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Lekired A, Cherif-Silini H, Silini A, Ben Yahia H, Ouzari HI. Comparative genomics reveals the acquisition of mobile genetic elements by the plant growth-promoting Pantoea eucrina OB49 in polluted environments. Genomics 2023; 115:110579. [PMID: 36792019 DOI: 10.1016/j.ygeno.2023.110579] [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: 06/17/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023]
Abstract
Heavy metal-tolerant plant growth-promoting bacteria (PGPB) have gained popularity in bioremediation in recent years. A genome-assisted study of a heavy metal-tolerant PGPB Pantoea eucrina OB49 isolated from the rhizosphere of wheat grown on a heavy metal-contaminated site is presented. Comparative pan-genome analysis indicated that OB49 acquired heavy metal resistance genes through horizontal gene transfer. On contigs S10 and S12, OB49 has two arsRBCH operons that give arsenic resistance. On the S12 contig, an arsRBCH operon was discovered in conjunction with the merRTPCADE operon, which provides mercury resistance. P. eucrina OB49 may be involved in an ecological alternative for heavy metal remediation and growth promotion of wheat grown in metal-polluted soils. Our results suggested the detection of mobile genetic elements that harbour the ars operon and the fluoride resistance genes adjacent to the mer operon.
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Affiliation(s)
- Abdelmalek Lekired
- Laboratory of Microorganisms and Active Biomolecules, MBA-LR03ES03, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hafsa Cherif-Silini
- Laboratory of Applied Microbiology, Department of Microbiology, Faculty of Natural and Life Sciences, Ferhat Abbas University, 19000, Setif, Algeria
| | - Allaoua Silini
- Laboratory of Applied Microbiology, Department of Microbiology, Faculty of Natural and Life Sciences, Ferhat Abbas University, 19000, Setif, Algeria
| | - Hamza Ben Yahia
- Laboratory of Microorganisms and Active Biomolecules, MBA-LR03ES03, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hadda-Imene Ouzari
- Laboratory of Microorganisms and Active Biomolecules, MBA-LR03ES03, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia.
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Balaji S. The transferred translocases: An old wine in a new bottle. Biotechnol Appl Biochem 2021; 69:1587-1610. [PMID: 34324237 DOI: 10.1002/bab.2230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/23/2021] [Indexed: 11/12/2022]
Abstract
The role of translocases was underappreciated and was not included as a separate class in the enzyme commission until August 2018. The recent research interests in proteomics of orphan enzymes, ionomics, and metallomics along with high-throughput sequencing technologies generated overwhelming data and revamped this enzyme into a separate class. This offers a great opportunity to understand the role of new or orphan enzymes in general and specifically translocases. The enzymes belonging to translocases regulate/permeate the transfer of ions or molecules across the membranes. These enzyme entries were previously associated with other enzyme classes, which are now transferred to a new enzyme class 7 (EC 7). The entries that are reclassified are important to extend the enzyme list, and it is the need of the hour. Accordingly, there is an upgradation of entries of this class of enzymes in several databases. This review is a concise compilation of translocases with reference to the number of entries currently available in the databases. This review also focuses on function as well as dysfunction of translocases during normal and disordered states, respectively.
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Affiliation(s)
- S Balaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576 104, India
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Jayakanthan S, Braiterman LT, Hasan NM, Unger VM, Lutsenko S. Human copper transporter ATP7B (Wilson disease protein) forms stable dimers in vitro and in cells. J Biol Chem 2017; 292:18760-18774. [PMID: 28842499 DOI: 10.1074/jbc.m117.807263] [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: 07/18/2017] [Revised: 08/21/2017] [Indexed: 11/06/2022] Open
Abstract
ATP7B is a copper-transporting P1B-type ATPase (Cu-ATPase) with an essential role in human physiology. Mutations in ATP7B cause the potentially fatal Wilson disease, and changes in ATP7B expression are observed in several cancers. Despite its physiologic importance, the biochemical information about ATP7B remains limited because of a complex multidomain organization of the protein. By analogy with the better characterized prokaryotic Cu-ATPases, ATP7B is assumed to be a single-chain monomer. We show that in eukaryotic cells, human ATP7B forms dimers that can be purified following solubilization. Deletion of the four N-terminal metal-binding domains, characteristic for human ATP7B, does not disrupt dimerization, i.e. the dimer interface is formed by the domains that are conserved among Cu-ATPases. Unlike the full-length ATP7B, which is targeted to the trans-Golgi network, 1-4ΔMBD-7B is targeted primarily to vesicles. This result and the analysis of differentially tagged ATP7B variants indicate that the dimeric structure is retained during ATP7B trafficking between the intracellular compartments. Purified dimeric species of 1-4ΔMBD-7B were characterized by a negative stain electron microscopy in the presence of ADP/MgCl2 Single-particle analysis yielded a low-resolution 3D model that provides the first insight into an overall architecture of a human Cu-ATPase, positions of the main domains, and a dimer interface.
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Affiliation(s)
| | - Lelita T Braiterman
- Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 and
| | | | - Vinzenz M Unger
- the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
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Mayerhofer H, Sautron E, Rolland N, Catty P, Seigneurin-Berny D, Pebay-Peyroula E, Ravaud S. Structural Insights into the Nucleotide-Binding Domains of the P1B-type ATPases HMA6 and HMA8 from Arabidopsis thaliana. PLoS One 2016; 11:e0165666. [PMID: 27802305 PMCID: PMC5089723 DOI: 10.1371/journal.pone.0165666] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 10/14/2016] [Indexed: 01/24/2023] Open
Abstract
Copper is a crucial ion in cells, but needs to be closely controlled due to its toxic potential and ability to catalyse the formation of radicals. In chloroplasts, an important step for the proper functioning of the photosynthetic electron transfer chain is the delivery of copper to plastocyanin in the thylakoid lumen. The main route for copper transport to the thylakoid lumen is driven by two PIB-type ATPases, Heavy Metal ATPase 6 (HMA6) and HMA8, located in the inner membrane of the chloroplast envelope and in the thylakoid membrane, respectively. Here, the crystal structures of the nucleotide binding domain of HMA6 and HMA8 from Arabidopsis thaliana are reported at 1.5Å and 1.75Å resolution, respectively, providing the first structural information on plants Cu+-ATPases. The structures reveal a compact domain, with two short helices on both sides of a twisted beta-sheet. A double mutant, aiding in the crystallization, provides a new crystal contact, but also avoids an internal clash highlighting the benefits of construct modifications. Finally, the histidine in the HP motif of the isolated domains, unable to bind ATP, shows a side chain conformation distinct from nucleotide bound structures.
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Affiliation(s)
- Hubert Mayerhofer
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Emeline Sautron
- Laboratoire de Physiologie Cellulaire et Végétale (LPCV), Institut de Biosciences et Biotechnologies de Grenoble (BIG), Université Grenoble Alpes, CEA, CNRS, INRA, Grenoble, France
| | - Norbert Rolland
- Laboratoire de Physiologie Cellulaire et Végétale (LPCV), Institut de Biosciences et Biotechnologies de Grenoble (BIG), Université Grenoble Alpes, CEA, CNRS, INRA, Grenoble, France
| | - Patrice Catty
- Laboratoire de Chimie et Biologie des Métaux (LCBM), BIG, Université Grenoble Alpes, CEA, CNRS, INRA, Grenoble, France
| | - Daphné Seigneurin-Berny
- Laboratoire de Physiologie Cellulaire et Végétale (LPCV), Institut de Biosciences et Biotechnologies de Grenoble (BIG), Université Grenoble Alpes, CEA, CNRS, INRA, Grenoble, France
| | - Eva Pebay-Peyroula
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Stéphanie Ravaud
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
- * E-mail:
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Smith AT, Smith KP, Rosenzweig AC. Diversity of the metal-transporting P1B-type ATPases. J Biol Inorg Chem 2014; 19:947-60. [PMID: 24729073 PMCID: PMC4119550 DOI: 10.1007/s00775-014-1129-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 03/21/2014] [Indexed: 01/23/2023]
Abstract
The P1B-ATPases are integral membrane proteins that couple ATP hydrolysis to metal cation transport. Widely distributed across all domains of life, these enzymes have been previously shown to transport copper, zinc, cobalt, and other thiophilic heavy metals. Recent data suggest that these enzymes may also be involved in nickel and/or iron transport. Here we have exploited large amounts of genomic data to examine and classify the various P1B-ATPase subfamilies. Specifically, we have combined new methods of data partitioning and network visualization known as Transitivity Clustering and Protein Similarity Networks with existing biochemical data to examine properties such as length, speciation, and metal-binding motifs of the P1B-ATPase subfamily sequences. These data reveal interesting relationships among the enzyme sequences of previously established subfamilies, indicate the presence of two new subfamilies, and suggest the existence of new regulatory elements in certain subfamilies. Taken together, these findings underscore the importance of P1B-ATPases in homeostasis of nearly every biologically relevant transition metal and provide an updated framework for future studies.
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Affiliation(s)
- Aaron T. Smith
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Kyle P. Smith
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Amy C. Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
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