1
|
Li X, Li Z, Wei Y, Chen Z, Xie S. Identification and characterization of the TetR family transcriptional regulator NffT in Rhizobium johnstonii. Appl Environ Microbiol 2024; 90:e0185123. [PMID: 38426790 PMCID: PMC10952539 DOI: 10.1128/aem.01851-23] [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: 10/17/2023] [Accepted: 02/02/2024] [Indexed: 03/02/2024] Open
Abstract
Symbiotic nitrogen fixation (SNF) by rhizobia is not only the main natural bionitrogen-source for organisms but also a green process leveraged to increase the fertility of soil for agricultural production. However, an insufficient understanding of the regulatory mechanism of SNF hinders its practical application. During SNF, nifA-fixA signaling is essential for the biosynthesis of nitrogenases and electron transfer chain proteins. In the present study, the TetR regulator NffT, whose mutation increased fixA expression, was discovered through a fixA-promoter-β-glucuronidase fusion assay performed with Rhizobium johnstonii. Real-time quantitative PCR analysis showed that nffT deletion increased the expression of symbiotic genes including nifA and fixA in nifA-fixA signaling, and fixL, fixK, fnrN, and fixN9 in fixL-fixN signaling. nffT overexpression resulted in disordered nodules and reduced nitrogen-fixing efficiency. Electrophoretic mobility shift assays revealed that NffT directly regulated the transcription of RL0091-93, which encode an ATP-binding ABC transporter predicted to be involved in carbohydrate transport. Purified His-tagged NffT bound to a 68 bp DNA sequence located -32 to -99 bp upstream of RL0091-93 and NffT deletion significantly increased the expression of RL0091-93. nffT-promoter-β-glucuronidase fusion assay indicated that nffT expression was regulated by the cobNTS genes and cobalamin. Mutations in cobNTS significantly decreased the expression of nffT, and cobalamin restored its expression. These results revealed that NffT affects nodule development and nitrogen-fixing reaction by participating in a complex regulatory network of symbiotic and carbohydrate metabolic genes and, thus, plays a pivotal regulatory role during symbiosis of R. johnstonii-Pisum sativum.IMPORTANCESymbiotic nitrogen fixation (SNF) by rhizobia is a green way to maintain soil fertility without causing environmental pollution or consuming chemical energy. A detailed understanding of the regulatory mechanism of this complex process is essential for promoting sustainable agriculture. In this study, we discovered the TetR-type regulator NffT, which suppressed the expression of fixA in Rhizobium johnstonii. Furthermore, NffT was confirmed to play pleiotropic roles in R. johnstonii-Pisum sativum symbiosis; specifically, it inhibited rhizobial growth, nodule differentiation, and nitrogen-fixing reactions. We revealed that NffT indirectly affected R. johnstonii-P. sativum symbiosis by participating in a complex regulatory network of symbiotic and carbohydrate metabolic genes. Furthermore, cobalamin, a chemical molecule, was reported for the first time to be involved in TetR-type protein transcription during symbiosis. Thus, NffT identification connects SNF regulation with genetic, metabolic, and chemical signals and provides new insights into the complex regulation of SNF, laying an experimental basis for the targeted construction of rhizobial strains with highly efficient nitrogen-fixing capacity.
Collapse
Affiliation(s)
- Xiaofang Li
- Institute of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou, Zhejiang, China
| | - Zhangqun Li
- Institute of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou, Zhejiang, China
| | - Yajuan Wei
- Institute of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou, Zhejiang, China
| | - Zirui Chen
- Institute of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou, Zhejiang, China
| | - Shijie Xie
- Institute of Biopharmaceuticals, School of Pharmaceutical Sciences, Taizhou University, Taizhou, Zhejiang, China
| |
Collapse
|
2
|
He Y, Collado JT, Iuliano JN, Woroniecka HA, Hall CR, Gil AA, Laptenok SP, Greetham GM, Illarionov B, Bacher A, Fischer M, French JB, Lukacs A, Meech SR, Tonge PJ. Elucidating the Signal Transduction Mechanism of the Blue-Light-Regulated Photoreceptor YtvA: From Photoactivation to Downstream Regulation. ACS Chem Biol 2024; 19:696-706. [PMID: 38385342 PMCID: PMC10949197 DOI: 10.1021/acschembio.3c00722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/25/2024] [Accepted: 02/12/2024] [Indexed: 02/23/2024]
Abstract
The blue-light photoreceptor YtvA from Bacillus subtilis has an N-terminal flavin mononucleotide (FMN)-binding light-oxygen-voltage (LOV) domain that is fused to a C-terminal sulfate transporter and anti-σ factor antagonist (STAS) output domain. To interrogate the signal transduction pathway that leads to photoactivation, the STAS domain was replaced with a histidine kinase, so that photoexcitation of the flavin could be directly correlated with biological activity. N94, a conserved Asn that is hydrogen bonded to the FMN C2═O group, was replaced with Ala, Asp, and Ser residues to explore the role of this residue in triggering the structural dynamics that activate the output domain. Femtosecond to millisecond time-resolved multiple probe spectroscopy coupled with a fluorescence polarization assay revealed that the loss of the hydrogen bond between N94 and the C2═O group decoupled changes in the protein structure from photoexcitation. In addition, alterations in N94 also decreased the stability of the Cys-FMN adduct formed in the light-activated state by up to a factor of ∼25. Collectively, these studies shed light on the role of the hydrogen bonding network in the LOV β-scaffold in signal transduction.
Collapse
Affiliation(s)
- YongLe He
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | | | - James N. Iuliano
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Helena A. Woroniecka
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Christopher R. Hall
- Central
Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, U.K.
| | - Agnieszka A. Gil
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | | | - Gregory M. Greetham
- Central
Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, U.K.
| | - Boris Illarionov
- Institut
für Biochemie und Lebensmittelchemie, Universität Hamburg, Grindelallee 117, D-20146 Hamburg, Germany
| | - Adelbert Bacher
- Institut
für Biochemie und Lebensmittelchemie, Universität Hamburg, Grindelallee 117, D-20146 Hamburg, Germany
- TUM School
of Natural Sciences, Technical University
of Munich, 85747 Garching, Germany
| | - Markus Fischer
- Institut
für Biochemie und Lebensmittelchemie, Universität Hamburg, Grindelallee 117, D-20146 Hamburg, Germany
| | - Jarrod B. French
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
- The
Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
| | - Andras Lukacs
- School
of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K.
- Department
of Biophysics, Medical School, University
of Pecs, Szigeti ut 12, 7624 Pecs, Hungary
| | - Stephen R. Meech
- School
of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K.
| | - Peter J. Tonge
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| |
Collapse
|
3
|
Xiao M, Dhungel S, Azad R, Favaro DC, Rajesh RP, Gardner KH, Kikani CK. Signal-regulated Unmasking of Nuclear Localization Motif in the PAS Domain Regulates the Nuclear Translocation of PASK. J Mol Biol 2024; 436:168433. [PMID: 38182104 PMCID: PMC10922792 DOI: 10.1016/j.jmb.2023.168433] [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: 09/11/2023] [Revised: 12/22/2023] [Accepted: 12/29/2023] [Indexed: 01/07/2024]
Abstract
The ligand-regulated PAS domains are one of the most diverse signal-integrating domains found in proteins from prokaryotes to humans. By biochemically connecting cellular processes with their environment, PAS domains facilitate an appropriate cellular response. PAS domain-containing Kinase (PASK) is an evolutionarily conserved protein kinase that plays important signaling roles in mammalian stem cells to establish stem cell fate. We have shown that the nuclear translocation of PASK is stimulated by differentiation signaling cues in muscle stem cells. However, the mechanistic basis of the regulation of PASK nucleo-cytoplasmic translocation remains unknown. Here, we show that the PAS-A domain of PASK contains a putative monopartite nuclear localization sequence (NLS) motif. This NLS is inhibited in cells through intramolecular association with a short linear motif, termed the PAS Interacting Motif (PIM), found upstream of the kinase domain. This interaction serves to retain PASK in the cytosol in the absence of signaling cues. Consistent with that, we show that metabolic inputs induce PASK nuclear import, likely by disrupting this association. We suggest that a route for such linkage may occur through the PAS-A ligand binding cavity. We show that PIM recruitment and artificial ligand binding to the PAS-A domain occur at neighboring locations that could facilitate metabolic control of the PAS-PIM interaction. Thus, the intramolecular interaction in PASK integrates metabolic signaling cues for nuclear translocation and could be targeted to control the balance between self-renewal and differentiation in stem cells.
Collapse
Affiliation(s)
- Michael Xiao
- Department of Biology, University of Kentucky, Lexington, KY 40502, USA
| | - Sajina Dhungel
- Department of Biology, University of Kentucky, Lexington, KY 40502, USA
| | - Roksana Azad
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA; Ph.D. Program in Biochemistry, Graduate Center, City University of New York, NY 10016, USA
| | - Denize C Favaro
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA
| | | | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA; Department of Chemistry and Biochemistry, City College of New York, NY 10031, USA; Ph.D. Programs in Biochemistry, Chemistry and Biology Ph.D. Programs, Graduate Center, City University of New York, NY 10016, USA.
| | - Chintan K Kikani
- Department of Biology, University of Kentucky, Lexington, KY 40502, USA.
| |
Collapse
|
4
|
Mokdad A, Ang E, Desciak M, Ott C, Vilbert A, Beddow O, Butuc A, Larsen RW, Reynolds MF. Photoacoustic Calorimetry Studies of O 2-Sensing FixL and (R200, I209) Variants from Sinorhizobium meliloti Reveal Conformational Changes Coupled to Ligand Photodissociation from the Heme-PAS Domain. Biochemistry 2024; 63:116-127. [PMID: 38127721 PMCID: PMC10765370 DOI: 10.1021/acs.biochem.3c00438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/29/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
FixL is an oxygen-sensing heme-PAS protein that regulates nitrogen fixation in the root nodules of plants. In this paper, we present the first photothermal studies of the full-length wild-type FixL protein from Sinorhizobium meliloti and the first thermodynamic profile of a full-length heme-PAS protein. Photoacoustic calorimetry studies reveal a quadriphasic relaxation for SmFixL*WT and the five variant proteins (SmFixL*R200H, SmFixL*R200Q, SmFixL*R200E, SmFixL*R200A, and SmFixL*I209M) with four intermediates from <20 ns to ∼1.5 μs associated with the photodissociation of CO from the heme. The altered thermodynamic profiles of the full-length SmFixL* variant proteins confirm that the conserved heme domain residues R200 and I209 are important for signal transduction. In contrast, the truncated heme domain, SmFixLH128-264, shows only a single, fast monophasic relaxation at <50 ns associated with the fast disruption of a salt bridge and release of CO to the solvent, suggesting that the full-length protein is necessary to observe the conformational changes that propagate the signal from the heme domain to the kinase domain.
Collapse
Affiliation(s)
- Audrey Mokdad
- Department
of Chemistry, University of South Florida, 4202 East Fowler Avenue SCA 400, Tampa, Florida 33620, United States
| | - EuTchen Ang
- Department
of Chemistry and Biochemistry, Saint Joseph’s
University, 5600 City Avenue, Philadelphia, Pennsylvania 19131, United States
| | - Michael Desciak
- Department
of Chemistry and Biochemistry, Saint Joseph’s
University, 5600 City Avenue, Philadelphia, Pennsylvania 19131, United States
| | - Christine Ott
- Department
of Chemistry and Biochemistry, Saint Joseph’s
University, 5600 City Avenue, Philadelphia, Pennsylvania 19131, United States
| | - Avery Vilbert
- Department
of Chemistry and Biochemistry, Saint Joseph’s
University, 5600 City Avenue, Philadelphia, Pennsylvania 19131, United States
| | - Olivia Beddow
- Department
of Chemistry and Biochemistry, Saint Joseph’s
University, 5600 City Avenue, Philadelphia, Pennsylvania 19131, United States
| | - Artiom Butuc
- Department
of Chemistry and Biochemistry, Saint Joseph’s
University, 5600 City Avenue, Philadelphia, Pennsylvania 19131, United States
| | - Randy W. Larsen
- Department
of Chemistry, University of South Florida, 4202 East Fowler Avenue SCA 400, Tampa, Florida 33620, United States
| | - Mark F. Reynolds
- Department
of Chemistry and Biochemistry, Saint Joseph’s
University, 5600 City Avenue, Philadelphia, Pennsylvania 19131, United States
| |
Collapse
|
5
|
Xiao M, Dhungel S, Azad R, Favaro DC, Rajesh RP, Gardner KH, Kikani CK. Signal-regulated unmasking of the nuclear localization motif in the PAS domain regulates the nuclear translocation of PASK. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.06.556462. [PMID: 37732199 PMCID: PMC10508781 DOI: 10.1101/2023.09.06.556462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The ligand-regulated PAS domains are one of the most diverse signal-integrating domains found in proteins from prokaryotes to humans. By biochemically connecting cellular processes with their environment, PAS domains facilitate an appropriate cellular response. PAS domain-containing Kinase (PASK) is an evolutionarily conserved protein kinase that plays important signaling roles in mammalian stem cells to establish stem cell fate. We have shown that the nuclear translocation of PASK is stimulated by differentiation signaling cues in muscle stem cells. However, the mechanistic basis of the regulation of PASK nucleo-cytoplasmic translocation remains unknown. Here, we show that the PAS-A domain of PASK contains a putative monopartite nuclear localization sequence (NLS) motif. This NLS is inhibited in cells via intramolecular association with a short linear motif, termed the PAS Interacting Motif (PIM), found upstream of the kinase domain. The interaction between the PAS-A domain and PIM is evolutionarily conserved and serves to retain PASK in the cytosol in the absence of signaling cues. Consistent with that, we show that metabolic inputs induce PASK nuclear import, likely by disrupting the PAS-A: PIM association. We suggest that a route for such linkage may occur through the PAS-A ligand binding cavity. We show that PIM recruitment and artificial ligand binding to the PAS-A domain occur at neighboring locations that could facilitate metabolic control of the PAS-PIM interaction. Thus, the PAS-A domain of PASK integrates metabolic signaling cues for nuclear translocation and could be targeted to control the balance between self-renewal and differentiation in stem cells.
Collapse
Affiliation(s)
- Michael Xiao
- Department of Biology, University of Kentucky, Lexington, KY 40502, USA
| | - Sajina Dhungel
- Department of Biology, University of Kentucky, Lexington, KY 40502, USA
| | - Roksana Azad
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA
- Ph.D. Program in Biochemistry, Graduate Center, City University of New York, NY 10016, USA
| | - Denize C. Favaro
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA
| | | | - Kevin H. Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA
- Department of Chemistry and Biochemistry, City College of New York, NY 10031, USA
- Ph.D. Programs in Biochemistry, Chemistry and Biology Ph.D. Programs, Graduate Center, City University of New York, NY 10016, USA
| | - Chintan K. Kikani
- Department of Biology, University of Kentucky, Lexington, KY 40502, USA
| |
Collapse
|
6
|
Li X, Li Z. What determines symbiotic nitrogen fixation efficiency in rhizobium: recent insights into Rhizobium leguminosarum. Arch Microbiol 2023; 205:300. [PMID: 37542687 DOI: 10.1007/s00203-023-03640-7] [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: 06/01/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/07/2023]
Abstract
Symbiotic nitrogen fixation (SNF) by rhizobium, a Gram-negative soil bacterium, is an essential component in the nitrogen cycle and is a sustainable green way to maintain soil fertility without chemical energy consumption. SNF, which results from the processes of nodulation, rhizobial infection, bacteroid differentiation and nitrogen-fixing reaction, requires the expression of various genes from both symbionts with adaptation to the changing environment. To achieve successful nitrogen fixation, rhizobia and their hosts cooperate closely for precise regulation of symbiotic genes, metabolic processes and internal environment homeostasis. Many researches have progressed to reveal the ample information about regulatory aspects of SNF during recent decades, but the major bottlenecks regarding improvement of nitrogen-fixing efficiency has proven to be complex. In this mini-review, we summarize recent advances that have contributed to understanding the rhizobial regulatory aspects that determine SNF efficiency, focusing on the coordinated regulatory mechanism of symbiotic genes, oxygen, carbon metabolism, amino acid metabolism, combined nitrogen, non-coding RNAs and internal environment homeostasis. Unraveling regulatory determinants of SNF in the nitrogen-fixing protagonist rhizobium is expected to promote an improvement of nitrogen-fixing efficiency in crop production.
Collapse
Affiliation(s)
- Xiaofang Li
- Institute of Biopharmaceuticals, Taizhou University, 1139 Shifu Avenue, Taizhou, 318000, China.
- School of Pharmaceutical Sciences, Taizhou University, 1139 Shifu Avenue, Taizhou, 318000, China.
| | - Zhangqun Li
- School of Pharmaceutical Sciences, Taizhou University, 1139 Shifu Avenue, Taizhou, 318000, China
| |
Collapse
|
7
|
Chakravarty D, Sreenivasan S, Swint-Kruse L, Porter LL. Identification of a covert evolutionary pathway between two protein folds. Nat Commun 2023; 14:3177. [PMID: 37264049 DOI: 10.1038/s41467-023-38519-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 05/03/2023] [Indexed: 06/03/2023] Open
Abstract
Although homologous protein sequences are expected to adopt similar structures, some amino acid substitutions can interconvert α-helices and β-sheets. Such fold switching may have occurred over evolutionary history, but supporting evidence has been limited by the: (1) abundance and diversity of sequenced genes, (2) quantity of experimentally determined protein structures, and (3) assumptions underlying the statistical methods used to infer homology. Here, we overcome these barriers by applying multiple statistical methods to a family of ~600,000 bacterial response regulator proteins. We find that their homologous DNA-binding subunits assume divergent structures: helix-turn-helix versus α-helix + β-sheet (winged helix). Phylogenetic analyses, ancestral sequence reconstruction, and AlphaFold2 models indicate that amino acid substitutions facilitated a switch from helix-turn-helix into winged helix. This structural transformation likely expanded DNA-binding specificity. Our approach uncovers an evolutionary pathway between two protein folds and provides a methodology to identify secondary structure switching in other protein families.
Collapse
Affiliation(s)
- Devlina Chakravarty
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Shwetha Sreenivasan
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Liskin Swint-Kruse
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Lauren L Porter
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| |
Collapse
|
8
|
Dent MR, Weaver BR, Roberts MG, Burstyn JN. Carbon Monoxide-Sensing Transcription Factors: Regulators of Microbial Carbon Monoxide Oxidation Pathway Gene Expression. J Bacteriol 2023; 205:e0033222. [PMID: 37154694 PMCID: PMC10210986 DOI: 10.1128/jb.00332-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Carbon monoxide (CO) serves as a source of energy and carbon for a diverse set of microbes found in anaerobic and aerobic environments. The enzymes that bacteria and archaea use to oxidize CO depend upon complex metallocofactors that require accessory proteins for assembly and proper function. This complexity comes at a high energetic cost and necessitates strict regulation of CO metabolic pathways in facultative CO metabolizers to ensure that gene expression occurs only when CO concentrations and redox conditions are appropriate. In this review, we examine two known heme-dependent transcription factors, CooA and RcoM, that regulate inducible CO metabolism pathways in anaerobic and aerobic microorganisms. We provide an analysis of the known physiological and genomic contexts of these sensors and employ this analysis to contextualize known biochemical properties. In addition, we describe a growing list of putative transcription factors associated with CO metabolism that potentially use cofactors other than heme to sense CO.
Collapse
Affiliation(s)
- Matthew R. Dent
- Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brian R. Weaver
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Madeleine G. Roberts
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Judith N. Burstyn
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| |
Collapse
|
9
|
Jia X, Zhao K, Liu F, Lin J, Lin C, Chen J. Transcriptional factor OmpR positively regulates prodigiosin biosynthesis in Serratia marcescens FZSF02 by binding with the promoter of the prodigiosin cluster. Front Microbiol 2022; 13:1041146. [PMID: 36466667 PMCID: PMC9712742 DOI: 10.3389/fmicb.2022.1041146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/01/2022] [Indexed: 10/27/2023] Open
Abstract
Prodigiosin is a promising secondary metabolite mainly produced by Serratia marcescens. The production of prodigiosin by S. marcescens is regulated by different kinds of regulatory systems, including the EnvZ/OmpR system. In this study, we demonstrated that the regulatory factor OmpR positively regulated prodigiosin production in S. marcescens FZSF02 by directly binding to the promoter region of the prodigiosin biosynthesis cluster with a lacZ reporter assay and electrophoretic mobility shift assay (EMSA). The binding sequence with the pig promoter was identified by a DNase I footprinting assay. We further demonstrate that OmpR regulates its own expression by directly binding to the promoter region of envZ/ompR. For the first time, the regulatory mechanism of prodigiosin production by the transcriptional factor OmpR was revealed.
Collapse
Affiliation(s)
- Xianbo Jia
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences, Fujian Key Laboratory of Plant Nutrition and Fertilizer, Fuzhou, China
| | - Ke Zhao
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Fangchen Liu
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Junjie Lin
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chenqiang Lin
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences, Fujian Key Laboratory of Plant Nutrition and Fertilizer, Fuzhou, China
| | - Jichen Chen
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences, Fujian Key Laboratory of Plant Nutrition and Fertilizer, Fuzhou, China
| |
Collapse
|
10
|
Makino A, Nakai R, Yoneda Y, Toyama T, Tanaka Y, Meng XY, Mori K, Ike M, Morikawa M, Kamagata Y, Tamaki H. Isolation of Aquatic Plant Growth-Promoting Bacteria for the Floating Plant Duckweed (Lemna minor). Microorganisms 2022; 10:microorganisms10081564. [PMID: 36013982 PMCID: PMC9416352 DOI: 10.3390/microorganisms10081564] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/15/2022] [Accepted: 07/28/2022] [Indexed: 11/29/2022] Open
Abstract
Plant growth-promoting bacteria (PGPB) can exert beneficial growth effects on their host plants. Little is known about the phylogeny and growth-promoting mechanisms of PGPB associated with aquatic plants, although those of terrestrial PGPB have been well-studied. Here, we report four novel aquatic PGPB strains, MRB1–4 (NITE P-01645–P-01648), for duckweed Lemna minor from our rhizobacterial collection isolated from Lythrum anceps. The number of L. minor fronds during 14 days co-culture with the strains MRB1–4 increased by 2.1–3.8-fold, compared with an uninoculated control; the plant biomass and chlorophyll content in co-cultures also increased. Moreover, all strains possessed an indole-3-acetic acid production trait in common with a plant growth-promoting trait of terrestrial PGPB. Phylogenetic analysis showed that three strains, MRB-1, -3, and -4, were affiliated with known proteobacterial genera (Bradyrhizobium and Pelomonas); this report is the first to describe a plant-growth promoting activity of Pelomonas members. The gammaproteobacterial strain MRB2 was suggested to be phylogenetically novel at the genus level. Under microscopic observation, the Pelomonas strain MRB3 was epiphytic and adhered to both the root surfaces and fronds of duckweed. The duckweed PGPB obtained here could serve as a new model for understanding unforeseen mechanisms behind aquatic plant-microbe interactions.
Collapse
Affiliation(s)
- Ayaka Makino
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Hokkaido, Japan; (A.M.); (R.N.)
| | - Ryosuke Nakai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Hokkaido, Japan; (A.M.); (R.N.)
| | - Yasuko Yoneda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan; (Y.Y.); (X.-Y.M.); (Y.K.)
| | - Tadashi Toyama
- Graduate School of Engineering, University of Yamanashi, Kofu 400-8511, Yamanashi, Japan; (T.T.); (K.M.)
| | - Yasuhiro Tanaka
- Graduate School of Life and Environmental Sciences, University of Yamanashi, Kofu 400-8510, Yamanashi, Japan;
| | - Xian-Ying Meng
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan; (Y.Y.); (X.-Y.M.); (Y.K.)
| | - Kazuhiro Mori
- Graduate School of Engineering, University of Yamanashi, Kofu 400-8511, Yamanashi, Japan; (T.T.); (K.M.)
| | - Michihiko Ike
- Graduate School of Engineering, Osaka University, Suita 565-0871, Osaka, Japan;
| | - Masaaki Morikawa
- Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Hokkaido, Japan;
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan; (Y.Y.); (X.-Y.M.); (Y.K.)
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan; (Y.Y.); (X.-Y.M.); (Y.K.)
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8577, Ibaraki, Japan
- Biotechnology Research Center, University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Correspondence: ; Tel.: +81-29-861-6592
| |
Collapse
|
11
|
Huo H, Zong L, Liu Y, Chen W, Chen J, Wei G. Rhizobial HmuS pSym as a heme-binding factor is required for optimal symbiosis between Mesorhizobium amorphae CCNWGS0123 and Robinia pseudoacacia. PLANT, CELL & ENVIRONMENT 2022; 45:2191-2210. [PMID: 35419804 DOI: 10.1111/pce.14335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 01/15/2022] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Nitrogen-fixing root nodules are formed by symbiotic association of legume hosts with rhizobia in nitrogen-deprived soils. Successful symbiosis is regulated by signals from both legume hosts and their rhizobial partners. HmuS is a heme degrading factor widely distributed in bacteria, but little is known about the role of rhizobial hmuS in symbiosis with legumes. Here, we found that inactivation of hmuSpSym in the symbiotic plasmid of Mesorhizobium amorphae CCNWGS0123 disrupted rhizobial infection, primordium formation, and nitrogen fixation in symbiosis with Robinia pseudoacacia. Although there was no difference in bacteroids differentiation, infected plant cells were shrunken and bacteroids were disintegrated in nodules of plants infected by the ΔhmuSpSym mutant strain. The balance of defence reaction was also impaired in ΔhmuSpSym strain-infected root nodules. hmuSpSym was strongly expressed in the nitrogen-fixation zone of mature nodules. Furthermore, the HmuSpSym protein could bind to heme but not degrade it. Inactivation of hmuSpSym led to significantly decreased expression levels of oxygen-sensing related genes in nodules. In summary, hmuSpSym of M. amorphae CCNWGS0123 plays an essential role in nodule development and maintenance of bacteroid survival within R. pseudoacacia cells, possibly through heme-binding in symbiosis.
Collapse
Affiliation(s)
- Haibo Huo
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
| | - Le Zong
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
| | - Yao Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
| | - Wenfeng Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences and Rhizobium Research Center, Ministry of Agriculture Key Laboratory of Soil Microbiology, China Agricultural University, Beijing, China
| | - Juan Chen
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling, Shaanxi, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
| |
Collapse
|
12
|
Abstract
Methylesterase/deamidase CheB is a key component of bacterial chemotaxis systems. It is also a prominent example of a two-component response regulator in which the effector domain is an enzyme. Like other response regulators, CheB is activated by phosphorylation of an aspartyl residue in its regulatory domain, creating an open conformation between its two domains. Studies of CheB in Escherichia coli and related organisms have shown that its enzymatic action is also enhanced by a pentapeptide-binding site for the enzyme at the chemoreceptor carboxyl terminus. Related carboxyl-terminal pentapeptides are found on >25,000 chemoreceptor sequences distributed across 11 bacterial phyla and many bacterial species, in which they presumably play similar roles. Yet, little is known about the interrelationship of CheB phosphorylation, pentapeptide binding, and interactions with its substrate methylesters and amides on the body of the chemoreceptor. We investigated by characterizing the binding kinetics of CheB to Nanodisc-inserted chemoreceptor dimers. The resulting kinetic and thermodynamic constants revealed a synergy between CheB phosphorylation and pentapeptide binding in which a phosphorylation mimic enhanced pentapeptide binding, and the pentapeptide served not only as a high-affinity tether for CheB but also selected the activated conformation of the enzyme. The basis of this selection was revealed by molecular modeling that predicted a pentapeptide-binding site on CheB which existed only in the open, activated enzyme. Recruitment of activated enzyme by selective tethering represents a previously unappreciated strategy for regulating response regulator action, one that may well occur in other two-component systems.
Collapse
|
13
|
Diversity in Sensing and Signaling of Bacterial Sensor Histidine Kinases. Biomolecules 2021; 11:biom11101524. [PMID: 34680156 PMCID: PMC8534201 DOI: 10.3390/biom11101524] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/13/2021] [Accepted: 10/13/2021] [Indexed: 11/17/2022] Open
Abstract
Two-component signal transduction systems (TCSs) are widely conserved in bacteria to respond to and adapt to the changing environment. Since TCSs are also involved in controlling the expression of virulence, biofilm formation, quorum sensing, and antimicrobial resistance in pathogens, they serve as candidates for novel drug targets. TCSs consist of a sensor histidine kinase (HK) and its cognate response regulator (RR). Upon perception of a signal, HKs autophosphorylate their conserved histidine residues, followed by phosphotransfer to their partner RRs. The phosphorylated RRs mostly function as transcriptional regulators and control the expression of genes necessary for stress response. HKs sense their specific signals not only in their extracytoplasmic sensor domain but also in their cytoplasmic and transmembrane domains. The signals are sensed either directly or indirectly via cofactors and accessory proteins. Accumulating evidence shows that a single HK can sense and respond to multiple signals in different domains. The underlying molecular mechanisms of how HK activity is controlled by these signals have been extensively studied both biochemically and structurally. In this article, we introduce the wide diversity of signal perception in different domains of HKs, together with their recently clarified structures and molecular mechanisms.
Collapse
|
14
|
Gonzaga de França Lopes L, Gouveia Júnior FS, Karine Medeiros Holanda A, Maria Moreira de Carvalho I, Longhinotti E, Paulo TF, Abreu DS, Bernhardt PV, Gilles-Gonzalez MA, Cirino Nogueira Diógenes I, Henrique Silva Sousa E. Bioinorganic systems responsive to the diatomic gases O2, NO, and CO: From biological sensors to therapy. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
15
|
Pardoux R, Dolla A, Aubert C. Metal-containing PAS/GAF domains in bacterial sensors. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
|
16
|
Ma P, Phillips-Jones MK. Membrane Sensor Histidine Kinases: Insights from Structural, Ligand and Inhibitor Studies of Full-Length Proteins and Signalling Domains for Antibiotic Discovery. Molecules 2021; 26:molecules26165110. [PMID: 34443697 PMCID: PMC8399564 DOI: 10.3390/molecules26165110] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/02/2021] [Accepted: 08/19/2021] [Indexed: 12/19/2022] Open
Abstract
There is an urgent need to find new antibacterial agents to combat bacterial infections, including agents that inhibit novel, hitherto unexploited targets in bacterial cells. Amongst novel targets are two-component signal transduction systems (TCSs) which are the main mechanism by which bacteria sense and respond to environmental changes. TCSs typically comprise a membrane-embedded sensory protein (the sensor histidine kinase, SHK) and a partner response regulator protein. Amongst promising targets within SHKs are those involved in environmental signal detection (useful for targeting specific SHKs) and the common themes of signal transmission across the membrane and propagation to catalytic domains (for targeting multiple SHKs). However, the nature of environmental signals for the vast majority of SHKs is still lacking, and there is a paucity of structural information based on full-length membrane-bound SHKs with and without ligand. Reasons for this lack of knowledge lie in the technical challenges associated with investigations of these relatively hydrophobic membrane proteins and the inherent flexibility of these multidomain proteins that reduces the chances of successful crystallisation for structural determination by X-ray crystallography. However, in recent years there has been an explosion of information published on (a) methodology for producing active forms of full-length detergent-, liposome- and nanodisc-solubilised membrane SHKs and their use in structural studies and identification of signalling ligands and inhibitors; and (b) mechanisms of signal sensing and transduction across the membrane obtained using sensory and transmembrane domains in isolation, which reveal some commonalities as well as unique features. Here we review the most recent advances in these areas and highlight those of potential use in future strategies for antibiotic discovery. This Review is part of a Special Issue entitled “Interactions of Bacterial Molecules with Their Ligands and Other Chemical Agents” edited by Mary K. Phillips-Jones.
Collapse
Affiliation(s)
- Pikyee Ma
- Laboratory of Biomolecular Research, Paul Scherrer Institute, CH-5232 Villigen, Switzerland;
| | - Mary K. Phillips-Jones
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
- Correspondence:
| |
Collapse
|
17
|
Silva MA, Salgueiro CA. Multistep Signaling in Nature: A Close-Up of Geobacter Chemotaxis Sensing. Int J Mol Sci 2021; 22:ijms22169034. [PMID: 34445739 PMCID: PMC8396549 DOI: 10.3390/ijms22169034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/30/2021] [Accepted: 08/09/2021] [Indexed: 11/23/2022] Open
Abstract
Environmental changes trigger the continuous adaptation of bacteria to ensure their survival. This is possible through a variety of signal transduction pathways involving chemoreceptors known as methyl-accepting chemotaxis proteins (MCP) that allow the microorganisms to redirect their mobility towards favorable environments. MCP are two-component regulatory (or signal transduction) systems (TCS) formed by a sensor and a response regulator domain. These domains synchronize transient protein phosphorylation and dephosphorylation events to convert the stimuli into an appropriate cellular response. In this review, the variability of TCS domains and the most common signaling mechanisms are highlighted. This is followed by the description of the overall cellular topology, classification and mechanisms of MCP. Finally, the structural and functional properties of a new family of MCP found in Geobacter sulfurreducens are revisited. This bacterium has a diverse repertoire of chemosensory systems, which represents a striking example of a survival mechanism in challenging environments. Two G. sulfurreducens MCP—GSU0582 and GSU0935—are members of a new family of chemotaxis sensor proteins containing a periplasmic PAS-like sensor domain with a c-type heme. Interestingly, the cellular location of this domain opens new routes to the understanding of the redox potential sensing signaling transduction pathways.
Collapse
Affiliation(s)
- Marta A. Silva
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal;
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Carlos A. Salgueiro
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal;
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- Correspondence:
| |
Collapse
|
18
|
Yamawaki T, Mizuno M, Ishikawa H, Takemura K, Kitao A, Shiro Y, Mizutani Y. Regulatory Switching by Concerted Motions on the Microsecond Time Scale of the Oxygen Sensor Protein FixL. J Phys Chem B 2021; 125:6847-6856. [PMID: 34133147 DOI: 10.1021/acs.jpcb.1c01885] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Signal transduction proteins perceive external stimuli in their sensor module and regulate the biological activities of the effector module, allowing cellular adaptation in response to environmental changes. FixL is a dimeric heme protein kinase that senses the oxygen level in plant root nodules to regulate the transcription of nitrogen fixation genes via the phosphorylation of its cognate transcriptional activator. Dissociation of oxygen from the heme induces conformational changes in the protein, converting it from the inactive form for phosphorylation to the active form. However, how FixL undergoes conformational change to regulate kinase activity upon oxygen dissociation remains poorly understood. Here we report time-resolved ultraviolet resonance Raman spectra showing conformational changes for FixL from Sinorhizobium meliloti. We observed spectral changes with a time constant of about 3 μs, which were oxygen-specific. Furthermore, we found that the conformational changes in the sensor and kinase domains are coupled, enabling allosteric control of kinase activity. Our results demonstrate that concerted structural changes on the microsecond time scale serve as the regulatory switch in FixL.
Collapse
Affiliation(s)
- Takeo Yamawaki
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Haruto Ishikawa
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Kazuhiro Takemura
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro, Tokyo 152-8550, Japan
| | - Akio Kitao
- School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro, Tokyo 152-8550, Japan
| | - Yoshitsugu Shiro
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| |
Collapse
|
19
|
Multiple sensors provide spatiotemporal oxygen regulation of gene expression in a Rhizobium-legume symbiosis. PLoS Genet 2021; 17:e1009099. [PMID: 33539353 PMCID: PMC7888657 DOI: 10.1371/journal.pgen.1009099] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 02/17/2021] [Accepted: 12/04/2020] [Indexed: 01/04/2023] Open
Abstract
Regulation by oxygen (O2) in rhizobia is essential for their symbioses with plants and involves multiple O2 sensing proteins. Three sensors exist in the pea microsymbiont Rhizobium leguminosarum Rlv3841: hFixL, FnrN and NifA. At low O2 concentrations (1%) hFixL signals via FxkR to induce expression of the FixK transcription factor, which activates transcription of downstream genes. These include fixNOQP, encoding the high-affinity cbb3-type terminal oxidase used in symbiosis. In free-living Rlv3841, the hFixL-FxkR-FixK pathway was active at 1% O2, and confocal microscopy showed hFixL-FxkR-FixK activity in the earliest stages of Rlv3841 differentiation in nodules (zones I and II). Work on Rlv3841 inside and outside nodules showed that the hFixL-FxkR-FixK pathway also induces transcription of fnrN at 1% O2 and in the earliest stages of Rlv3841 differentiation in nodules. We confirmed past findings suggesting a role for FnrN in fixNOQP expression. However, unlike hFixL-FxkR-FixK, Rlv3841 FnrN was only active in the near-anaerobic zones III and IV of pea nodules. Quantification of fixNOQP expression in nodules showed this was driven primarily by FnrN, with minimal direct hFixL-FxkR-FixK induction. Thus, FnrN is key for full symbiotic expression of fixNOQP. Without FnrN, nitrogen fixation was reduced by 85% in Rlv3841, while eliminating hFixL only reduced fixation by 25%. The hFixL-FxkR-FixK pathway effectively primes the O2 response by increasing fnrN expression in early differentiation (zones I-II). In zone III of mature nodules, near-anaerobic conditions activate FnrN, which induces fixNOQP transcription to the level required for wild-type nitrogen fixation activity. Modelling and transcriptional analysis indicates that the different O2 sensitivities of hFixL and FnrN lead to a nuanced spatiotemporal pattern of gene regulation in different nodule zones in response to changing O2 concentration. Multi-sensor O2 regulation is prevalent in rhizobia, suggesting the fine-tuned control this enables is common and maximizes the effectiveness of the symbioses. Rhizobia are soil bacteria that form a symbiosis with legume plants. In exchange for shelter from the plant, rhizobia provide nitrogen fertilizer, produced by nitrogen fixation. Fixation is catalysed by the nitrogenase enzyme, which is inactivated by oxygen. To prevent this, plants house rhizobia in root nodules, which create a low oxygen environment. However, rhizobia need oxygen, and must adapt to survive the low oxygen concentration in the nodule. Key to this is regulating their genes based on oxygen concentration. We studied one Rhizobium species which uses three different protein sensors of oxygen, each turning on at a different oxygen concentration. As the bacteria get deeper inside the plant nodule and the oxygen concentration drops, each sensor switches on in turn. Our results also show that the first sensor to turn on, hFixL, primes the second sensor, FnrN. This prepares the rhizobia for the core region of the nodule where oxygen concentration is lowest and most nitrogen fixation takes place. If both sensors are removed, the bacteria cannot fix nitrogen. Many rhizobia have several oxygen sensing proteins, so using multiple sensors is likely a common strategy enabling rhizobia to adapt to low oxygen precisely and in stages during symbiosis.
Collapse
|
20
|
Xie M, Wu M, Han A. Structural insights into the signal transduction mechanism of the K +-sensing two-component system KdpDE. Sci Signal 2020; 13:13/643/eaaz2970. [PMID: 32753477 DOI: 10.1126/scisignal.aaz2970] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Two-component systems (TCSs), which consist of a histidine kinase (HK) sensor and a response regulator (RR), are important for bacteria to quickly sense and respond to various environmental signals. HKs and RRs typically function as a cognate pair, interacting only with one another to transduce signaling. Precise signal transduction in a TCS depends on the specific interactions between the receiver domain (RD) of the RR and the dimerization and histidine phosphorylation domain (DHp) of the HK. Here, we determined the complex structure of KdpDE, a TCS consisting of the HK KdpD and the RR KdpE, which is responsible for K+ homeostasis. Both the RD and the DNA binding domain (DBD) of KdpE interacted with KdpD. Although the RD of KdpE and the DHp of KdpD contributed to binding specificity, the DBD mediated a distinct interaction with the catalytic ATP-binding (CA) domain of KdpD that was indispensable for KdpDE-mediated signal transduction. Moreover, the DBD-CA interface largely overlapped with that of the DBD-DNA complex, leading to competition between KdpD and its target promoter in a KdpE phosphorylation-dependent manner. In addition, the extended C-terminal tail of the CA domain was critical for stabilizing the interaction with KdpDE and for signal transduction. Together, these data provide a molecular basis for specific KdpD and KdpE interactions that play key roles in efficient signal transduction and transcriptional regulation by this TCS.
Collapse
Affiliation(s)
- Mingquan Xie
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Mengyuan Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Aidong Han
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China.
| |
Collapse
|
21
|
Négrerie M. Iron transitions during activation of allosteric heme proteins in cell signaling. Metallomics 2020; 11:868-893. [PMID: 30957812 DOI: 10.1039/c8mt00337h] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Allosteric heme proteins can fulfill a very large number of different functions thanks to the remarkable chemical versatility of heme through the entire living kingdom. Their efficacy resides in the ability of heme to transmit both iron coordination changes and iron redox state changes to the protein structure. Besides the properties of iron, proteins may impose a particular heme geometry leading to distortion, which allows selection or modulation of the electronic properties of heme. This review focusses on the mechanisms of allosteric protein activation triggered by heme coordination changes following diatomic binding to proteins as diverse as the human NO-receptor, cytochromes, NO-transporters and sensors, and a heme-activated potassium channel. It describes at the molecular level the chemical capabilities of heme to achieve very different tasks and emphasizes how the properties of heme are determined by the protein structure. Particularly, this reviews aims at giving an overview of the exquisite adaptability of heme, from bacteria to mammals.
Collapse
Affiliation(s)
- Michel Négrerie
- Laboratoire d'Optique et Biosciences, INSERM, CNRS, Ecole Polytechnique, 91120 Palaiseau, France.
| |
Collapse
|
22
|
Leitner DM, Yamato T. Recent developments in the computational study of protein structural and vibrational energy dynamics. Biophys Rev 2020; 12:317-322. [PMID: 32124240 DOI: 10.1007/s12551-020-00661-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/23/2020] [Indexed: 12/11/2022] Open
Abstract
Recent developments in the computational study of energy transport in proteins are reviewed, including advances in both methodology and applications. The concept of energy exchange network (EEN) is discussed, and a recent calculation of EENs for the allosteric protein FixL is reviewed, which illustrates how residues and protein regions involved in the allosteric transition can be identified. Recent work has examined relations between EENs and protein dynamics as well as structure. We review some of the computational studies carried out on several proteins that explore connections between energy conductivity across polar contacts in proteins and between proteins and water and equilibrium dynamics of the contacts, and we discuss some of the recent experimental work that addresses this topic.
Collapse
Affiliation(s)
- David M Leitner
- Department of Chemistry and Chemical Physics Program, University of Nevada, Reno, NV, 89557, USA.
- Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.
| | - Takahisa Yamato
- Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.
| |
Collapse
|
23
|
Hirota K. Basic Biology of Hypoxic Responses Mediated by the Transcription Factor HIFs and its Implication for Medicine. Biomedicines 2020; 8:biomedicines8020032. [PMID: 32069878 PMCID: PMC7168341 DOI: 10.3390/biomedicines8020032] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 02/08/2020] [Accepted: 02/12/2020] [Indexed: 12/19/2022] Open
Abstract
Oxygen (O2) is essential for human life. Molecular oxygen is vital for the production of adenosine triphosphate (ATP) in human cells. O2 deficiency leads to a reduction in the energy levels that are required to maintain biological functions. O2 acts as the final acceptor of electrons during oxidative phosphorylation, a series of ATP synthesis reactions that occur in conjunction with the electron transport system in mitochondria. Persistent O2 deficiency may cause death due to malfunctioning biological processes. The above account summarizes the classic view of oxygen. However, this classic view has been reviewed over the last two decades. Although O2 is essential for life, higher organisms such as mammals are unable to biosynthesize molecular O2 in the body. Because the multiple organs of higher organisms are constantly exposed to the risk of “O2 deficiency,” living organisms have evolved elaborate strategies to respond to hypoxia. In this review, I will describe the system that governs oxygen homeostasis in the living body from the point-of-view of the transcription factor hypoxia-inducible factor (HIF).
Collapse
Affiliation(s)
- Kiichi Hirota
- Department of Human Stress Response Science, Institute of Biomedical Science, Kansai Medical University, Hirakata, Osaka 573-1010, Japan
| |
Collapse
|
24
|
Abstract
Rhizobia are α- and β-proteobacteria that form a symbiotic partnership with legumes, fixing atmospheric dinitrogen to ammonia and providing it to the plant. Oxygen regulation is key in this symbiosis. Fixation is performed by an oxygen-intolerant nitrogenase enzyme but requires respiration to meet its high energy demands. To satisfy these opposing constraints the symbiotic partners cooperate intimately, employing a variety of mechanisms to regulate and respond to oxygen concentration. During symbiosis rhizobia undergo significant changes in gene expression to differentiate into nitrogen-fixing bacteroids. Legumes host these bacteroids in specialized root organs called nodules. These generate a near-anoxic environment using an oxygen diffusion barrier, oxygen-binding leghemoglobin and control of mitochondria localization. Rhizobia sense oxygen using multiple interconnected systems which enable a finely-tuned response to the wide range of oxygen concentrations they experience when transitioning from soil to nodules. The oxygen-sensing FixL-FixJ and hybrid FixL-FxkR two-component systems activate at relatively high oxygen concentration and regulate fixK transcription. FixK activates the fixNOQP and fixGHIS operons producing a high-affinity terminal oxidase required for bacterial respiration in the microaerobic nodule. Additionally or alternatively, some rhizobia regulate expression of these operons by FnrN, an FNR-like oxygen-sensing protein. The final stage of symbiotic establishment is activated by the NifA protein, regulated by oxygen at both the transcriptional and protein level. A cross-species comparison of these systems highlights differences in their roles and interconnections but reveals common regulatory patterns and themes. Future work is needed to establish the complete regulon of these systems and identify other regulatory signals.
Collapse
Affiliation(s)
- Paul J Rutten
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
25
|
Abstract
Response regulators function as the output components of two-component systems, which couple the sensing of environmental stimuli to adaptive responses. Response regulators typically contain conserved receiver (REC) domains that function as phosphorylation-regulated switches to control the activities of effector domains that elicit output responses. This modular design is extremely versatile, enabling different regulatory strategies tuned to the needs of individual signaling systems. This review summarizes structural features that underlie response regulator function. An abundance of atomic resolution structures and complementary biochemical data have defined the mechanisms for response regulator enzymatic activities, revealed trends in regulatory strategies utilized by response regulators of different subfamilies, and provided insights into interactions of response regulators with their cognate histidine kinases. Among the hundreds of thousands of response regulators identified, variations abound. This article provides a framework for understanding structural features that enable function of canonical response regulators and a basis for distinguishing noncanonical configurations.
Collapse
Affiliation(s)
- Rong Gao
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA; , ,
| | - Sophie Bouillet
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA; , ,
| | - Ann M Stock
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA; , ,
| |
Collapse
|
26
|
Lobão JBDS, Gondim ACS, Guimarães WG, Gilles‐Gonzalez M, Lopes LGDF, Sousa EHS. Oxygen triggers signal transduction in the DevS (DosS) sensor of
Mycobacterium tuberculosis
by modulating the quaternary structure. FEBS J 2019; 286:479-494. [DOI: 10.1111/febs.14734] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 11/05/2018] [Accepted: 12/14/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Josiane Bezerra da Silva Lobão
- Laboratory of Bioinorganic Chemistry Department of Organic and Inorganic Chemistry Federal University of Ceara Center for Sciences Fortaleza Brazil
| | - Ana C. S. Gondim
- Laboratory of Bioinorganic Chemistry Department of Organic and Inorganic Chemistry Federal University of Ceara Center for Sciences Fortaleza Brazil
| | - Wellinson G. Guimarães
- Laboratory of Bioinorganic Chemistry Department of Organic and Inorganic Chemistry Federal University of Ceara Center for Sciences Fortaleza Brazil
| | | | - Luiz Gonzaga de França Lopes
- Laboratory of Bioinorganic Chemistry Department of Organic and Inorganic Chemistry Federal University of Ceara Center for Sciences Fortaleza Brazil
| | - Eduardo H. S. Sousa
- Laboratory of Bioinorganic Chemistry Department of Organic and Inorganic Chemistry Federal University of Ceara Center for Sciences Fortaleza Brazil
| |
Collapse
|
27
|
Ota K, Yamato T. Energy Exchange Network Model Demonstrates Protein Allosteric Transition: An Application to an Oxygen Sensor Protein. J Phys Chem B 2019; 123:768-775. [DOI: 10.1021/acs.jpcb.8b10489] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kunitaka Ota
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Takahisa Yamato
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
- Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, 1 rue Laurent Fries Parc d’Innovation, 67404 Illkirch, Cedex, France
| |
Collapse
|
28
|
Ryo M, Yamashino T, Yamakawa H, Fujita Y, Aoki S. PAS-histidine kinases PHK1 and PHK2 exert oxygen-dependent dual and opposite effects on gametophore formation in the moss Physcomitrella patens. Biochem Biophys Res Commun 2018; 503:2861-2865. [DOI: 10.1016/j.bbrc.2018.08.056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 08/06/2018] [Indexed: 10/28/2022]
|
29
|
VanHook AM. New connections: The complexity of simple signaling systems. Sci Signal 2018. [DOI: 10.1126/scisignal.aat7921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Bacterial two-component systems are efficient and versatile but not always simple.
Collapse
|