1
|
Okumura K, Mikami B, Oiki S, Ogura K, Hashimoto W. Expression, purification and preliminary crystallographic analysis of bacterial transmembrane protein EfeU for iron import. Protein Expr Purif 2024; 219:106487. [PMID: 38657915 DOI: 10.1016/j.pep.2024.106487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 04/10/2024] [Accepted: 04/20/2024] [Indexed: 04/26/2024]
Abstract
The bacterial Efe system functions as an importer of free Fe2+ into cells independently of iron-chelating compounds such as siderophores and consisted of iron-binding protein EfeO, peroxidase EfeB, and transmembrane permease EfeU. While we and other researchers reported crystal structures of EfeO and EfeB, that of EfeU remains undetermined. In this study, we constructed expression system of EfeU derived from Escherichia coli, selected E. coli Rosetta-gami 2 (DE3) as an expression host, and succeeded in purification of the proteins which were indicated to form an oligomer by blue native PAGE. We obtained preliminary data of the X-ray crystallography, suggesting that expression and purification methods we established in this study enable structural analysis of the bacterial Efe system.
Collapse
Affiliation(s)
- Kenji Okumura
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Japan
| | - Bunzo Mikami
- Laboratory of Metabolic Sciences of Forest Plants and Microorganisms, Research Institute for Sustainable Humanosphere, Kyoto University, Japan
| | - Sayoko Oiki
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Japan
| | - Kohei Ogura
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Japan
| | - Wataru Hashimoto
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Japan.
| |
Collapse
|
2
|
Werner MH, Mehner-Breitfeld D, Brüser T. A larger TatBC complex associates with TatA clusters for transport of folded proteins across the bacterial cytoplasmic membrane. Sci Rep 2024; 14:13754. [PMID: 38877109 PMCID: PMC11178869 DOI: 10.1038/s41598-024-64547-x] [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: 04/03/2024] [Accepted: 06/10/2024] [Indexed: 06/16/2024] Open
Abstract
The twin-arginine translocation (Tat) system transports folded proteins across energized biological membranes in bacteria, plastids, and plant mitochondria. In Escherichia coli, the three membrane proteins TatA, TatB and TatC associate to enable Tat transport. While TatB and TatC together form complexes that bind Tat-dependently transported proteins, the TatA component is responsible for the permeabilization of the membrane during transport. With wild type Tat systems, the TatB- and TatC-containing Tat complexes TC1 and TC2 can be differentiated. Their TatA content has not been resolved, nor could they be assigned to any step of the translocation mechanism. It is therefore a key question of current Tat research to understand how TatA associates with Tat systems during transport. By analyzing affinity-purified Tat complexes with mutations in TatC that selectively enrich either TC1 or TC2, we now for the first time demonstrate that both Tat complexes associate with TatA, but the larger TC2 recruits significantly more TatA than the smaller TC1. Most TatA co-purified as multimeric clusters. Using site-specific photo cross-linking, we could detect TatA-TatC interactions only near TatC transmembrane helices 5 and 6. Substrate-binding did not change the interacting positions but affected the stability of the interaction, pointing to a substrate-induced conformational transition. Together, our findings indicate that TatA clusters associate with TatBC without being integrated into the complex by major rearrangements. The increased TatA affinity of the larger Tat complex TC2 suggests that functional assembly is advanced in this complex.
Collapse
Affiliation(s)
- Max-Hinrich Werner
- Institute of Microbiology, Leibniz Universität Hannover, Herrenhäuser Straße 2, 30419, Hannover, Germany
| | - Denise Mehner-Breitfeld
- Institute of Microbiology, Leibniz Universität Hannover, Herrenhäuser Straße 2, 30419, Hannover, Germany
| | - Thomas Brüser
- Institute of Microbiology, Leibniz Universität Hannover, Herrenhäuser Straße 2, 30419, Hannover, Germany.
| |
Collapse
|
3
|
Diao S, Duan Y, Wang M, Feng Y, Miao H, Zhao Y. Multi-Omics Study on Molecular Mechanisms of Single-Atom Fe-Doped Two-Dimensional Conjugated Phthalocyanine Framework for Photocatalytic Antibacterial Performance. Molecules 2024; 29:1601. [PMID: 38611880 PMCID: PMC11013413 DOI: 10.3390/molecules29071601] [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: 02/19/2024] [Revised: 03/21/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Currently, photocatalysis of the two-dimensional (2D) conjugated phthalocyanine framework with a single Fe atom (CPF-Fe) has shown efficient photocatalytic activities for the removal of harmful effluents and antibacterial activity. Their photocatalytic mechanisms are dependent on the redox reaction-which is led by the active species generated from the photocatalytic process. Nevertheless, the molecular mechanism of CPF-Fe antimicrobial activity has not been sufficiently explored. In this study, we successfully synthesized CPF-Fe with great broad-spectrum antibacterial properties under visible light and used it as an antibacterial agent. The molecular mechanism of CPF-Fe against Escherichia coli and Salmonella enteritidis was explored through multi-omics analyses (transcriptomics and metabolomics correlation analyses). The results showed that CPF-Fe not only led to the oxidative stress of bacteria by generating large amounts of h+ and ROS but also caused failure in the synthesis of bacterial cell wall components as well as an osmotic pressure imbalance by disrupting glycolysis, oxidative phosphorylation, and TCA cycle pathways. More surprisingly, CPF-Fe could disrupt the metabolism of amino acids and nucleic acids, as well as inhibit their energy metabolism, resulting in the death of bacterial cells. The research further revealed the antibacterial mechanism of CPF-Fe from a molecular perspective, providing a theoretical basis for the application of CPF-Fe photocatalytic antibacterial nanomaterials.
Collapse
Affiliation(s)
- Shihong Diao
- Chongqing Key Laboratory of Herbivore Science, College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (S.D.); (Y.D.); (M.W.)
| | - Yixin Duan
- Chongqing Key Laboratory of Herbivore Science, College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (S.D.); (Y.D.); (M.W.)
| | - Mengying Wang
- Chongqing Key Laboratory of Herbivore Science, College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (S.D.); (Y.D.); (M.W.)
| | - Yuanjiao Feng
- The Faculty of Pharmacy, Chongqing Medical and Pharmaceutical College, Chongqing 401331, China
| | - Hong Miao
- Chongqing Key Laboratory of Herbivore Science, College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (S.D.); (Y.D.); (M.W.)
| | - Yongju Zhao
- Chongqing Key Laboratory of Herbivore Science, College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (S.D.); (Y.D.); (M.W.)
| |
Collapse
|
4
|
Unexpected diversity of dye-decolorizing peroxidases. Biochem Biophys Rep 2023; 33:101401. [DOI: 10.1016/j.bbrep.2022.101401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
|
5
|
Rajasekaran MB, Hussain R, Siligardi G, Andrews SC, Watson KA. Crystal structure and metal binding properties of the periplasmic iron component EfeM from Pseudomonas syringae EfeUOB/M iron-transport system. Biometals 2022; 35:573-589. [PMID: 35348940 PMCID: PMC9174327 DOI: 10.1007/s10534-022-00389-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/14/2022] [Indexed: 11/08/2022]
Abstract
EfeUOB/M has been characterised in Pseudomonas syringae pathovar. syringae as a novel type of ferrous-iron transporter, consisting of an inner-membrane protein (EfeUPsy) and three periplasmic proteins (EfeOPsy, EfeMPsy and EfeBPsy). The role of an iron permease and peroxidase function has been identified for the EfeU and EfeB proteins, respectively, but the role of EfeO/M remains unclear. EfeMPsy is an 'M75-only' EfeO-like protein with a C-terminal peptidase-M75 domain (EfeOII/EfeM family). Herein, we report the 1.6 Å resolution crystal structure of EfeMPsy, the first structural report for an EfeM component of P. syringae pv. syringae. The structure possesses the bi-lobate architecture found in other bacterial periplasmic substrate/solute binding proteins. Metal binding studies, using SRCD and ICP-OES, reveal a preference of EfeMPsy for copper, iron and zinc. This work provides detailed knowledge of the structural scaffold, the metal site geometry, and the divalent metal binding potential of EfeM. This work provides crucial underpinning for a more detailed understanding of the role of EfeM/EfeO proteins and the peptidase-M75 domains in EfeUOB/M iron uptake systems in bacteria.
Collapse
Affiliation(s)
- Mohan B Rajasekaran
- School of Biological Sciences, Health and Life Sciences Building, University of Reading, Whiteknights Campus, Reading, RG6 6EX, UK
- Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN19QJ, UK
| | - Rohanah Hussain
- B23 Beamline, Diamond Light Source, Harwell Science Innovation Campus, Chilton, Didcot, OX11 0DE, UK
| | - Giuliano Siligardi
- B23 Beamline, Diamond Light Source, Harwell Science Innovation Campus, Chilton, Didcot, OX11 0DE, UK
| | - Simon C Andrews
- School of Biological Sciences, Health and Life Sciences Building, University of Reading, Whiteknights Campus, Reading, RG6 6EX, UK
| | - Kimberly A Watson
- School of Biological Sciences, Health and Life Sciences Building, University of Reading, Whiteknights Campus, Reading, RG6 6EX, UK.
| |
Collapse
|
6
|
Steunou AS, Vigouroux A, Aumont‐Nicaise M, Plancqueel S, Boussac A, Ouchane S, Moréra S. New insights into the mechanism of iron transport through the bacterial Ftr system present in pathogens. FEBS J 2022; 289:6286-6307. [DOI: 10.1111/febs.16476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/11/2022] [Accepted: 05/06/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Anne Soisig Steunou
- Université Paris‐Saclay, CEA CNRS Institute for Integrative Biology of the Cell (I2BC) Gif‐sur‐Yvette France
| | - Armelle Vigouroux
- Université Paris‐Saclay, CEA CNRS Institute for Integrative Biology of the Cell (I2BC) Gif‐sur‐Yvette France
| | - Magali Aumont‐Nicaise
- Université Paris‐Saclay, CEA CNRS Institute for Integrative Biology of the Cell (I2BC) Gif‐sur‐Yvette France
| | - Stéphane Plancqueel
- Université Paris‐Saclay, CEA CNRS Institute for Integrative Biology of the Cell (I2BC) Gif‐sur‐Yvette France
| | - Alain Boussac
- Université Paris‐Saclay, CEA CNRS Institute for Integrative Biology of the Cell (I2BC) Gif‐sur‐Yvette France
| | - Soufian Ouchane
- Université Paris‐Saclay, CEA CNRS Institute for Integrative Biology of the Cell (I2BC) Gif‐sur‐Yvette France
| | - Solange Moréra
- Université Paris‐Saclay, CEA CNRS Institute for Integrative Biology of the Cell (I2BC) Gif‐sur‐Yvette France
| |
Collapse
|
7
|
Banerjee S, Chanakira MN, Hall J, Kerkan A, Dasgupta S, Martin DW. A review on bacterial redox dependent iron transporters and their evolutionary relationship. J Inorg Biochem 2022; 229:111721. [PMID: 35033753 DOI: 10.1016/j.jinorgbio.2022.111721] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 02/05/2023]
Abstract
Iron is an essential yet toxic micronutrient and its transport across biological membranes is tightly regulated in all living organisms. One such iron transporter, the Ftr-type permeases, is found in both eukaryotic and prokaryotic cells. These Ftr-type transporters are required for iron transport, predicted to form α-helical transmembrane structures, and conserve two ArgGluxxGlu (x = any amino acid) motifs. In the yeast Ftr transporter (Ftr1p), a ferroxidase (Fet3p) is required for iron transport in an oxidation coupled transport step. None of the bacterial Ftr-type transporters (EfeU and FetM from E. coli; cFtr from Campylobacter jejuni; FtrC from Brucella, Bordetella, and Burkholderia spp.) contain a ferroxidase protein. Bioinformatics report predicted periplasmic EfeO and FtrB (from the EfeUOB and FtrABCD systems) as novel cupredoxins. The Cu2+ binding and the ferrous oxidation properties of these proteins are uncharacterized and the other two bacterial Ftr-systems are expressed without any ferroxidase/cupredoxin, leading to controversy about the mode of function of these transporters. Here, we review published data on Ftr-type transporters to gain insight into their functional diversity. Based on original bioinformatics data presented here evolutionary relations between these systems are presented.
Collapse
Affiliation(s)
- Sambuddha Banerjee
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA.
| | - Mina N Chanakira
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
| | - Jonathan Hall
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
| | - Alexa Kerkan
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
| | - Saumya Dasgupta
- Department of Chemistry, Amity Institute of Applied Sciences, Amity University Kolkata, WB 700135, India
| | - Daniel W Martin
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA
| |
Collapse
|
8
|
Schoenborn AA, Yannarell SM, Wallace ED, Clapper H, Weinstein IC, Shank EA. Defining the Expression, Production, and Signaling Roles of Specialized Metabolites during Bacillus subtilis Differentiation. J Bacteriol 2021; 203:e0033721. [PMID: 34460312 PMCID: PMC8544424 DOI: 10.1128/jb.00337-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/11/2021] [Indexed: 11/20/2022] Open
Abstract
Bacterial specialized (or secondary) metabolites are structurally diverse molecules that mediate intra- and interspecies interactions by altering growth and cellular physiology and differentiation. Bacillus subtilis, a Gram-positive model bacterium commonly used to study biofilm formation and sporulation, has the capacity to produce more than 10 specialized metabolites. Some of these B. subtilis specialized metabolites have been investigated for their role in facilitating cellular differentiation, but only rarely has the behavior of multiple metabolites been simultaneously investigated. In this study, we explored the interconnectivity of differentiation (biofilm and sporulation) and specialized metabolites in B. subtilis. Specifically, we interrogated how development influences specialized metabolites and vice versa. Using the sporulation-inducing medium DSM, we found that the majority of the specialized metabolites examined are expressed and produced during biofilm formation and sporulation. Additionally, we found that six of these metabolites (surfactin, ComX, bacillibactin, bacilysin, subtilosin A, and plipastatin) are necessary signaling molecules for proper progression of B. subtilis differentiation. This study further supports the growing body of work demonstrating that specialized metabolites have essential physiological functions as cell-cell communication signals in bacteria. IMPORTANCE Bacterially produced specialized metabolites are frequently studied for their potential use as antibiotics and antifungals. However, a growing body of work has suggested that the antagonistic potential of specialized metabolites is not their only function. Here, using Bacillus subtilis as our model bacterium, we demonstrated that developmental processes such as biofilm formation and sporulation are tightly linked to specialized metabolite gene expression and production. Additionally, under our differentiation-inducing conditions, six out of the nine specialized metabolites investigated behave as intraspecific signals that impact B. subtilis physiology and influence biofilm formation and sporulation. Our work supports the viewpoint that specialized metabolites have a clear role as cell-cell signaling molecules within differentiated populations of bacteria.
Collapse
Affiliation(s)
- Alexi A. Schoenborn
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sarah M. Yannarell
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - E. Diane Wallace
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Haley Clapper
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ilon C. Weinstein
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Elizabeth A. Shank
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| |
Collapse
|
9
|
Cesinger MR, Schwardt NH, Halsey CR, Thomason MK, Reniere ML. Investigating the Roles of Listeria monocytogenes Peroxidases in Growth and Virulence. Microbiol Spectr 2021; 9:e0044021. [PMID: 34287055 PMCID: PMC8552690 DOI: 10.1128/spectrum.00440-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/23/2021] [Indexed: 11/25/2022] Open
Abstract
Bacteria have necessarily evolved a protective arsenal of proteins to contend with peroxides and other reactive oxygen species generated in aerobic environments. Listeria monocytogenes encounters an onslaught of peroxide both in the environment and during infection of the mammalian host, where it is the causative agent of the foodborne illness listeriosis. Despite the importance of peroxide for the immune response to bacterial infection, the strategy by which L. monocytogenes protects against peroxide toxicity has yet to be illuminated. Here, we investigated the expression and essentiality of all the peroxidase-encoding genes during L. monocytogenes growth in vitro and during infection of murine cells in tissue culture. We found that chdC and kat were required for aerobic growth in vitro, and fri and ahpA were each required for L. monocytogenes to survive acute peroxide stress. Despite increased expression of fri, ahpA, and kat during infection of macrophages, only fri proved necessary for cytosolic growth. In contrast, the proteins encoded by lmo0367, lmo0983, tpx, lmo1609, and ohrA were dispensable for aerobic growth, acute peroxide detoxification, and infection. Together, our results provide insight into the multifaceted L. monocytogenes peroxide detoxification strategy and demonstrate that L. monocytogenes encodes a functionally diverse set of peroxidase enzymes. IMPORTANCE Listeria monocytogenes is a facultative intracellular pathogen and the causative agent of the foodborne illness listeriosis. L. monocytogenes must contend with reactive oxygen species generated extracellularly during aerobic growth and intracellularly by the host immune system. However, the mechanisms by which L. monocytogenes defends against peroxide toxicity have not yet been defined. Here, we investigated the roles of each of the peroxidase-encoding genes in L. monocytogenes growth, peroxide stress response, and virulence in mammalian cells.
Collapse
Affiliation(s)
- Monica R. Cesinger
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Nicole H. Schwardt
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Cortney R. Halsey
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Maureen K. Thomason
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Michelle L. Reniere
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| |
Collapse
|
10
|
Sugano Y, Yoshida T. DyP-Type Peroxidases: Recent Advances and Perspectives. Int J Mol Sci 2021; 22:5556. [PMID: 34074047 PMCID: PMC8197335 DOI: 10.3390/ijms22115556] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/16/2022] Open
Abstract
In this review, we chart the major milestones in the research progress on the DyP-type peroxidase family over the past decade. Though mainly distributed among bacteria and fungi, this family actually exhibits more widespread diversity. Advanced tertiary structural analyses have revealed common and different features among members of this family. Notably, the catalytic cycle for the peroxidase activity of DyP-type peroxidases appears to be different from that of other ubiquitous heme peroxidases. DyP-type peroxidases have also been reported to possess activities in addition to peroxidase function, including hydrolase or oxidase activity. They also show various cellular distributions, functioning not only inside cells but also outside of cells. Some are also cargo proteins of encapsulin. Unique, noteworthy functions include a key role in life-cycle switching in Streptomyces and the operation of an iron transport system in Staphylococcus aureus, Bacillus subtilis and Escherichia coli. We also present several probable physiological roles of DyP-type peroxidases that reflect the widespread distribution and function of these enzymes. Lignin degradation is the most common function attributed to DyP-type peroxidases, but their activity is not high compared with that of standard lignin-degrading enzymes. From an environmental standpoint, degradation of natural antifungal anthraquinone compounds is a specific focus of DyP-type peroxidase research. Considered in its totality, the DyP-type peroxidase family offers a rich source of diverse and attractive materials for research scientists.
Collapse
Affiliation(s)
- Yasushi Sugano
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women’s University, Tokyo 112-8681, Japan;
| | | |
Collapse
|
11
|
Laothamteep N, Kawano H, Vejarano F, Suzuki-Minakuchi C, Shintani M, Nojiri H, Pinyakong O. Effects of environmental factors and coexisting substrates on PAH degradation and transcriptomic responses of the defined bacterial consortium OPK. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 277:116769. [PMID: 33676341 DOI: 10.1016/j.envpol.2021.116769] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 02/10/2021] [Accepted: 02/13/2021] [Indexed: 05/12/2023]
Abstract
The present study showed that syntrophic associations in a defined bacterial consortium, named OPK, containing Mycolicibacterium strains PO1 and PO2, Novosphingobium pentaromativorans PY1 and Bacillus subtilis FW1, led to effective pyrene degradation over a wide range of pH values, temperatures and salinities, as well as in the presence of a second polycyclic aromatic hydrocarbon (PAH). Anthracene, phenanthrene or fluorene facilitated complete pyrene degradation within 9 days, while fluoranthene delayed pyrene degradation. Interestingly, fluoranthene degradation was enhanced in the presence of pyrene. Transcriptome analysis confirmed that Mycolicibacterium strains were the key PAH-degraders during the cometabolism of pyrene and fluoranthene. Notably, the transcription of genes encoding pyrene-degrading enzymes were shown to be important for enhanced fluoranthene degradation. NidAB was the major initial oxygenase involved in the degradation of pyrene and fluoranthene mixture. Other functional genes encoding ribosomal proteins, an iron transporter, ABC transporters and stress response proteins were induced in strains PO1 and PO2. Furthermore, an intermediate pyrene-degrading Novosphingobium strain contributed to protocatechuate degradation. The results demonstrated that synergistic interactions among the bacterial members (PO1, PO2 and PY1) of the consortium OPK promoted the simultaneous degradation of two high molecular weight (HMW) PAHs.
Collapse
Affiliation(s)
- Natthariga Laothamteep
- Department of Microbiology, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok, 10330, Thailand; Microbial Technology for Marine Pollution Treatment Research Unit, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok, 10330, Thailand; Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hibiki Kawano
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Felipe Vejarano
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Chiho Suzuki-Minakuchi
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Masaki Shintani
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka, 432-8561, Japan
| | - Hideaki Nojiri
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Onruthai Pinyakong
- Department of Microbiology, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok, 10330, Thailand; Microbial Technology for Marine Pollution Treatment Research Unit, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok, 10330, Thailand; Research Program on Remediation Technologies for Petroleum Contamination, Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok, 10330, Thailand; Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok, 10330, Thailand.
| |
Collapse
|
12
|
Clarkson SM, Haja DK, Adams MWW. The hyperthermophilic archaeon Pyrococcus furiosus utilizes environmental iron sulfide cluster complexes as an iron source. Extremophiles 2021; 25:249-256. [PMID: 33779854 DOI: 10.1007/s00792-021-01224-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/10/2021] [Indexed: 11/27/2022]
Abstract
Iron is an essential nutrient for almost all known organisms, but in aerobic, neutral pH environments, it is present primarily as precipitated oxyhydroxide minerals. In contrast, in anaerobic environments, iron can exist in its ferrous form (Fe2+) and remain soluble. In sulfide-rich, anaerobic environments, Fe2+ and sulfide react to form iron sulfide cluster complexes of the form FexSx (FeSaq), which further condense to form the mineral mackinawite, which itself is partly soluble. However, the ability of microorganisms to utilize iron sulfide as an iron source is not known. Here, we show that the anaerobic, hyperthermophilic archaeon Pyrococcus furiosus can directly assimilate the iron in dissolved iron sulfide cluster complexes (FeSaq) without further dissolution to Fe2+. Growth is only inhibited in the presence of a Fe2+-specific chelator. The FeSaq that is utilized can be formed either by reaction of chelated Fe2+ with sulfide or dissolved from mackinawite. Pyrococcus furiosus can utilize FeSaq larger than 3.5 kDa, or Fe40S40, and may actively aid in the dissolution of mackinawite to the assimilated FeSaq. A model for iron sulfide assimilation from an insoluble mineral is proposed.
Collapse
Affiliation(s)
- Sonya M Clarkson
- Department of Biochemistry and Molecular Biology, University of Georgia, Life Sciences Bldg, Athens, GA, 30602-7229, USA
- Conagen Inc, Bedford, MA, 01730, USA
| | - Dominik K Haja
- Department of Biochemistry and Molecular Biology, University of Georgia, Life Sciences Bldg, Athens, GA, 30602-7229, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Life Sciences Bldg, Athens, GA, 30602-7229, USA.
| |
Collapse
|
13
|
Engineering Bacillus subtilis Cells as Factories: Enzyme Secretion and Value-added Chemical Production. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-020-0104-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
14
|
Prajapati B, Bernal-Cabas M, López-Álvarez M, Schaffer M, Bartel J, Rath H, Steil L, Becher D, Völker U, Mäder U, van Dijl JM. Double trouble: Bacillus depends on a functional Tat machinery to avoid severe oxidative stress and starvation upon entry into a NaCl-depleted environment. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118914. [PMID: 33245978 DOI: 10.1016/j.bbamcr.2020.118914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/08/2020] [Accepted: 11/20/2020] [Indexed: 11/17/2022]
Abstract
The widely conserved twin-arginine translocases (Tat) allow the transport of fully folded cofactor-containing proteins across biological membranes. In doing so, these translocases serve different biological functions ranging from energy conversion to cell division. In the Gram-positive soil bacterium Bacillus subtilis, the Tat machinery is essential for effective growth in media lacking iron or NaCl. It was previously shown that this phenomenon relates to the Tat-dependent export of the heme-containing peroxidase EfeB, which converts Fe2+ to Fe3+ at the expense of hydrogen peroxide. However, the reasons why the majority of tat mutant bacteria perish upon dilution in NaCl-deprived medium and how, after several hours, a sub-population adapts to this condition was unknown. Here we show that, upon growth in the absence of NaCl, the bacteria face two major problems, namely severe oxidative stress at the membrane and starvation leading to death. The tat mutant cells can overcome these challenges if they are fed with arginine, which implies that severe arginine depletion is a major cause of death and resumed arginine synthesis permits their survival. Altogether, our findings show that the Tat system of B. subtilis is needed to preclude severe oxidative stress and starvation upon sudden drops in the environmental Na+ concentration as caused by flooding or rain.
Collapse
Affiliation(s)
- Bimal Prajapati
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands
| | - Margarita Bernal-Cabas
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands
| | - Marina López-Álvarez
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands
| | - Marc Schaffer
- University Medicine Greifswald, Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, Greifswald, Germany
| | - Jürgen Bartel
- University of Greifswald, Institute of Microbiology, Department of Microbial Proteomics, Greifswald, Germany
| | - Hermann Rath
- University Medicine Greifswald, Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, Greifswald, Germany
| | - Leif Steil
- University Medicine Greifswald, Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, Greifswald, Germany
| | - Dörte Becher
- University of Greifswald, Institute of Microbiology, Department of Microbial Proteomics, Greifswald, Germany
| | - Uwe Völker
- University Medicine Greifswald, Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, Greifswald, Germany
| | - Ulrike Mäder
- University Medicine Greifswald, Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, Greifswald, Germany.
| | - Jan Maarten van Dijl
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands.
| |
Collapse
|
15
|
Chan ACK, Lin H, Koch D, Grass G, Nies DH, Murphy MEP. A copper site is required for iron transport by the periplasmic proteins P19 and FetP. Metallomics 2020; 12:1530-1541. [PMID: 32780051 DOI: 10.1039/d0mt00130a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Campylobacter jejuni is a leading cause of food-borne gastrointestinal disease in humans and uropathogenic Escherichia coli is a leading cause of urinary tract infections. Both human pathogens harbour a homologous iron uptake system (termed cjFetM-P19 in C. jejuni and ecFetM-FetP in E. coli). Although these systems are important for growth under iron limitation, the mechanisms by which these systems function during iron transport remain undefined. The copper ions bound to P19 and FetP, the homologous periplasmic proteins, are coordinated in an uncommon penta-dentate manner involving a Met-Glu-His3 motif and exhibit positional plasticity. Here we demonstrate the function of the Met and Glu residues in modulating copper binding and controlling copper positioning through site-directed variants, binding assays, and crystal structures. Growth of C. jejuni strains with these p19 variants is impaired under iron limited conditions as compared to the wild-type strain. Additionally, an acidic residue-rich secondary site is required for binding iron and function in vivo. Finally, western blot analyses demonstrate direct and specific interactions between periplasmic P19 and FetP with the large periplasmic domain of their respective inner membrane transporters cjFetM and ecFetM.
Collapse
Affiliation(s)
- Anson C K Chan
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Canada.
| | - Helen Lin
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Canada.
| | - Doreen Koch
- Department of Molecular Microbiology, Martin-Luther-University Halle, Wittenberg, European Community, Germany
| | - Gregor Grass
- Bundeswehr Institute for Microbiology, Munich, Germany
| | - Dietrich H Nies
- Department of Molecular Microbiology, Martin-Luther-University Halle, Wittenberg, European Community, Germany
| | - Michael E P Murphy
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Canada.
| |
Collapse
|
16
|
Park J, Lee S, Lee MJ, Park K, Lee S, Kim JF, Kim P. Accelerated Growth of Corynebacterium glutamicum by Up-Regulating Stress- Responsive Genes Based on Transcriptome Analysis of a Fast-Doubling Evolved Strain. J Microbiol Biotechnol 2020; 30:1420-1429. [PMID: 32699195 PMCID: PMC9728273 DOI: 10.4014/jmb.2006.06035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/06/2020] [Accepted: 07/09/2020] [Indexed: 12/15/2022]
Abstract
Corynebacterium glutamicum, an important industrial strain, has a relatively slower reproduction rate. To acquire a growth-boosted C. glutamicum, a descendant strain was isolated from a continuous culture after 600 generations. The isolated descendant C. glutamicum, JH41 strain, was able to double 58% faster (td=1.15 h) than the parental type strain (PT, td=1.82 h). To understand the factors boosting reproduction, the transcriptomes of JH41 and PT strains were compared. The mRNAs involved in respiration and TCA cycle were upregulated. The intracellular ATP of the JH41 strain was 50% greater than the PT strain. The upregulation of NCgl1610 operon (a putative dyp-type heme peroxidase, a putative copper chaperone, and a putative copper importer) that presumed to role in the assembly and redox control of cytochrome c oxidase was found in the JH41 transcriptome. Plasmid-driven expression of the operon enabled the PT strain to double 19% faster (td=1.82 h) than its control (td=2.17 h) with 14% greater activity of cytochrome c oxidase and 27% greater intracellular ATP under the oxidative stress conditions. Upregulations of genes those might enhance translation fitness were also found in the JH41 transcriptome. Plasmid-driven expressions of NCgl0171 (encoding a cold-shock protein) and NCgl2435 (encoding a putative peptidyl-tRNA hydrolase) enabled the PT to double 22% and 32% faster than its control, respectively (empty vector: td=1.93 h, CspA: td=1.58 h, and Pth: td=1.44 h). Based on the results, the factors boosting growth rate in C. gluctamicum were further discussed in the viewpoints of cellular energy state, oxidative stress management, and translation.
Collapse
Affiliation(s)
- Jihoon Park
- Department of Biotechnology, The Catholic University of Korea, Gyeonggi 14662, Republic of Korea
| | - SuRin Lee
- Department of Biotechnology, The Catholic University of Korea, Gyeonggi 14662, Republic of Korea
| | - Min Ju Lee
- Department of Biotechnology, The Catholic University of Korea, Gyeonggi 14662, Republic of Korea
| | - Kyunghoon Park
- Department of Biotechnology, The Catholic University of Korea, Gyeonggi 14662, Republic of Korea
| | - Seungki Lee
- Department of Biotechnology, The Catholic University of Korea, Gyeonggi 14662, Republic of Korea
| | - Jihyun F. Kim
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Pil Kim
- Department of Biotechnology, The Catholic University of Korea, Gyeonggi 14662, Republic of Korea,Corresponding author Phone/Fax: +82-2-2164-4922 E-mail:
| |
Collapse
|
17
|
Corretto E, Antonielli L, Sessitsch A, Höfer C, Puschenreiter M, Widhalm S, Swarnalakshmi K, Brader G. Comparative Genomics of Microbacterium Species to Reveal Diversity, Potential for Secondary Metabolites and Heavy Metal Resistance. Front Microbiol 2020; 11:1869. [PMID: 32903828 PMCID: PMC7438953 DOI: 10.3389/fmicb.2020.01869] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/16/2020] [Indexed: 12/11/2022] Open
Abstract
Microbacterium species have been isolated from a wide range of hosts and environments, including heavy metal-contaminated sites. Here, we present a comprehensive analysis on the phylogenetic distribution and the genetic potential of 70 Microbacterium belonging to 20 different species isolated from heavy metal-contaminated and non-contaminated sites with particular attention to secondary metabolites gene clusters. The analyzed Microbacterium species are divided in three main functional clades. They share a small core genome (331 gene families covering basic functions) pointing to high genetic diversity. The most common secondary metabolite gene clusters encode pathways for the production of terpenoids, type III polyketide synthases and non-ribosomal peptide synthetases, potentially responsible of the synthesis of siderophore-like compounds. In vitro tests showed that many Microbacterium strains produce siderophores, ACC deaminase, auxins (IAA) and are able to solubilize phosphate. Microbacterium isolates from heavy metal contaminated sites are on average more resistant to heavy metals and harbor more genes related to metal homeostasis (e.g., metalloregulators). On the other hand, the ability to increase the metal mobility in a contaminated soil through the secretion of specific molecules seems to be widespread among all. Despite the widespread capacity of strains to mobilize several metals, plants inoculated with selected Microbacterium isolates showed only slightly increased iron concentrations, whereas concentrations of zinc, cadmium and lead were decreased.
Collapse
Affiliation(s)
- Erika Corretto
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Livio Antonielli
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Angela Sessitsch
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Christoph Höfer
- Institute of Soil Research, Department of Forest- and Soil Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Markus Puschenreiter
- Institute of Soil Research, Department of Forest- and Soil Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Siegrid Widhalm
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | | | - Günter Brader
- Bioresouces Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| |
Collapse
|
18
|
Bernal-Cabas M, Miethke M, Antelo-Varela M, Aguilar Suárez R, Neef J, Schön L, Gabarrini G, Otto A, Becher D, Wolf D, van Dijl JM. Functional association of the stress-responsive LiaH protein and the minimal TatAyCy protein translocase in Bacillus subtilis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118719. [DOI: 10.1016/j.bbamcr.2020.118719] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 01/07/2023]
|
19
|
Garber AI, Nealson KH, Okamoto A, McAllister SM, Chan CS, Barco RA, Merino N. FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies. Front Microbiol 2020; 11:37. [PMID: 32082281 PMCID: PMC7005843 DOI: 10.3389/fmicb.2020.00037] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 01/09/2020] [Indexed: 01/15/2023] Open
Abstract
Iron is a micronutrient for nearly all life on Earth. It can be used as an electron donor and electron acceptor by iron-oxidizing and iron-reducing microorganisms and is used in a variety of biological processes, including photosynthesis and respiration. While it is the fourth most abundant metal in the Earth's crust, iron is often limiting for growth in oxic environments because it is readily oxidized and precipitated. Much of our understanding of how microorganisms compete for and utilize iron is based on laboratory experiments. However, the advent of next-generation sequencing and surge in publicly available sequence data has made it possible to probe the structure and function of microbial communities in the environment. To bridge the gap between our understanding of iron acquisition, iron redox cycling, iron storage, and magnetosome formation in model microorganisms and the plethora of sequence data available from environmental studies, we have created a comprehensive database of hidden Markov models (HMMs) based on genes related to iron acquisition, storage, and reduction/oxidation in Bacteria and Archaea. Along with this database, we present FeGenie, a bioinformatics tool that accepts genome and metagenome assemblies as input and uses our comprehensive HMM database to annotate provided datasets with respect to iron-related genes and gene neighborhood. An important contribution of this tool is the efficient identification of genes involved in iron oxidation and dissimilatory iron reduction, which have been largely overlooked by standard annotation pipelines. We validated FeGenie against a selected set of 28 isolate genomes and showcase its utility in exploring iron genes present in 27 metagenomes, 4 isolate genomes from human oral biofilms, and 17 genomes from candidate organisms, including members of the candidate phyla radiation. We show that FeGenie accurately identifies iron genes in isolates. Furthermore, analysis of metagenomes using FeGenie demonstrates that the iron gene repertoire and abundance of each environment is correlated with iron richness. While this tool will not replace the reliability of culture-dependent analyses of microbial physiology, it provides reliable predictions derived from the most up-to-date genetic markers. FeGenie's database will be maintained and continually updated as new genes are discovered. FeGenie is freely available: https://github.com/Arkadiy-Garber/FeGenie.
Collapse
Affiliation(s)
- Arkadiy I. Garber
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
- Department of Earth Sciences, University of Delaware, Newark, DE, United States
| | - Kenneth H. Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Akihiro Okamoto
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, Tsukuba, Japan
| | - Sean M. McAllister
- School of Marine Science and Policy, University of Delaware, Newark, DE, United States
| | - Clara S. Chan
- Department of Earth Sciences, University of Delaware, Newark, DE, United States
- School of Marine Science and Policy, University of Delaware, Newark, DE, United States
| | - Roman A. Barco
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Nancy Merino
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
| |
Collapse
|
20
|
Abstract
The Tat pathway for protein translocation across bacterial membranes stands out for its selective handling of fully folded cargo proteins. In this review, we provide a comprehensive summary of our current understanding of the different known Tat components, their assembly into different complexes, and their specific roles in the protein translocation process. In particular, this overview focuses on the Gram-negative bacterium Escherichia coli and the Gram-positive bacterium Bacillus subtilis. Using these organisms as examples, we discuss structural features of Tat complexes alongside mechanistic models that allow for the Tat pathway's unique protein proofreading and transport capabilities. Finally, we highlight recent advances in exploiting the Tat pathway for biotechnological benefit, the production of high-value pharmaceutical proteins.
Collapse
|
21
|
Reis AC, Kolvenbach BA, Chami M, Gales L, Egas C, Corvini PFX, Nunes OC. Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader 'Candidatus Leucobacter sulfamidivorax' strain GP. BMC Genomics 2019; 20:885. [PMID: 31752666 PMCID: PMC6868719 DOI: 10.1186/s12864-019-6206-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 10/21/2019] [Indexed: 02/01/2023] Open
Abstract
Background Microbial communities recurrently establish metabolic associations resulting in increased fitness and ability to perform complex tasks, such as xenobiotic degradation. In a previous study, we have described a sulfonamide-degrading consortium consisting of a novel low-abundant actinobacterium, named strain GP, and Achromobacter denitrificans PR1. However, we found that strain GP was unable to grow independently and could not be further purified. Results Previous studies suggested that strain GP might represent a new putative species within the Leucobacter genus (16S rRNA gene similarity < 97%). In this study, we found that average nucleotide identity (ANI) with other Leucobacter spp. ranged between 76.8 and 82.1%, further corroborating the affiliation of strain GP to a new provisional species. The average amino acid identity (AAI) and percentage of conserved genes (POCP) values were near the lower edge of the genus delimitation thresholds (65 and 55%, respectively). Phylogenetic analysis of core genes between strain GP and Leucobacter spp. corroborated these findings. Comparative genomic analysis indicates that strain GP may have lost genes related to tetrapyrrole biosynthesis and thiol transporters, both crucial for the correct assembly of cytochromes and aerobic growth. However, supplying exogenous heme and catalase was insufficient to abolish the dependent phenotype. The actinobacterium harbors at least two copies of a novel genetic element containing a sulfonamide monooxygenase (sadA) flanked by a single IS1380 family transposase. Additionally, two homologs of sadB (4-aminophenol monooxygenase) were identified in the metagenome-assembled draft genome of strain GP, but these were not located in the vicinity of sadA nor of mobile or integrative elements. Conclusions Comparative genomics of the genus Leucobacter suggested the absence of some genes encoding for important metabolic traits in strain GP. Nevertheless, although media and culture conditions were tailored to supply its potential metabolic needs, these conditions were insufficient to isolate the PR1-dependent actinobacterium further. This study gives important insights regarding strain GP metabolism; however, gene expression and functional studies are necessary to characterize and further isolate strain GP. Based on our data, we propose to classify strain GP in a provisional new species within the genus Leucobacter, ‘Candidatus Leucobacter sulfamidivorax‘.
Collapse
Affiliation(s)
- Ana C Reis
- Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering - LEPABE, Department of Chemical Engineering, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.,Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Gruendenstrasse 40, 4132, Muttenz, Switzerland
| | - Boris A Kolvenbach
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Gruendenstrasse 40, 4132, Muttenz, Switzerland
| | - Mohamed Chami
- BioEM lab, C-Cina, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Luís Gales
- Instituto de Investigação e Inovação em Saúde - i3S, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,Instituto de Biologia Molecular e Celular - IBMC, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar - ICBAS, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Conceição Egas
- Next Generation Sequencing Unit, Biocant, BiocantPark, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal.,Center for Neuroscience and Cell Biology, University of Coimbra, Faculty of Medicine, Rua Larga, Pólo I, 3004-504, Coimbra, Portugal
| | - Philippe F-X Corvini
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Gruendenstrasse 40, 4132, Muttenz, Switzerland
| | - Olga C Nunes
- Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering - LEPABE, Department of Chemical Engineering, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.
| |
Collapse
|
22
|
Battu L, Ulaganathan K. Whole genome sequencing and identification of host-interactive genes in the rice endophytic Leifsonia sp. ku-ls. Funct Integr Genomics 2019; 20:237-243. [PMID: 31482368 DOI: 10.1007/s10142-019-00713-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 08/11/2019] [Accepted: 08/23/2019] [Indexed: 12/12/2022]
Abstract
Leifsonia sp. ku-ls is an endophytic bacterial strain colonizing in high numbers the stem and leaf of the high-yielding and widely grown indica rice cultivar RP Bio-226. Whole genome sequencing of this strain using Illumina Hiseq-2500 system resulted in generation of 10,103,994 paired-end reads of 150 nucleotides length. De novo assembly of the reads with A5MySeq resulted in 51 scaffolds. Kmer analysis with KAT estimated the genome size as 3.83 Mbp with 70% GC content. Annotation of the genome resulted in identification of 3930 protein-coding genes, 45 tRNA genes, and 3 rRNA genes. Detailed analysis of the genes predicted resulted in identification of host beneficial genes which include genes associated with hormone production, nitrogen metabolism, and stress response. There is an elaborate defense against oxidative stress present in this bacterium which also can mitigate plant oxidative stress resulting from disease/abiotic stress. Comparison of this endophytic bacterial genome with non-endophytic Leifsonia sp. showed presence of additional genes, increase in copy number of some of the genes and regulators. Many genes with eukaryotic-like domains have also been identified in this bacterium.
Collapse
Affiliation(s)
- Latha Battu
- Centre for Plant Molecular Biology, Osmania University, Hyderabad, Telangana, 500007, India
| | - Kandasamy Ulaganathan
- Centre for Plant Molecular Biology, Osmania University, Hyderabad, Telangana, 500007, India.
| |
Collapse
|
23
|
Abstract
The twin-arginine protein translocation (Tat) system has been characterized in bacteria, archaea and the chloroplast thylakoidal membrane. This system is distinct from other protein transport systems with respect to two key features. Firstly, it accepts cargo proteins with an N-terminal signal peptide that carries the canonical twin-arginine motif, which is essential for transport. Second, the Tat system only accepts and translocates fully folded cargo proteins across the respective membrane. Here, we review the core essential features of folded protein transport via the bacterial Tat system, using the three-component TatABC system of Escherichia coli and the two-component TatAC systems of Bacillus subtilis as the main examples. In particular, we address features of twin-arginine signal peptides, the essential Tat components and how they assemble into different complexes, mechanistic features and energetics of Tat-dependent protein translocation, cytoplasmic chaperoning of Tat cargo proteins, and the remarkable proofreading capabilities of the Tat system. In doing so, we present the current state of our understanding of Tat-dependent protein translocation across biological membranes, which may serve as a lead for future investigations.
Collapse
Affiliation(s)
- Kelly M. Frain
- The School of Biosciences, University of Kent, Canterbury, CT2 7NZ UK
| | - Colin Robinson
- The School of Biosciences, University of Kent, Canterbury, CT2 7NZ UK
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen (UMCG), Hanzeplein 1, P.O. Box 30001, 9700 RB Groningen, The Netherlands
| |
Collapse
|
24
|
Anand A, Olson CA, Yang L, Sastry AV, Catoiu E, Choudhary KS, Phaneuf PV, Sandberg TE, Xu S, Hefner Y, Szubin R, Feist AM, Palsson BO. Pseudogene repair driven by selection pressure applied in experimental evolution. Nat Microbiol 2019; 4:386-389. [DOI: 10.1038/s41564-018-0340-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/05/2018] [Indexed: 11/09/2022]
|
25
|
Abstract
SIGNIFICANCE Iron is required for growth and is often redox active under cytosolic conditions. As a result of its facile redox chemistry, iron homeostasis is intricately involved with oxidative stress. Bacterial adaptation to iron limitation and oxidative stress often involves ferric uptake regulator (Fur) proteins: a diverse set of divalent cation-dependent, DNA-binding proteins that vary widely in both metal selectivity and sensitivity to metal-catalyzed oxidation. Recent Advances: Bacteria contain two Fur family metalloregulators that use ferrous iron (Fe2+) as their cofactor, Fur and PerR. Fur functions to regulate iron homeostasis in response to changes in intracellular levels of Fe2+. PerR also binds Fe2+, which enables metal-catalyzed protein oxidation as a mechanism for sensing hydrogen peroxide (H2O2). CRITICAL ISSUES To effectively regulate iron homeostasis, Fur has an Fe2+ affinity tuned to monitor the labile iron pool of the cell and may be under selective pressure to minimize iron oxidation, which would otherwise lead to an inappropriate increase in iron uptake under oxidative stress conditions. Conversely, Fe2+ is bound more tightly to PerR but exhibits high H2O2 reactivity, which enables a rapid induction of peroxide stress genes. FUTURE DIRECTIONS The features that determine the disparate reactivity of these proteins with oxidants are still poorly understood. A controlled, comparative analysis of the affinities of Fur/PerR proteins for their metal cofactors and their rate of reactivity with H2O2, combined with structure/function analyses, will be needed to define the molecular mechanisms that have facilitated this divergence of function between these two paralogous regulators.
Collapse
Affiliation(s)
| | - John D Helmann
- Department of Microbiology, Cornell University , Ithaca, New York
| |
Collapse
|
26
|
Mannala GK, Koettnitz J, Mohamed W, Sommer U, Lips KS, Spröer C, Bunk B, Overmann J, Hain T, Heiss C, Domann E, Alt V. Whole-genome comparison of high and low virulent Staphylococcus aureus isolates inducing implant-associated bone infections. Int J Med Microbiol 2018; 308:505-513. [DOI: 10.1016/j.ijmm.2018.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/08/2018] [Accepted: 04/22/2018] [Indexed: 11/16/2022] Open
|
27
|
Chander AM, Kochhar R, Dhawan DK, Bhadada SK, Mayilraj S. Genome sequence and comparative genomic analysis of a clinically important strain CD11-4 of Janibacter melonis isolated from celiac disease patient. Gut Pathog 2018; 10:2. [PMID: 29387173 PMCID: PMC5778662 DOI: 10.1186/s13099-018-0229-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 01/06/2018] [Indexed: 12/22/2022] Open
Abstract
Background Janibacter melonis and other member of this genus are known to cause bacteremia and serious clinical comorbidities, but there is no study reporting about pathogenicity attributes of J. melonis. Janibacter terrae is known to cause lethal infection. Reporting the genome of J. melonis CD11-4 and comparative genomics with other members of genus has provided some novel insights that can enable us to understand the mechanisms responsible for its pathogenicity in humans. Results Comparative genomic analysis by Rapid Annotation Server and Technology revealed the presence of similar virulence determinant genes in both J. terrae NBRC 107853T and J. melonis CD11-4. Like J. terrae NBRC 107853T, J. melonis CD11-4 contained two genes responsible for resistance against β-lactam class of antibiotics and two genes for resistance against fluoroquinolones. Interestingly, J. melonis CD11-4 contained a unique gene coding for multidrug resistance efflux pumps unlike all other members of this genus. It also contained two genes involved in Toxin-antitoxin Systems that were absent in J. terrae NBRC 107853T but were present in some other members of genus. Conclusions Genome annotations of J. melonis CD11-4 revealed that it contained similar or more virulence repertoire like J. terrae NBRC 107853T. Like other gut pathogens, J. melonis possesses key virulence determinant genes for antibiotic resistance, invasion, adhesion, biofilm formation, iron acquisition and to cope with stress response, thereby indicating that strain J. melonis CD11-4 could be a gut pathogen.
Collapse
Affiliation(s)
- Atul Munish Chander
- 1Department of Biophysics, Panjab University, Chandigarh, India.,3Department of Endocrinology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Rakesh Kochhar
- 2Department of Gastroenterology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | | | - Sanjay Kumar Bhadada
- 3Department of Endocrinology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Shanmugam Mayilraj
- 4Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Chandigarh, 160036 India
| |
Collapse
|
28
|
Pham NP, Layec S, Dugat-Bony E, Vidal M, Irlinger F, Monnet C. Comparative genomic analysis of Brevibacterium strains: insights into key genetic determinants involved in adaptation to the cheese habitat. BMC Genomics 2017; 18:955. [PMID: 29216827 PMCID: PMC5719810 DOI: 10.1186/s12864-017-4322-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 11/21/2017] [Indexed: 11/10/2022] Open
Abstract
Background Brevibacterium strains are widely used for the manufacturing of surface-ripened cheeses, contributing to the breakdown of lipids and proteins and producing volatile sulfur compounds and red-orange pigments. The objective of the present study was to perform comparative genomic analyses in order to better understand the mechanisms involved in their ability to grow on the cheese surface and the differences between the strains. Results The genomes of 23 Brevibacterium strains, including twelve strains isolated from cheeses, were compared for their gene repertoire involved in salt tolerance, iron acquisition, bacteriocin production and the ability to use the energy compounds present in cheeses. All or almost all the genomes encode the enzymes involved in ethanol, acetate, lactate, 4-aminobutyrate and glycerol catabolism, and in the synthesis of the osmoprotectants ectoine, glycine-betaine and trehalose. Most of the genomes contain two contiguous genes encoding extracellular proteases, one of which was previously characterized for its activity on caseins. Genes encoding a secreted triacylglycerol lipase or involved in the catabolism of galactose and D-galactonate or in the synthesis of a hydroxamate-type siderophore are present in part of the genomes. Numerous Fe3+/siderophore ABC transport components are present, part of them resulting from horizontal gene transfers. Two cheese-associated strains have also acquired catecholate-type siderophore biosynthesis gene clusters by horizontal gene transfer. Predicted bacteriocin biosynthesis genes are present in most of the strains, and one of the corresponding gene clusters is located in a probable conjugative transposon that was only found in cheese-associated strains. Conclusions Brevibacterium strains show differences in their gene repertoire potentially involved in the ability to grow on the cheese surface. Part of these differences can be explained by different phylogenetic positions or by horizontal gene transfer events. Some of the distinguishing features concern biotic interactions with other strains such as the secretion of proteases and triacylglycerol lipases, and competition for iron or bacteriocin production. In the future, it would be interesting to take the properties deduced from genomic analyses into account in order to improve the screening and selection of Brevibacterium strains, and their association with other ripening culture components. Electronic supplementary material The online version of this article (10.1186/s12864-017-4322-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Nguyen-Phuong Pham
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Séverine Layec
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Eric Dugat-Bony
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Marie Vidal
- US 1426, GeT-PlaGe, Genotoul, INRA, 31326, Castanet-Tolosan, France
| | - Françoise Irlinger
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850, Thiverval-Grignon, France
| | - Christophe Monnet
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850, Thiverval-Grignon, France.
| |
Collapse
|
29
|
Gallois N, Alpha-Bazin B, Ortet P, Barakat M, Piette L, Long J, Berthomieu C, Armengaud J, Chapon V. Proteogenomic insights into uranium tolerance of a Chernobyl's Microbacterium bacterial isolate. J Proteomics 2017; 177:148-157. [PMID: 29223802 DOI: 10.1016/j.jprot.2017.11.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/15/2017] [Accepted: 11/27/2017] [Indexed: 10/18/2022]
Abstract
Microbacterium oleivorans A9 is a uranium-tolerant actinobacteria isolated from the trench T22 located near the Chernobyl nuclear power plant. This site is contaminated with different radionuclides including uranium. To observe the molecular changes at the proteome level occurring in this strain upon uranyl exposure and understand molecular mechanisms explaining its uranium tolerance, we established its draft genome and used this raw information to perform an in-depth proteogenomics study. High-throughput proteomics were performed on cells exposed or not to 10μM uranyl nitrate sampled at three previously identified phases of uranyl tolerance. We experimentally detected and annotated 1532 proteins and highlighted a total of 591 proteins for which abundances were significantly differing between conditions. Notably, proteins involved in phosphate and iron metabolisms show high dynamics. A large ratio of proteins more abundant upon uranyl stress, are distant from functionally-annotated known proteins, highlighting the lack of fundamental knowledge regarding numerous key molecular players from soil bacteria. BIOLOGICAL SIGNIFICANCE Microbacterium oleivorans A9 is an interesting environmental model to understand biological processes engaged in tolerance to radionuclides. Using an innovative proteogenomics approach, we explored its molecular mechanisms involved in uranium tolerance. We sequenced its genome, interpreted high-throughput proteomic data against a six-reading frame ORF database deduced from the draft genome, annotated the identified proteins and compared protein abundances from cells exposed or not to uranyl stress after a cascade search. These data show that a complex cellular response to uranium occurs in Microbacterium oleivorans A9, where one third of the experimental proteome is modified. In particular, the uranyl stress perturbed the phosphate and iron metabolic pathways. Furthermore, several transporters have been identified to be specifically associated to uranyl stress, paving the way to the development of biotechnological tools for uranium decontamination.
Collapse
Affiliation(s)
- Nicolas Gallois
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire des Interactions Protéine Métal, 13108 Saint-Paul-lez-Durance, France
| | - Béatrice Alpha-Bazin
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols sur Cèze, France
| | - Philippe Ortet
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire d'écologie microbienne de la rhizosphère et d'environnements extrêmes, 13108 Saint-Paul-lez-Durance, France
| | - Mohamed Barakat
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire d'écologie microbienne de la rhizosphère et d'environnements extrêmes, 13108 Saint-Paul-lez-Durance, France
| | - Laurie Piette
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire des Interactions Protéine Métal, 13108 Saint-Paul-lez-Durance, France
| | - Justine Long
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire d'écologie microbienne de la rhizosphère et d'environnements extrêmes, 13108 Saint-Paul-lez-Durance, France
| | - Catherine Berthomieu
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire des Interactions Protéine Métal, 13108 Saint-Paul-lez-Durance, France
| | - Jean Armengaud
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols sur Cèze, France.
| | - Virginie Chapon
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire des Interactions Protéine Métal, 13108 Saint-Paul-lez-Durance, France
| |
Collapse
|
30
|
Sequential induction of Fur-regulated genes in response to iron limitation in Bacillus subtilis. Proc Natl Acad Sci U S A 2017; 114:12785-12790. [PMID: 29133393 DOI: 10.1073/pnas.1713008114] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Bacterial cells modulate transcription in response to changes in iron availability. The ferric uptake regulator (Fur) senses intracellular iron availability and plays a central role in maintaining iron homeostasis in Bacillus subtilis Here we utilized FrvA, a high-affinity Fe2+ efflux transporter from Listeria monocytogenes, as an inducible genetic tool to deplete intracellular iron. We then characterized the responses of the Fur, FsrA, and PerR regulons as cells transition from iron sufficiency to deficiency. Our results indicate that the Fur regulon is derepressed in three distinct waves. First, uptake systems for elemental iron (efeUOB), ferric citrate (fecCDEF), and petrobactin (fpbNOPQ) are induced to prevent iron deficiency. Second, B. subtilis synthesizes its own siderophore bacillibactin (dhbACEBF) and turns on bacillibactin (feuABC) and hydroxamate siderophore (fhuBCGD) uptake systems to scavenge iron from the environment and flavodoxins (ykuNOP) to replace ferredoxins. Third, as iron levels decline further, an "iron-sparing" response (fsrA, fbpAB, and fbpC) is induced to block the translation of abundant iron-utilizing proteins and thereby permit the most essential iron-dependent enzymes access to the limited iron pools. ChIP experiments demonstrate that in vivo occupancy of Fur correlates with derepression of each operon, and the graded response observed here results, at least in part, from higher-affinity binding of Fur to the "late"-induced genes.
Collapse
|
31
|
Temtrirath K, Okumura K, Maruyama Y, Mikami B, Murata K, Hashimoto W. Binding mode of metal ions to the bacterial iron import protein EfeO. Biochem Biophys Res Commun 2017; 493:1095-1101. [PMID: 28919419 DOI: 10.1016/j.bbrc.2017.09.057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 09/12/2017] [Indexed: 01/18/2023]
Abstract
The tripartite EfeUOB system functions as a low pH iron importer in Gram-negative bacteria. In the alginate-assimilating bacterium Sphingomonas sp. strain A1, an additional EfeO-like protein (Algp7) is encoded downstream of the efeUOB operon. Here we show the metal binding mode of Algp7, which carries a M_75 metallopeptidase motif. The Algp7 protein was purified from recombinant E. coli cells and was subsequently characterized using differential scanning fluorimetry, fluorescence spectrometry, atomic absorption spectroscopy, and X-ray crystallography. The fluorescence of a dye, SYPRO Orange, bound to denatured Algp7 in the absence and presence of metal ions was measured during heat treatment. The fluorescence profile of Algp7 in the presence of metals such as ferric, ferrous, and zinc ions, shifted to a higher temperature, suggesting that Algp7 binds these metal ions and that metal ion-bound Algp7 is more thermally stable than the ligand-free form. Algp7 was directly demonstrated to show an ability to bind copper ion by atomic absorption spectroscopy. Crystal structure of metal ion-bound Algp7 revealed that the metal ion is bound to the cleft surrounded by several acidic residues. Four residues, Glu79, Glu82, Asp96, and Glu178, distinct from the M_75 motif (His115xxGlu118), are coordinated to the metal ion. This is the first report to provide structural insights into metal binding by the bacterial EfeO element.
Collapse
Affiliation(s)
- Kanate Temtrirath
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Kenji Okumura
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Yukie Maruyama
- Laboratory of Food Microbiology, Department of Life Science, Faculty of Science and Engineering, Setsunan University, Neyagawa, Osaka 572-8508, Japan
| | - Bunzo Mikami
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Kousaku Murata
- Laboratory of Food Microbiology, Department of Life Science, Faculty of Science and Engineering, Setsunan University, Neyagawa, Osaka 572-8508, Japan
| | - Wataru Hashimoto
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan.
| |
Collapse
|
32
|
Abstract
Iron is an essential micronutrient for both microbes and humans alike. For well over half a century we have known that this element, in particular, plays a pivotal role in health and disease and, most especially, in shaping host-pathogen interactions. Intracellular iron concentrations serve as a critical signal in regulating the expression not only of high-affinity iron acquisition systems in bacteria, but also of toxins and other noted virulence factors produced by some major human pathogens. While we now are aware of many strategies that the host has devised to sequester iron from invading microbes, there are as many if not more sophisticated mechanisms by which successful pathogens overcome nutritional immunity imposed by the host. This review discusses some of the essential components of iron sequestration and scavenging mechanisms of the host, as well as representative Gram-negative and Gram-positive pathogens, and highlights recent advances in the field. Last, we address how the iron acquisition strategies of pathogenic bacteria may be exploited for the development of novel prophylactics or antimicrobials.
Collapse
|
33
|
Abstract
Acquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4733 protein coding genes. The largest of these regions are enriched for genes involved in siderophore acquisition, and are widely distributed in cheese rinds in both Europe and the US. These results suggest that HGT is prevalent in cheese rind microbiomes, and that identification of genes that are frequently transferred in a particular environment may provide insight into the selective forces shaping microbial communities. DOI:http://dx.doi.org/10.7554/eLife.22144.001 From the depths of the ocean to the lining of the human gut, almost every environment on Earth is home to a unique community of microorganisms referred to as a microbiome. Within these communities, unrelated microorganisms can exchange genetic information through a process known as horizontal gene transfer. For example, genes linked to antibiotic resistance are often transferred between different microorganisms, which can create increasingly drug resistant microbes and has important implications for human health. Horizontal gene transfer has been studied for almost 100 years, but examining it directly is challenging because, almost by definition, it requires studying a community of microbes rather than one microbe in isolation. As such, researchers are looking for simple models of microbial communities that can be easily manipulated in experiments. Bonham et al. have now turned to the outer surface of cheese, also known as cheese rind, to better understand horizontal gene transfer. As a model system, the cheese rind microbiome is relatively simple to work with because cheese rind is easy to replicate in the laboratory, and the microbes growing on cheese can be grown on their own or in combinations with other microbes. By comparing the genetic material of 165 cheese-associated bacteria to one another, Bonham et al. identified over 4,000 genes that were shared between the bacteria, including several large clusters of genes that were shared by many species. Many of the identified genes (about 23% to be precise) appear to help the microorganisms acquire nutrients that are known to be in short supply on the surface of cheese surface, including iron. Bacteria typically use specialized molecules called siderophores to scavenge for iron and uptake systems to carry the iron-bound siderophore back into the cell. Notably, only the genes associated with the uptake systems were found in some of the shared gene clusters. This finding suggests that horizontal gene transfer has allowed some microbes to “cheat” and take up iron-bound siderophores without expending energy to produce the siderophores themselves. Using the cheese rind microbiome as a model system, it becomes possible to explore how horizontal gene transfer works in more detail than before. A better understanding of this process can then be applied to other important microbiomes, including those where genes conferring antibiotic resistance are commonly exchanged. DOI:http://dx.doi.org/10.7554/eLife.22144.002
Collapse
Affiliation(s)
- Kevin S Bonham
- Division of Biological Sciences, University of California, San Diego, San Diego, United States
| | | | - Rachel J Dutton
- Division of Biological Sciences, University of California, San Diego, San Diego, United States.,Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, San Diego, United States
| |
Collapse
|
34
|
Roy EM, Griffith KL. Characterization of a Novel Iron Acquisition Activity That Coordinates the Iron Response with Population Density under Iron-Replete Conditions in Bacillus subtilis. J Bacteriol 2017; 199:e00487-16. [PMID: 27795321 PMCID: PMC5165090 DOI: 10.1128/jb.00487-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/24/2016] [Indexed: 01/10/2023] Open
Abstract
Iron is an essential micronutrient required for the viability of many organisms. Under oxidizing conditions, ferric iron is highly insoluble (∼10-9 to 10-18 M), yet bacteria typically require ∼10-6 M for survival. To overcome this disparity, many bacteria have adopted the use of extracellular iron-chelating siderophores coupled with specific iron-siderophore uptake systems. In the case of Bacillus subtilis, undomesticated strains produce the siderophore bacillibactin. However, many laboratory strains, e.g., JH642, have lost the ability to produce bacillibactin during the process of domestication. In this work, we identified a novel iron acquisition activity from strain JH642 that accumulates in the growth medium and coordinates the iron response with population density. The molecule(s) responsible for this activity was named elemental Fe(II/III) (Efe) acquisition factor because efeUOB (ywbLMN) is required for its activity. Unlike most iron uptake molecules, including siderophores and iron reductases, Efe acquisition factor is present under iron-replete conditions and is regulated independently of Fur repressor. Restoring bacillibactin production in strain JH642 inhibits the activity of Efe acquisition factor, presumably by sequestering available iron. A similar iron acquisition activity is produced from a mutant of Escherichia coli unable to synthesize the siderophore enterobactin. Given the conservation of efeUOB and its regulation by catecholic siderophores in B. subtilis and E. coli, we speculate that Efe acquisition factor is utilized by many bacteria, serves as an alternative to Fur-mediated iron acquisition systems, and provides cells with biologically available iron that would normally be inaccessible during aerobic growth under iron-replete conditions. IMPORTANCE Iron is an essential micronutrient required for a variety of biological processes, yet ferric iron is highly insoluble during aerobic growth. In this work, we identified a novel iron acquisition activity that coordinates the iron response with population density in laboratory strains of Bacillus subtilis We named the molecule(s) responsible for this activity elemental Fe(II/III) (Efe) acquisition factor after the efeUOB (ywbLMN) operon required for its uptake into cells. Unlike most iron uptake systems, Efe acquisition factor is present under iron-replete conditions and is regulated independently of Fur, the master regulator of the iron response. We speculate that Efe acquisition factor is highly conserved among bacteria and serves as a backup to Fur-mediated iron acquisition systems.
Collapse
Affiliation(s)
- Emily M Roy
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Kevin L Griffith
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| |
Collapse
|
35
|
Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression. Microbiol Mol Biol Rev 2016; 80:1029-1057. [PMID: 27784798 DOI: 10.1128/mmbr.00026-16] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bacteria can employ widely diverse RNA molecules to regulate their gene expression. Such molecules include trans-acting small regulatory RNAs, antisense RNAs, and a variety of transcriptional attenuation mechanisms in the 5' untranslated region. Thus far, most regulatory RNA research has focused on Gram-negative bacteria, such as Escherichia coli and Salmonella. Hence, there is uncertainty about whether the resulting insights can be extrapolated directly to other bacteria, such as the Gram-positive soil bacterium Bacillus subtilis. A recent study identified 1,583 putative regulatory RNAs in B. subtilis, whose expression was assessed across 104 conditions. Here, we review the current understanding of RNA-based regulation in B. subtilis, and we categorize the newly identified putative regulatory RNAs on the basis of their conservation in other bacilli and the stability of their predicted secondary structures. Our present evaluation of the publicly available data indicates that RNA-mediated gene regulation in B. subtilis mostly involves elements at the 5' ends of mRNA molecules. These can include 5' secondary structure elements and metabolite-, tRNA-, or protein-binding sites. Importantly, sense-independent segments are identified as the most conserved and structured potential regulatory RNAs in B. subtilis. Altogether, the present survey provides many leads for the identification of new regulatory RNA functions in B. subtilis.
Collapse
|
36
|
Petrus MLC, Vijgenboom E, Chaplin AK, Worrall JAR, van Wezel GP, Claessen D. The DyP-type peroxidase DtpA is a Tat-substrate required for GlxA maturation and morphogenesis in Streptomyces. Open Biol 2016; 6:150149. [PMID: 26740586 PMCID: PMC4736821 DOI: 10.1098/rsob.150149] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The filamentous bacterium Streptomyces lividans depends on the radical copper oxidase GlxA for the formation of reproductive aerial structures and, in liquid environments, for the formation of pellets. Incorporation of copper into the active site is essential for the formation of a cross-linked tyrosyl-cysteine cofactor, which is needed for enzymatic activity. In this study, we show a crucial link between GlxA maturation and a group of copper-related proteins including the chaperone Sco and a novel DyP-type peroxidase hereinafter called DtpA. Under copper-limiting conditions, the sco and dtpA deletion mutants are blocked in aerial growth and pellet formation, similarly to a glxA mutant. Western blot analysis showed that GlxA maturation is perturbed in the sco and dtpA mutants, but both maturation and morphology can by rescued by increasing the bioavailability of copper. DtpA acts as a peroxidase in the presence of GlxA and is a substrate for the twin-arginine translocation (Tat) translocation pathway. In agreement, the maturation status of GlxA is also perturbed in tat mutants, which can be compensated for by the addition of copper, thereby partially restoring their morphological defects. Our data support a model wherein a copper-trafficking pathway and Tat-dependent secretion of DtpA link to the GlxA-dependent morphogenesis pathway.
Collapse
Affiliation(s)
- Marloes L C Petrus
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Erik Vijgenboom
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Amanda K Chaplin
- School of Biological Science, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Jonathan A R Worrall
- School of Biological Science, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Dennis Claessen
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| |
Collapse
|
37
|
Abstract
Bacillus subtilis is one of the best-studied organisms. Due to the broad knowledge and annotation and the well-developed genetic system, this bacterium is an excellent starting point for genome minimization with the aim of constructing a minimal cell. We have analyzed the genome of B. subtilis and selected all genes that are required to allow life in complex medium at 37°C. This selection is based on the known information on essential genes and functions as well as on gene and protein expression data and gene conservation. The list presented here includes 523 and 119 genes coding for proteins and RNAs, respectively. These proteins and RNAs are required for the basic functions of life in information processing (replication and chromosome maintenance, transcription, translation, protein folding, and secretion), metabolism, cell division, and the integrity of the minimal cell. The completeness of the selected metabolic pathways, reactions, and enzymes was verified by the development of a model of metabolism of the minimal cell. A comparison of the MiniBacillus genome to the recently reported designed minimal genome of Mycoplasma mycoides JCVI-syn3.0 indicates excellent agreement in the information-processing pathways, whereas each species has a metabolism that reflects specific evolution and adaptation. The blueprint of MiniBacillus presented here serves as the starting point for a successive reduction of the B. subtilis genome.
Collapse
|
38
|
Xu N, Qiu GW, Lou WJ, Li ZK, Jiang HB, Price NM, Qiu BS. Identification of an iron permease, cFTR1, in cyanobacteria involved in the iron reduction/re-oxidation uptake pathway. Environ Microbiol 2016; 18:5005-5017. [DOI: 10.1111/1462-2920.13464] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/19/2016] [Accepted: 07/23/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Ning Xu
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology; Central China Normal University; Wuhan Hubei 430079 People's Republic of China
| | - Guo-Wei Qiu
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology; Central China Normal University; Wuhan Hubei 430079 People's Republic of China
| | - Wen-Jing Lou
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology; Central China Normal University; Wuhan Hubei 430079 People's Republic of China
| | - Zheng-Ke Li
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology; Central China Normal University; Wuhan Hubei 430079 People's Republic of China
| | - Hai-Bo Jiang
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology; Central China Normal University; Wuhan Hubei 430079 People's Republic of China
| | - Neil M. Price
- Department of Biology; McGill University; 1205 Docteur Penfield Montreal Québec H3A 1B1 Canada
| | - Bao-Sheng Qiu
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology; Central China Normal University; Wuhan Hubei 430079 People's Republic of China
| |
Collapse
|
39
|
Mishra S, Gupta S, Raghuvanshi S, Pal P. Energetic assessment of fixation of CO2 and subsequent biofuel production using B. cereus SM1 isolated from sewage treatment plant. Bioprocess Biosyst Eng 2016; 39:1247-58. [PMID: 27071767 DOI: 10.1007/s00449-016-1603-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 04/03/2016] [Indexed: 12/15/2022]
Abstract
The ongoing work on global warming resulting from green house gases (GHGs) has led to explore the possibility of bacterial strains which can fix carbon dioxide (CO2) and can generate value-added products. The present work is an effort in this direction and has carried out an exhaustive batch experiments for the fixation of CO2 using B. Cereus SM1 isolated from sewage treatment plant (STP). The work has incorporated 5-day batch run for gaseous phase inlet CO2 concentration of 13 ± 1 % (%v/v). 84.6 (±5.76) % of CO2 removal was obtained in the gaseous phase at mentioned CO2 concentration (%v/v). Energetic requirement for CO2 fixation was assessed by varying Fe[II] ion concentration (0-200 ppm) on the per-day basis. The cell lysate obtained from CO2 fixation studies (Fe[II] ion = 100 ppm) was analyzed using Fourier transformation infrared spectroscopy (FTIR) and gas chromatography-mass spectroscopy (GC-MS). This analysis confirmed the presence of fatty acids and hydrocarbon as valuable products. The hydrocarbons were found in the range of C11-C22 which is equivalent to light oil. The obtained fatty acids were found in the range of C11-C19. The possibility of fatty acid conversion to biodiesel was explored by carrying out the transesterification reaction. The yield of biodiesel was obtained as 86.5 (±0.048) % under the transesterification reaction conditions. Results of this research work can provide the valuable information in the implementation of biomitigation of CO2 at real scenario.
Collapse
Affiliation(s)
- Somesh Mishra
- Department of Chemical Engineering, Birla Institute of Technology and Science (BITS), Pilani, 333031, Rajasthan, India
| | - Suresh Gupta
- Department of Chemical Engineering, Birla Institute of Technology and Science (BITS), Pilani, 333031, Rajasthan, India
| | - Smita Raghuvanshi
- Department of Chemical Engineering, Birla Institute of Technology and Science (BITS), Pilani, 333031, Rajasthan, India.
| | - Pratibha Pal
- Department of Chemical Engineering, Birla Institute of Technology and Science (BITS), Pilani, 333031, Rajasthan, India
| |
Collapse
|
40
|
Abstract
Twin-arginine protein translocation systems (Tat) translocate fully folded and co-factor-containing proteins across biological membranes. In this review, we focus on the Tat pathway of Gram-positive bacteria. The minimal Tat pathway is composed of two components, namely a TatA and TatC pair, which are often complemented with additional TatA-like proteins. We provide overviews of our current understanding of Tat pathway composition and mechanistic aspects related to Tat-dependent cargo protein translocation. This includes Tat pathway flexibility, requirements for the correct folding and incorporation of co-factors in cargo proteins and the functions of known cargo proteins. Tat pathways of several Gram-positive bacteria are discussed in detail, with emphasis on the Tat pathway of Bacillus subtilis. We discuss both shared and unique features of the different Gram-positive bacterial Tat pathways. Lastly, we highlight topics for future research on Tat, including the development of this protein transport pathway for the biotechnological secretion of high-value proteins and its potential applicability as an antimicrobial drug target in pathogens.
Collapse
Affiliation(s)
- Vivianne J Goosens
- MRC Centre for Molecular Bacteriology and Infection, Section of Microbiology, Imperial College London, London, SW7 2AZ, UK
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700, RB, Groningen, The Netherlands.
| |
Collapse
|
41
|
A Tat ménage à trois — The role of Bacillus subtilis TatAc in twin-arginine protein translocation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:2745-53. [DOI: 10.1016/j.bbamcr.2015.07.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/28/2015] [Accepted: 07/30/2015] [Indexed: 11/19/2022]
|
42
|
Guan G, Pinochet-Barros A, Gaballa A, Patel SJ, Argüello JM, Helmann JD. PfeT, a P1B4 -type ATPase, effluxes ferrous iron and protects Bacillus subtilis against iron intoxication. Mol Microbiol 2015; 98:787-803. [PMID: 26261021 DOI: 10.1111/mmi.13158] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2015] [Indexed: 11/30/2022]
Abstract
Iron is an essential element for nearly all cells and limited iron availability often restricts growth. However, excess iron can also be deleterious, particularly when cells expressing high affinity iron uptake systems transition to iron rich environments. Bacillus subtilis expresses numerous iron importers, but iron efflux has not been reported. Here, we describe the B. subtilis PfeT protein (formerly YkvW/ZosA) as a P1B4 -type ATPase in the PerR regulon that serves as an Fe(II) efflux pump and protects cells against iron intoxication. Iron and manganese homeostasis in B. subtilis are closely intertwined: a pfeT mutant is iron sensitive, and this sensitivity can be suppressed by low levels of Mn(II). Conversely, a pfeT mutant is more resistant to Mn(II) overload. In vitro, the PfeT ATPase is activated by both Fe(II) and Co(II), although only Fe(II) efflux is physiologically relevant in wild-type cells, and null mutants accumulate elevated levels of intracellular iron. Genetic studies indicate that PfeT together with the ferric uptake repressor (Fur) cooperate to prevent iron intoxication, with iron sequestration by the MrgA mini-ferritin playing a secondary role. Protection against iron toxicity may also be a key role for related P1B4 -type ATPases previously implicated in bacterial pathogenesis.
Collapse
Affiliation(s)
- Guohua Guan
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA.,State Key Laboratories for Agro-biotechnology and College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | | | - Ahmed Gaballa
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Sarju J Patel
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - José M Argüello
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA, 01609, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| |
Collapse
|
43
|
Celis AI, DuBois JL. Substrate, product, and cofactor: The extraordinarily flexible relationship between the CDE superfamily and heme. Arch Biochem Biophys 2015; 574:3-17. [PMID: 25778630 PMCID: PMC4414885 DOI: 10.1016/j.abb.2015.03.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 03/06/2015] [Accepted: 03/08/2015] [Indexed: 12/21/2022]
Abstract
PFam Clan 0032, also known as the CDE superfamily, is a diverse group of at least 20 protein families sharing a common α,β-barrel domain. Of these, six different groups bind heme inside the barrel's interior, using it alternately as a cofactor, substrate, or product. Focusing on these six, an integrated picture of structure, sequence, taxonomy, and mechanism is presented here, detailing how a single structural motif might be able to mediate such an array of functions with one of nature's most important small molecules.
Collapse
Affiliation(s)
- Arianna I Celis
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States
| | - Jennifer L DuBois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States.
| |
Collapse
|
44
|
Sheldon JR, Heinrichs DE. Recent developments in understanding the iron acquisition strategies of gram positive pathogens. FEMS Microbiol Rev 2015; 39:592-630. [DOI: 10.1093/femsre/fuv009] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2015] [Indexed: 12/26/2022] Open
|
45
|
Mielcarek A, Blauenburg B, Miethke M, Marahiel MA. Molecular insights into frataxin-mediated iron supply for heme biosynthesis in Bacillus subtilis. PLoS One 2015; 10:e0122538. [PMID: 25826316 PMCID: PMC4380498 DOI: 10.1371/journal.pone.0122538] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 02/13/2015] [Indexed: 11/19/2022] Open
Abstract
Iron is required as an element to sustain life in all eukaryotes and most bacteria. Although several bacterial iron acquisition strategies have been well explored, little is known about the intracellular trafficking pathways of iron and its entry into the systems for co-factor biogenesis. In this study, we investigated the iron-dependent process of heme maturation in Bacillus subtilis and present, for the first time, structural evidence for the physical interaction of a frataxin homologue (Fra), which is suggested to act as a regulatory component as well as an iron chaperone in different cellular pathways, and a ferrochelatase (HemH), which catalyses the final step of heme b biogenesis. Specific interaction between Fra and HemH was observed upon co-purification from crude cell lysates and, further, by using the recombinant proteins for analytical size-exclusion chromatography. Hydrogen-deuterium exchange experiments identified the landscape of the Fra/HemH interaction interface and revealed Fra as a specific ferrous iron donor for the ferrochelatase HemH. The functional utilisation of the in vitro-generated heme b co-factor upon Fra-mediated iron transfer was confirmed by using the B. subtilis nitric oxide synthase bsNos as a metabolic target enzyme. Complementary mutational analyses confirmed that Fra acts as an essential component for maturation and subsequent targeting of the heme b co-factor, hence representing a key player in the iron-dependent physiology of B. subtilis.
Collapse
Affiliation(s)
- Andreas Mielcarek
- Philipps-University Marburg, Department of Chemistry/Biochemistry, Marburg, Germany
| | - Bastian Blauenburg
- Philipps-University Marburg, Department of Chemistry/Biochemistry, Marburg, Germany
| | - Marcus Miethke
- Philipps-University Marburg, Department of Chemistry/Biochemistry, Marburg, Germany
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
| | - Mohamed A. Marahiel
- Philipps-University Marburg, Department of Chemistry/Biochemistry, Marburg, Germany
| |
Collapse
|
46
|
Lechowicz J, Krawczyk-Balska A. An update on the transport and metabolism of iron in Listeria monocytogenes: the role of proteins involved in pathogenicity. Biometals 2015; 28:587-603. [PMID: 25820385 PMCID: PMC4481299 DOI: 10.1007/s10534-015-9849-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 03/17/2015] [Indexed: 12/21/2022]
Abstract
Listeria monocytogenes is a Gram-positive bacterium that causes a rare but severe human disease with high mortality rate. The microorganism is widespread in the natural environment where it shows a saprophytic lifestyle. In the human body it infects many different cell types, where it lives intracellularly, however it may also temporarily live extracellularly. The ability to survive and grow in such diverse niches suggests that this bacterium has a wide range of mechanisms for both the acquisition of various sources of iron and effective management of this microelement. In this review, data about the mechanisms of transport, metabolism and regulation of iron, including recent findings in these areas, are summarized with focus on the importance of these mechanisms for the virulence of L. monocytogenes. These data indicate the key role of haem transport and maintenance of intracellular iron homeostasis for the pathogenesis of L. monocytogenes. Furthermore, some of the proteins involved in iron homeostasis like Fri and FrvA seem to deserve special attention due to their potential use in the development of new therapeutic antilisterial strategies.
Collapse
Affiliation(s)
- Justyna Lechowicz
- Department of Applied Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | | |
Collapse
|
47
|
The multihued palette of dye-decolorizing peroxidases. Arch Biochem Biophys 2015; 574:56-65. [PMID: 25743546 DOI: 10.1016/j.abb.2015.01.014] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 01/11/2015] [Accepted: 01/16/2015] [Indexed: 12/31/2022]
Abstract
Dye-decolorizing peroxidases (DyPs; EC 1.11.1.19) are heme enzymes that comprise a family of the dimeric α+β barrel structural superfamily of proteins. The first DyP, identified relatively recently in the fungus Bjerkandera adusta, was characterized for its ability to catalyze the decolorization of anthraquinone-based industrial dyes. These enzymes are now known to be present in all three domains of life, but do not appear to occur in plants or animals. They are involved in a range of physiological processes, although in many cases their roles remain unknown. This has not prevented the development of their biocatalytic potential, which includes the transformation of lignin. This review highlights the functional diversity of DyPs in the light of phylogenetic, structural and biochemical data. The phylogenetic analysis reveals the existence of at least five classes of DyPs. Their potential physiological roles are discussed based in part on synteny analyses. Finally, the considerable biotechnological potential of DyPs is summarized.
Collapse
|
48
|
Halbedel S, Reiss S, Hahn B, Albrecht D, Mannala GK, Chakraborty T, Hain T, Engelmann S, Flieger A. A systematic proteomic analysis of Listeria monocytogenes house-keeping protein secretion systems. Mol Cell Proteomics 2014; 13:3063-81. [PMID: 25056936 DOI: 10.1074/mcp.m114.041327] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Listeria monocytogenes is a firmicute bacterium causing serious infections in humans upon consumption of contaminated food. Most of its virulence factors are secretory proteins either released to the medium or attached to the bacterial surface. L. monocytogenes encodes at least six different protein secretion pathways. Although great efforts have been made in the past to predict secretory proteins and their secretion routes using bioinformatics, experimental evidence is lacking for most secretion systems. Therefore, we constructed mutants in the main housekeeping protein secretion systems, which are the Sec-dependent transport, the YidC membrane insertases SpoIIIJ and YqjG, as well as the twin-arginine pathway, and analyzed their secretion and virulence defects. Our results demonstrate that Sec-dependent secretion and membrane insertion of proteins via YidC proteins are essential for viability of L. monocytogenes. Depletion of SecA or YidC activity severely affected protein secretion, whereas loss of the Tat-pathway was without any effect on secretion, viability, and virulence. Two-dimensional gel electrophoresis combined with protein identification by mass spectrometry revealed that secretion of many virulence factors and of enzymes synthesizing and degrading the cell wall depends on the SecA route. This finding was confirmed by SecA inhibition experiments using sodium azide. Analysis of secretion of substrates typically dependent on the accessory SecA2 ATPase in wild type and azide resistant mutants of L. monocytogenes revealed for the first time that SecA2-dependent protein secretion also requires the ATPase activity of the house-keeping SecA protein.
Collapse
Affiliation(s)
- Sven Halbedel
- From the ‡Robert Koch Institute, FG11 - Division of Enteropathogenic Bacteria and Legionella, Burgstrasse 37, 38855 Wernigerode, Germany;
| | - Swantje Reiss
- §Institute of Microbiology, University of Greifswald, F.-L.-Jahn-Strasse 15, 17487 Greifswald, Germany
| | - Birgit Hahn
- From the ‡Robert Koch Institute, FG11 - Division of Enteropathogenic Bacteria and Legionella, Burgstrasse 37, 38855 Wernigerode, Germany
| | - Dirk Albrecht
- §Institute of Microbiology, University of Greifswald, F.-L.-Jahn-Strasse 15, 17487 Greifswald, Germany
| | - Gopala Krishna Mannala
- ¶Institute of Medical Microbiology, University of Gießen, Schubertstrasse 81, 35392 Gießen, Germany
| | - Trinad Chakraborty
- ¶Institute of Medical Microbiology, University of Gießen, Schubertstrasse 81, 35392 Gießen, Germany
| | - Torsten Hain
- ¶Institute of Medical Microbiology, University of Gießen, Schubertstrasse 81, 35392 Gießen, Germany
| | - Susanne Engelmann
- §Institute of Microbiology, University of Greifswald, F.-L.-Jahn-Strasse 15, 17487 Greifswald, Germany; ‖Institute of Microbiology, Technical University of Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany; **Helmholtz Centre for Infection Research, Microbial Proteomics, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Antje Flieger
- From the ‡Robert Koch Institute, FG11 - Division of Enteropathogenic Bacteria and Legionella, Burgstrasse 37, 38855 Wernigerode, Germany;
| |
Collapse
|
49
|
Stentzel S, Vu HC, Weyrich AM, Jehmlich N, Schmidt F, Salazar MG, Steil L, Völker U, Bröker BM. Altered immune proteome ofStaphylococcus aureusunder iron-restricted growth conditions. Proteomics 2014; 14:1857-67. [DOI: 10.1002/pmic.201300512] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 04/16/2014] [Accepted: 05/22/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Sebastian Stentzel
- Department of Immunology; Institute of Immunology and Transfusion Medicine; University Medicine Greifswald; Greifswald Germany
| | - Hai Chi Vu
- Department of Immunology; Institute of Immunology and Transfusion Medicine; University Medicine Greifswald; Greifswald Germany
| | - Anna Maria Weyrich
- Department of Immunology; Institute of Immunology and Transfusion Medicine; University Medicine Greifswald; Greifswald Germany
| | - Nico Jehmlich
- Interfaculty Institute of Genetics and Functional Genomics; University Medicine Greifswald; Greifswald Germany
| | - Frank Schmidt
- Interfaculty Institute of Genetics and Functional Genomics; University Medicine Greifswald; Greifswald Germany
- ZIK-FunGene Junior Research Group “Applied Proteomics”; University Medicine Greifswald; Greifswald Germany
| | - Manuela Gesell Salazar
- Interfaculty Institute of Genetics and Functional Genomics; University Medicine Greifswald; Greifswald Germany
| | - Leif Steil
- Interfaculty Institute of Genetics and Functional Genomics; University Medicine Greifswald; Greifswald Germany
| | - Uwe Völker
- Interfaculty Institute of Genetics and Functional Genomics; University Medicine Greifswald; Greifswald Germany
| | - Barbara M. Bröker
- Department of Immunology; Institute of Immunology and Transfusion Medicine; University Medicine Greifswald; Greifswald Germany
| |
Collapse
|
50
|
Behrendt J, Brüser T. The TatBC complex of the Tat protein translocase in Escherichia coli and its transition to the substrate-bound TatABC complex. Biochemistry 2014; 53:2344-54. [PMID: 24654648 DOI: 10.1021/bi500169s] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The twin-arginine translocation (Tat) system serves to transport folded proteins across membranes of prokaryotes and plant plastids. In Escherichia coli, a complex consisting of multiple copies of TatB and TatC initiates the transport by binding the signal peptides of the Tat substrates. Using blue-native polyacrylamide gel electrophoresis, bands of TatBC-containing complexes can be detected at molecular masses of 440 and 580 kDa. We systematically analyzed the formation of Tat complexes with TatB or TatC variants that carried point mutations at selected positions. Several mutations resulted in specific disassembly patterns and alterations in the 440 kDa:580 kDa complex ratios. The 440 kDa complex contains only TatBC, whereas the 580 kDa complex consists of TatABC. Substrate binding results in a TatBC-Tat substrate complex at ~500 kDa and a TatABC-Tat substrate complex at ~600 kDa. Only the ~600 kDa complex was detected with nonrecombinant substrate levels and thus could be the physiologically most relevant species. The results suggest that some TatA is usually associated with TatBC, regardless of substrate binding.
Collapse
Affiliation(s)
- Jana Behrendt
- Institute of Microbiology, Leibniz University Hannover , Schneiderberg 50, 30167 Hannover, Germany
| | | |
Collapse
|