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Tang Y, Qin D, Tian Z, Chen W, Ma Y, Wang J, Yang J, Yan D, Dixon R, Wang YP. Diurnal switches in diazotrophic lifestyle increase nitrogen contribution to cereals. Nat Commun 2023; 14:7516. [PMID: 37980355 PMCID: PMC10657418 DOI: 10.1038/s41467-023-43370-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/07/2023] [Indexed: 11/20/2023] Open
Abstract
Uncoupling of biological nitrogen fixation from ammonia assimilation is a prerequisite step for engineering ammonia excretion and improvement of plant-associative nitrogen fixation. In this study, we have identified an amino acid substitution in glutamine synthetase, which provides temperature sensitive biosynthesis of glutamine, the intracellular metabolic signal of the nitrogen status. As a consequence, negative feedback regulation of genes and enzymes subject to nitrogen regulation, including nitrogenase is thermally controlled, enabling ammonia excretion in engineered Escherichia coli and the plant-associated diazotroph Klebsiella oxytoca at 23 °C, but not at 30 °C. We demonstrate that this temperature profile can be exploited to provide diurnal oscillation of ammonia excretion when variant bacteria are used to inoculate cereal crops. We provide evidence that diurnal temperature variation improves nitrogen donation to the plant because the inoculant bacteria have the ability to recover and proliferate at higher temperatures during the daytime.
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Affiliation(s)
- Yuqian Tang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences & School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Debin Qin
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences & School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Zhexian Tian
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences & School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Wenxi Chen
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences & School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Yuanxi Ma
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences & School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Jilong Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences & School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Jianguo Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences & School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Dalai Yan
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK.
| | - Yi-Ping Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences & School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China.
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2
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Nagatani H, Mae Y, Konishi M, Matsuzaki M, Kita K, Daldal F, Sakamoto K. UbiN, a novel Rhodobacter capsulatus decarboxylative hydroxylase involved in aerobic ubiquinone biosynthesis. FEBS Open Bio 2023; 13:2081-2093. [PMID: 37716914 PMCID: PMC10626278 DOI: 10.1002/2211-5463.13707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 08/01/2023] [Accepted: 09/15/2023] [Indexed: 09/18/2023] Open
Abstract
Ubiquinone (UQ) is a lipophilic electron carrier that functions in the respiratory and photosynthetic electron transfer chains of proteobacteria and eukaryotes. Bacterial UQ biosynthesis is well studied in the gammaproteobacterium Escherichia coli, in which most bacterial UQ-biosynthetic enzymes have been identified. However, these enzymes are not always conserved among UQ-containing bacteria. In particular, the alphaproteobacterial UQ biosynthesis pathways contain many uncharacterized steps with unknown features. In this work, we identified in the alphaproteobacterium Rhodobacter capsulatus a new decarboxylative hydroxylase and named it UbiN. Remarkably, the UbiN sequence is more similar to a salicylate hydroxylase than the conventional flavin-containing UQ-biosynthetic monooxygenases. Under aerobic conditions, R. capsulatus ΔubiN mutant cells accumulate 3-decaprenylphenol, which is a UQ-biosynthetic intermediate. In addition, 3-decaprenyl-4-hydroxybenzoic acid, which is the substrate of UQ-biosynthetic decarboxylase UbiD, also accumulates in ΔubiN cells under aerobic conditions. Considering that the R. capsulatus ΔubiD-X double mutant strain (UbiX produces a prenylated FMN required for UbiD) grows as a wild-type strain under aerobic conditions, these results indicate that UbiN catalyzes the aerobic decarboxylative hydroxylation of 3-decaprenyl-4-hydroxybenzoic acid. This is the first example of the involvement of decarboxylative hydroxylation in ubiquinone biosynthesis. This finding suggests that the C1 hydroxylation reaction is, at least in R. capsulatus, the first step among the three hydroxylation steps involved in UQ biosynthesis. Although the C5 hydroxylation reaction is often considered to be the first hydroxylation step in bacterial UQ biosynthesis, it appears that the R. capsulatus pathway is more similar to that found in mammalians.
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Affiliation(s)
- Haruka Nagatani
- United Graduate School of Agricultural SciencesIwate UniversityMoriokaJapan
| | - Yoshiyuki Mae
- Faculty of Agriculture and Life ScienceHirosaki UniversityJapan
| | - Miharu Konishi
- Faculty of Agriculture and Life ScienceHirosaki UniversityJapan
| | | | - Kiyoshi Kita
- School of Tropical Medicine and Global HealthNagasaki UniversityJapan
- Department of Host‐Defense Biochemistry, Institute of Tropical Medicine (NEKKEN)Nagasaki UniversityJapan
| | - Fevzi Daldal
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Kimitoshi Sakamoto
- United Graduate School of Agricultural SciencesIwate UniversityMoriokaJapan
- Faculty of Agriculture and Life ScienceHirosaki UniversityJapan
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3
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Alim NTB, Koppenhöfer S, Lang AS, Beatty JT. Extracellular Polysaccharide Receptor and Receptor-Binding Proteins of the Rhodobacter capsulatus Bacteriophage-like Gene Transfer Agent RcGTA. Genes (Basel) 2023; 14:genes14051124. [PMID: 37239483 DOI: 10.3390/genes14051124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
A variety of prokaryotes produce a bacteriophage-like gene transfer agent (GTA), and the alphaproteobacterial Rhodobacter capsulatus RcGTA is a model GTA. Some environmental isolates of R. capsulatus lack the ability to acquire genes transferred by the RcGTA (recipient capability). In this work, we investigated the reason why R. capsulatus strain 37b4 lacks recipient capability. The RcGTA head spike fiber and tail fiber proteins have been proposed to bind extracellular oligosaccharide receptors, and strain 37b4 lacks a capsular polysaccharide (CPS). The reason why strain 37b4 lacks a CPS was unknown, as was whether the provision of a CPS to 37b4 would result in recipient capability. To address these questions, we sequenced and annotated the strain 37b4 genome and used BLAST interrogations of this genome sequence to search for homologs of genes known to be needed for R. capsulatus recipient capability. We also created a cosmid-borne genome library from a wild-type strain, mobilized the library into 37b4, and used the cosmid-complemented strain 37b4 to identify genes needed for a gain of function, allowing for the acquisition of RcGTA-borne genes. The relative presence of CPS around a wild-type strain, 37b4, and cosmid-complemented 37b4 cells was visualized using light microscopy of stained cells. Fluorescently tagged head spike fiber and tail fiber proteins of the RcGTA particle were created and used to measure the relative binding to wild-type and 37b4 cells. We found that strain 37b4 lacks recipient capability because of an inability to bind RcGTA; the reason it is incapable of binding is that it lacks CPS, and the absence of CPS is due to the absence of genes previously shown to be needed for CPS production in another strain. In addition to the head spike fiber, we found that the tail fiber protein also binds to the CPS.
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Affiliation(s)
- Nawshin T B Alim
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Sonja Koppenhöfer
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1C 5S7, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1C 5S7, Canada
| | - J Thomas Beatty
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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4
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Guo XP, Yan HQ, Yang W, Yin Z, Vadyvaloo V, Zhou D, Sun YC. A frameshift in Yersinia pestis rcsD alters canonical Rcs signalling to preserve flea-mammal plague transmission cycles. eLife 2023; 12:e83946. [PMID: 37010269 PMCID: PMC10191623 DOI: 10.7554/elife.83946] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 04/02/2023] [Indexed: 04/04/2023] Open
Abstract
Multiple genetic changes in the enteric pathogen Yersinia pseudotuberculosis have driven the emergence of Yesinia pestis, the arthropod-borne, etiological agent of plague. These include developing the capacity for biofilm-dependent blockage of the flea foregut to enable transmission by flea bite. Previously, we showed that pseudogenization of rcsA, encoding a component of the Rcs signalling pathway, is an important evolutionary step facilitating Y. pestis flea-borne transmission. Additionally, rcsD, another important gene in the Rcs system, harbours a frameshift mutation. Here, we demonstrated that this rcsD mutation resulted in production of a small protein composing the C-terminal RcsD histidine-phosphotransferase domain (designated RcsD-Hpt) and full-length RcsD. Genetic analysis revealed that the rcsD frameshift mutation followed the emergence of rcsA pseudogenization. It further altered the canonical Rcs phosphorylation signal cascade, fine-tuning biofilm production to be conducive with retention of the pgm locus in modern lineages of Y. pestis. Taken together, our findings suggest that a frameshift mutation in rcsD is an important evolutionary step that fine-tuned biofilm production to ensure perpetuation of flea-mammal plague transmission cycles.
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Affiliation(s)
- Xiao-Peng Guo
- NHC key laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Hai-Qin Yan
- Department of Basic Medical Sciences, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical CollegeBengbuChina
- Paul G. Allen School for Global Health, Washington State UniversityPullmanUnited States
| | - Wenhui Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Viveka Vadyvaloo
- Paul G. Allen School for Global Health, Washington State UniversityPullmanUnited States
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Yi-Cheng Sun
- NHC key laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
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Ong A, O’Brian MR. The Bradyrhizobium japonicum fsrB gene is essential for utilization of structurally diverse ferric siderophores to fulfill its nutritional iron requirement. Mol Microbiol 2023; 119:340-349. [PMID: 36648393 PMCID: PMC10411499 DOI: 10.1111/mmi.15028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023]
Abstract
In Bradyrhizobium japonicum, iron uptake from ferric siderophores involves selective outer membrane proteins and non-selective periplasmic and cytoplasmic membrane components that accommodate numerous structurally diverse siderophores. Free iron traverses the cytoplasmic membrane through the ferrous (Fe2+ ) transporter system FeoAB, but the other non-selective components have not been described. Here, we identify fsrB as an iron-regulated gene required for growth on iron chelates of catecholate- and hydroxymate-type siderophores, but not on inorganic iron. Utilization of the non-physiological iron chelator EDDHA as an iron source was also dependent on fsrB. Uptake activities of 55 Fe3+ bound to ferrioxamine B, ferrichrome or enterobactin were severely diminished in the fsrB mutant compared with the wild type. Growth of the fsrB or feoB strains on ferrichrome were rescued with plasmid-borne E. coli fhuCDB ferrichrome transport genes, suggesting that FsrB activity occurs in the periplasm rather than the cytoplasm. Whole cells of an fsrB mutant are defective in ferric reductase activity. Both whole cells and spheroplasts catalyzed the demetallation of ferric siderophores that were defective in an fsrB mutant. Collectively, the data support a model whereby FsrB is required for reduction of iron and its dissociation from the siderophore in the periplasm, followed by transport of the ferrous ion into the cytoplasm by FeoAB.
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Affiliation(s)
- Alasteir Ong
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, The University at Buffalo, 955 Main Street, Room 4102, Buffalo, New York 14203-1121
| | - Mark R. O’Brian
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, The University at Buffalo, 955 Main Street, Room 4102, Buffalo, New York 14203-1121
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6
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Shao Y, Yin C, Lv F, Jiang S, Wu S, Han Y, Xue W, Ma Y, Zheng J, Zhan Y, Ke X, Lu W, Lin M, Shang L, Yan Y. The Sigma Factor AlgU Regulates Exopolysaccharide Production and Nitrogen-Fixing Biofilm Formation by Directly Activating the Transcription of pslA in Pseudomonas stutzeri A1501. Genes (Basel) 2022; 13:genes13050867. [PMID: 35627252 PMCID: PMC9141998 DOI: 10.3390/genes13050867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 11/29/2022] Open
Abstract
Pseudomonas stutzeri A1501, a plant-associated diazotrophic bacterium, prefers to conform to a nitrogen-fixing biofilm state under nitrogen-deficient conditions. The extracytoplasmic function (ECF) sigma factor AlgU is reported to play key roles in exopolysaccharide (EPS) production and biofilm formation in the Pseudomonas genus; however, the function of AlgU in P. stutzeri A1501 is still unclear. In this work, we mainly investigated the role of algU in EPS production, biofilm formation and nitrogenase activity in A1501. The algU mutant ΔalgU showed a dramatic decrease both in the EPS production and the biofilm formation capabilities. In addition, the biofilm-based nitrogenase activity was reduced by 81.4% in the ΔalgU mutant. The transcriptional level of pslA, a key Psl-like (a major EPS in A1501) synthesis-related gene, was almost completely inhibited in the algU mutant and was upregulated by 2.8-fold in the algU-overexpressing strain. A predicted AlgU-binding site was identified in the promoter region of pslA. The DNase I footprinting assays indicated that AlgU could directly bind to the pslA promoter, and β-galactosidase activity analysis further revealed mutations of the AlgU-binding boxes drastically reduced the transcriptional activity of the pslA promoter; moreover, we also demonstrated that AlgU was positively regulated by RpoN at the transcriptional level and negatively regulated by the RNA-binding protein RsmA at the posttranscriptional level. Taken together, these data suggest that AlgU promotes EPS production and nitrogen-fixing biofilm formation by directly activating the transcription of pslA, and the expression of AlgU is controlled by RpoN and RsmA at different regulatory levels.
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Affiliation(s)
- Yahui Shao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Changyan Yin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Fanyang Lv
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Shanshan Jiang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Shaoyu Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Yueyue Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Wei Xue
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Yiyuan Ma
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Juan Zheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Yuhua Zhan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Xiubin Ke
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Wei Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
| | - Liguo Shang
- School of Basic Medicine, GuangXi University of Chinese Medicine, Nanning 530200, China
- Correspondence: (L.S.); (Y.Y.)
| | - Yongliang Yan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.S.); (C.Y.); (F.L.); (S.J.); (S.W.); (Y.H.); (W.X.); (Y.M.); (J.Z.); (Y.Z.); (X.K.); (W.L.); (M.L.)
- Correspondence: (L.S.); (Y.Y.)
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7
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Misawa N, Maoka T, Takemura M. Carotenoids: Carotenoid and apocarotenoid analysis—Use of E. coli to produce carotenoid standards. Methods Enzymol 2022; 670:87-137. [DOI: 10.1016/bs.mie.2022.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Zhang Y, Yuan J. CRISPR/Cas12a-mediated genome engineering in the photosynthetic bacterium Rhodobacter capsulatus. Microb Biotechnol 2021; 14:2700-2710. [PMID: 33773050 PMCID: PMC8601187 DOI: 10.1111/1751-7915.13805] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 12/11/2022] Open
Abstract
Purple non-sulfur photosynthetic bacteria (PNSB) such as Rhodobacter capsulatus serve as a versatile platform for fundamental studies and various biotechnological applications. In this study, we sought to develop the class II RNA-guided CRISPR/Cas12a system from Francisella novicida for genome editing and transcriptional regulation in R. capsulatus. Template-free disruption method mediated by CRISPR/Cas12a reached ˜ 90% editing efficiency when targeting ccoO or nifH gene. When both genes were simultaneously edited, the multiplex editing efficiency reached > 63%. In addition, CRISPR interference (CRISPRi) using deactivated Cas12a was also evaluated using reporter genes egfp and lacZ, and the transcriptional repression efficiency reached ˜ 80%. In summary, our work represents the first report to develop CRISPR/Cas12a-mediated genome editing and transcriptional regulation in R. capsulatus, which would greatly accelerate PNSB-related researches.
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Affiliation(s)
- Yang Zhang
- State Key Laboratory of Cellular Stress BiologyInnovation Center for Cell Signaling NetworkSchool of Life SciencesXiamen UniversityFujian361102China
| | - Jifeng Yuan
- State Key Laboratory of Cellular Stress BiologyInnovation Center for Cell Signaling NetworkSchool of Life SciencesXiamen UniversityFujian361102China
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9
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Öztürk Y, Blaby-Haas CE, Daum N, Andrei A, Rauch J, Daldal F, Koch HG. Maturation of Rhodobacter capsulatus Multicopper Oxidase CutO Depends on the CopA Copper Efflux Pathway and Requires the cutF Product. Front Microbiol 2021; 12:720644. [PMID: 34566924 PMCID: PMC8456105 DOI: 10.3389/fmicb.2021.720644] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/18/2021] [Indexed: 11/15/2022] Open
Abstract
Copper (Cu) is an essential cofactor required for redox enzymes in all domains of life. Because of its toxicity, tightly controlled mechanisms ensure Cu delivery for cuproenzyme biogenesis and simultaneously protect cells against toxic Cu. Many Gram-negative bacteria contain extracytoplasmic multicopper oxidases (MCOs), which are involved in periplasmic Cu detoxification. MCOs are unique cuproenzymes because their catalytic center contains multiple Cu atoms, which are required for the oxidation of Cu1+ to the less toxic Cu2+. Hence, Cu is both substrate and essential cofactor of MCOs. Here, we investigated the maturation of Rhodobacter capsulatus MCO CutO and its role in periplasmic Cu detoxification. A survey of CutO activity of R. capsulatus mutants with known defects in Cu homeostasis and in the maturation of the cuproprotein cbb 3-type cytochrome oxidase (cbb 3-Cox) was performed. This revealed that CutO activity is largely independent of the Cu-delivery pathway for cbb 3-Cox biogenesis, except for the cupric reductase CcoG, which is required for full CutO activity. The most pronounced decrease of CutO activity was observed with strains lacking the cytoplasmic Cu chaperone CopZ, or the Cu-exporting ATPase CopA, indicating that CutO maturation is linked to the CopZ-CopA mediated Cu-detoxification pathway. Our data demonstrate that CutO is important for cellular Cu resistance under both aerobic and anaerobic growth conditions. CutO is encoded in the cutFOG operon, but only CutF, and not CutG, is essential for CutO activity. No CutO activity is detectable when cutF or its putative Cu-binding motif are mutated, suggesting that the cutF product serves as a Cu-binding component required for active CutO production. Bioinformatic analyses of CutF-like proteins support their widespread roles as putative Cu-binding proteins for several Cu-relay pathways. Our overall findings show that the cytoplasmic CopZ-CopA dependent Cu detoxification pathway contributes to providing Cu to CutO maturation, a process that strictly relies on cutF.
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Affiliation(s)
- Yavuz Öztürk
- Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
| | - Crysten E. Blaby-Haas
- Biology Department, Brookhaven National Laboratory, Upton, NY, United States
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, United States
| | - Noel Daum
- Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Andreea Andrei
- Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
- Fakultät für Biologie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Juna Rauch
- Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Fevzi Daldal
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
| | - Hans-Georg Koch
- Institut für Biochemie und Molekularbiologie, ZBMZ, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
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10
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Geiger O, Sohlenkamp C, Vera-Cruz D, Medeot DB, Martínez-Aguilar L, Sahonero-Canavesi DX, Weidner S, Pühler A, López-Lara IM. ExoS/ChvI Two-Component Signal-Transduction System Activated in the Absence of Bacterial Phosphatidylcholine. FRONTIERS IN PLANT SCIENCE 2021; 12:678976. [PMID: 34367203 PMCID: PMC8343143 DOI: 10.3389/fpls.2021.678976] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Sinorhizobium meliloti contains the negatively charged phosphatidylglycerol and cardiolipin as well as the zwitterionic phosphatidylethanolamine (PE) and phosphatidylcholine (PC) as major membrane phospholipids. In previous studies we had isolated S. meliloti mutants that lack PE or PC. Although mutants deficient in PE are able to form nitrogen-fixing nodules on alfalfa host plants, mutants lacking PC cannot sustain development of any nodules on host roots. Transcript profiles of mutants unable to form PE or PC are distinct; they differ from each other and they are different from the wild type profile. For example, a PC-deficient mutant of S. meliloti shows an increase of transcripts that encode enzymes required for succinoglycan biosynthesis and a decrease of transcripts required for flagellum formation. Indeed, a PC-deficient mutant is unable to swim and overproduces succinoglycan. Some suppressor mutants, that regain swimming and form normal levels of succinoglycan, are altered in the ExoS sensor. Our findings suggest that the lack of PC in the sinorhizobial membrane activates the ExoS/ChvI two-component regulatory system. ExoS/ChvI constitute a molecular switch in S. meliloti for changing from a free-living to a symbiotic life style. The periplasmic repressor protein ExoR controls ExoS/ChvI function and it is thought that proteolytic ExoR degradation would relieve repression of ExoS/ChvI thereby switching on this system. However, as ExoR levels are similar in wild type, PC-deficient mutant and suppressor mutants, we propose that lack of PC in the bacterial membrane provokes directly a conformational change of the ExoS sensor and thereby activation of the ExoS/ChvI two-component system.
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Affiliation(s)
- Otto Geiger
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Christian Sohlenkamp
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Diana Vera-Cruz
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Daniela B. Medeot
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | | | - Stefan Weidner
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Alfred Pühler
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Isabel M. López-Lara
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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11
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Pech-Canul ÁDLC, Rivera-Hernández G, Nogales J, Geiger O, Soto MJ, López-Lara IM. Role of Sinorhizobium meliloti and Escherichia coli Long-Chain Acyl-CoA Synthetase FadD in Long-Term Survival. Microorganisms 2020; 8:microorganisms8040470. [PMID: 32225039 PMCID: PMC7232532 DOI: 10.3390/microorganisms8040470] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 11/16/2022] Open
Abstract
FadD is an acyl-coenzyme A (CoA) synthetase specific for long-chain fatty acids (LCFA). Strains mutated in fadD cannot produce acyl-CoA and thus cannot grow on exogenous LCFA as the sole carbon source. Mutants in the fadD (smc02162) of Sinorhizobium meliloti are unable to grow on oleate as the sole carbon source and present an increased surface motility and accumulation of free fatty acids at the entry of the stationary phase of growth. In this study, we found that constitutive expression of the closest FadD homologues of S. meliloti, encoded by sma0150 and smb20650, could not revert any of the mutant phenotypes. In contrast, the expression of Escherichia coli fadD could restore the same functions as S. meliloti fadD. Previously, we demonstrated that FadD is required for the degradation of endogenous fatty acids released from membrane lipids. Here, we show that absence of a functional fadD provokes a significant loss of viability in cultures of E. coli and of S. meliloti in the stationary phase, demonstrating a crucial role of fatty acid degradation in survival capacity.
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Affiliation(s)
- Ángel de la Cruz Pech-Canul
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México. Cuernavaca, Morelos, C.P. 62210, Mexico; (Á.d.l.C.P.-C.); (G.R.-H.); (O.G.)
| | - Geovanny Rivera-Hernández
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México. Cuernavaca, Morelos, C.P. 62210, Mexico; (Á.d.l.C.P.-C.); (G.R.-H.); (O.G.)
| | - Joaquina Nogales
- Departamento de Microbiología del Suelo y Sistemas Simbióticos. Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (J.N.); (M.J.S.)
| | - Otto Geiger
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México. Cuernavaca, Morelos, C.P. 62210, Mexico; (Á.d.l.C.P.-C.); (G.R.-H.); (O.G.)
| | - María J. Soto
- Departamento de Microbiología del Suelo y Sistemas Simbióticos. Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (J.N.); (M.J.S.)
| | - Isabel M. López-Lara
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México. Cuernavaca, Morelos, C.P. 62210, Mexico; (Á.d.l.C.P.-C.); (G.R.-H.); (O.G.)
- Correspondence: ; Tel.: +52-7773291703
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12
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Abstract
The rhizobium-legume symbiosis contributes around 65% of biological nitrogen fixation in agriculture systems and is critical for sustainable agriculture by reducing the amount of chemical nitrogen fertilizer being used. Rhizobial inocula have been commercialized for more than 100 years, but the efficiency of inoculation can vary among legume cultivars, field sites, and years. These long-lasting challenging problems impede the establishment of a sustainable agriculture, particularly in developing countries. Here, we report that rhizobial zinc starvation machinery containing a conserved high-affinity zinc transporter and accessory components makes cumulative contributions to modulating rhizobial symbiotic compatibility. This work highlights a critical role of largely unexplored nutritional immunity in the rhizobium-legume symbiosis, which makes zinc starvation machinery an attractive target for improving rhizobial symbiotic compatibility. Pathogenic bacteria need high-affinity zinc uptake systems to counteract the nutritional immunity exerted by infected hosts. However, our understanding of zinc homeostasis in mutualistic systems such as the rhizobium-legume symbiosis is limited. Here, we show that the conserved high-affinity zinc transporter ZnuABC and accessory transporter proteins (Zip1, Zip2, and c06450) made cumulative contributions to nodulation of the broad-host-range strain Sinorhizobium fredii CCBAU45436. Zur acted as a zinc-dependent repressor for the znuC-znuB-zur operon, znuA, and c06450 by binding to the associated Zur box, but did not regulate zip1 and zip2. ZnuABC was the major zinc transporter. Combined mutants lacking znuA and one of the three accessory genes had more severe defects in nodulation and growth under zinc starvation conditions than the znuA mutant, though rhizoplane colonization by these mutants was not impaired. In contrast to the elite strain CCBAU45436, more drastic symbiotic defects were observed for the znuA mutants of other Sinorhizobium strains, which lack at least one of the three accessory genes in their genomes and are characterized by their limited host range and geographical distribution. The znu-derived mutants showed a higher expression level of nod genes involved in Nod factor biosynthesis and a reduced expression of genes encoding a type three secretion system and its effector NopP, which can interfere with the host immune system. Application of exogenous zinc restored the nodulation ability of these znu-derived mutants. Therefore, the conserved ZnuABC and accessory components in the zinc starvation machinery play an important role in modulating symbiotic compatibility.
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Yu Z, Yu D, Mao Y, Zhang M, Ding M, Zhang J, Wu S, Qiu J, Yin J. Identification and characterization of a LuxI/R-type quorum sensing system in Pseudoalteromonas. Res Microbiol 2019; 170:243-255. [DOI: 10.1016/j.resmic.2019.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/04/2019] [Accepted: 07/09/2019] [Indexed: 12/30/2022]
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Tan YJC, Zhao C, Nasreen M, O'Rourke L, Dhouib R, Roberts L, Wan Y, Beatson SA, Kappler U. Control of Bacterial Sulfite Detoxification by Conserved and Species-Specific Regulatory Circuits. Front Microbiol 2019; 10:960. [PMID: 31139157 PMCID: PMC6527743 DOI: 10.3389/fmicb.2019.00960] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 04/16/2019] [Indexed: 11/15/2022] Open
Abstract
Although sulfite, a by-product of the degradation of many sulfur compounds, is highly reactive and can cause damage to DNA, proteins and lipids, comparatively little is known about the regulation of sulfite-oxidizing enzyme (SOEs) expression. Here we have investigated the regulation of SOE-encoding genes in two species of α-Proteobacteria, Sinorhizobium meliloti and Starkeya novella, that degrade organo- and inorganic sulfur compounds, respectively, and contain unrelated types of SOEs that show different expression patterns. Our work revealed that in both cases, the molecular signal that triggers SOE gene expression is sulfite, and strong up-regulation depends on the presence of a sulfite-responsive, cognate Extracytoplasmic function (ECF) sigma factor, making sulfite oxidation a bacterial stress response. An additional RpoE1-like ECF sigma factor was also involved in the regulation, but was activated by different molecular signals, taurine (Sm) and tetrathionate (Sn), respectively, targeted different gene promoters, and also differed in the magnitude of the response generated. We therefore propose that RpoE1 is a secondary, species-specific regulator of SOE gene expression rather than a general, conserved regulatory circuit. Sulfite produced by major dissimilatory processes appeared to be the trigger for SOE gene expression in both species, as we were unable to find evidence for an increase of SOE activity in stationary growth phase. The basic regulation of bacterial sulfite oxidation by cognate ECF sigma factors is likely to be applicable to three groups of alpha and beta-Proteobacteria in which we identified similar SOE operon structures.
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Affiliation(s)
- Yi Jie Chelsea Tan
- Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Chengzhi Zhao
- Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Marufa Nasreen
- Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Leo O'Rourke
- Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Rabeb Dhouib
- Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Leah Roberts
- Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Ying Wan
- Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Scott A Beatson
- Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Ulrike Kappler
- Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
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15
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Breitenbach J, Pollmann H, Sandmann G. Genetic modification of the carotenoid pathway in the red yeast Xanthophyllomyces dendrorhous: Engineering of a high-yield zeaxanthin strain. J Biotechnol 2019; 289:112-117. [DOI: 10.1016/j.jbiotec.2018.11.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/11/2018] [Accepted: 11/25/2018] [Indexed: 12/23/2022]
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16
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Francia F, Khalfaoui-Hassani B, Lanciano P, Musiani F, Noodleman L, Venturoli G, Daldal F. The cytochrome b lysine 329 residue is critical for ubihydroquinone oxidation and proton release at the Q o site of bacterial cytochrome bc 1. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1860:167-179. [PMID: 30550726 DOI: 10.1016/j.bbabio.2018.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 12/06/2018] [Accepted: 12/07/2018] [Indexed: 11/16/2022]
Abstract
The ubihydroquinone:cytochrome (cyt) c oxidoreductase (or cyt bc1) is an important enzyme for photosynthesis and respiration. In bacteria like Rhodobacter capsulatus, this membrane complex has three subunits, the iron‑sulfur protein (ISP) with its Fe2S2 cluster, cyt c1 and cyt b, forming two catalytic domains, the Qo (hydroquinone (QH2) oxidation) and Qi (quinone (Q) reduction) sites. At the Qo site, the electron transfer pathways originating from QH2 oxidation are known, but their associated proton release routes are less well defined. Earlier, we demonstrated that the His291 of cyt b is important for this latter process. In this work, using the bacterial cyt bc1 and site directed mutagenesis, we show that Lys329 of cyt b is also critical for electron and proton transfer at the Qo site. Of the mutants examined, Lys329Arg was photosynthesis proficient and had quasi-wild type cyt bc1 activity. In contrast, the Lys329Ala and Lys329Asp were photosynthesis-impaired and contained defective but assembled cyt bc1. In particular, the bifurcated electron transfer and associated proton(s) release reactions occurring during QH2 oxidation were drastically impaired in Lys329Asp mutant. Furthermore, in silico docking studies showed that in this mutant the location and the H-bonding network around the Fe2S2 cluster of ISP on cyt b surface was different than the wild type enzyme. Based on these experimental findings and theoretical considerations, we propose that the presence of a positive charge at position 329 of cyt b is critical for efficient electron transfer and proton release for QH2 oxidation at the Qo site of cyt bc1.
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Affiliation(s)
- Francesco Francia
- Dipartimento di Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy
| | | | - Pascal Lanciano
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Francesco Musiani
- Dipartimento di Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy
| | - Louis Noodleman
- The Scripps Research Institute, Department of Integrative Structural and Computational Biology, La Jolla, CA 92037, USA
| | - Giovanni Venturoli
- Dipartimento di Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy; Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), Dipartimento di Fisica, Università di Bologna, 40127 Bologna, Italy
| | - Fevzi Daldal
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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17
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Hu Y, Jiao J, Liu LX, Sun YW, Chen WF, Sui XH, Chen WX, Tian CF. Evidence for Phosphate Starvation of Rhizobia without Terminal Differentiation in Legume Nodules. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:1060-1068. [PMID: 29663866 DOI: 10.1094/mpmi-02-18-0031-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Phosphate homeostasis is tightly modulated in all organisms, including bacteria, which harbor both high- and low-affinity transporters acting under conditions of fluctuating phosphate levels. It was thought that nitrogen-fixing rhizobia, named bacteroids, inhabiting root nodules of legumes are not phosphate limited. Here, we show that the high-affinity phosphate transporter PstSCAB, rather than the low-affinity phosphate transporter Pit, is essential for effective nitrogen fixation of Sinorhizobium fredii in soybean nodules. Symbiotic and growth defects of the pst mutant can be effectively restored by knocking out PhoB, the transcriptional repressor of pit. The pst homologs of representative rhizobia were actively transcribed in bacteroids without terminal differentiation in nodules of diverse legumes (soybean, pigeonpea, cowpea, common bean, and Sophora flavescens) but exhibited a basal expression level in terminally differentiated bacteroids (alfalfa, pea, and peanut). Rhizobium leguminosarum bv. viciae Rlv3841 undergoes characteristic nonterminal and terminal differentiations in nodules of S. flavescens and pea, respectively. The pst mutant of Rlv3841 showed impaired adaptation to the nodule environment of S. flavescens but was indistinguishable from the wild-type strain in pea nodules. Taken together, root nodule rhizobia can be either phosphate limited or nonlimited regarding the rhizobial differentiation fate, which is a host-dependent feature.
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Affiliation(s)
- Yue Hu
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Jian Jiao
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Li Xue Liu
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Yan Wei Sun
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Wen Feng Chen
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Xin Hua Sui
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Wen Xin Chen
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Chang Fu Tian
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, 100193, Beijing, China
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18
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Fukaya Y, Takemura M, Koyanagi T, Maoka T, Shindo K, Misawa N. Structural and functional analysis of the carotenoid biosynthesis genes of a Pseudomonas strain isolated from the excrement of Autumn Darter. Biosci Biotechnol Biochem 2018; 82:1043-1052. [DOI: 10.1080/09168451.2017.1398069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Abstract
There are many reports about carotenoid-producing bacteria and carotenoid biosynthesis genes. In databases for Pseudomonas genome sequences, there are genes homologous to carotenoid biosynthesis genes, but the function of these genes in Pseudomonas has not been elucidated. In this study, we cloned the carotenoid biosynthesis genes from a Pseudomonas sp. strain, named Akiakane, which was isolated from the excrement of the Autumn Darter dragonfly. Using an Escherichia coli functional expression system, we confirmed that the idi, crtE, crtB, crtI, and crtY gene products of the Akiakane strain show predictable catalytic activities. A cluster of six genes was also found, which was comparable to other carotenoid-producing bacteria that belong to the α-Proteobacteria or γ-Proteobacteria class.
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Affiliation(s)
- Yuki Fukaya
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Japan
| | - Miho Takemura
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Japan
| | - Takashi Koyanagi
- Department of Food Science, Ishikawa Prefectural University, Nonoichi, Japan
| | - Takashi Maoka
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Japan
- Research Institute for Production Development, Kyoto, Japan
| | - Kazutoshi Shindo
- Department of Food and Nutrition, Japan Women’s University, Tokyo, Japan
| | - Norihiko Misawa
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Japan
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NsrA, a Predicted β-Barrel Outer Membrane Protein Involved in Plant Signal Perception and the Control of Secondary Infection in Sinorhizobium meliloti. J Bacteriol 2018. [PMID: 29531182 DOI: 10.1128/jb.00019-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An ongoing signal exchange fine-tunes the symbiotic interactions between rhizobia and legumes, ensuring the establishment and maintenance of mutualism. In a recently identified regulatory loop, endosymbiotic Sinorhizobium meliloti exerts negative feedback on root infection in response to unknown plant cues. Upon signal perception, three bacterial adenylate cyclases (ACs) of the inner membrane, namely, CyaD1, CyaD2, and CyaK, synthesize the second messenger cAMP, which, together with the cAMP-dependent Clr transcriptional activator, activates the expression of genes involved in root infection control. The pathway that links signal perception at the surface of the cell to cytoplasmic cAMP production by ACs was thus far unknown. Here we first show that CyaK is the cognate AC for the plant signal, called signal 1, that was observed previously in mature nodule and shoot extracts. We also show that inactivation of the gene immediately upstream of cyaK, nsrA (smb20775), which encodes a β-barrel protein of the outer membrane, abolished signal 1 perception ex planta, whereas nsrA overexpression increased signal 1 responsiveness. Inactivation of the nsrA gene abolished all Clr-dependent gene expression in nodules and led to a marked hyperinfection phenotype on plants, similar to that of a cyaD1 cyaD2 cyaK triple mutant. We suggest that the NsrA protein acts as the (co)receptor for two signal molecules, signal 1 and a hypothetical signal 1', in mature and young nodules that cooperate in controlling secondary infection in S. meliloti-Medicago symbiosis. The predicted topology and domain composition of the NsrA protein hint at a mechanism of transmembrane signaling.IMPORTANCE Symbiotic interactions, especially mutualistic ones, rely on a continuous signal exchange between the symbionts. Here we report advances regarding a recently discovered signal transduction pathway that fine-tunes the symbiotic interaction between S. meliloti and its Medicago host plant. We have identified an outer membrane protein of S. meliloti, called NsrA, that transduces Medicago plant signals to adenylate cyclases in the inner membrane, thereby triggering a cAMP signaling cascade that controls infection. Besides their relevance for the rhizobium-legume symbiosis, these findings shed light on the mechanisms of signal perception and transduction by adenylate cyclases and transmembrane signaling in bacteria.
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20
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Guerrero-Castro J, Lozano L, Sohlenkamp C. Dissecting the Acid Stress Response of Rhizobium tropici CIAT 899. Front Microbiol 2018; 9:846. [PMID: 29760688 PMCID: PMC5936775 DOI: 10.3389/fmicb.2018.00846] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 04/12/2018] [Indexed: 11/27/2022] Open
Abstract
Rhizobium tropici CIAT899 is a nodule-forming α-proteobacterium displaying intrinsic resistance to several abiotic stress conditions such as low pH and high temperatures, which are common in tropical environments. It is a good competitor for Phaseolus vulgaris (common bean) nodule occupancy at low pH values, however little is known about the genetic and physiological basis of the tolerance to acidic conditions. To identify genes in R. tropici involved in pH stress response we combined two different approaches: (1) A Tn5 mutant library of R. tropici CIAT899 was screened and 26 acid-sensitive mutants were identified. For 17 of these mutants, the transposon insertion sites could be identified. (2) We also studied the transcriptomes of cells grown under different pH conditions using RNA-Seq. RNA was extracted from cells grown for several generations in minimal medium at 6.8 or 4.5 (adapted cells). In addition, we acid-shocked cells pre-grown at pH 6.8 for 45 min at pH 4.5. Of the 6,289 protein-coding genes annotated in the genome of R. tropici CIAT 899, 383 were differentially expressed under acidic conditions (pH 4.5) vs. control condition (pH 6.8). Three hundred and fifty one genes were induced and 32 genes were repressed; only 11 genes were induced upon acid shock. The acid stress response of R. tropici CIAT899 is versatile: we found genes encoding response regulators and membrane transporters, enzymes involved in amino acid and carbohydrate metabolism and proton extrusion, in addition to several hypothetical genes. Our findings enhance our understanding of the core genes that are important during the acid stress response in R. tropici.
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Affiliation(s)
- Julio Guerrero-Castro
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,Programa de Doctorado en Ciencias Biomédicas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Luis Lozano
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Christian Sohlenkamp
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Lang C, Smith LS, Haney CH, Long SR. Characterization of Novel Plant Symbiosis Mutants Using a New Multiple Gene-Expression Reporter Sinorhizobium meliloti Strain. FRONTIERS IN PLANT SCIENCE 2018; 9:76. [PMID: 29467773 PMCID: PMC5808326 DOI: 10.3389/fpls.2018.00076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/15/2018] [Indexed: 06/08/2023]
Abstract
The formation of nitrogen fixing root nodules by Medicago truncatula and Sinorhizobium meliloti requires communication between both organisms and coordinated differentiation of plant and bacterial cells. After an initial signal exchange, the bacteria invade the tissue of the growing nodule via plant-derived tubular structures, called infection threads. The bacteria are released from the infection threads into invasion-competent plant cells, where they differentiate into nitrogen-fixing bacteroids. Both organisms undergo dramatic transcriptional, metabolic and morphological changes during nodule development. To identify plant processes that are essential for the formation of nitrogen fixing nodules after nodule development has been initiated, large scale mutageneses have been conducted to discover underlying plant symbiosis genes. Such screens yield numerous uncharacterized plant lines with nitrogen fixation deficient nodules. In this study, we report construction of a S. meliloti strain carrying four distinct reporter constructs to reveal stages of root nodule development. The strain contains a constitutively expressed lacZ reporter construct; a PexoY-mTFP fusion that is expressed in infection threads but not in differentiated bacteroids; a PbacA-mcherry construct that is expressed in infection threads and during bacteroid differentiation; and a PnifH-uidA construct that is expressed during nitrogen fixation. We used this strain together with fluorescence microscopy to study nodule development over time in wild type nodules and to characterize eight plant mutants from a fast neutron bombardment screen. Based on the signal intensity and the localization patterns of the reporter genes, we grouped mutants with similar phenotypes and placed them in a developmental context.
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Affiliation(s)
| | | | | | - Sharon R. Long
- Gilbert Lab, Department of Biology, Stanford University, Stanford, CA, United States
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Onder O, Verissimo AF, Khalfaoui-Hassani B, Peters A, Koch HG, Daldal F. Absence of Thiol-Disulfide Oxidoreductase DsbA Impairs cbb3-Type Cytochrome c Oxidase Biogenesis in Rhodobacter capsulatus. Front Microbiol 2017; 8:2576. [PMID: 29312253 PMCID: PMC5742617 DOI: 10.3389/fmicb.2017.02576] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/11/2017] [Indexed: 12/20/2022] Open
Abstract
The thiol-disulfide oxidoreductase DsbA carries out oxidative folding of extra-cytoplasmic proteins by catalyzing the formation of intramolecular disulfide bonds. It has an important role in various cellular functions, including cell division. The purple non-sulfur bacterium Rhodobacter capsulatus mutants lacking DsbA show severe temperature-sensitive and medium-dependent respiratory growth defects. In the presence of oxygen, at normal growth temperature (35°C), DsbA− mutants form colonies on minimal medium, but they do not grow on enriched medium where cells elongate and lyse. At lower temperatures (i.e., 25°C), cells lacking DsbA grow normally in both minimum and enriched media, however, they do not produce the cbb3-type cytochrome c oxidase (cbb3-Cox) on enriched medium. Availability of chemical oxidants (e.g., Cu2+ or a mixture of cysteine and cystine) in the medium becomes critical for growth and cbb3-Cox production in the absence of DsbA. Indeed, addition of Cu2+ to the enriched medium suppresses, and conversely, omission of Cu2+ from the minimal medium induces, growth and cbb3-Cox defects. Alleviation of these defects by addition of redox-active chemicals indicates that absence of DsbA perturbs cellular redox homeostasis required for the production of an active cbb3-Cox, especially in enriched medium where bioavailable Cu2+ is scarce. This is the first report describing that DsbA activity is required for full respiratory capability of R. capsulatus, and in particular, for proper biogenesis of its cbb3-Cox. We propose that absence of DsbA, besides impairing the maturation of the c-type cytochrome subunits, also affects the incorporation of Cu into the catalytic subunit of cbb3-Cox. Defective high affinity Cu acquisition pathway, which includes the MFS-type Cu importer CcoA, and lower production of the c-type cytochrome subunits lead together to improper assembly and degradation of cbb3-Cox.
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Affiliation(s)
- Ozlem Onder
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
| | - Andreia F Verissimo
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
| | | | - Annette Peters
- Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Institut für Biochemie und Molekularbiologie, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Hans-Georg Koch
- Zentrum für Biochemie und Molekulare Zellforschung (ZBMZ), Institut für Biochemie und Molekularbiologie, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Fevzi Daldal
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
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Raberg M, Volodina E, Lin K, Steinbüchel A. Ralstonia eutrophaH16 in progress: Applications beside PHAs and establishment as production platform by advanced genetic tools. Crit Rev Biotechnol 2017; 38:494-510. [DOI: 10.1080/07388551.2017.1369933] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Matthias Raberg
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Elena Volodina
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Kaichien Lin
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
- Environmental Science Department, King Abdulaziz University, Jeddah, Saudi Arabia
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24
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Calatrava-Morales N, Nogales J, Ameztoy K, van Steenbergen B, Soto MJ. The NtrY/NtrX System of Sinorhizobium meliloti GR4 Regulates Motility, EPS I Production, and Nitrogen Metabolism but Is Dispensable for Symbiotic Nitrogen Fixation. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:566-577. [PMID: 28398840 DOI: 10.1094/mpmi-01-17-0021-r] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Sinorhizobium meliloti can translocate over surfaces. However, little is known about the regulatory mechanisms that control this trait and its relevance for establishing symbiosis with alfalfa plants. To gain insights into this field, we isolated Tn5 mutants of S. meliloti GR4 with impaired surface motility. In mutant strain GRS577, the transposon interrupted the ntrY gene encoding the sensor kinase of the NtrY/NtrX two-component regulatory system. GRS577 is impaired in flagella synthesis and overproduces succinoglycan, which is responsible for increased biofilm formation. The mutant also shows altered cell morphology and higher susceptibility to salt stress. GRS577 induces nitrogen-fixing nodules in alfalfa but exhibits decreased competitive nodulation. Complementation experiments indicate that both ntrY and ntrX account for all the phenotypes displayed by the ntrY::Tn5 mutant. Ectopic overexpression of VisNR, the motility master regulator, was sufficient to rescue motility and competitive nodulation of the transposant. A transcriptome profiling of GRS577 confirmed differential expression of exo and flagellar genes, and led to the demonstration that NtrY/NtrX allows for optimal expression of denitrification and nifA genes under microoxic conditions in response to nitrogen compounds. This study extends our knowledge of the complex role played by NtrY/NtrX in S. meliloti.
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Affiliation(s)
- Nieves Calatrava-Morales
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Profesor Albareda 1, 18008 Granada, Spain
| | - Joaquina Nogales
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Profesor Albareda 1, 18008 Granada, Spain
| | - Kinia Ameztoy
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Profesor Albareda 1, 18008 Granada, Spain
| | - Bart van Steenbergen
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Profesor Albareda 1, 18008 Granada, Spain
| | - María J Soto
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Profesor Albareda 1, 18008 Granada, Spain
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25
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Fazli M, Rybtke M, Steiner E, Weidel E, Berthelsen J, Groizeleau J, Bin W, Zhi BZ, Yaming Z, Kaever V, Givskov M, Hartmann RW, Eberl L, Tolker-Nielsen T. Regulation of Burkholderia cenocepacia biofilm formation by RpoN and the c-di-GMP effector BerB. Microbiologyopen 2017; 6. [PMID: 28419759 PMCID: PMC5552954 DOI: 10.1002/mbo3.480] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 03/01/2017] [Accepted: 03/07/2017] [Indexed: 11/25/2022] Open
Abstract
Knowledge about the molecular mechanisms that are involved in the regulation of biofilm formation is essential for the development of biofilm‐control measures. It is well established that the nucleotide second messenger cyclic diguanosine monophosphate (c‐di‐GMP) is a positive regulator of biofilm formation in many bacteria, but more knowledge about c‐di‐GMP effectors is needed. We provide evidence that c‐di‐GMP, the alternative sigma factor RpoN (σ54), and the enhancer‐binding protein BerB play a role in biofilm formation of Burkholderia cenocepacia by regulating the production of a biofilm‐stabilizing exopolysaccharide. Our findings suggest that BerB binds c‐di‐GMP, and activates RpoN‐dependent transcription of the berA gene coding for a c‐di‐GMP‐responsive transcriptional regulator. An increased level of the BerA protein in turn induces the production of biofilm‐stabilizing exopolysaccharide in response to high c‐di‐GMP levels. Our findings imply that the production of biofilm exopolysaccharide in B. cenocepacia is regulated through a cascade involving two consecutive transcription events that are both activated by c‐di‐GMP. This type of regulation may allow tight control of the expenditure of cellular resources.
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Affiliation(s)
- Mustafa Fazli
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark.,Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten Rybtke
- Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Elisabeth Steiner
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Elisabeth Weidel
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
| | - Jens Berthelsen
- Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Julie Groizeleau
- Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Wu Bin
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Boo Zhao Zhi
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Zhang Yaming
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Volkhard Kaever
- Research Core Unit Metabolomics, Institute of Pharmacology, Hannover Medical School, Hannover, Germany
| | - Michael Givskov
- Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Rolf W Hartmann
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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26
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diCenzo GC, Zamani M, Ludwig HN, Finan TM. Heterologous Complementation Reveals a Specialized Activity for BacA in the Medicago-Sinorhizobium meliloti Symbiosis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:312-324. [PMID: 28398123 DOI: 10.1094/mpmi-02-17-0030-r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The bacterium Sinorhizobium meliloti Rm2011 forms N2-fixing root nodules on alfalfa and other leguminous plants. The pSymB chromid contains a 110-kb region (the ETR region) showing high synteny to a chromosomally located region in Sinorhizobium fredii NGR234 and related rhizobia. We recently introduced the ETR region from S. fredii NGR234 into the S. meliloti chromosome. Here, we report that, unexpectedly, the S. fredii NGR234 ETR region did not complement deletion of the S. meliloti ETR region in symbiosis with Medicago sativa. This phenotype was due to the bacA gene of NGR234 not being functionally interchangeable with the S. meliloti bacA gene during M. sativa symbiosis. Further analysis revealed that, whereas bacA genes from S. fredii or Rhizobium leguminosarum bv. viciae 3841 failed to complement the Fix- phenotype of a S. meliloti bacA mutant with M. sativa, they allowed for further developmental progression prior to a loss of viability. In contrast, with Melilotus alba, bacA from S. fredii and R. leguminosarum supported N2 fixation by a S. meliloti bacA mutant. Additionally, the S. meliloti bacA gene can support N2 fixation of a R. leguminosarum bacA mutant during symbiosis with Pisum sativum. A phylogeny of BacA proteins illustrated that S. meliloti BacA has rapidly diverged from most rhizobia and has converged toward the sequence of pathogenic genera Brucella and Escherichia. These data suggest that the S. meliloti BacA has evolved toward a specific interaction with Medicago and highlights the limitations of using a single model system for the study of complex biological topics.
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Affiliation(s)
- George C diCenzo
- Department of Biology, McMaster University, 1280 Main St. W., Hamilton, Ontario L8S 4K1, Canada
| | - Maryam Zamani
- Department of Biology, McMaster University, 1280 Main St. W., Hamilton, Ontario L8S 4K1, Canada
| | - Hannah N Ludwig
- Department of Biology, McMaster University, 1280 Main St. W., Hamilton, Ontario L8S 4K1, Canada
| | - Turlough M Finan
- Department of Biology, McMaster University, 1280 Main St. W., Hamilton, Ontario L8S 4K1, Canada
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27
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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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28
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Gruber S, Schwendenwein D, Magomedova Z, Thaler E, Hagen J, Schwab H, Heidinger P. Design of inducible expression vectors for improved protein production in Ralstonia eutropha H16 derived host strains. J Biotechnol 2016; 235:92-9. [DOI: 10.1016/j.jbiotec.2016.04.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 04/11/2016] [Accepted: 04/12/2016] [Indexed: 11/16/2022]
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29
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Kilmartin JR, Bernhardt PV, Dhouib R, Hanson GR, Riley MJ, Kappler U. Effects of mutations in active site heme ligands on the spectroscopic and catalytic properties of SoxAX cytochromes. J Inorg Biochem 2016; 162:309-318. [PMID: 27112898 DOI: 10.1016/j.jinorgbio.2016.04.015] [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: 11/05/2015] [Revised: 04/04/2016] [Accepted: 04/12/2016] [Indexed: 10/21/2022]
Abstract
By attaching a sulfur substrate to a conserved cysteine of the SoxYZ carrier protein SoxAX cytochromes initiate the reaction cycle of the Sox (sulfur oxidation) multienzyme complex, which is the major pathway for microbial reoxidation of sulfur compounds in the environment. Despite their important role in this process, the reaction mechanism of the SoxAX cytochromes has not been fully elucidated. Here we report the effects of several active site mutations on the spectroscopic and enzymatic properties of the type II SoxAX protein from Starkeya novella, which in addition to two heme groups also contains a Cu redox centre. All substituted proteins contained these redox centres except for His231Ala which was unable to bind Cu(II). Substitution of the SoxA active site heme cysteine ligand with histidine resulted in increased microheterogeneity around the SoxA heme as determined by CW-EPR, while a SnSoxAXC236A substituted protein revealed a completely new, nitrogenous SoxA heme ligand. The same novel ligand was present in SnSoxAXH231A CW-EPR spectra, the first time that a ligand switch of the SoxA heme involving a nearby amino acid has been demonstrated. Kinetically, SnSoxAXC236A and SnSoxAXC236H showed reduced turnover, and in assays containing SoxYZ these mutants retained only ~25% of the wildtype activity. Together, these data indicate that the Cu redox centre can mediate a low level of activity, and that a possible ligand switch can occur during catalysis. It also appears that the SoxA heme cysteine ligand (and possibly the low redox potential) is important for an efficient reaction with SnSoxYZ/thiosulfate.
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Affiliation(s)
- James R Kilmartin
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Rabeb Dhouib
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Graeme R Hanson
- Centre for Advanced Imaging, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Mark J Riley
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Ulrike Kappler
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld 4072, Australia.
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30
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Wang D, Wang YC, Wu LJ, Liu JX, Zhang P, Jiao J, Yan H, Liu T, Tian CF, Chen WX. Construction and pilot screening of a signature-tagged mutant library of Sinorhizobium fredii. Arch Microbiol 2016; 198:91-9. [PMID: 26472206 DOI: 10.1007/s00203-015-1161-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 08/02/2015] [Accepted: 10/03/2015] [Indexed: 11/28/2022]
Abstract
Sinorhizobium fredii is well known for its ability to establish symbiosis with diverse legumes such as Glycine max (soybean, determinate nodules) and Cajanus cajan (pigeon pea, indeterminate nodules). In order to make screening of S. fredii genes related to symbiosis cost-effective, we constructed a large Tn5 insertion mutant library of S. fredii CCBAU45436 using the signature-tagged mutagenesis (STM) technique. This STM library contains a total of 25,500 independent mutants distributed in 17 sublibraries tagged by corresponding distinct DNA bar-code sequences. After the pilot screening of 255 mutants in 15 batches, Tag85-4, Tag4-17, Tag4-11 and Tag10-13 were found to have attenuated competitiveness (0-30 % in nodule occupation) compared to the wild-type strain when inoculated on soybean. Further characterization of these mutants suggests that Tag4-11 (a pyrC mutant) and Tag10-13 (a nrdJ mutant) are defective in establishing symbiosis with soybean. The pyrC mutant induced uninfected pseudonodules while the nrdJ mutant formed significantly more nodules containing bacteroids with poor persistence ability. When these two mutants were tested on pigeon pea, host-specific symbiotic defects were found. These results demonstrated the STM library as a valuable resource for identifying S. fredii genes relevant to symbiosis.
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Affiliation(s)
- Dan Wang
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Yuan Chun Wang
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Li Juan Wu
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Jian Xin Liu
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Pan Zhang
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Jian Jiao
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Hui Yan
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Tao Liu
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Chang Fu Tian
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China.
- Rhizobium Research Center, China Agricultural University, Beijing, China.
| | - Wen Xin Chen
- State Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
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31
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Godino A, Príncipe A, Fischer S. A ptsP deficiency in PGPR Pseudomonas fluorescens SF39a affects bacteriocin production and bacterial fitness in the wheat rhizosphere. Res Microbiol 2015; 167:178-89. [PMID: 26708985 DOI: 10.1016/j.resmic.2015.12.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 12/04/2015] [Accepted: 12/07/2015] [Indexed: 11/26/2022]
Abstract
Pseudomonas fluorescens SF39a is a plant-growth-promoting bacterium isolated from wheat rhizosphere. In this report, we demonstrate that this native strain secretes bacteriocins that inhibit growth of phytopathogenic strains of the genera Pseudomonas and Xanthomonas. An S-type pyocin gene was detected in the genome of strain SF39a and named pys. A non-polar pys::Km mutant was constructed. The bacteriocin production was impaired in this mutant. To identify genes involved in bacteriocin regulation, random transposon mutagenesis was carried out. A miniTn5Km1 mutant, called P. fluorescens SF39a-451, showed strongly reduced bacteriocin production. This phenotype was caused by inactivation of the ptsP gene which encodes a phosphoenolpyruvate phosphotransferase (EI(Ntr)) of the nitrogen-related phosphotransferase system (PTS(Ntr)). In addition, this mutant showed a decrease in biofilm formation and protease production, and an increase in surface motility and pyoverdine production compared with the wild-type strain. Moreover, we investigated the ability of strain SF39a-451 to colonize the wheat rhizosphere under greenhouse conditions. Interestingly, the mutant was less competitive than the wild-type strain in the rhizosphere. To our knowledge, this study provides the first evidence of both the relevance of the ptsP gene in bacteriocin production and functional characterization of a pyocin S in P. fluorescens.
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Affiliation(s)
- Agustina Godino
- Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta 36-Km 601-5800, Río Cuarto, Córdoba, Argentina.
| | - Analía Príncipe
- Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta 36-Km 601-5800, Río Cuarto, Córdoba, Argentina.
| | - Sonia Fischer
- Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Ruta 36-Km 601-5800, Río Cuarto, Córdoba, Argentina.
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32
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Ramírez-Mata A, López-Lara LI, Xiqui-Vázquez ML, Jijón-Moreno S, Romero-Osorio A, Baca BE. The cyclic-di-GMP diguanylate cyclase CdgA has a role in biofilm formation and exopolysaccharide production in Azospirillum brasilense. Res Microbiol 2015; 167:190-201. [PMID: 26708984 DOI: 10.1016/j.resmic.2015.12.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 12/09/2015] [Accepted: 12/10/2015] [Indexed: 11/25/2022]
Abstract
In bacteria, proteins containing GGDEF domains are involved in production of the second messenger c-di-GMP. Here we report that the cdgA gene encoding diguanylate cyclase A (CdgA) is involved in biofilm formation and exopolysaccharide (EPS) production in Azospirillum brasilense Sp7. Biofilm quantification using crystal violet staining revealed that inactivation of cdgA decreased biofilm formation. In addition, confocal laser scanning microscopy analysis of green-fluorescent protein-labeled bacteria showed that, during static growth, the biofilms had differential levels of development: bacteria harboring a cdgA mutation exhibited biofilms with considerably reduced thickness compared with those of the wild-type Sp7 strain. Moreover, DNA-specific staining and treatment with DNase I, and epifluorescence studies demonstrated that extracellular DNA and EPS are components of the biofilm matrix in Azospirillum. After expression and purification of the CdgA protein, diguanylate cyclase activity was detected. The enzymatic activity of CdgA-producing cyclic c-di-GMP was determined using GTP as a substrate and flavin adenine dinucleotide (FAD(+)) and Mg(2)(+) as cofactors. Together, our results revealed that A. brasilense possesses a functional c-di-GMP biosynthesis pathway.
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Affiliation(s)
- Alberto Ramírez-Mata
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Edif. 103J, Av. San Claudio S/N, Col. San Manuel, Puebla Pue CP 72570, Mexico.
| | - Lilia I López-Lara
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Edif. 103J, Av. San Claudio S/N, Col. San Manuel, Puebla Pue CP 72570, Mexico.
| | - Ma Luisa Xiqui-Vázquez
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Edif. 103J, Av. San Claudio S/N, Col. San Manuel, Puebla Pue CP 72570, Mexico.
| | - Saúl Jijón-Moreno
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Edif. 103J, Av. San Claudio S/N, Col. San Manuel, Puebla Pue CP 72570, Mexico.
| | - Angelica Romero-Osorio
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Edif. 103J, Av. San Claudio S/N, Col. San Manuel, Puebla Pue CP 72570, Mexico.
| | - Beatriz E Baca
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Edif. 103J, Av. San Claudio S/N, Col. San Manuel, Puebla Pue CP 72570, Mexico.
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Tittabutr P, Sripakdi S, Boonkerd N, Tanthanuch W, Minamisawa K, Teaumroong N. Possible Role of 1-Aminocyclopropane-1-Carboxylate (ACC) Deaminase Activity of Sinorhizobium sp. BL3 on Symbiosis with Mung Bean and Determinate Nodule Senescence. Microbes Environ 2015; 30:310-20. [PMID: 26657304 PMCID: PMC4676554 DOI: 10.1264/jsme2.me15120] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 10/19/2015] [Indexed: 01/03/2023] Open
Abstract
Sinorhizobium sp. BL3 forms symbiotic interactions with mung bean (Vigna radiata) and contains lrpL-acdS genes, which encode the 1-aminocyclopropane-1-carboxylate (ACC) deaminase enzyme that cleaves ACC, a precursor of plant ethylene synthesis. Since ethylene interferes with nodule formation in some legumes and plays a role in senescence in plant cells, BL3-enhancing ACC deaminase activity (BL3(+)) and defective mutant (BL3(-)) strains were constructed in order to investigate the effects of this enzyme on symbiosis and nodule senescence. Nodulation competitiveness was weaker in BL3(-) than in the wild-type, but was stronger in BL3(+). The inoculation of BL3(-) into mung bean resulted in less plant growth, a lower nodule dry weight, and smaller nodule number than those in the wild-type, whereas the inoculation of BL3(+) had no marked effects. However, similar nitrogenase activity was observed with all treatments; it was strongly detected 3 weeks after the inoculation and gradually declined with time, indicating senescence. The rate of plant nodulation by BL3(+) increased in a time-dependent manner. Nodules occupied by BL3(-) formed smaller symbiosomes, and bacteroid degradation was more prominent than that in the wild-type 7 weeks after the inoculation. Changes in biochemical molecules during nodulation were tracked by Fourier Transform Infrared (FT-IR) microspectroscopy, and the results obtained confirmed that aging processes differed in nodules occupied by BL3 and BL3(-). This is the first study to show the possible role of ACC deaminase activity in senescence in determinate nodules. Our results suggest that an increase in ACC deaminase activity in this strain does not extend the lifespan of nodules, whereas the lack of this activity may accelerate nodule senescence.
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Affiliation(s)
- Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of TechnologyNakhon Ratchasima, 30000Thailand
| | - Sudarat Sripakdi
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of TechnologyNakhon Ratchasima, 30000Thailand
| | - Nantakorn Boonkerd
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of TechnologyNakhon Ratchasima, 30000Thailand
| | - Waraporn Tanthanuch
- Synchrotron Light Research Institute (public organization)Nakhon Ratchasima 30000Thailand
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577Japan
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of TechnologyNakhon Ratchasima, 30000Thailand
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Versatile plasmid-based expression systems for Gram-negative bacteria—General essentials exemplified with the bacterium Ralstonia eutropha H16. N Biotechnol 2015; 32:552-8. [DOI: 10.1016/j.nbt.2015.03.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 03/12/2015] [Accepted: 03/20/2015] [Indexed: 12/13/2022]
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Jiao YS, Liu YH, Yan H, Wang ET, Tian CF, Chen WX, Guo BL, Chen WF. Rhizobial Diversity and Nodulation Characteristics of the Extremely Promiscuous Legume Sophora flavescens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:1338-1352. [PMID: 26389798 DOI: 10.1094/mpmi-06-15-0141-r] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In present study, we report our extensive survey on the diversity and biogeography of rhizobia associated with Sophora flavescens, a sophocarpidine (matrine)-containing medicinal legume. We additionally investigated the cross nodulation, infection pattern, light and electron microscopies of root nodule sections of S. flavescens infected by various rhizobia. Seventeen genospecies of rhizobia belonging to five genera with seven types of symbiotic nodC genes were found to nodulate S. flavescens in natural soils. In the cross-nodulation tests, most representative rhizobia in class α-Proteobacteria, whose host plants belong to different cross-nodulation groups, form effective indeterminate nodules, while representative rhizobia in class β-Proteobacteria form ineffective nodules on S. flavescens. Highly host-specific biovars of Rhizobium leguminosarum (bv. trifolii and bv. viciae) and Rhizobium etli bv. phaseoli could establish symbioses with S. flavescens, providing further evidence that S. flavescens is an extremely promiscuous legume and it does not have strict selectivity on either the symbiotic genes or the species-determining housekeeping genes of rhizobia. Root-hair infection is found as the pattern that rhizobia have gained entry into the curled root hairs. Electron microscopies of ultra-thin sections of S. flavescens root nodules formed by different rhizobia show that the bacteroids are regular or irregular rod shape and nonswollen types. Some bacteroids contain poly-β-hydroxybutyrate (PHB), while others do not, indicating the synthesis of PHB in bacteroids is rhizobia-dependent. The extremely promiscuous symbiosis between S. flavescens and different rhizobia provide us a basis for future studies aimed at understanding the molecular interactions of rhizobia and legumes.
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Affiliation(s)
- Yin Shan Jiao
- 1 State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
| | - Yuan Hui Liu
- 1 State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
| | - Hui Yan
- 1 State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
| | - En Tao Wang
- 1 State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
- 2 Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D. F. 11340, México
| | - Chang Fu Tian
- 1 State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
| | - Wen Xin Chen
- 1 State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
| | - Bao Lin Guo
- 3 Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Wen Feng Chen
- 1 State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
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DNA Microarray-Based Identification of Genes Regulated by NtrC in Bradyrhizobium japonicum. Appl Environ Microbiol 2015; 81:5299-308. [PMID: 26025905 DOI: 10.1128/aem.00609-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/18/2015] [Indexed: 11/20/2022] Open
Abstract
The Bradyrhizobium japonicum NtrBC two-component system is a critical regulator of cellular nitrogen metabolism, including the acquisition and catabolism of nitrogenous compounds. To better define the roles of this system, genome-wide transcriptional profiling was performed to identify the NtrC regulon during the response to nitrogen limitation. Upon cells perceiving low intracellular nitrogen, they stimulate the phosphorylation of NtrC, which induces genes responsible for alteration of the core glutamine synthetase/glutamate synthase nitrogen assimilation pathway, including the genes for the glutamine synthetases and PII proteins. In addition, genes responsible for the import and utilization of multiple nitrogen sources, specifically nitrate and nitrite, were upregulated by NtrC activation. Mutational analysis of a candidate nitrite reductase revealed a role for NtrC in regulating the assimilation of nitrite, since mutations in both ntrC and the gene encoding the candidate nitrite reductase abolished the ability to grow on nitrite as a sole nitrogen source.
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Nybo SE, Khan NE, Woolston BM, Curtis WR. Metabolic engineering in chemolithoautotrophic hosts for the production of fuels and chemicals. Metab Eng 2015; 30:105-120. [PMID: 25959019 DOI: 10.1016/j.ymben.2015.04.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 04/06/2015] [Accepted: 04/29/2015] [Indexed: 12/19/2022]
Abstract
The ability of autotrophic organisms to fix CO2 presents an opportunity to utilize this 'greenhouse gas' as an inexpensive substrate for biochemical production. Unlike conventional heterotrophic microorganisms that consume carbohydrates and amino acids, prokaryotic chemolithoautotrophs have evolved the capacity to utilize reduced chemical compounds to fix CO2 and drive metabolic processes. The use of chemolithoautotrophic hosts as production platforms has been renewed by the prospect of metabolically engineered commodity chemicals and fuels. Efforts such as the ARPA-E electrofuels program highlight both the potential and obstacles that chemolithoautotrophic biosynthetic platforms provide. This review surveys the numerous advances that have been made in chemolithoautotrophic metabolic engineering with a focus on hydrogen oxidizing bacteria such as the model chemolithoautotrophic organism (Ralstonia), the purple photosynthetic bacteria (Rhodobacter), and anaerobic acetogens. Two alternative strategies of microbial chassis development are considered: (1) introducing or enhancing autotrophic capabilities (carbon fixation, hydrogen utilization) in model heterotrophic organisms, or (2) improving tools for pathway engineering (transformation methods, promoters, vectors etc.) in native autotrophic organisms. Unique characteristics of autotrophic growth as they relate to bioreactor design and process development are also discussed in the context of challenges and opportunities for genetic manipulation of organisms as production platforms.
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Affiliation(s)
- S Eric Nybo
- Department of Pharmaceutical Sciences, College of Pharmacy, Ferris State University, Big Rapids, MI, United States
| | - Nymul E Khan
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, United States
| | - Benjamin M Woolston
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Wayne R Curtis
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, United States.
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Biswas I. Genetic tools for manipulating Acinetobacter baumannii genome: an overview. J Med Microbiol 2015; 64:657-669. [PMID: 25948809 DOI: 10.1099/jmm.0.000081] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Acinetobacter baumannii is an emerging nosocomial pathogen involved in a variety of infections ranging from minor soft-tissue infections to more severe infections such as ventilator-associated pneumonia and bacteraemia. A. baumannii has become resistant to most of the commonly used antibiotics and multidrug-resistant isolates are becoming a severe problem in the healthcare setting. In the past few years, whole-genome sequences of >200 A. baumannii isolates have been generated. Several methods and molecular tools have been used for genetic manipulation of various Acinetobacter spp. Here, we review recent developments of various genetic tools used for modification of the A. baumannii genome, including various ways to inactivate gene function, chromosomal integration and transposon mutagenesis.
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Affiliation(s)
- Indranil Biswas
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
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Autenrieth C, Ghosh R. Random mutagenesis and overexpression of rhodopin-3,4-desaturase allows the production of highly conjugated carotenoids in Rhodospirillum rubrum. Arch Biochem Biophys 2015; 572:134-141. [DOI: 10.1016/j.abb.2015.01.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 01/23/2015] [Accepted: 01/24/2015] [Indexed: 12/01/2022]
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Sahonero-Canavesi DX, Sohlenkamp C, Sandoval-Calderón M, Lamsa A, Pogliano K, López-Lara IM, Geiger O. Fatty acid-releasing activities in Sinorhizobium meliloti include unusual diacylglycerol lipase. Environ Microbiol 2015; 17:3391-406. [PMID: 25711932 DOI: 10.1111/1462-2920.12814] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/11/2015] [Accepted: 02/11/2015] [Indexed: 11/28/2022]
Abstract
Phospholipids are well known for their membrane-forming properties and thereby delimit any cell from the exterior world. In addition, membrane phospholipids can act as precursors for signals and other biomolecules during their turnover. Little is known about phospholipid signalling, turnover and remodelling in bacteria. Recently, we showed that a FadD-deficient mutant of Sinorhizobium meliloti, unable to convert free fatty acids to their coenzyme A derivatives, accumulates free fatty acids during the stationary phase of growth. Enzymatic activities responsible for the generation of these free fatty acids were unknown in rhizobia. Searching the genome of S. meliloti, we identified a potential lysophospholipase (SMc04041) and two predicted patatin-like phospholipases A (SMc00930, SMc01003). Although SMc00930 as well as SMc01003 contribute to the release of free fatty acids in S. meliloti, neither one can use phospholipids as substrates. Here we show that SMc01003 converts diacylglycerol to monoacylglycerol and a fatty acid, and that monoacylglycerol can be further degraded by SMc01003 to another fatty acid and glycerol. A SMc01003-deficient mutant of S. meliloti transiently accumulates diacylglycerol, suggesting that SMc01003 also acts as diacylglycerol lipase (DglA) in its native background. Expression of the DglA lipase in Escherichia coli causes lysis of cells in stationary phase of growth.
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Affiliation(s)
- Diana X Sahonero-Canavesi
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Apdo. Postal 565-A, Cuernavaca, Morelos, CP 62210, Mexico
| | - Christian Sohlenkamp
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Apdo. Postal 565-A, Cuernavaca, Morelos, CP 62210, Mexico
| | - Mario Sandoval-Calderón
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Apdo. Postal 565-A, Cuernavaca, Morelos, CP 62210, Mexico
| | - Anne Lamsa
- Division of Biological Sciences, University of California, San Diego, CA, 92093, USA
| | - Kit Pogliano
- Division of Biological Sciences, University of California, San Diego, CA, 92093, USA
| | - Isabel M López-Lara
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Apdo. Postal 565-A, Cuernavaca, Morelos, CP 62210, Mexico
| | - Otto Geiger
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Apdo. Postal 565-A, Cuernavaca, Morelos, CP 62210, Mexico
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Liu J, Yang J, Wen J, Yang Y, Wei X, Zhang X, Wang YP. Mutational analysis of dimeric linkers in peri- and cytoplasmic domains of histidine kinase DctB reveals their functional roles in signal transduction. Open Biol 2015; 4:140023. [PMID: 24898140 PMCID: PMC4077058 DOI: 10.1098/rsob.140023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Membrane-associated histidine kinases (HKs) in two-component systems respond to environmental stimuli by autophosphorylation and phospho-transfer. HK typically contains a periplasmic sensor domain that regulates the cytoplasmic kinase domain through a conserved cytoplasmic linker. How signal is transduced from the ligand-binding site across the membrane barrier remains unclear. Here, we analyse two linker regions of a typical HK, DctB. One region connects the first transmembrane helix with the periplasmic Per-ARNT-Sim domains, while the other one connects the second transmembrane helix with the cytoplasmic kinase domains. We identify a leucine residue in the first linker region to be essential for the signal transduction and for maintaining the delicate balance of the dimeric interface, which is key to its activities. We also show that the other linker, belonging to the S-helix coiled-coil family, plays essential roles in signal transduction inside the cell. Furthermore, by combining mutations with opposing activities in the two regions, we show that these two signalling transduction elements are integrated to produce a combined effect on the final activity of DctB.
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Affiliation(s)
- Jiwei Liu
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Jianguo Yang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Jin Wen
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Yun Yang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Xiaolu Wei
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
| | - Xiaodong Zhang
- Department of Life Sciences, Centre for Structural Biology, Imperial College London, London SW7 2AZ, UK
| | - Yi-Ping Wang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
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Abstract
ABSTRACT
The scientific and technical ambition of contemporary synthetic biology is the engineering of biological objects with a degree of predictability comparable to those made through electric and industrial manufacturing. To this end, biological parts with given specifications are sequence-edited, standardized, and combined into devices, which are assembled into complete systems. This goal, however, faces the customary context dependency of biological ingredients and their amenability to mutation. Biological orthogonality (i.e., the ability to run a function in a fashion minimally influenced by the host) is thus a desirable trait in any deeply engineered construct. Promiscuous conjugative plasmids found in environmental bacteria have evolved precisely to autonomously deploy their encoded activities in a variety of hosts, and thus they become excellent sources of basic building blocks for genetic and metabolic circuits. In this article we review a number of such reusable functions that originated in environmental plasmids and keep their properties and functional parameters in a variety of hosts. The properties encoded in the corresponding sequences include
inter alia
origins of replication, DNA transfer machineries, toxin-antitoxin systems, antibiotic selection markers, site-specific recombinases, effector-dependent transcriptional regulators (with their cognate promoters), and metabolic genes and operons. Several of these sequences have been standardized as BioBricks and/or as components of the SEVA (Standard European Vector Architecture) collection. Such formatting facilitates their physical composability, which is aimed at designing and deploying complex genetic constructs with new-to-nature properties.
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Guo XP, Ren GX, Zhu H, Mao XJ, Sun YC. Differential regulation of the hmsCDE operon in Yersinia pestis and Yersinia pseudotuberculosis by the Rcs phosphorelay system. Sci Rep 2015; 5:8412. [PMID: 25672461 PMCID: PMC4325325 DOI: 10.1038/srep08412] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 01/19/2015] [Indexed: 11/19/2022] Open
Abstract
Yersinia pestis, the agent of plague, forms a biofilm in its flea vector to enhance transmission. Y. pestis biofilm development is positively regulated by hmsT and hmsD, encoding diguanylate cyclases (DGCs) involved in synthesis of the bacterial second messenger c-di-GMP. rcsA, encoding an auxiliary protein in Rcs phosphorelay, is nonfunctional in Y. pestis, while in Yersinia pseudotuberculosis, rcsA is functional and represses biofilms. Previously we showed that Rcs phosphorelay negatively regulates transcription of hmsT in Y. pestis and its ancestor Yersinia pseudotuberculosis. In this study, we show that Rcs positively regulates hmsCDE operon (encoding HmsD) in Y. pestis; while in the presence of functional rcsA, Rcs represses hmsCDE operon in Y. pseudotuberculosis. Loss of rcsA's function in Y. pestis not only causes derepression of hmsT but also causes activation of hmsD, which may account for the increased biofilm formation in Y. pestis. In addition, differential regulation of the two DGCs, HmsT and HmsD by Rcs may help Y. pestis to adapt to different environment.
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Affiliation(s)
- Xiao-Peng Guo
- MOH key laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 9, Dongdan Santiao, Dongcheng District, Beijing, 100730, China
| | - Gai-Xian Ren
- MOH key laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 9, Dongdan Santiao, Dongcheng District, Beijing, 100730, China
| | - Hui Zhu
- MOH key laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 9, Dongdan Santiao, Dongcheng District, Beijing, 100730, China
| | - Xu-Jian Mao
- MOH key laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 9, Dongdan Santiao, Dongcheng District, Beijing, 100730, China
| | - Yi-Cheng Sun
- MOH key laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 9, Dongdan Santiao, Dongcheng District, Beijing, 100730, China
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Duarte AS, Cavaleiro E, Pereira C, Merino S, Esteves AC, Duarte EP, Tomás JM, Correia AC. Aeromonas piscicola AH-3 expresses an extracellular collagenase with cytotoxic properties. Lett Appl Microbiol 2014; 60:288-97. [PMID: 25443157 DOI: 10.1111/lam.12373] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 11/10/2014] [Accepted: 11/26/2014] [Indexed: 01/01/2023]
Abstract
UNLABELLED The aim of this study was to investigate the presence and the phenotypic expression of a gene coding for a putative collagenase. This gene (AHA_0517) was identified in Aeromonas hydrophila ATCC 7966 genome and named colAh. We constructed and characterized an Aeromonas piscicola AH-3::colAh knockout mutant. Collagenolytic activity of the wild-type and mutant strains was determined, demonstrating that colAh encodes for a collagenase. ColAh-collagen interaction was assayed by Far-Western blot, and cytopathic effects were investigated in Vero cells. We demonstrated that ColAh is a gluzincin metallopeptidase (approx. 100 kDa), able to cleave and physically interact with collagen, that contributes for Aeromonas collagenolytic activity and cytotoxicity. ColAh possess the consensus HEXXH sequence and a glutamic acid as the third zinc binding positioned downstream the HEXXH motif, but has low sequence similarity and distinct domain architecture to the well-known clostridial collagenases. In addition, these results highlight the importance of exploring new microbial collagenases that may have significant relevance for the health and biotechnological industries. SIGNIFICANCE AND IMPACT OF THE STUDY Collagenases play a central role in processes where collagen digestion is needed, for example host invasion by pathogenic micro-organisms. We identified a new collagenase from Aeromonas using an integrated in silico/in vitro strategy. This enzyme is able to bind and cleave collagen, contributes for AH-3 cytotoxicity and shares low similarity with known bacterial collagenases. This is the first report of an enzyme belonging to the gluzincin subfamily of the M9 family of peptidases in Aeromonas. This study increases the current knowledge on collagenolytic enzymes bringing new perspectives for biotechnology/medical purposes.
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Affiliation(s)
- A S Duarte
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
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Gruber S, Hagen J, Schwab H, Koefinger P. Reprint of “Versatile and stable vectors for efficient gene expression in Ralstonia eutropha H16”. J Biotechnol 2014; 192 Pt B:410-8. [DOI: 10.1016/j.jbiotec.2014.09.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Gruber S, Hagen J, Schwab H, Koefinger P. Versatile and stable vectors for efficient gene expression in Ralstonia eutropha H16. J Biotechnol 2014; 186:74-82. [DOI: 10.1016/j.jbiotec.2014.06.030] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 06/11/2014] [Accepted: 06/25/2014] [Indexed: 10/25/2022]
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Pooyan S, George MLC, Borthakur D. Characterization of a Rhizobium etli chromosomal gene required for nodule development on Phaseolus vulgaris L. World J Microbiol Biotechnol 2014; 10:583-9. [DOI: 10.1007/bf00367673] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/27/1994] [Accepted: 06/01/1994] [Indexed: 11/30/2022]
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Amino acid residues of RegA important for interactions with the CbbR-DNA complex of Rhodobacter sphaeroides. J Bacteriol 2014; 196:3179-90. [PMID: 24957624 DOI: 10.1128/jb.01842-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
CbbR and RegA (PrrA) are transcriptional regulators of the Calvin-Benson-Bassham (CBB) CO2 fixation pathway (cbbI and cbbII) operons of Rhodobacter sphaeroides. The CbbR and RegA proteins interact, but CbbR must be bound to the promoter DNA in order for RegA-CbbR protein-protein interactions to occur. RegA greatly enhances the ability of CbbR to bind the cbbI promoter or greatly enhances the stability of the CbbR/promoter complex. The N-terminal receiver domain and the DNA binding domain of RegA were shown to interact with CbbR. Residues in α-helix 7 and α-helix 8 of the DNA binding domain (helix-turn-helix) of RegA directly interacted with CbbR, with α-helix 7 positioned immediately above the DNA and α-helix 8 located in the major groove of the DNA. A CbbR protein containing only the DNA binding motif and the linker helix was capable of binding to RegA. In contrast, a truncated CbbR containing only the linker helix and recognition domains I and II (required for effector binding) was not able to interact with RegA. The accumulated results strongly suggest that the DNA binding domains of both proteins interact to facilitate optimal transcriptional control over the cbb operons. In vivo analysis, using constitutively active mutant CbbR proteins, further indicated that CbbR must interact with phosphorylated RegA in order to accomplish transcriptional activation.
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Evaluation of a pooled strategy for high-throughput sequencing of cosmid clones from metagenomic libraries. PLoS One 2014; 9:e98968. [PMID: 24911009 PMCID: PMC4049660 DOI: 10.1371/journal.pone.0098968] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 05/09/2014] [Indexed: 11/19/2022] Open
Abstract
High-throughput sequencing methods have been instrumental in the growing field of metagenomics, with technological improvements enabling greater throughput at decreased costs. Nonetheless, the economy of high-throughput sequencing cannot be fully leveraged in the subdiscipline of functional metagenomics. In this area of research, environmental DNA is typically cloned to generate large-insert libraries from which individual clones are isolated, based on specific activities of interest. Sequence data are required for complete characterization of such clones, but the sequencing of a large set of clones requires individual barcode-based sample preparation; this can become costly, as the cost of clone barcoding scales linearly with the number of clones processed, and thus sequencing a large number of metagenomic clones often remains cost-prohibitive. We investigated a hybrid Sanger/Illumina pooled sequencing strategy that omits barcoding altogether, and we evaluated this strategy by comparing the pooled sequencing results to reference sequence data obtained from traditional barcode-based sequencing of the same set of clones. Using identity and coverage metrics in our evaluation, we show that pooled sequencing can generate high-quality sequence data, without producing problematic chimeras. Though caveats of a pooled strategy exist and further optimization of the method is required to improve recovery of complete clone sequences and to avoid circumstances that generate unrecoverable clone sequences, our results demonstrate that pooled sequencing represents an effective and low-cost alternative for sequencing large sets of metagenomic clones.
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Heterologous expression of pyrroloquinoline quinone (pqq) gene cluster confers mineral phosphate solubilization ability to Herbaspirillum seropedicae Z67. Appl Microbiol Biotechnol 2014; 98:5117-29. [DOI: 10.1007/s00253-014-5610-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 02/10/2014] [Accepted: 02/11/2014] [Indexed: 11/26/2022]
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