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Neira G, Vergara E, Holmes DS. Genome-guided prediction of acid resistance mechanisms in acidophilic methanotrophs of phylogenetically deep-rooted Verrucomicrobia isolated from geothermal environments. Front Microbiol 2022; 13:900531. [PMID: 36212841 PMCID: PMC9543262 DOI: 10.3389/fmicb.2022.900531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Verrucomicrobia are a group of microorganisms that have been proposed to be deeply rooted in the Tree of Life. Some are methanotrophs that oxidize the potent greenhouse gas methane and are thus important in decreasing atmospheric concentrations of the gas, potentially ameliorating climate change. They are widespread in various environments including soil and fresh or marine waters. Recently, a clade of extremely acidophilic Verrucomicrobia, flourishing at pH < 3, were described from high-temperature geothermal ecosystems. This novel group could be of interest for studies about the emergence of life on Earth and to astrobiologists as homologs for possible extraterrestrial life. In this paper, we describe predicted mechanisms for survival of this clade at low pH and suggest its possible evolutionary trajectory from an inferred neutrophilic ancestor. Extreme acidophiles are defined as organisms that thrive in extremely low pH environments (≤ pH 3). Many are polyextremophiles facing high temperatures and high salt as well as low pH. They are important to study for both providing fundamental insights into biological mechanisms of survival and evolution in such extreme environments and for understanding their roles in biotechnological applications such as industrial mineral recovery (bioleaching) and mitigation of acid mine drainage. They are also, potentially, a rich source of novel genes and pathways for the genetic engineering of microbial strains. Acidophiles of the Verrucomicrobia phylum are unique as they are the only known aerobic methanotrophs that can grow optimally under acidic (pH 2–3) and moderately thermophilic conditions (50–60°C). Three moderately thermophilic genera, namely Methylacidiphilum, Methylacidimicrobium, and Ca. Methylacidithermus, have been described in geothermal environments. Most of the investigations of these organisms have focused on their methane oxidizing capabilities (methanotrophy) and use of lanthanides as a protein cofactor, with no extensive study that sheds light on the mechanisms that they use to flourish at extremely low pH. In this paper, we extend the phylogenetic description of this group of acidophiles using whole genome information and we identify several mechanisms, potentially involved in acid resistance, including “first line of defense” mechanisms that impede the entry of protons into the cell. These include the presence of membrane-associated hopanoids, multiple copies of the outer membrane protein (Slp), and inner membrane potassium channels (kup, kdp) that generate a reversed membrane potential repelling the intrusion of protons. Acidophilic Verrucomicrobia also display a wide array of proteins potentially involved in the “second line of defense” where protons that evaded the first line of defense and entered the cell are expelled or neutralized, such as the glutamate decarboxylation (gadAB) and phosphate-uptake systems. An exclusive N-type ATPase F0-F1 was identified only in acidophiles of Verrucomicrobia and is predicted to be a specific adaptation in these organisms. Phylogenetic analyses suggest that many predicted mechanisms are evolutionarily conserved and most likely entered the acidophilic lineage of Verrucomicrobia by vertical descent from a common ancestor. However, it is likely that some defense mechanisms such as gadA and kup entered the acidophilic Verrucomicrobia lineage by horizontal gene transfer.
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Affiliation(s)
- Gonzalo Neira
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Eva Vergara
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
- *Correspondence: David S. Holmes
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Boase K, González C, Vergara E, Neira G, Holmes D, Watkin E. Prediction and Inferred Evolution of Acid Tolerance Genes in the Biotechnologically Important Acidihalobacter Genus. Front Microbiol 2022; 13:848410. [PMID: 35516430 PMCID: PMC9062700 DOI: 10.3389/fmicb.2022.848410] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/28/2022] [Indexed: 11/18/2022] Open
Abstract
Acidihalobacter is a genus of acidophilic, gram-negative bacteria known for its ability to oxidize pyrite minerals in the presence of elevated chloride ions, a capability rare in other iron-sulfur oxidizing acidophiles. Previous research involving Acidihalobacter spp. has focused on their applicability in saline biomining operations and their genetic arsenal that allows them to cope with chloride, metal and oxidative stress. However, an understanding of the molecular adaptations that enable Acidihalobacter spp. to thrive under both acid and chloride stress is needed to provide a more comprehensive understanding of how this genus can thrive in such extreme biomining conditions. Currently, four genomes of the Acidihalobacter genus have been sequenced: Acidihalobacter prosperus DSM 5130T, Acidihalobacter yilgarnensis DSM 105917T, Acidihalobacter aeolianus DSM 14174T, and Acidihalobacter ferrooxydans DSM 14175T. Phylogenetic analysis shows that the Acidihalobacter genus roots to the Chromatiales class consisting of mostly halophilic microorganisms. In this study, we aim to advance our knowledge of the genetic repertoire of the Acidihalobacter genus that has enabled it to cope with acidic stress. We provide evidence of gene gain events that are hypothesized to help the Acidihalobacter genus cope with acid stress. Potential acid tolerance mechanisms that were found in the Acidihalobacter genomes include multiple potassium transporters, chloride/proton antiporters, glutamate decarboxylase system, arginine decarboxylase system, urease system, slp genes, squalene synthesis, and hopanoid synthesis. Some of these genes are hypothesized to have entered the Acidihalobacter via vertical decent from an inferred non-acidophilic ancestor, however, horizontal gene transfer (HGT) from other acidophilic lineages is probably responsible for the introduction of many acid resistance genes.
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Affiliation(s)
- Katelyn Boase
- Curtin Medical School, Curtin University, Perth, WA, Australia
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Santiago, Chile
| | - Eva Vergara
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Santiago, Chile
| | - Gonzalo Neira
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Santiago, Chile
| | - David Holmes
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencias, Universidad San Sebastián, Santiago, Chile
- *Correspondence: David S. Holmes,
| | - Elizabeth Watkin
- Curtin Medical School, Curtin University, Perth, WA, Australia
- Elizabeth Watkin,
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3
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Sweet ME, Zhang X, Erdjument-Bromage H, Dubey V, Khandelia H, Neubert TA, Pedersen BP, Stokes DL. Serine phosphorylation regulates the P-type potassium pump KdpFABC. eLife 2020; 9:55480. [PMID: 32955430 PMCID: PMC7535926 DOI: 10.7554/elife.55480] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 09/19/2020] [Indexed: 12/22/2022] Open
Abstract
KdpFABC is an ATP-dependent K+ pump that ensures bacterial survival in K+-deficient environments. Whereas transcriptional activation of kdpFABC expression is well studied, a mechanism for down-regulation when K+ levels are restored has not been described. Here, we show that KdpFABC is inhibited when cells return to a K+-rich environment. The mechanism of inhibition involves phosphorylation of Ser162 on KdpB, which can be reversed in vitro by treatment with serine phosphatase. Mutating Ser162 to Alanine produces constitutive activity, whereas the phosphomimetic Ser162Asp mutation inactivates the pump. Analyses of the transport cycle show that serine phosphorylation abolishes the K+-dependence of ATP hydrolysis and blocks the catalytic cycle after formation of the aspartyl phosphate intermediate (E1~P). This regulatory mechanism is unique amongst P-type pumps and this study furthers our understanding of how bacteria control potassium homeostasis to maintain cell volume and osmotic potential.
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Affiliation(s)
- Marie E Sweet
- Skirball Institute, Dept. of Cell Biology, New York University School of Medicine, New York, United States
| | - Xihui Zhang
- Skirball Institute, Dept. of Cell Biology, New York University School of Medicine, New York, United States
| | - Hediye Erdjument-Bromage
- Skirball Institute, Dept. of Cell Biology, New York University School of Medicine, New York, United States
| | - Vikas Dubey
- PHYLIFE, Physical Life Science, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Himanshu Khandelia
- PHYLIFE, Physical Life Science, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Thomas A Neubert
- Skirball Institute, Dept. of Cell Biology, New York University School of Medicine, New York, United States
| | - Bjørn P Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - David L Stokes
- Skirball Institute, Dept. of Cell Biology, New York University School of Medicine, New York, United States
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4
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Abstract
In bacteria, K+ is used to maintain cell volume and osmotic potential. Homeostasis normally involves a network of constitutively expressed transport systems, but in K+ deficient environments, the KdpFABC complex uses ATP to pump K+ into the cell. This complex appears to be a hybrid of two types of transporters, with KdpA descending from the superfamily of K+ transporters and KdpB belonging to the superfamily of P-type ATPases. Studies of enzymatic activity documented a catalytic cycle with hallmarks of classical P-type ATPases and studies of ion transport indicated that K+ import into the cytosol occurred in the second half of this cycle in conjunction with hydrolysis of an aspartyl phosphate intermediate. Atomic structures of the KdpFABC complex from X-ray crystallography and cryo-EM have recently revealed conformations before and after formation of this aspartyl phosphate that appear to contradict the functional studies. Specifically, structural comparisons with the archetypal P-type ATPase, SERCA, suggest that K+ transport occurs in the first half of the cycle, accompanying formation of the aspartyl phosphate. Further controversy has arisen regarding the path by which K+ crosses the membrane. The X-ray structure supports the conventional view that KdpA provides the conduit, whereas cryo-EM structures suggest that K+ moves from KdpA through a long, intramembrane tunnel to reach canonical ion binding sites in KdpB from which they are released to the cytosol. This review discusses evidence supporting these contradictory models and identifies key experiments needed to resolve discrepancies and produce a unified model for this fascinating mechanistic hybrid.
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Affiliation(s)
- Bjørn P Pedersen
- a Department of Molecular Biology and Genetics, Aarhus University , Aarhus C , Denmark
| | - David L Stokes
- b Department of Cell Biology, New York University School of Medicine, Skirball Institute , New York , NY , USA
| | - Hans-Jürgen Apell
- c Department of Biology, University of Konstanz , Konstanz , Germany
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Cryo-EM structures of KdpFABC suggest a K + transport mechanism via two inter-subunit half-channels. Nat Commun 2018; 9:4971. [PMID: 30478378 PMCID: PMC6255902 DOI: 10.1038/s41467-018-07319-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 10/24/2018] [Indexed: 12/16/2022] Open
Abstract
P-type ATPases ubiquitously pump cations across biological membranes to maintain vital ion gradients. Among those, the chimeric K+ uptake system KdpFABC is unique. While ATP hydrolysis is accomplished by the P-type ATPase subunit KdpB, K+ has been assumed to be transported by the channel-like subunit KdpA. A first crystal structure uncovered its overall topology, suggesting such a spatial separation of energizing and transporting units. Here, we report two cryo-EM structures of the 157 kDa, asymmetric KdpFABC complex at 3.7 Å and 4.0 Å resolution in an E1 and an E2 state, respectively. Unexpectedly, the structures suggest a translocation pathway through two half-channels along KdpA and KdpB, uniting the alternating-access mechanism of actively pumping P-type ATPases with the high affinity and selectivity of K+ channels. This way, KdpFABC would function as a true chimeric complex, synergizing the best features of otherwise separately evolved transport mechanisms.
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Abstract
Cellular potassium import systems play a fundamental role in osmoregulation, pH homeostasis and membrane potential in all domains of life. In bacteria, the kdp operon encodes a four subunit potassium pump that maintains intracellular homeostasis as well as cell shape and turgor under conditions where potassium is limiting1. This membrane complex, called KdpFABC, has one channel-like subunit (KdpA) belonging to the Superfamily of Potassium Transporters and another pump-like subunit (KdpB) belonging to the Superfamily of P-type ATPases. Although there is considerable structural and functional information about members from both superfamilies, the mechanism by which uphill potassium transport through KdpA is coupled with ATP hydrolysis by KdpB remains poorly understood. Here we report the 2.9 Å X-ray structure of the complete Escherichia coli KdpFABC complex with a potassium ion within the selectivity filter of KdpA as well as a water molecule at a canonical cation site in the transmembrane domain of KdpB. The structure also reveals two structural elements that appear to mediate the coupling between these two subunits. Specifically, a protein-embedded tunnel runs between these potassium and water sites and a helix controlling the cytoplasmic gate of KdpA is linked to the phosphorylation domain of KdpB. Based on these observations, we propose an unprecedented mechanism that repurposes protein channel architecture for active transport across biomembranes.
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Affiliation(s)
- Ching-Shin Huang
- Molecular Biophysics Graduate Program, New York University School of Medicine, Skirball Institute, 540 First Avenue, New York, New York 10016, USA
| | - Bjørn Panyella Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C, Denmark.,Aarhus Institute of Advanced Studies, Aarhus University, Høegh-Guldbergs Gade 6B, DK-8000 Aarhus C, Denmark
| | - David L Stokes
- Department of Cell Biology, New York University School of Medicine, Skirball Institute, 540 First Avenue, New York, New York 10016, USA
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Bräuer S, Cadillo-Quiroz H, Kyrpides N, Woyke T, Goodwin L, Detter C, Podell S, Yavitt JB, Zinder SH. Genome of Methanoregula boonei 6A8 reveals adaptations to oligotrophic peatland environments. MICROBIOLOGY-SGM 2015; 161:1572-1581. [PMID: 25998264 DOI: 10.1099/mic.0.000117] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Analysis of the genome sequence of Methanoregula boonei strain 6A8, an acidophilic methanogen isolated from an ombrotrophic (rain-fed) peat bog, has revealed unique features that likely allow it to survive in acidic, nutrient-poor conditions. First, M. boonei is predicted to generate ATP using protons that are abundant in peat, rather than sodium ions that are scarce, and the sequence of a membrane-bound methyltransferase, believed to pump Na+ in all methanogens, shows differences in key amino acid residues. Further, perhaps reflecting the hypokalemic status of many peat bogs, M. boonei demonstrates redundancy in the predicted potassium uptake genes trk, kdp and kup, some of which may have been horizontally transferred to methanogens from bacteria, possibly Geobacter spp. Overall, the putative functions of the potassium uptake, ATPase and methyltransferase genes may, at least in part, explain the cosmopolitan success of group E1/E2 and related methanogenic archaea in acidic peat bogs.
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Affiliation(s)
- Suzanna Bräuer
- Department of Biology, Appalachian State University, Boone, NC 28608, USA
| | - Hinsby Cadillo-Quiroz
- Swette Center for Environmental Biotechnology at the Biodesign Institute, Arizona State University, Tempe, AZ 85287-4501, USA
| | - Nikos Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Lynne Goodwin
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Chris Detter
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Sheila Podell
- Scripps Institution of Oceanography, La Jolla, CA 92093, USA
| | - Joseph B Yavitt
- Department of Natural Resources, Cornell University, Ithaca, NY 14853, USA
| | - Stephen H Zinder
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
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8
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Hänelt I, Tholema N, Kröning N, Vor der Brüggen M, Wunnicke D, Bakker EP. KtrB, a member of the superfamily of K+ transporters. Eur J Cell Biol 2011; 90:696-704. [DOI: 10.1016/j.ejcb.2011.04.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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9
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Nie L, Lavinder JJ, Sarkar M, Stephany K, Magliery TJ. Synthetic approach to stop-codon scanning mutagenesis. J Am Chem Soc 2011; 133:6177-86. [PMID: 21452871 DOI: 10.1021/ja106894g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A general combinatorial mutagenesis strategy using common dimethoxytrityl-protected mononucleotide phosphoramidites and a single orthogonally protected trinucleotide phosphoramidite (Fmoc-TAG; Fmoc = 9-fluorenylmethoxycarbonyl) was developed to scan a gene with the TAG amber stop codon with complete synthetic control. In combination with stop-codon suppressors that insert natural (e.g., alanine) or unnatural (e.g., p-benzoylphenylalanine, Bpa) amino acids, a single DNA library can be used to incorporate different amino acids for diverse purposes. Here, we scanned TAG codons through part of the gene for a model four-helix bundle protein, Rop, which regulates the copy number of ColE1 plasmids. Alanine was incorporated into Rop for mapping its binding site using an in vivo activity screen, and subtle but important differences from in vitro gel-shift studies of Rop function are evident. As a test, Bpa was incorporated using a Phe14 amber mutant isolated from the scanning library. Surprisingly, Phe14Bpa-Rop is weakly active, despite the critical role of Phe14 in Rop activity. Bpa is a photoaffinity label unnatural amino acid that can form covalent bonds with adjacent molecules upon UV irradiation. Irradiation of Phe14Bpa-Rop, which is a dimer in solution like wild-type Rop, results in covalent dimers, trimers, and tetramers. This suggests that Phe14Bpa-Rop weakly associates as a tetramer in solution and highlights the use of Bpa cross-linking as a means of trapping weak and transient interactions.
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Affiliation(s)
- Lihua Nie
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
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Becker D, Fendler K, Altendorf K, Greie JC. The Conserved Dipole in Transmembrane Helix 5 of KdpB in the Escherichia coli KdpFABC P-Type ATPase Is Crucial for Coupling and the Electrogenic K+-Translocation Step. Biochemistry 2007; 46:13920-8. [DOI: 10.1021/bi701394h] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Doris Becker
- Abteilung Mikrobiologie, Fachbereich Biologie/Chemie, Universität Osnabrück, 49069 Osnabrück, and Max Planck Institut für Biophysik, Max-von-Laue-Strasse 3, 60438 Frankfurt/Main, Germany
| | - Klaus Fendler
- Abteilung Mikrobiologie, Fachbereich Biologie/Chemie, Universität Osnabrück, 49069 Osnabrück, and Max Planck Institut für Biophysik, Max-von-Laue-Strasse 3, 60438 Frankfurt/Main, Germany
| | - Karlheinz Altendorf
- Abteilung Mikrobiologie, Fachbereich Biologie/Chemie, Universität Osnabrück, 49069 Osnabrück, and Max Planck Institut für Biophysik, Max-von-Laue-Strasse 3, 60438 Frankfurt/Main, Germany
| | - Jörg-Christian Greie
- Abteilung Mikrobiologie, Fachbereich Biologie/Chemie, Universität Osnabrück, 49069 Osnabrück, and Max Planck Institut für Biophysik, Max-von-Laue-Strasse 3, 60438 Frankfurt/Main, Germany
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11
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Haupt M, Bramkamp M, Coles M, Kessler H, Altendorf K. Prokaryotic Kdp-ATPase: recent insights into the structure and function of KdpB. J Mol Microbiol Biotechnol 2006; 10:120-31. [PMID: 16645309 DOI: 10.1159/000091559] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
P-type ATPases are amongst the most abundant enzymes that are responsible for active transport of ions across biological membranes. Within the last 5 years a detailed picture of the structure and function of these transport ATPases has emerged. Here, we report on the recent progress in elucidating the molecular mechanism of a unique, prokaryotic member of P-type ATPases, the Kdp-ATPase. The review focuses on the catalytic parts of the central subunit, KdpB. The structure of the nucleotide-binding domain was solved by NMR spectroscopy at high resolution and a model of the nucleotide-binding mode was presented. The nucleotide turned out to be 'clipped' into the binding pocket by a pi-pi interaction to F377 on one side and a cation-pi interaction to K395 on the other. The 395KGXXD/E motif and thus the nucleotide-binding mode seems to be conserved in all P-type ATPases, except the heavy metal-transporting (class IB) ATPases. Hence, it can be concluded that KdpB is currently misgrouped as class IA. Mutational studies on two highly conserved residues (D583 and K586) in the transmembrane helix 5 of KdpB revealed that they are indispensable in coupling ATP hydrolysis to ion translocation. Based on these results, two possible pathways for the reaction cycle are discussed.
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Affiliation(s)
- Melina Haupt
- Institut für Organische Chemie und Biochemie, Technische Universität Munchen, Garching, Germany
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12
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Haupt M, Bramkamp M, Heller M, Coles M, Deckers-Hebestreit G, Herkenhoff-Hesselmann B, Altendorf K, Kessler H. The holo-form of the nucleotide binding domain of the KdpFABC complex from Escherichia coli reveals a new binding mode. J Biol Chem 2005; 281:9641-9. [PMID: 16354672 DOI: 10.1074/jbc.m508290200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
P-type ATPases are ubiquitously abundant enzymes involved in active transport of charged residues across biological membranes. The KdpB subunit of the prokaryotic Kdp-ATPase (KdpFABC complex) shares characteristic regions of homology with class II-IV P-type ATPases and has been shown previously to be misgrouped as a class IA P-type ATPase. Here, we present the NMR structure of the AMP-PNP-bound nucleotide binding domain KdpBN of the Escherichia coli Kdp-ATPase at high resolution. The aromatic moiety of the nucleotide is clipped into the binding pocket by Phe(377) and Lys(395) via a pi-pi stacking and a cation-pi interaction, respectively. Charged residues at the outer rim of the binding pocket (Arg(317), Arg(382), Asp(399), and Glu(348)) stabilize and direct the triphosphate group via electrostatic attraction and repulsion toward the phosphorylation domain. The nucleotide binding mode was corroborated by the replacement of critical residues. The conservative mutation F377Y produced a high residual nucleotide binding capacity, whereas replacement by alanine resulted in low nucleotide binding capacities and a considerable loss of ATPase activity. Similarly, mutation K395A resulted in loss of ATPase activity and nucleotide binding affinity, even though the protein was properly folded. We present a schematic model of the nucleotide binding mode that allows for both high selectivity and a low nucleotide binding constant, necessary for the fast and effective turnover rate realized in the reaction cycle of the Kdp-ATPase.
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Affiliation(s)
- Melina Haupt
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
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13
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Tholema N, Vor der Brüggen M, Mäser P, Nakamura T, Schroeder JI, Kobayashi H, Uozumi N, Bakker EP. All four putative selectivity filter glycine residues in KtrB are essential for high affinity and selective K+ uptake by the KtrAB system from Vibrio alginolyticus. J Biol Chem 2005; 280:41146-54. [PMID: 16210320 DOI: 10.1074/jbc.m507647200] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The subunit KtrB of bacterial Na+-dependent K+-translocating KtrAB systems belongs to a superfamily of K+ transporters. These proteins contain four repeated domains, each composed of two transmembrane helices connected by a putative pore loop (p-loop). The four p-loops harbor a conserved glycine residue at a position equivalent to a glycine selectivity filter residue in K+ channels. We investigated whether these glycines also form a selectivity filter in KtrB. The single residues Gly70, Gly185, Gly290, and Gly402 from p-loops P(A) to P(D) of Vibrio alginolyticus KtrB were replaced with alanine, serine, or aspartate. The three alanine variants KtrB(A70), KtrB(A185), and KtrB(A290) maintained a substantial activity in KtrAB-mediated K+ uptake in Escherichia coli. This activity was associated with a decrease in the affinity for K+ by 2 orders of magnitude, with little effect on Vmax. Minor activities were also observed for three other variants: KtrB(A402), KtrB(S70), and KtrB(D185). With all of these variants, the property of Na+ dependence of K+ transport was preserved. Only the four serine variants mediated Na+ uptake, and these variants differed considerably in their K+/Na+ selectivity. Experiments on cloned ktrB in the pBAD18 vector showed that V. alginolyticus KtrB alone was still active in E. coli. It mediated Na+-independent, slow, high affinity, and mutation-specific K+ uptake as well as K+-independent Na+ uptake. These data demonstrate that KtrB contains a selectivity filter for K+ ions and that all four conserved p-loop glycine residues are part of this filter. They also indicate that the role of KtrA lies in conferring velocity and ion coupling to the Ktr complex.
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Affiliation(s)
- Nancy Tholema
- Abteilung Mikrobiologie, Universität Osnabrück, D-49069 Osnabrück, Germany
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14
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Bramkamp M, Altendorf K. Functional modules of KdpB, the catalytic subunit of the Kdp-ATPase from Escherichia coli. Biochemistry 2004; 43:12289-96. [PMID: 15379567 DOI: 10.1021/bi048727d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The large cytoplasmic domain (H4H5) of KdpB of the KdpFABC complex (P-type ATPase) from Escherichia coli consists of two separate modules, the phosphorylation domain (KdpBP) and the nucleotide binding domain (KdpBN). The H4H5 and the KdpBN domains were purified as soluble 10His-tagged fusion proteins. Both proteins exhibit a mainly alpha-helical secondary structure as judged by CD spectroscopy. Fluorescein 5-isothiocyanate (FITC) labeling studies revealed that both proteins form a proper nucleotide binding site. Adenosine nucleotides protect the H4H5 loop but not KdpBN against FITC modification. Trinitrophenyl (TNP)-nucleotide binding studies revealed that both H4H5 and KdpBN bind nucleotides with high affinity. Furthermore, the H4H5 loop was still able to hydrolyze ATP, as well as p-nitrophenyl phosphate (pNPP). These results lend support to the notion that the separately synthesized H4H5 and KdpBN domains retain their native structure and that they reveal properties of both P2-type ATPases (e.g., Na(+),K(+)-ATPase and Ca(2+)-ATPase) and P1b-type ATPases (e.g., heavy metal transporting ATPases). Furthermore, this report also emphasizes the unique position of the Kdp-ATPase within the P-type ATPase family.
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Affiliation(s)
- Marc Bramkamp
- Universität Osnabrück, Fachbereich Biologie/Chemie, Abteilung Mikrobiologie, D-49069 Osnabrück, Germany
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Bertrand J, Altendorf K, Bramkamp M. Amino acid substitutions in putative selectivity filter regions III and IV in KdpA alter ion selectivity of the KdpFABC complex from Escherichia coli. J Bacteriol 2004; 186:5519-22. [PMID: 15292155 PMCID: PMC490938 DOI: 10.1128/jb.186.16.5519-5522.2004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
When grown under conditions of potassium limitation or high osmolality, Escherichia coli synthesizes the K(+)-translocating KdpFABC complex. The KdpA subunit, which has sequence homology to potassium channels of the KcsA type, has been shown to be important for potassium binding and transport. Replacement of the glycine residues in KdpA at positions 345 and 470, members of putative selectivity filter regions III and IV, alters the ion selectivity of the KdpFABC complex.
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Affiliation(s)
- Jessica Bertrand
- Abteilung Mikrobiologie, Fachbereich Biologie/Chemie, Universität Osnabrück, D-49076 Osnabrueck, Germany
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Epstein W. The roles and regulation of potassium in bacteria. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2003; 75:293-320. [PMID: 14604015 DOI: 10.1016/s0079-6603(03)75008-9] [Citation(s) in RCA: 337] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Potassium is the major intracellular cation in bacteria as well as in eucaryotic cells. Bacteria accumulate K+ by a number of different transport systems that vary in kinetics, energy coupling, and regulation. The Trk and Kdp systems of enteric organisms have been well studied and are found in many distantly related species. The Ktr system, resembling Trk in many ways, is also found in many bacteria. In most species two or more independent saturable K(+)-transport systems are present. The KefB and KefC type of system that is activated by treatment of cells with toxic electrophiles is the only specific K(+)-efflux system that has been well characterized. Pressure-activated channels of at least three types are found in bacteria; these represent nonspecific paths of efflux when turgor pressure is dangerously high. A close homolog of eucaryotic K+ channels is found in many bacteria, but its role remains obscure. K+ transporters are regulated both by ion concentrations and turgor. A very general property is activation of K+ uptake by an increase in medium osmolarity. This response is modulated by both internal and external concentrations of K+. Kdp is the only K(+)-transport system whose expression is regulated by environmental conditions. Decrease in turgor pressure and/or reduction in external K+ rapidly increase expression of Kdp. The signal created by these changes, inferred to be reduced turgor, is transmitted by the KdpD sensor kinase to the KdpE-response regulator that in turn stimulates transcription of the kdp genes. K+ acts as a cytoplasmic-signaling molecule, activating and/or inducing enzymes and transport systems that allow the cell to adapt to elevated osmolarity. The signal could be ionic strength or specifically K+. This signaling response is probably mediated by a direct sensing of internal ionic strength by each particular system and not by a component or system that coordinates this response by different systems to elevated K+.
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Affiliation(s)
- Wolfgang Epstein
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
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van der Laan M, Gassel M, Altendorf K. Characterization of amino acid substitutions in KdpA, the K+-binding and -translocating subunit of the KdpFABC complex of Escherichia coli. J Bacteriol 2002; 184:5491-4. [PMID: 12218037 PMCID: PMC135338 DOI: 10.1128/jb.184.19.5491-5494.2002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
When grown under K+ limitation, Escherichia coli induces the K+-translocating KdpFABC complex. The stimulation of ATPase activity by NH4+ ions was shown for the first time. Substitutions in KdpA, which is responsible for K+ binding and translocation, revealed that enzyme complexes KdpA:G232A and KdpA:G232S have completely lost their cation selectivity.
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Affiliation(s)
- Martin van der Laan
- Abteilung Mikrobiologie, Fachbereich Biologie/Chemie, Universität Osnabrück, D-49069 Osnabrück, Germany
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Sardesai AA, Gowrishankar J. Improvement in K+-limited growth rate associated with expression of the N-terminal fragment of one subunit (KdpA) of the multisubunit Kdp transporter in Escherichia coli. J Bacteriol 2001; 183:3515-20. [PMID: 11344160 PMCID: PMC99650 DOI: 10.1128/jb.183.11.3515-3520.2001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mutations in any one of three genes, kdpA, -B, or -C, in Escherichia coli abolish the activity of Kdp, a multisubunit K+-ATPase that belongs to the P-type ATPase family of cation transporters. We found in this study that expression in vivo of a 135-amino-acid-long N-terminal fragment (KdpA'), less than one-quarter the length of native KdpA, was able to mediate an improvement in K+-limited growth rates in two different contexts, even in the absence of both KdpC and the ATPase subunit KdpB. The first context was when KdpA' was overexpressed in cells from a heterologous inducible promoter, and the second was when KdpA' was provided with a C-terminally altered extension (following a spontaneous genetic rearrangement). Our results suggest that KdpA' provides an incipient pathway for K+ translocation which can serve to transport K+ into the cells in response to the cytoplasmic membrane potential.
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Affiliation(s)
- A A Sardesai
- Centre for Cellular and Molecular Biology, Hyderabad 500 007, India
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