: effect on tacrolimus biosynthesis. Microbiol Res 2018; 217:14-22. [DOI: 10.1016/j.micres.2018.08.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/04/2018] [Accepted: 08/29/2018] [Indexed: 11/29/2022]
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72
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Caron K, Trowell SC. Highly Sensitive and Selective Biosensor for a Disaccharide Based on an AraC-Like Transcriptional Regulator Transduced with Bioluminescence Resonance Energy Transfer. Anal Chem 2018; 90:12986-12993. [PMID: 30234965 DOI: 10.1021/acs.analchem.8b03689] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sensitive and selective quantification of individual sugars in complex media is technically challenging and usually requires HPLC separation. Accurate measurement without the need for separation would be highly desirable. The measurement of trace levels of lactose in lactose-reduced milk exemplifies the problem, with the added challenge that trace lactose must be measured in the presence of ≈140 mM glucose and galactose, the products of lactase digestion of lactose. Biosensing is an alternative to HPLC, but current biosensing methods, based on coupled-enzyme assays, tend to have poor sensitivity and complex biochemistry and can be time-consuming. We explored a fundamentally different approach, based on identifying a lactose-specific binding protein compatible with photonic transduction. We identified the BgaR transcriptional regulator of Clostridium perfringens, which is highly selective for lactose, as a suitable ligand binding domain and combined it with a bioluminescence energy resonance transfer transduction system. This BRET-based biosensor showed a 27% decrease in the BRET ratio in the presence of saturating (1 mM) lactose. Using a 5 min assay, the half maximal effective concentration (EC50) for lactose in phosphate-buffered saline (PBS) was 12 μM. The biosensor was 200 times more sensitive to lactose than to glucose or galactose. Sensitivity and selectivity were not significantly affected by the presence of 10% (v/v) dialyzed milk. The biosensor is suitable for direct determination of residual lactose in lactase-treated milk, with a limit of detection of 0.2 μM, 100 times below the most stringent lactose-free standard and without the need to remove fat or protein from the sample.
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Affiliation(s)
- Karine Caron
- CSIRO Health and Biosecurity , Canberra , Australian Capital Territory , 2601 , Australia
| | - Stephen C Trowell
- CSIRO Health and Biosecurity , Canberra , Australian Capital Territory , 2601 , Australia
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73
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Pinheiro J, Lisboa J, Pombinho R, Carvalho F, Carreaux A, Brito C, Pöntinen A, Korkeala H, dos Santos NM, Morais-Cabral JH, Sousa S, Cabanes D. MouR controls the expression of the Listeria monocytogenes Agr system and mediates virulence. Nucleic Acids Res 2018; 46:9338-9352. [PMID: 30011022 PMCID: PMC6182135 DOI: 10.1093/nar/gky624] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 06/25/2018] [Accepted: 06/28/2018] [Indexed: 12/11/2022] Open
Abstract
The foodborne pathogen Listeria monocytogenes (Lm) causes invasive infection in susceptible animals and humans. To survive and proliferate within hosts, this facultative intracellular pathogen tightly coordinates the expression of a complex regulatory network that controls the expression of virulence factors. Here, we identified and characterized MouR, a novel virulence regulator of Lm. Through RNA-seq transcriptomic analysis, we determined the MouR regulon and demonstrated how MouR positively controls the expression of the Agr quorum sensing system (agrBDCA) of Lm. The MouR three-dimensional structure revealed a dimeric DNA-binding transcription factor belonging to the VanR class of the GntR superfamily of regulatory proteins. We also showed that by directly binding to the agr promoter region, MouR ultimately modulates chitinase activity and biofilm formation. Importantly, we demonstrated by in vitro cell invasion assays and in vivo mice infections the role of MouR in Lm virulence.
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Affiliation(s)
- Jorge Pinheiro
- Group of Molecular Microbiology, IBMC – Institute for Molecular and Cell Biology; i3S – Institute for Research and Innovation in Health, Porto 4200-135, Portugal
- ICBAS- Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto 4200-135, Portugal
| | - Johnny Lisboa
- Group of Fish Immunology & Vaccinology, IBMC – Institute for Molecular and Cell Biology; i3S – Institute for Research and Innovation in Health, Porto 4200-135, Portugal
| | - Rita Pombinho
- Group of Molecular Microbiology, IBMC – Institute for Molecular and Cell Biology; i3S – Institute for Research and Innovation in Health, Porto 4200-135, Portugal
- ICBAS- Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto 4200-135, Portugal
| | - Filipe Carvalho
- Group of Molecular Microbiology, IBMC – Institute for Molecular and Cell Biology; i3S – Institute for Research and Innovation in Health, Porto 4200-135, Portugal
- ICBAS- Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto 4200-135, Portugal
| | - Alexis Carreaux
- Group of Molecular Microbiology, IBMC – Institute for Molecular and Cell Biology; i3S – Institute for Research and Innovation in Health, Porto 4200-135, Portugal
- SDV - UFR Sciences Du Vivant: Université Paris Diderot-Paris 7, Paris 75013, France
| | - Cláudia Brito
- Group of Molecular Microbiology, IBMC – Institute for Molecular and Cell Biology; i3S – Institute for Research and Innovation in Health, Porto 4200-135, Portugal
- ICBAS- Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto 4200-135, Portugal
| | - Anna Pöntinen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki 00014, Finland
| | - Hannu Korkeala
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki 00014, Finland
| | - Nuno M S dos Santos
- Group of Fish Immunology & Vaccinology, IBMC – Institute for Molecular and Cell Biology; i3S – Institute for Research and Innovation in Health, Porto 4200-135, Portugal
| | - João H Morais-Cabral
- Group of Structural Biochemistry, IBMC – Institute for Molecular and Cell Biology; i3S – Institute for Research and Innovation in Health, Porto 4200-135, Portugal
| | - Sandra Sousa
- Group of Molecular Microbiology, IBMC – Institute for Molecular and Cell Biology; i3S – Institute for Research and Innovation in Health, Porto 4200-135, Portugal
| | - Didier Cabanes
- Group of Molecular Microbiology, IBMC – Institute for Molecular and Cell Biology; i3S – Institute for Research and Innovation in Health, Porto 4200-135, Portugal
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Tanabe T, Isshiki A, Miyamoto K, Tsujibo H, Yamamoto S, Funahashi T. Transcriptional regulation of the ferric aerobactin receptor gene by a GntR-like repressor IutR in Vibrio furnissii. FEMS Microbiol Lett 2018; 365:5092603. [PMID: 30203068 DOI: 10.1093/femsle/fny220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 09/06/2018] [Indexed: 12/26/2022] Open
Abstract
We found that Vibrio furnissii can utilize aerobactin (AERO) as a xenosiderophore. A homology search of its genome revealed that this bacterium possesses genes encoding an AERO-mediated iron acquisition system similar to that of V. vulnificus. The system consists of the ABC transporter gene vatCDB, the GntR-type transcriptional repressor gene iutR, and the outer membrane receptor gene iutA. The functions of the vatCDB operon and iutA in V. furnissii were confirmed by the inability of the corresponding deletion mutants to utilize AERO. Reverse transcription-quantitative PCR revealed that iutA transcription under iron-limiting conditions was extensively activated by the addition of AERO to the growth medium; therefore, we focused on elucidating this phenomenon. Electrophoretic mobility shift and DNase I footprinting assays revealed that glutathione S-transferase-fused IutR (GST-IutR) bound directly to a specific palindromic sequence in the iutA promoter region. However, GST-IutR did not bind to this sequence when either AERO or ferric AERO was present in the assay mixture. These in vitro findings suggest that, under iron-limiting conditions, iutA transcription in V. furnissii is artfully regulated both by IutR, acting as a direct repressor of iutA, and by AERO, acting as an effector for IutR, leading to the derepression of iutA transcription.
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Affiliation(s)
- Tomotaka Tanabe
- Laboratory of Hygienic Chemistry, College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, 790-8578 Ehime, Japan
| | - Ayaka Isshiki
- Laboratory of Hygienic Chemistry, College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, 790-8578 Ehime, Japan
| | - Katsushiro Miyamoto
- Department of Microbiology, Osaka University of Pharmaceutical Sciences, Takatsuki, 569-1094 Osaka, Japan
| | - Hiroshi Tsujibo
- Department of Microbiology, Osaka University of Pharmaceutical Sciences, Takatsuki, 569-1094 Osaka, Japan
| | - Shigeo Yamamoto
- Laboratory of Hygienic Chemistry, College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, 790-8578 Ehime, Japan
| | - Tatsuya Funahashi
- Laboratory of Hygienic Chemistry, College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, 790-8578 Ehime, Japan
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Woods EC, Edwards AN, Childress KO, Jones JB, McBride SM. The C. difficile clnRAB operon initiates adaptations to the host environment in response to LL-37. PLoS Pathog 2018; 14:e1007153. [PMID: 30125334 PMCID: PMC6117091 DOI: 10.1371/journal.ppat.1007153] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/30/2018] [Accepted: 07/16/2018] [Indexed: 01/05/2023] Open
Abstract
To cause disease, Clostridioides (Clostridium) difficile must resist killing by innate immune effectors in the intestine, including the host antimicrobial peptide, cathelicidin (LL-37). The mechanisms that enable C. difficile to adapt to the intestine in the presence of antimicrobial peptides are unknown. Expression analyses revealed an operon, CD630_16170-CD630_16190 (clnRAB), which is highly induced by LL-37 and is not expressed in response to other cell-surface active antimicrobials. This operon encodes a predicted transcriptional regulator (ClnR) and an ABC transporter system (ClnAB), all of which are required for function. Analyses of a clnR mutant indicate that ClnR is a pleiotropic regulator that directly binds to LL-37 and controls expression of numerous genes, including many involved in metabolism, cellular transport, signaling, gene regulation, and pathogenesis. The data suggest that ClnRAB is a novel regulatory mechanism that senses LL-37 as a host signal and regulates gene expression to adapt to the host intestinal environment during infection.
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Affiliation(s)
- Emily C. Woods
- Department of Microbiology and Immunology, and Emory University Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, United States of America
| | - Adrianne N. Edwards
- Department of Microbiology and Immunology, and Emory University Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, United States of America
| | - Kevin O. Childress
- Department of Microbiology and Immunology, and Emory University Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, United States of America
| | - Joshua B. Jones
- Department of Microbiology and Immunology, and Emory University Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, United States of America
| | - Shonna M. McBride
- Department of Microbiology and Immunology, and Emory University Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, United States of America
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Casados-Vázquez LE, Bideshi DK, Barboza-Corona JE. Regulator ThnR and the ThnDE ABC transporter proteins confer autoimmunity to thurincin H in Bacillus thuringiensis. Antonie Van Leeuwenhoek 2018; 111:2349-2360. [DOI: 10.1007/s10482-018-1124-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/06/2018] [Indexed: 10/28/2022]
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Yousuf S, Angara RK, Roy A, Gupta SK, Misra R, Ranjan A. Mce2R/Rv0586 of Mycobacterium tuberculosis is the functional homologue of FadR E. coli. MICROBIOLOGY-SGM 2018; 164:1133-1145. [PMID: 29993358 DOI: 10.1099/mic.0.000686] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Lipid metabolism is critical to Mycobacterium tuberculosis survival and infection. Unlike Escherichia coli, which has a single FadR, the M. tuberculosis genome encodes five proteins of the FadR sub-family. While the role of E. coli FadR as a regulator of fatty acid metabolism is well known, the definitive functions of M. tuberculosis FadR proteins are still under investigation. An interesting question about the M. tuberculosis FadRs remains open: which one of these proteins is the functional homologue of E. coli FadR? To address this, we have applied two different approaches. The first one was the bioinformatics approach and the second one was the classical molecular genetic approach involving complementation studies. Surprisingly, the results of these two approaches did not agree. Among the five M. tuberculosis FadRs, Rv0494 shared the highest sequence similarity with FadRE. coli and Rv0586 was the second best match. However, only Rv0586, but not Rv0494, could complement E. coli ∆fadR, indicating that Rv0586 is the M. tuberculosis functional homologue of FadRE. coli. Further studies showed that both regulators, Rv0494 and Rv0586, show similar responsiveness to LCFA, and have conserved critical residues for DNA binding. However, analysis of the operator site indicated that the inter-palindromic distance required for DNA binding differs for the two regulators. The differences in the binding site selection helped in the success of Rv0586 binding to fadB upstream over Rv0494 and may have played a critical role in complementing E. coli ∆fadR. Further, for the first time, we report the lipid-responsive nature of Rv0586.
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Affiliation(s)
- Suhail Yousuf
- 1Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500039, India
- 2Graduate studies, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Rajendra Kumar Angara
- 1Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500039, India
- 2Graduate studies, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Ajit Roy
- 1Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500039, India
- 2Graduate studies, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Shailesh Kumar Gupta
- 1Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500039, India
- 2Graduate studies, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Rohan Misra
- 1Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500039, India
- 2Graduate studies, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Akash Ranjan
- 1Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, 500039, India
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78
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Tramonti A, Nardella C, di Salvo ML, Pascarella S, Contestabile R. The MocR-like transcription factors: pyridoxal 5'-phosphate-dependent regulators of bacterial metabolism. FEBS J 2018; 285:3925-3944. [PMID: 29974999 DOI: 10.1111/febs.14599] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/14/2018] [Accepted: 06/25/2018] [Indexed: 12/22/2022]
Abstract
Many biological functions played by current proteins were not created by evolution from scratch, rather they were obtained combining already available protein scaffolds. This is the case of MocR-like bacterial transcription factors (MocR-TFs), a subclass of GntR transcription regulators, whose structure is the outcome of the fusion between DNA-binding proteins and pyridoxal 5'-phosphate (PLP)-dependent enzymes. The resultant chimeras can count on the properties of both protein classes, i.e. the capability to recognize specific DNA sequences and to bind PLP and amino-compounds; it is the modulation of such binding properties to confer to MocR-TFs chimeras the ability to interact with effector molecules and DNA so as to regulate transcription. MocR-TFs control different metabolic processes involving vitamin B6 and amino acids, which are canonical ligands of PLP-dependent enzymes. However, MocR-TFs are also implicated in the metabolism of compounds that are not substrates of PLP-dependent enzymes, such as rhizopine and ectoine. Genomic analyses show that MocR-TFs are widespread among eubacteria, implying an essential role in their metabolism and highlighting the scarcity of our knowledge on these important players in microbial metabolism. Although MocR-TFs have been discovered 15 years ago, the research activity on these transcriptional regulators has only recently intensified, producing a wealth of information that needs to be brought back to general principles. This is the main task of this review, which reports and analyses the available information concerning MocR-TFs functional role, structural features, interaction with effector molecules and the characteristics of DNA transcriptional factor-binding sites of MocR-based regulatory systems.
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Affiliation(s)
- Angela Tramonti
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Roma, Italy.,Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Italy
| | - Caterina Nardella
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Italy
| | - Martino L di Salvo
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Italy
| | - Stefano Pascarella
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Italy
| | - Roberto Contestabile
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Italy
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79
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Interaction of the GntR-family transcription factor Sll1961 with thioredoxin in the cyanobacterium Synechocystis sp. PCC 6803. Sci Rep 2018; 8:6666. [PMID: 29703909 PMCID: PMC5923263 DOI: 10.1038/s41598-018-25077-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 04/16/2018] [Indexed: 11/23/2022] Open
Abstract
Changes in the redox state of the photosynthetic electron transport chain act as a signal to trigger acclimation responses to environmental cues and thioredoxin has been suggested to work as a key factor connecting the redox change with transcriptional regulation in the cyanobacterium Synechocystis sp. PCC 6803. We screened for redox-dependent transcription factors interacting with thioredoxin M (TrxM) and isolated the GntR-type transcription factor Sll1961 previously reported to be involved in acclimation responses of the photosynthetic machinery. Biochemical analyses using recombinant Sll1961 proteins of wild type and mutants of three cysteine residues, C124, C229 and C307, revealed that an intramolecular disulfide bond is formed between C229 and C307 under oxidizing conditions and TrxM can reduce it by attacking C307. Sll1961 exists in a dimeric form of about 80 kDa both under reducing and oxidizing conditions. C124 can form an intermolecular disulfide bond but it is not essential for dimerization. Based on these observations, tertiary structure models of the Sll1961 homodimer and the Sll1961-TrxM complex were constructed.
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80
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Zhou Y, Nie R, Liu X, Kong J, Wang X, Li J. GntR is involved in the expression of virulence in strain Streptococcus suis P1/7. FEMS Microbiol Lett 2018; 365:4964750. [DOI: 10.1093/femsle/fny091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/06/2018] [Indexed: 12/16/2022] Open
Affiliation(s)
- Ying Zhou
- Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, People's Republic of China
| | - Ruonan Nie
- Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, People's Republic of China
| | - Xiaoyue Liu
- Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, People's Republic of China
| | - Jinghui Kong
- Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, People's Republic of China
| | - Xiaohong Wang
- Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, People's Republic of China
| | - Jinquan Li
- Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, People's Republic of China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei, People's Republic of China
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81
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Czech L, Hermann L, Stöveken N, Richter AA, Höppner A, Smits SHJ, Heider J, Bremer E. Role of the Extremolytes Ectoine and Hydroxyectoine as Stress Protectants and Nutrients: Genetics, Phylogenomics, Biochemistry, and Structural Analysis. Genes (Basel) 2018; 9:genes9040177. [PMID: 29565833 PMCID: PMC5924519 DOI: 10.3390/genes9040177] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 03/13/2018] [Accepted: 03/15/2018] [Indexed: 01/26/2023] Open
Abstract
Fluctuations in environmental osmolarity are ubiquitous stress factors in many natural habitats of microorganisms, as they inevitably trigger osmotically instigated fluxes of water across the semi-permeable cytoplasmic membrane. Under hyperosmotic conditions, many microorganisms fend off the detrimental effects of water efflux and the ensuing dehydration of the cytoplasm and drop in turgor through the accumulation of a restricted class of organic osmolytes, the compatible solutes. Ectoine and its derivative 5-hydroxyectoine are prominent members of these compounds and are synthesized widely by members of the Bacteria and a few Archaea and Eukarya in response to high salinity/osmolarity and/or growth temperature extremes. Ectoines have excellent function-preserving properties, attributes that have led to their description as chemical chaperones and fostered the development of an industrial-scale biotechnological production process for their exploitation in biotechnology, skin care, and medicine. We review, here, the current knowledge on the biochemistry of the ectoine/hydroxyectoine biosynthetic enzymes and the available crystal structures of some of them, explore the genetics of the underlying biosynthetic genes and their transcriptional regulation, and present an extensive phylogenomic analysis of the ectoine/hydroxyectoine biosynthetic genes. In addition, we address the biochemistry, phylogenomics, and genetic regulation for the alternative use of ectoines as nutrients.
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Affiliation(s)
- Laura Czech
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
| | - Lucas Hermann
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
| | - Nadine Stöveken
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany.
| | - Alexandra A Richter
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
| | - Astrid Höppner
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, Universitäts Str. 1, D-40225 Düsseldorf, Germany.
| | - Sander H J Smits
- Center for Structural Studies, Heinrich-Heine University Düsseldorf, Universitäts Str. 1, D-40225 Düsseldorf, Germany.
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitäts Str. 1, D-40225 Düsseldorf, Germany.
| | - Johann Heider
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany.
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043 Marburg, Germany.
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany.
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82
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Milano T, Gulzar A, Narzi D, Guidoni L, Pascarella S. Molecular dynamics simulation unveils the conformational flexibility of the interdomain linker in the bacterial transcriptional regulator GabR from Bacillus subtilis bound to pyridoxal 5'-phosphate. PLoS One 2017; 12:e0189270. [PMID: 29253008 PMCID: PMC5734734 DOI: 10.1371/journal.pone.0189270] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 11/22/2017] [Indexed: 11/18/2022] Open
Abstract
GabR from Bacillus subtilis is a transcriptional regulator belonging to the MocR subfamily of the GntR regulators. The structure of the MocR regulators is characterized by the presence of two domains: i) a N-terminal domain, about 60 residue long, possessing the winged-Helix-Turn-Helix (wHTH) architecture with DNA recognition and binding capability; ii) a C-terminal domain (about 350 residue) folded as the pyridoxal 5'-phosphate (PLP) dependent aspartate aminotransferase (AAT) with dimerization and effector binding functions. The two domains are linked to each other by a peptide bridge. Although structural and functional characterization of MocRs is proceeding at a fast pace, virtually nothing is know about the molecular changes induced by the effector binding and on how these modifications influence the properties of the regulator. An extensive molecular dynamics simulation on the crystallographic structure of the homodimeric B. subtilis GabR has been undertaken with the aim to envisage the role and the importance of conformational flexibility in the action of GabR. Molecular dynamics has been calculated for the apo (without PLP) and holo (with PLP bound) forms of the GabR. A comparison between the molecular dynamics trajectories calculated for the two GabR forms suggested that one of the wHTH domain detaches from the AAT-like domain in the GabR PLP-bound form. The most evident conformational change in the holo PLP-bound form is represented by the rotation and the subsequent detachment from the subunit surface of one of the wHTH domains. The movement is mediated by a rearrangement of the linker connecting the AAT domain possibly triggered by the presence of the negative charge of the PLP cofactor. This is the second most significant conformational modification. The C-terminal section of the linker docks into the "active site" pocket and establish stabilizing contacts consisting of hydrogen-bonds, salt-bridges and hydrophobic interactions.
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Affiliation(s)
- Teresa Milano
- Dipartimento di Scienze biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Italy
| | - Adnan Gulzar
- Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi dell’Aquila, L’Aquila, Italy
| | - Daniele Narzi
- Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi dell’Aquila, L’Aquila, Italy
| | - Leonardo Guidoni
- Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi dell’Aquila, L’Aquila, Italy
| | - Stefano Pascarella
- Dipartimento di Scienze biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Italy
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83
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Schulz A, Hermann L, Freibert SA, Bönig T, Hoffmann T, Riclea R, Dickschat JS, Heider J, Bremer E. Transcriptional regulation of ectoine catabolism in response to multiple metabolic and environmental cues. Environ Microbiol 2017; 19:4599-4619. [PMID: 28892254 DOI: 10.1111/1462-2920.13924] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 08/29/2017] [Accepted: 08/31/2017] [Indexed: 01/04/2023]
Abstract
Ectoine and hydroxyectoine are effective microbial osmostress protectants, but can also serve as versatile nutrients for bacteria. We have studied the genetic regulation of ectoine and hydroxyectoine import and catabolism in the marine Roseobacter species Ruegeria pomeroyi and identified three transcriptional regulators involved in these processes: the GabR/MocR-type repressor EnuR, the feast and famine-type regulator AsnC and the two-component system NtrYX. The corresponding genes are widely associated with ectoine and hydroxyectoine uptake and catabolic gene clusters (enuR, asnC), and with microorganisms predicted to consume ectoines (ntrYX). EnuR contains a covalently bound pyridoxal-5'-phosphate as a co-factor and the chemistry underlying the functioning of MocR/GabR-type regulators typically requires a system-specific low molecular mass effector molecule. Through ligand binding studies with purified EnuR, we identified N-(alpha)-L-acetyl-2,4-diaminobutyric acid and L-2,4-diaminobutyric acid as inducers for EnuR that are generated through ectoine catabolism. AsnC/Lrp-type proteins can wrap DNA into nucleosome-like structures, and we found that the asnC gene was essential for use of ectoines as nutrients. Furthermore, we discovered through transposon mutagenesis that the NtrYX two-component system is required for their catabolism. Database searches suggest that our findings have important ramifications for an understanding of the molecular biology of most microbial consumers of ectoines.
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Affiliation(s)
- Annina Schulz
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, D-35043 Marburg, Germany
| | - Lucas Hermann
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, D-35043 Marburg, Germany
| | - Sven-Andreas Freibert
- Department of Medicine, Institute for Cytobiology and Cytopathology, Philipps-University Marburg, Robert-Koch Str. 6, D-35032 Marburg, Germany
| | - Tobias Bönig
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, D-35043 Marburg, Germany
| | - Tamara Hoffmann
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, D-35043 Marburg, Germany
| | - Ramona Riclea
- Institute of Organic Chemistry, Technical University Braunschweig, D-38106 Braunschweig, Germany.,Kekulé-Institute for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-Universität Bonn, D-53121 Bonn, Germany
| | - Jeroen S Dickschat
- Institute of Organic Chemistry, Technical University Braunschweig, D-38106 Braunschweig, Germany.,Kekulé-Institute for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-Universität Bonn, D-53121 Bonn, Germany
| | - Johann Heider
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, D-35043 Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, D-35043 Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, D-35043 Marburg, Germany
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84
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Matelska D, Steczkiewicz K, Ginalski K. Comprehensive classification of the PIN domain-like superfamily. Nucleic Acids Res 2017; 45:6995-7020. [PMID: 28575517 PMCID: PMC5499597 DOI: 10.1093/nar/gkx494] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 05/24/2017] [Indexed: 12/21/2022] Open
Abstract
PIN-like domains constitute a widespread superfamily of nucleases, diverse in terms of the reaction mechanism, substrate specificity, biological function and taxonomic distribution. Proteins with PIN-like domains are involved in central cellular processes, such as DNA replication and repair, mRNA degradation, transcription regulation and ncRNA maturation. In this work, we identify and classify the most complete set of PIN-like domains to provide the first comprehensive analysis of sequence–structure–function relationships within the whole PIN domain-like superfamily. Transitive sequence searches using highly sensitive methods for remote homology detection led to the identification of several new families, including representatives of Pfam (DUF1308, DUF4935) and CDD (COG2454), and 23 other families not classified in the public domain databases. Further sequence clustering revealed relationships between individual sequence clusters and showed heterogeneity within some families, suggesting a possible functional divergence. With five structural groups, 70 defined clusters, over 100,000 proteins, and broad biological functions, the PIN domain-like superfamily constitutes one of the largest and most diverse nuclease superfamilies. Detailed analyses of sequences and structures, domain architectures, and genomic contexts allowed us to predict biological function of several new families, including new toxin-antitoxin components, proteins involved in tRNA/rRNA maturation and transcription/translation regulation.
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Affiliation(s)
- Dorota Matelska
- University of Warsaw, CeNT, Laboratory of Bioinformatics and Systems Biology, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Kamil Steczkiewicz
- University of Warsaw, CeNT, Laboratory of Bioinformatics and Systems Biology, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Krzysztof Ginalski
- University of Warsaw, CeNT, Laboratory of Bioinformatics and Systems Biology, Zwirki i Wigury 93, 02-089 Warsaw, Poland
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85
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Okrent RA, Trippe KM, Maselko M, Manning V. Functional analysis of a biosynthetic cluster essential for production of 4-formylaminooxyvinylglycine, a germination-arrest factor from Pseudomonas fluorescens WH6. MICROBIOLOGY-SGM 2017; 163:207-217. [PMID: 28270265 DOI: 10.1099/mic.0.000418] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Rhizosphere-associated Pseudomonas fluorescens WH6 produces the germination-arrest factor 4-formylaminooxyvinylglycine (FVG). FVG has previously been shown to both arrest the germination of weedy grasses and inhibit the growth of the bacterial plant pathogen Erwinia amylovora. Very little is known about the mechanism by which FVG is produced. Although a previous study identified a region of the genome that may be involved in FVG biosynthesis, it has not yet been determined which genes within that region are sufficient and necessary for FVG production. In the current study, we explored the role of each of the putative genes encoded in that region by constructing deletion mutations. Mutant strains were assayed for their ability to produce FVG with a combination of biological assays and TLC analyses. This work defined the core FVG biosynthetic gene cluster and revealed several interesting characteristics of FVG production. We determined that FVG biosynthesis requires two small ORFs of less than 150 nucleotides and that multiple transporters have overlapping but distinct functionality. In addition, two genes in the centre of the biosynthetic gene cluster are not required for FVG production, suggesting that additional products may be produced from the cluster. Transcriptional analysis indicated that at least three active promoters play a role in the expression of genes within this cluster. The results of this study enrich our knowledge regarding the diversity of mechanisms by which bacteria produce non-proteinogenic amino acids like vinylglycines.
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Affiliation(s)
- Rachel A Okrent
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.,USDA-ARS Forage Seed and Cereal Research Unit, Corvallis, OR, USA
| | - Kristin M Trippe
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, USA.,USDA-ARS Forage Seed and Cereal Research Unit, Corvallis, OR, USA
| | - Maciej Maselko
- Present address: Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN, USA.,USDA-ARS Forage Seed and Cereal Research Unit, Corvallis, OR, USA
| | - Viola Manning
- USDA-ARS Forage Seed and Cereal Research Unit, Corvallis, OR, USA
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86
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Li Z, Wang S, Zhang H, Xi L, Zhang J, Zhang X, Han J, Zhang J. Immunization with recombinant GntR plasmid confers protection against Brucella challenge in BALB/c mice. Microb Pathog 2017; 111:357-361. [PMID: 28916314 DOI: 10.1016/j.micpath.2017.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 07/27/2017] [Accepted: 09/11/2017] [Indexed: 10/18/2022]
Abstract
It is essential to improve animal vaccine for brucellosis since conventional vaccines are residual virulent and poor protective effect, limit their applications. To solve these problems, the recombinant DNA vaccines were appeared, which could improve protective immunity and were attenuated to animals. In current research, the recombinant DNA vaccine (pVGntR) based on transcriptional regulator GntR of Brucella abortus (B. abortus) was constructed. The results show that pVGntR is significantly more protective than the conventional RB51 vaccine. Immunization with pVGntR increases the production of immunoglobulin G (IgG) and elicits elevated numbers of gamma interferon (IFN-γ) and interleukin-4 (IL-4). These results suggest that pVGntR is a highly efficacious vaccine candidate that confers protection against wild-type B. abortus challenge.
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Affiliation(s)
- Zhiqiang Li
- School of Biotechnology and Food, Shangqiu Normal University, Shangqiu 476000, Henan, China
| | - Shuli Wang
- School of Biotechnology and Food, Shangqiu Normal University, Shangqiu 476000, Henan, China
| | - Hui Zhang
- College of Animal Science and Technology, Shihezi University, Shihezi 832003, Xinjiang, China.
| | - Li Xi
- School of Biotechnology and Food, Shangqiu Normal University, Shangqiu 476000, Henan, China
| | - Jinliang Zhang
- School of Biotechnology and Food, Shangqiu Normal University, Shangqiu 476000, Henan, China
| | - Xiaogen Zhang
- School of Biotechnology and Food, Shangqiu Normal University, Shangqiu 476000, Henan, China
| | - Jincheng Han
- School of Biotechnology and Food, Shangqiu Normal University, Shangqiu 476000, Henan, China
| | - Junbo Zhang
- College of Biology, Agriculture and Forestry, Tongren University, Tongren 554300, Guizhou, China
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87
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Yesudhas D, Batool M, Anwar MA, Panneerselvam S, Choi S. Proteins Recognizing DNA: Structural Uniqueness and Versatility of DNA-Binding Domains in Stem Cell Transcription Factors. Genes (Basel) 2017; 8:genes8080192. [PMID: 28763006 PMCID: PMC5575656 DOI: 10.3390/genes8080192] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/22/2017] [Accepted: 07/25/2017] [Indexed: 12/17/2022] Open
Abstract
Proteins in the form of transcription factors (TFs) bind to specific DNA sites that regulate cell growth, differentiation, and cell development. The interactions between proteins and DNA are important toward maintaining and expressing genetic information. Without knowing TFs structures and DNA-binding properties, it is difficult to completely understand the mechanisms by which genetic information is transferred between DNA and proteins. The increasing availability of structural data on protein-DNA complexes and recognition mechanisms provides deeper insights into the nature of protein-DNA interactions and therefore, allows their manipulation. TFs utilize different mechanisms to recognize their cognate DNA (direct and indirect readouts). In this review, we focus on these recognition mechanisms as well as on the analysis of the DNA-binding domains of stem cell TFs, discussing the relative role of various amino acids toward facilitating such interactions. Unveiling such mechanisms will improve our understanding of the molecular pathways through which TFs are involved in repressing and activating gene expression.
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Affiliation(s)
- Dhanusha Yesudhas
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Maria Batool
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Muhammad Ayaz Anwar
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Suresh Panneerselvam
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
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88
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Chu HY, Sprouffske K, Wagner A. The role of recombination in evolutionary adaptation of Escherichia coli to a novel nutrient. J Evol Biol 2017; 30:1692-1711. [PMID: 28612351 DOI: 10.1111/jeb.13132] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/11/2017] [Accepted: 06/05/2017] [Indexed: 12/11/2022]
Abstract
The benefits and detriments of recombination for adaptive evolution have been studied both theoretically and experimentally, with conflicting predictions and observations. Most pertinent experiments examine recombination's effects in an unchanging environment and do not study its genomewide effects. Here, we evolved six replicate populations of either highly recombining R+ or lowly recombining R- E. coli strains in a changing environment, by introducing the novel nutrients L-arabinose or indole into the environment. The experiment's ancestral strains are not viable on these nutrients, but 130 generations of adaptive evolution were sufficient to render them viable. Recombination conferred a more pronounced advantage to populations adapting to indole. To study the genomic changes associated with this advantage, we sequenced the genomes of 384 clones isolated from selected replicates at the end of the experiment. These genomes harbour complex changes that range from point mutations to large-scale DNA amplifications. Among several candidate adaptive mutations, those in the tryptophanase regulator tnaC stand out, because the tna operon in which it resides has a known role in indole metabolism. One of the highly recombining populations also shows a significant excess of large-scale segmental DNA amplifications that include the tna operon. This lineage also shows a unique and potentially adaptive combination of point mutations and DNA amplifications that may have originated independently from one another, to be joined later by recombination. Our data illustrate that the advantages of recombination for adaptive evolution strongly depend on the environment and that they can be associated with complex genomic changes.
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Affiliation(s)
- H-Y Chu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - K Sprouffske
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - A Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,The Swiss Institute of Bioinformatics, Quartier Sorge, Batiment Genopode, Lausanne, Switzerland.,The Santa Fe Institute, Santa Fe, NM, USA
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89
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Control of gdhR Expression in Neisseria gonorrhoeae via Autoregulation and a Master Repressor (MtrR) of a Drug Efflux Pump Operon. mBio 2017; 8:mBio.00449-17. [PMID: 28400529 PMCID: PMC5388806 DOI: 10.1128/mbio.00449-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The MtrCDE efflux pump of Neisseria gonorrhoeae contributes to gonococcal resistance to a number of antibiotics used previously or currently in treatment of gonorrhea, as well as to host-derived antimicrobials that participate in innate defense. Overexpression of the MtrCDE efflux pump increases gonococcal survival and fitness during experimental lower genital tract infection of female mice. Transcription of mtrCDE can be repressed by the DNA-binding protein MtrR, which also acts as a global regulator of genes involved in important metabolic, physiologic, or regulatory processes. Here, we investigated whether a gene downstream of mtrCDE, previously annotated gdhR in Neisseria meningitidis, is a target for regulation by MtrR. In meningococci, GdhR serves as a regulator of genes involved in glucose catabolism, amino acid transport, and biosynthesis, including gdhA, which encodes an l-glutamate dehydrogenase and is located next to gdhR but is transcriptionally divergent. We report here that in N. gonorrhoeae, expression of gdhR is subject to autoregulation by GdhR and direct repression by MtrR. Importantly, loss of GdhR significantly increased gonococcal fitness compared to a complemented mutant strain during experimental murine infection. Interestingly, loss of GdhR did not influence expression of gdhA, as reported for meningococci. This variance is most likely due to differences in promoter localization and utilization between gonococci and meningococci. We propose that transcriptional control of gonococcal genes through the action of MtrR and GdhR contributes to fitness of N. gonorrhoeae during infection.IMPORTANCE The pathogenic Neisseria species are strict human pathogens that can cause a sexually transmitted infection (N. gonorrhoeae) or meningitis or fulminant septicemia (N. meningitidis). Although they share considerable genetic information, little attention has been directed to comparing transcriptional regulatory systems that modulate expression of their conserved genes. We hypothesized that transcriptional regulatory differences exist between these two pathogens, and we used the gdh locus as a model to test this idea. For this purpose, we studied two conserved genes (gdhR and gdhA) within the locus. Despite general conservation of the gdh locus in gonococci and meningococci, differences exist in noncoding sequences that correspond to promoter elements or potential sites for interacting with DNA-binding proteins, such as GdhR and MtrR. Our results indicate that implications drawn from studying regulation of conserved genes in one pathogen are not necessarily translatable to a genetically related pathogen.
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90
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PLP and GABA trigger GabR-mediated transcription regulation in Bacillus subtilis via external aldimine formation. Proc Natl Acad Sci U S A 2017; 114:3891-3896. [PMID: 28348215 DOI: 10.1073/pnas.1703019114] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Bacillus subtilis protein regulator of the gabTD operon and its own gene (GabR) is a transcriptional activator that regulates transcription of γ-aminobutyric acid aminotransferase (GABA-AT; GabT) upon interactions with pyridoxal-5'-phosphate (PLP) and GABA, and thereby promotes the biosynthesis of glutamate from GABA. We show here that the external aldimine formed between PLP and GABA is apparently responsible for triggering the GabR-mediated transcription activation. Details of the "active site" in the structure of the GabR effector-binding/oligomerization (Eb/O) domain suggest that binding a monocarboxylic γ-amino acid such as GABA should be preferred over dicarboxylic acid ligands. A reactive GABA analog, (S)-4-amino-5-fluoropentanoic acid (AFPA), was used as a molecular probe to examine the reactivity of PLP in both GabR and a homologous aspartate aminotransferase (Asp-AT) from Escherichia coli as a control. A comparison between the structures of the Eb/O-PLP-AFPA complex and Asp-AT-PLP-AFPA complex revealed that GabR is incapable of facilitating further steps of the transamination reaction after the formation of the external aldimine. Results of in vitro and in vivo assays using full-length GabR support the conclusion that AFPA is an agonistic ligand capable of triggering GabR-mediated transcription activation via formation of an external aldimine with PLP.
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91
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Ibáñez MI, Cabello P, Luque-Almagro VM, Sáez LP, Olaya A, Sánchez de Medina V, Luque de Castro MD, Moreno-Vivián C, Roldán MD. Quantitative proteomic analysis of Pseudomonas pseudoalcaligenes CECT5344 in response to industrial cyanide-containing wastewaters using Liquid Chromatography-Mass Spectrometry/Mass Spectrometry (LC-MS/MS). PLoS One 2017; 12:e0172908. [PMID: 28253357 PMCID: PMC5333837 DOI: 10.1371/journal.pone.0172908] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/31/2017] [Indexed: 11/20/2022] Open
Abstract
Biological treatments to degrade cyanide are a powerful technology for cyanide removal from industrial wastewaters. It has been previously demonstrated that the alkaliphilic bacterium Pseudomonas pseudoalcaligenes CECT5344 is able to use free cyanide and several metal−cyanide complexes as the sole nitrogen source. In this work, the strain CECT5344 has been used for detoxification of the different chemical forms of cyanide that are present in alkaline wastewaters from the jewelry industry. This liquid residue also contains large concentrations of metals like iron, copper and zinc, making this wastewater even more toxic. To elucidate the molecular mechanisms involved in the bioremediation process, a quantitative proteomic analysis by LC-MS/MS has been carried out in P. pseudoalcaligenes CECT5344 cells grown with the jewelry residue as sole nitrogen source. Different proteins related to cyanide and cyanate assimilation, as well as other proteins involved in transport and resistance to metals were induced by the cyanide-containing jewelry residue. GntR-like regulatory proteins were also induced by this industrial residue and mutational analysis revealed that GntR-like regulatory proteins may play a role in the regulation of cyanide assimilation in P. pseudoalcaligenes CECT5344. The strain CECT5344 has been used in a batch reactor to remove at pH 9 the different forms of cyanide present in industrial wastewaters from the jewelry industry (0.3 g/L, ca. 12 mM total cyanide, including both free cyanide and metal−cyanide complexes). This is the first report describing the biological removal at alkaline pH of such as elevated concentration of cyanide present in a heterogeneous mixture from an industrial source.
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Affiliation(s)
- María Isabel Ibáñez
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Purificación Cabello
- Departamento de Botánica, Ecología y Fisiología Vegetal, Edificio Celestino Mutis, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Víctor Manuel Luque-Almagro
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Lara P. Sáez
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Alfonso Olaya
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Verónica Sánchez de Medina
- Departamento de Química Analítica, Edificio Marie Curie, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - María Dolores Luque de Castro
- Departamento de Química Analítica, Edificio Marie Curie, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - Conrado Moreno-Vivián
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
| | - María Dolores Roldán
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, Córdoba, Spain
- * E-mail:
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92
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Zhou X, Yan Q, Wang N. Deciphering the regulon of a GntR family regulator via transcriptome and ChIP-exo analyses and its contribution to virulence in Xanthomonas citri. MOLECULAR PLANT PATHOLOGY 2017; 18:249-262. [PMID: 26972728 PMCID: PMC6638223 DOI: 10.1111/mpp.12397] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 02/08/2016] [Accepted: 03/07/2016] [Indexed: 05/14/2023]
Abstract
Xanthomonas contains a large group of plant-associated species, many of which cause severe diseases on important crops worldwide. Six gluconate-operon repressor (GntR) family transcriptional regulators are predicted in Xanthomonas, one of which, belonging to the YtrA subfamily, plays a prominent role in bacterial virulence. However, the direct targets and comprehensive regulatory profile of YtrA remain unknown. Here, we performed microarray and high-resolution chromatin immunoprecipitation-exonuclease (ChIP-exo) experiments to identify YtrA direct targets and its DNA binding motif in X. citri ssp. citri (Xac), the causal agent of citrus canker. Integrative microarray and ChIP-exo data analysis revealed that YtrA directly regulates three operons by binding to a palindromic motif GGTG-N16 -CACC at the promoter region. A similar palindromic motif and YtrA homologues were also identified in many other bacteria, including Stenotrophomonas, Pseudoxanthomonas and Frateuria, indicating a widespread phenomenon. Deletion of ytrA in Xac abolishes bacterial virulence and induction of the hypersensitive response (HR). We found that YtrA regulates the expression of hrp/hrc genes encoding the bacterial type III secretion system (T3SS) and controls multiple biological processes, including motility and adhesion, oxidative stress, extracellular enzyme production and iron uptake. YtrA represses the expression of its direct targets in artificial medium or in planta. Importantly, over-expression of yro3, one of the YtrA directly regulated operons which contains trmL and XAC0231, induced weaker canker symptoms and down-regulation of hrp/hrc gene expression, suggesting a negative regulation in Xac virulence and T3SS. Our study has significantly advanced the mechanistic understanding of YtrA regulation and its contribution to bacterial virulence.
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Affiliation(s)
- Xiaofeng Zhou
- Citrus Research and Education CenterDepartment of Microbiology and Cell Science, IFAS, University of Florida700 Experiment Station RoadLake AlfredFL33850USA
| | - Qing Yan
- Citrus Research and Education CenterDepartment of Microbiology and Cell Science, IFAS, University of Florida700 Experiment Station RoadLake AlfredFL33850USA
| | - Nian Wang
- Citrus Research and Education CenterDepartment of Microbiology and Cell Science, IFAS, University of Florida700 Experiment Station RoadLake AlfredFL33850USA
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93
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Tramonti A, Milano T, Nardella C, di Salvo ML, Pascarella S, Contestabile R. Salmonella typhimurium PtsJ is a novel MocR-like transcriptional repressor involved in regulating the vitamin B 6 salvage pathway. FEBS J 2017; 284:466-484. [PMID: 27987384 DOI: 10.1111/febs.13994] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 12/09/2016] [Accepted: 12/13/2016] [Indexed: 12/11/2022]
Abstract
The vitamin B6 salvage pathway, involving pyridoxine 5'-phosphate oxidase (PNPOx) and pyridoxal kinase (PLK), recycles B6 vitamers from nutrients and protein turnover to produce pyridoxal 5'-phosphate (PLP), the catalytically active form of the vitamin. Regulation of this pathway, widespread in living organisms including humans and many bacteria, is very important to vitamin B6 homeostasis but poorly understood. Although some information is available on the enzymatic regulation of PNPOx and PLK, little is known on their regulation at the transcriptional level. In the present work, we identified a new MocR-like regulator, PtsJ from Salmonella typhimurium, which controls the expression of the pdxK gene encoding one of the two PLKs expressed in this organism (PLK1). Analysis of pdxK expression in a ptsJ knockout strain demonstrated that PtsJ acts as a transcriptional repressor. This is the first case of a MocR-like regulator acting as repressor of its target gene. Expression and purification of PtsJ allowed a detailed characterisation of its effector and DNA-binding properties. PLP is the only B6 vitamer acting as effector molecule for PtsJ. A DNA-binding region composed of four repeated nucleotide sequences is responsible for binding of PtsJ to its target promoter. Analysis of binding stoichiometry revealed that protein subunits/DNA molar ratio varies from 4 : 1 to 2 : 1, depending on the presence or absence of PLP. Structural characteristics of DNA transcriptional factor-binding sites suggest that PtsJ binds DNA according to a different model with respect to other characterised members of the MocR subgroup.
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Affiliation(s)
- Angela Tramonti
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy.,Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Teresa Milano
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Caterina Nardella
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Martino L di Salvo
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Stefano Pascarella
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Roberto Contestabile
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
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94
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Negative Regulation of Ectoine Uptake and Catabolism in Sinorhizobium meliloti: Characterization of the EhuR Gene. J Bacteriol 2016; 199:JB.00119-16. [PMID: 27795315 DOI: 10.1128/jb.00119-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 09/20/2016] [Indexed: 12/21/2022] Open
Abstract
Ectoine has osmoprotective effects on Sinorhizobium meliloti that differ from its effects in other bacteria. Ectoine does not accumulate in S. meliloti cells; instead, it is degraded. The products of the ehuABCD-eutABCDE operon were previously discovered to be responsible for the uptake and catabolism of ectoine in S. meliloti However, the mechanism by which ectoine is involved in the regulation of the ehuABCD-eutABCDE operon remains unclear. The ehuR gene, which is upstream of and oriented in the same direction as the ehuABCD-eutABCDE operon, encodes a member of the MocR/GntR family of transcriptional regulators. Quantitative reverse transcription-PCR and promoter-lacZ reporter fusion experiments revealed that EhuR represses transcription of the ehuABCD-eutABCDE operon, but this repression is inhibited in the presence of ectoine. Electrophoretic mobility shift assays and DNase I footprinting assays revealed that EhuR bound specifically to the DNA regions overlapping the -35 region of the ehuA promoter and the +1 region of the ehuR promoter. Surface plasmon resonance assays further demonstrated direct interactions between EhuR and the two promoters, although EhuR was found to have higher affinity for the ehuA promoter than for the ehuR promoter. In vitro, DNA binding by EhuR could be directly inhibited by a degradation product of ectoine. Our work demonstrates that EhuR is an important negative transcriptional regulator involved in the regulation of ectoine uptake and catabolism and is likely regulated by one or more end products of ectoine catabolism. IMPORTANCE Sinorhizobium meliloti is an important soil bacterium that displays symbiotic interactions with legume hosts. Ectoine serves as a key osmoprotectant for S. meliloti However, ectoine does not accumulate in the cells; rather, it is degraded. In this study, we characterized the transcriptional regulation of the operon responsible for ectoine uptake and catabolism in S. meliloti We identified and characterized the transcription repressor EhuR, which is the first MocR/GntR family member found to be involved in the regulation of compatible solute uptake and catabolism. More importantly, we demonstrated for the first time that an ectoine catabolic end product could modulate EhuR DNA-binding activity. Therefore, this work provides new insights into the unique mechanism of ectoine-induced osmoprotection in S. meliloti.
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95
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Labella JI, Obrebska A, Espinosa J, Salinas P, Forcada-Nadal A, Tremiño L, Rubio V, Contreras A. Expanding the Cyanobacterial Nitrogen Regulatory Network: The GntR-Like Regulator PlmA Interacts with the PII-PipX Complex. Front Microbiol 2016; 7:1677. [PMID: 27840625 PMCID: PMC5083789 DOI: 10.3389/fmicb.2016.01677] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/06/2016] [Indexed: 11/17/2022] Open
Abstract
Cyanobacteria, phototrophic organisms that perform oxygenic photosynthesis, perceive nitrogen status by sensing 2-oxoglutarate levels. PII, a widespread signaling protein, senses and transduces nitrogen and energy status to target proteins, regulating metabolism and gene expression. In cyanobacteria, under conditions of low 2-oxoglutarate, PII forms complexes with the enzyme N-acetyl glutamate kinase, increasing arginine biosynthesis, and with PII-interacting protein X (PipX), making PipX unavailable for binding and co-activation of the nitrogen regulator NtcA. Both the PII-PipX complex structure and in vivo functional data suggested that this complex, as such, could have regulatory functions in addition to PipX sequestration. To investigate this possibility we performed yeast three-hybrid screening of genomic libraries from Synechococcus elongatus PCC7942, searching for proteins interacting simultaneously with PII and PipX. The only prey clone found in the search expressed PlmA, a member of the GntR family of transcriptional regulators proven here by gel filtration to be homodimeric. Interactions analyses further confirmed the simultaneous requirement of PII and PipX, and showed that the PlmA contacts involve PipX elements exposed in the PII-PipX complex, specifically the C-terminal helices and one residue of the tudor-like body. In contrast, PII appears not to interact directly with PlmA, possibly being needed indirectly, to induce an extended conformation of the C-terminal helices of PipX and for modulating the surface polarity at the PII-PipX boundary, two elements that appear crucial for PlmA binding. Attempts to inactive plmA confirmed that this gene is essential in S. elongatus. Western blot assays revealed that S. elongatus PlmA, irrespective of the nitrogen regime, is a relatively abundant transcriptional regulator, suggesting the existence of a large PlmA regulon. In silico studies showed that PlmA is universally and exclusively found in cyanobacteria. Based on interaction data, on the relative amounts of the proteins involved in PII-PipX-PlmA complexes, determined in western assays, and on the restrictions imposed by the symmetries of trimeric PII and dimeric PlmA molecules, a structural and regulatory model for PlmA function is discussed in the context of the cyanobacterial nitrogen interaction network.
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Affiliation(s)
- Jose I Labella
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante Alicante, Spain
| | - Anna Obrebska
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante Alicante, Spain
| | - Javier Espinosa
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante Alicante, Spain
| | - Paloma Salinas
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante Alicante, Spain
| | | | - Lorena Tremiño
- Instituto de Biomedicina de Valencia of the CSIC Valencia, Spain
| | - Vicente Rubio
- Instituto de Biomedicina de Valencia of the CSICValencia, Spain; Group 739, CIBER de Enfermedades Raras (CIBERER-ISCIII)Valencia, Spain
| | - Asunción Contreras
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante Alicante, Spain
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96
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Abstract
The virulence of many bacterial pathogens, including the important human pathogen Staphylococcus aureus, depends on the secretion of frequently large amounts of toxins. Toxin production involves the need for the bacteria to make physiological adjustments for energy conservation. While toxins are primarily targets of gene regulation, such changes may be accomplished by regulatory functions of the toxins themselves. However, mechanisms by which toxins regulate gene expression have remained poorly understood. We show here that the staphylococcal phenol-soluble modulin (PSM) toxins have gene regulatory functions that, in particular, include inducing expression of their own transport system by direct interference with a GntR-type repressor protein. This capacity was most pronounced in PSMs with low cytolytic capacity, demonstrating functional specification among closely related members of that toxin family during evolution. Our study presents a molecular mechanism of gene regulation by a bacterial toxin that adapts bacterial physiology to enhanced toxin production. Toxins play a major role in many bacterial diseases. When toxins are produced during infection, the bacteria need to balance this energy-consuming task with other physiological processes. However, it has remained poorly understood how toxins can impact gene expression to trigger such adaptations. We found that specific members of a toxin family in the major human pathogen Staphylococcus aureus have evolved for gene regulatory purposes. These specific toxins interact with a DNA-binding regulator protein to enable production of the toxin export machinery and ascertain that the machinery is not expressed when toxins are not made and it is not needed. Our study gives mechanistic insight into how toxins may directly adjust bacterial physiology to times of toxin production during infection.
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97
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The thnR gene is a negative transcription regulator of the thurincin H genetic cassette in Bacillus thuringiensis subsp. morrisoni. Arch Microbiol 2016; 199:385-390. [DOI: 10.1007/s00203-016-1298-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 09/15/2016] [Accepted: 09/21/2016] [Indexed: 10/20/2022]
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98
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Conjugative DNA-transfer in Streptomyces, a mycelial organism. Plasmid 2016; 87-88:1-9. [PMID: 27687731 DOI: 10.1016/j.plasmid.2016.09.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/13/2016] [Accepted: 09/25/2016] [Indexed: 02/06/2023]
Abstract
Conjugative DNA-transfer in the Gram-positive mycelial soil bacterium Streptomyces, well known for the production of numerous antibiotics, is a unique process involving the transfer of a double-stranded DNA molecule. Apparently it does not depend on a type IV secretion system but resembles the segregation of chromosomes during bacterial cell division. A single plasmid-encoded protein, TraB, directs the transfer from the plasmid-carrying donor to the recipient. TraB is a FtsK-like DNA-translocase, which recognizes a specific plasmid sequence, clt, via interaction with specific 8-bp repeats. Chromosomal markers are mobilized by the recognition of clt-like sequences randomly distributed all over the Streptomyces chromosomes. Fluorescence microcopy with conjugative reporter plasmids and differentially labelled recipient strains revealed conjugative plasmid transfer at the lateral walls of the hyphae, when getting in contact. Subsequently, the newly transferred plasmids cross septal cross walls, which occur at irregular distances in the mycelium and invade the neighboring compartments, thus efficiently colonizing the recipient mycelium. This intramycelial plasmid spreading requires the DNA-translocase TraB and a complex of several Spd proteins. Inactivation of a single spd gene interferes with intramycelial plasmid spreading. The molecular function of the Spd proteins is widely unknown. Spd proteins of different plasmids are highly diverse, none showing sequence similarity to a functionally characterized protein. The integral membrane protein SpdB2 binds DNA, peptidoglycan and forms membrane pores in vivo and in vitro. Intramycelial plasmid spreading is an adaptation to the mycelial growth characteristics of Streptomyces and ensures the rapid dissemination of the plasmid within the recipient colony before the onset of sporulation.
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99
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Amidani D, Tramonti A, Canosa AV, Campanini B, Maggi S, Milano T, di Salvo ML, Pascarella S, Contestabile R, Bettati S, Rivetti C. Study of DNA binding and bending by Bacillus subtilis GabR, a PLP-dependent transcription factor. Biochim Biophys Acta Gen Subj 2016; 1861:3474-3489. [PMID: 27640111 DOI: 10.1016/j.bbagen.2016.09.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 09/02/2016] [Accepted: 09/11/2016] [Indexed: 12/23/2022]
Abstract
BACKGROUND GabR is a transcriptional regulator belonging to the MocR/GabR family, characterized by a N-terminal wHTH DNA-binding domain and a C-terminal effector binding and/or oligomerization domain, structurally homologous to aminotransferases (ATs). In the presence of γ-aminobutyrate (GABA) and pyridoxal 5'-phosphate (PLP), GabR activates the transcription of gabT and gabD genes involved in GABA metabolism. METHODS Here we report a biochemical and atomic force microscopy characterization of Bacillus subtilis GabR in complex with DNA. Complexes were assembled in vitro to study their stoichiometry, stability and conformation. RESULTS The fractional occupancy of the GabR cognate site suggests that GabR binds as a dimer with Kd of 10nM. Upon binding GabR bends the DNA by 80° as measured by anomalous electrophoretic mobility. With GABA we observed a decrease in affinity and conformational rearrangements compatible with a less compact nucleo-protein complex but no changes of the DNA bending angle. By employing promoter and GabR mutants we found that basic residues of the positively charged groove on the surface of the AT domain affect DNA affinity. CONCLUSIONS The present data extend current understanding of the GabR-DNA interaction and the effect of GABA and PLP. A model for the GabR-DNA complex, corroborated by a docking simulation, is proposed. GENERAL SIGNIFICANCE Characterization of the GabR DNA binding mode highlights the key role of DNA bending and interactions with bases outside the canonical direct repeats, and might be of general relevance for the action mechanism of MocR transcription factors.
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Affiliation(s)
- Davide Amidani
- Dipartimento di Bioscienze, Università degli Studi di Parma, Parma, Italy
| | - Angela Tramonti
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Roma, Italy; Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | | | | | - Stefano Maggi
- Dipartimento di Bioscienze, Università degli Studi di Parma, Parma, Italy
| | - Teresa Milano
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Martino L di Salvo
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Stefano Pascarella
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Roberto Contestabile
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Stefano Bettati
- Dipartimento di Neuroscienze, Università di Parma, Parma, Italy; National Institute of Biostructures and Biosystems, Rome, Italy
| | - Claudio Rivetti
- Dipartimento di Bioscienze, Università degli Studi di Parma, Parma, Italy.
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Schulz A, Stöveken N, Binzen IM, Hoffmann T, Heider J, Bremer E. Feeding on compatible solutes: A substrate-induced pathway for uptake and catabolism of ectoines and its genetic control by EnuR. Environ Microbiol 2016; 19:926-946. [PMID: 27318028 DOI: 10.1111/1462-2920.13414] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/19/2016] [Indexed: 01/19/2023]
Abstract
Ectoine and 5-hydroxyectoine are widely synthesized microbial osmostress protectants. They are also versatile nutrients but their catabolism and the genetic regulation of the corresponding genes are incompletely understood. Using the marine bacterium Ruegeria pomeroyi DSS-3, we investigated the utilization of ectoines and propose a seven steps comprising catabolic route that entails an initial conversion of 5-hydroxyectoine to ectoine, the opening of the ectoine ring, and the subsequent degradation of this intermediate to l-aspartate. The catabolic genes are co-transcribed with three genes encoding a 5-hydroxyectoine/ectoine-specific TRAP transporter. A chromosomal deletion of this entire gene cluster abolishes the utilization of ectoines as carbon and nitrogen sources. The presence of ectoines in the growth medium triggers enhanced expression of the importer and catabolic operon, a process dependent on a substrate-inducible promoter that precedes this gene cluster. EnuR, a member of the MocR/GabR-type transcriptional regulators, controls the activity of this promoter and functions as a repressor. EnuR contains a covalently bound pyridoxal-5'-phosphate, and we suggest that this co-factor is critical for the substrate-mediated induction of the 5-hydroxyectoine/ectoine import and catabolic genes. Bioinformatics showed that ectoine consumers are restricted to the Proteobacteria and that EnuR is likely a central regulator for most ectoine/5-hydroxyectoine catabolic genes.
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Affiliation(s)
- Annina Schulz
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg, D-35043, Germany
| | - Nadine Stöveken
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg, D-35043, Germany.,Philipps-University Marburg, LOEWE-Center for Synthetic Microbiology, Hans-Meerwein Str. 6, Marburg, D-35043, Germany
| | - Ina M Binzen
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg, D-35043, Germany
| | - Tamara Hoffmann
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg, D-35043, Germany
| | - Johann Heider
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg, D-35043, Germany.,Philipps-University Marburg, LOEWE-Center for Synthetic Microbiology, Hans-Meerwein Str. 6, Marburg, D-35043, Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg, D-35043, Germany.,Philipps-University Marburg, LOEWE-Center for Synthetic Microbiology, Hans-Meerwein Str. 6, Marburg, D-35043, Germany
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