1
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Ulmer LD, Canzani D, Woods CN, Stone NL, Janowska MK, Klevit RE, Bush MF. High-Performance Workflow for Identifying Site-Specific Crosslinks Originating from a Genetically Incorporated, Photoreactive Amino Acid. J Proteome Res 2024; 23:3560-3570. [PMID: 38968604 PMCID: PMC11296897 DOI: 10.1021/acs.jproteome.4c00194] [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] [Indexed: 07/07/2024]
Abstract
In conventional crosslinking mass spectrometry, proteins are crosslinked using a highly selective, bifunctional chemical reagent, which limits crosslinks to residues that are accessible and reactive to the reagent. Genetically incorporating a photoreactive amino acid offers two key advantages: any site can be targeted, including those that are inaccessible to conventional crosslinking reagents, and photoreactive amino acids can potentially react with a broad range of interaction partners. However, broad reactivity imposes additional challenges for crosslink identification. In this study, we incorporate benzoylphenylalanine (BPA), a photoreactive amino acid, at selected sites in an intrinsically disordered region of the human protein HSPB5. We report and characterize a workflow for identifying and visualizing residue-level interactions originating from BPA. We routinely identify 30 to 300 crosslinked peptide spectral matches with this workflow, which is up to ten times more than existing tools for residue-level BPA crosslink identification. Most identified crosslinks are assigned to a precision of one or two residues, which is supported by a high degree of overlap between replicate analyses. Based on these results, we anticipate that this workflow will support the more general use of genetically incorporated, photoreactive amino acids for characterizing the structures of proteins that have resisted high-resolution characterization.
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Affiliation(s)
- Lindsey D. Ulmer
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Daniele Canzani
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
| | - Christopher N. Woods
- University of Washington, Department of Biochemistry, Box 357350, Seattle, WA 98195-7350
| | - Natalie L. Stone
- University of Washington, Department of Biochemistry, Box 357350, Seattle, WA 98195-7350
| | - Maria K. Janowska
- University of Washington, Department of Biochemistry, Box 357350, Seattle, WA 98195-7350
| | - Rachel E. Klevit
- University of Washington, Department of Biochemistry, Box 357350, Seattle, WA 98195-7350
| | - Matthew F. Bush
- University of Washington, Department of Chemistry, Box 351700, Seattle, WA 98195-1700
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2
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Oh J, Kim DK, Ahn SH, Kim HM, Cho H. A dual role of the conserved PEX19 helix in safeguarding peroxisomal membrane proteins. iScience 2024; 27:109537. [PMID: 38585659 PMCID: PMC10995880 DOI: 10.1016/j.isci.2024.109537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 02/13/2024] [Accepted: 03/18/2024] [Indexed: 04/09/2024] Open
Abstract
Accurate localization of membrane proteins is essential for proper cellular functioning and the integrity of cellular membranes. Post-translational targeting of peroxisomal membrane proteins (PMPs) is mediated by the cytosolic chaperone PEX19 and its membrane receptor PEX3. However, the molecular mechanisms underlying PMP targeting are poorly understood. Here, using biochemical and mass spectrometry analysis, we find that a conserved PEX19 helix, αd, is critical to prevent improper exposure of the PEX26 transmembrane domain (TMD) to cytosolic chaperones. Furthermore, the αd helix of PEX19 interacts with the cytosolic domain of the PEX3 receptor, thereby triggering PEX26 release at the correct destination membrane. The peroxisome-deficient PEX3-G138E mutant completely abolishes this secondary interaction, leading to lack of PEX3-induced PEX26 release from PEX19. These findings elucidate a dual molecular mechanism that is essential to membrane protein protection and destination-specific release by a molecular chaperone.
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Affiliation(s)
- Jeonghyun Oh
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Do Kyung Kim
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Seung Hae Ahn
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Ho Min Kim
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
- Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hyunju Cho
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
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3
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Havshøi NW, Nielsen J, Fuglsang AT. The mechanism behind tenuazonic acid-mediated inhibition of plant plasma membrane H +-ATPase and plant growth. J Biol Chem 2024; 300:107167. [PMID: 38490436 PMCID: PMC11002603 DOI: 10.1016/j.jbc.2024.107167] [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: 11/09/2023] [Revised: 02/29/2024] [Accepted: 03/06/2024] [Indexed: 03/17/2024] Open
Abstract
The increasing prevalence of herbicide-resistant weeds has led to a search for new herbicides that target plant growth processes differing from those targeted by current herbicides. In recent years, some studies have explored the use of natural compounds from microorganisms as potential new herbicides. We previously demonstrated that tenuazonic acid (TeA) from the phytopathogenic fungus Stemphylium loti inhibits the plant plasma membrane (PM) H+-ATPase, representing a new target for herbicides. In this study, we further investigated the mechanism by which TeA inhibits PM H+-ATPase and the effect of the toxin on plant growth using Arabidopsis thaliana. We also studied the biochemical effects of TeA on the PM H+-ATPases from spinach (Spinacia oleracea) and A. thaliana (AHA2) by examining PM H+-ATPase activity under different conditions and in different mutants. Treatment with 200 μM TeA-induced cell necrosis in larger plants and treatment with 10 μM TeA almost completely inhibited cell elongation and root growth in seedlings. We show that the isoleucine backbone of TeA is essential for inhibiting the ATPase activity of the PM H+-ATPase. Additionally, this inhibition depends on the C-terminal domain of AHA2, and TeA binding to PM H+-ATPase requires the Regulatory Region I of the C-terminal domain in AHA2. TeA likely has a higher binding affinity toward PM H+-ATPase than the phytotoxin fusicoccin. Finally, our findings show that TeA retains the H+-ATPase in an inhibited state, suggesting that it could act as a lead compound for creating new herbicides targeting the PM H+-ATPase.
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Affiliation(s)
- Nanna Weise Havshøi
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - John Nielsen
- Department of Drug Design and Pharmacology, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - Anja Thoe Fuglsang
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark.
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4
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Fuji S, Yamauchi S, Sugiyama N, Kohchi T, Nishihama R, Shimazaki KI, Takemiya A. Light-induced stomatal opening requires phosphorylation of the C-terminal autoinhibitory domain of plasma membrane H +-ATPase. Nat Commun 2024; 15:1195. [PMID: 38378726 PMCID: PMC10879506 DOI: 10.1038/s41467-024-45236-9] [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: 02/13/2023] [Accepted: 01/16/2024] [Indexed: 02/22/2024] Open
Abstract
Plasma membrane H+-ATPase provides the driving force for light-induced stomatal opening. However, the mechanisms underlying the regulation of its activity remain unclear. Here, we show that the phosphorylation of two Thr residues in the C-terminal autoinhibitory domain is crucial for H+-ATPase activation and stomatal opening in Arabidopsis thaliana. Using phosphoproteome analysis, we show that blue light induces the phosphorylation of Thr-881 within the C-terminal region I, in addition to penultimate Thr-948 in AUTOINHIBITED H+-ATPASE 1 (AHA1). Based on site-directed mutagenesis experiments, phosphorylation of both Thr residues is essential for H+ pumping and stomatal opening in response to blue light. Thr-948 phosphorylation is a prerequisite for Thr-881 phosphorylation by blue light. Additionally, red light-driven guard cell photosynthesis induces Thr-881 phosphorylation, possibly contributing to red light-dependent stomatal opening. Our findings provide mechanistic insights into H+-ATPase activation that exploits the ion transport across the plasma membrane and light signalling network in guard cells.
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Affiliation(s)
- Saashia Fuji
- Department of Biology, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8512, Japan
| | - Shota Yamauchi
- Department of Biology, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8512, Japan
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan
| | - Naoyuki Sugiyama
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Ken-Ichiro Shimazaki
- Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan
| | - Atsushi Takemiya
- Department of Biology, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8512, Japan.
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5
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Structural and Functional Diversity of Two ATP-Driven Plant Proton Pumps. Int J Mol Sci 2023; 24:ijms24054512. [PMID: 36901943 PMCID: PMC10003446 DOI: 10.3390/ijms24054512] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/09/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Two ATP-dependent proton pumps function in plant cells. Plasma membrane H+-ATPase (PM H+-ATPase) transfers protons from the cytoplasm to the apoplast, while vacuolar H+-ATPase (V-ATPase), located in tonoplasts and other endomembranes, is responsible for proton pumping into the organelle lumen. Both enzymes belong to two different families of proteins and, therefore, differ significantly in their structure and mechanism of action. The plasma membrane H+-ATPase is a member of the P-ATPases that undergo conformational changes, associated with two distinct E1 and E2 states, and autophosphorylation during the catalytic cycle. The vacuolar H+-ATPase represents rotary enzymes functioning as a molecular motor. The plant V-ATPase consists of thirteen different subunits organized into two subcomplexes, the peripheral V1 and the membrane-embedded V0, in which the stator and rotor parts have been distinguished. In contrast, the plant plasma membrane proton pump is a functional single polypeptide chain. However, when the enzyme is active, it transforms into a large twelve-protein complex of six H+-ATPase molecules and six 14-3-3 proteins. Despite these differences, both proton pumps can be regulated by the same mechanisms (such as reversible phosphorylation) and, in some processes, such as cytosolic pH regulation, may act in a coordinated way.
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6
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Blackburn MR, Minkoff BB, Sussman MR. Mass spectrometry-based technologies for probing the 3D world of plant proteins. PLANT PHYSIOLOGY 2022; 189:12-22. [PMID: 35139210 PMCID: PMC9070838 DOI: 10.1093/plphys/kiac039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 12/30/2021] [Indexed: 05/03/2023]
Abstract
Over the past two decades, mass spectrometric (MS)-based proteomics technologies have facilitated the study of signaling pathways throughout biology. Nowhere is this needed more than in plants, where an evolutionary history of genome duplications has resulted in large gene families involved in posttranslational modifications and regulatory pathways. For example, at least 5% of the Arabidopsis thaliana genome (ca. 1,200 genes) encodes protein kinases and protein phosphatases that regulate nearly all aspects of plant growth and development. MS-based technologies that quantify covalent changes in the side-chain of amino acids are critically important, but they only address one piece of the puzzle. A more crucially important mechanistic question is how noncovalent interactions-which are more difficult to study-dynamically regulate the proteome's 3D structure. The advent of improvements in protein 3D technologies such as cryo-electron microscopy, nuclear magnetic resonance, and X-ray crystallography has allowed considerable progress to be made at this level, but these methods are typically limited to analyzing proteins, which can be expressed and purified in milligram quantities. Newly emerging MS-based technologies have recently been developed for studying the 3D structure of proteins. Importantly, these methods do not require protein samples to be purified and require smaller amounts of sample, opening the wider proteome for structural analysis in complex mixtures, crude lysates, and even in intact cells. These MS-based methods include covalent labeling, crosslinking, thermal proteome profiling, and limited proteolysis, all of which can be leveraged by established MS workflows, as well as newly emerging methods capable of analyzing intact macromolecules and the complexes they form. In this review, we discuss these recent innovations in MS-based "structural" proteomics to provide readers with an understanding of the opportunities they offer and the remaining challenges for understanding the molecular underpinnings of plant structure and function.
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Affiliation(s)
- Matthew R Blackburn
- Department of Biochemistry and Center for Genomic Science Innovation, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Benjamin B Minkoff
- Department of Biochemistry and Center for Genomic Science Innovation, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Michael R Sussman
- Department of Biochemistry and Center for Genomic Science Innovation, University of Wisconsin, Madison, Wisconsin 53706, USA
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7
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Duckworth AT, Keck JL. Use of an unnatural amino acid to map helicase/DNA interfaces via photoactivated crosslinking. Methods Enzymol 2022; 672:55-74. [PMID: 35934485 PMCID: PMC10037347 DOI: 10.1016/bs.mie.2022.02.019] [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] [Indexed: 11/21/2022]
Abstract
Formation of protein/nucleic acid complexes is essential for life. From DNA replication and repair to transcription and translation, myriad different proteins bind nucleic acids to execute their essential cellular functions. Our understanding of the mechanisms underlying recognition and processing of nucleic acids can be greatly informed by mapping protein domains and residues that form interfaces with their DNA or RNA targets. Here we describe a crosslinking protocol in which the unnatural amino acid p-benzoyl-l-phenylalanine (Bpa) integrated at selected sites within the PriA DNA helicase is used to map surfaces of the protein that interact with specific positions in a synthetic DNA replication fork in vitro.
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Affiliation(s)
- Alexander T Duckworth
- Department of Biomolecular Chemistry, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States.
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8
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Zhao P, Zhao C, Chen D, Yun C, Li H, Bai L. Structure and activation mechanism of the hexameric plasma membrane H +-ATPase. Nat Commun 2021; 12:6439. [PMID: 34750373 PMCID: PMC8575881 DOI: 10.1038/s41467-021-26782-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 10/22/2021] [Indexed: 11/29/2022] Open
Abstract
The S. cerevisiae plasma membrane H+-ATPase, Pma1, is a P3A-type ATPase and the primary protein component of the membrane compartment of Pma1 (MCP). Like other plasma membrane H+-ATPases, Pma1 assembles and functions as a hexamer, a property unique to this subfamily among the larger family of P-type ATPases. It has been unclear how Pma1 organizes the yeast membrane into MCP microdomains, or why it is that Pma1 needs to assemble into a hexamer to establish the membrane electrochemical proton gradient. Here we report a high-resolution cryo-EM study of native Pma1 hexamers embedded in endogenous lipids. Remarkably, we found that the Pma1 hexamer encircles a liquid-crystalline membrane domain composed of 57 ordered lipid molecules. The Pma1-encircled lipid patch structure likely serves as the building block of the MCP. At pH 7.4, the carboxyl-terminal regulatory α-helix binds to the phosphorylation domains of two neighboring Pma1 subunits, locking the hexamer in the autoinhibited state. The regulatory helix becomes disordered at lower pH, leading to activation of the Pma1 hexamer. The activation process is accompanied by a 6.7 Å downward shift and a 40° rotation of transmembrane helices 1 and 2 that line the proton translocation path. The conformational changes have enabled us to propose a detailed mechanism for ATP-hydrolysis-driven proton pumping across the plasma membrane. Our structures will facilitate the development of antifungal drugs that target this essential protein.
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Affiliation(s)
- Peng Zhao
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Chaoran Zhao
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Dandan Chen
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Caihong Yun
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
| | - Lin Bai
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing, China.
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9
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Lee HC, Binos S, Chapman K, Pulsford SB, Ivanovici A, Rathjen JP, Djordjevic MA. A new method to visualize CEP hormone-CEP receptor interactions in vascular tissue in vivo. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6164-6174. [PMID: 34059899 DOI: 10.1093/jxb/erab244] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/29/2021] [Indexed: 06/12/2023]
Abstract
C-TERMINALLY ENCODED PEPTIDEs (CEPs) control diverse responses in plants including root development, root system architecture, nitrogen demand signalling, and nutrient allocation that influences yield, and there is evidence that different ligands impart different phenotypic responses. Thus, there is a need for a simple method that identifies bona fide CEP hormone-receptor pairings in vivo and examines whether different CEP family peptides bind the same receptor. We used formaldehyde or photoactivation to cross-link fluorescently tagged group 1 or group 2 CEPs to receptors in semi-purified Medicago truncatula or Arabidopsis thaliana leaf vascular tissues to verify that COMPACT ROOT ARCHITECTURE 2 (CRA2) is the Medicago CEP receptor, and to investigate whether sequence diversity within the CEP family influences receptor binding. Formaldehyde cross-linked the fluorescein isothiocyanate (FITC)-tagged Medicago group 1 CEP (MtCEP1) to wild-type Medicago or Arabidopsis vascular tissue cells, but not to the CEP receptor mutants, cra2 or cepr1. Binding competition showed that unlabelled MtCEP1 displaces FITC-MtCEP1 from CRA2. In contrast, the group 2 CEP, FITC-AtCEP14, bound to vascular tissue independently of CEPR1 or CRA2, and AtCEP14 did not complete with FITC-MtCEP1 to bind CEP receptors. The binding of a photoactivatable FITC-MtCEP1 to the periphery of Medicago vascular cells suggested that CRA2 localizes to the plasma membrane. We separated and visualized a fluorescent 105 kDa protein corresponding to the photo-cross-linked FITC-MtCEP1-CRA2 complex using SDS-PAGE. Mass spectrometry identified CRA2-specific peptides in this protein band. The results indicate that FITC-MtCEP1 binds to CRA2, MtCRA2 and AtCEPR1 are functionally equivalent, and the binding specificities of group 1 and group 2 CEPs are distinct. Using formaldehyde or photoactivated cross-linking of biologically active, fluorescently tagged ligands may find wider utility by identifying CEP-CEP receptor pairings in diverse plants.
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Affiliation(s)
- Han-Chung Lee
- Division of Plant Sciences, Research School of Biology, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Steve Binos
- Thermo Fisher Scientific, Bio21 Institute, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Kelly Chapman
- Division of Plant Sciences, Research School of Biology, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Sacha B Pulsford
- Division of Plant Sciences, Research School of Biology, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Ariel Ivanovici
- Division of Plant Sciences, Research School of Biology, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - John P Rathjen
- Division of Plant Sciences, Research School of Biology, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Michael A Djordjevic
- Division of Plant Sciences, Research School of Biology, College of Science, The Australian National University, Canberra, ACT 2601, Australia
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10
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Lee K, Ziegelhoffer T, Delewski W, Berger SE, Sabat G, Craig EA. Pathway of Hsp70 interactions at the ribosome. Nat Commun 2021; 12:5666. [PMID: 34580293 PMCID: PMC8476630 DOI: 10.1038/s41467-021-25930-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 09/08/2021] [Indexed: 11/09/2022] Open
Abstract
In eukaryotes, an Hsp70 molecular chaperone triad assists folding of nascent chains emerging from the ribosome tunnel. In fungi, the triad consists of canonical Hsp70 Ssb, atypical Hsp70 Ssz1 and J-domain protein cochaperone Zuo1. Zuo1 binds the ribosome at the tunnel exit. Zuo1 also binds Ssz1, tethering it to the ribosome, while its J-domain stimulates Ssb’s ATPase activity to drive efficient nascent chain interaction. But the function of Ssz1 and how Ssb engages at the ribosome are not well understood. Employing in vivo site-specific crosslinking, we found that Ssb(ATP) heterodimerizes with Ssz1. Ssb, in a manner consistent with the ADP conformation, also crosslinks to ribosomal proteins across the tunnel exit from Zuo1. These two modes of Hsp70 Ssb interaction at the ribosome suggest a functionally efficient interaction pathway: first, Ssb(ATP) with Ssz1, allowing optimal J-domain and nascent chain engagement; then, after ATP hydrolysis, Ssb(ADP) directly with the ribosome. Here, the authors use in vivo site-specific crosslinking to provide molecular-level insight into how the fungal Hsp70 chaperone system — the Ssb:Ssz1:Zuo1 triad — assists the folding process for the nascent peptide chain emerging from the ribosome tunnel.
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Affiliation(s)
- Kanghyun Lee
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.,Department of Biochemistry and Biophysics, Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, 94158, USA
| | - Thomas Ziegelhoffer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Wojciech Delewski
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Scott E Berger
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.,Department of Chemistry, Lafayette College, Easton, PA, 18042, USA.,Biophysics Program, Stanford University, Stanford, CA, 94305, USA
| | - Grzegorz Sabat
- Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Elizabeth A Craig
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.
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11
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Juurakko CL, Bredow M, Nakayama T, Imai H, Kawamura Y, diCenzo GC, Uemura M, Walker VK. The Brachypodium distachyon cold-acclimated plasma membrane proteome is primed for stress resistance. G3-GENES GENOMES GENETICS 2021; 11:6321953. [PMID: 34544140 PMCID: PMC8661430 DOI: 10.1093/g3journal/jkab198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 06/04/2021] [Indexed: 11/25/2022]
Abstract
In order to survive subzero temperatures, some plants undergo cold acclimation (CA) where low, nonfreezing temperatures, and/or shortened day lengths allow cold-hardening and survival during subsequent freeze events. Central to this response is the plasma membrane (PM), where low temperature is perceived and cellular homeostasis must be preserved by maintaining membrane integrity. Here, we present the first PM proteome of cold-acclimated Brachypodium distachyon, a model species for the study of monocot crops. A time-course experiment investigated CA-induced changes in the proteome following two-phase partitioning PM enrichment and label-free quantification by nano-liquid chromatography-mass spectrophotometry. Two days of CA were sufficient for membrane protection as well as an initial increase in sugar levels and coincided with a significant change in the abundance of 154 proteins. Prolonged CA resulted in further increases in soluble sugars and abundance changes in more than 680 proteins, suggesting both a necessary early response to low-temperature treatment, as well as a sustained CA response elicited over several days. A meta-analysis revealed that the identified PM proteins have known roles in low-temperature tolerance, metabolism, transport, and pathogen defense as well as drought, osmotic stress, and salt resistance suggesting crosstalk between stress responses, such that CA may prime plants for other abiotic and biotic stresses. The PM proteins identified here present keys to an understanding of cold tolerance in monocot crops and the hope of addressing economic losses associated with modern climate-mediated increases in frost events.
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Affiliation(s)
- Collin L Juurakko
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Melissa Bredow
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Takato Nakayama
- Department of Plant-Bioscience, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Hiroyuki Imai
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Yukio Kawamura
- Department of Plant-Bioscience, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan.,United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan
| | - George C diCenzo
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Matsuo Uemura
- Department of Plant-Bioscience, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan.,United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Virginia K Walker
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada.,Department of Biomedical and Molecular Sciences, School of Environmental Studies, Queen's University, Kingston, ON K7L 3N6, Canada
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12
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The transport mechanism of P4 ATPase lipid flippases. Biochem J 2021; 477:3769-3790. [PMID: 33045059 DOI: 10.1042/bcj20200249] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/02/2020] [Accepted: 09/16/2020] [Indexed: 12/18/2022]
Abstract
P4 ATPase lipid flippases are ATP-driven transporters that translocate specific lipids from the exoplasmic to the cytosolic leaflet of biological membranes, thus establishing a lipid gradient between the two leaflets that is essential for many cellular processes. While substrate specificity, subcellular and tissue-specific expression, and physiological functions have been assigned to a number of these transporters in several organisms, the mechanism of lipid transport has been a topic of intense debate in the field. The recent publication of a series of structural models based on X-ray crystallography and cryo-EM studies has provided the first glimpse into how P4 ATPases have adapted the transport mechanism used by the cation-pumping family members to accommodate a substrate that is at least an order of magnitude larger than cations.
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Lapshin NK, Piotrovskii MS, Trofimova MS. Involvement of plasma membrane H +-ATPase in diamide-induced extracellular alkalization by roots from pea seedlings. PLANTA 2021; 253:10. [PMID: 33389194 DOI: 10.1007/s00425-020-03532-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
MAIN CONCLUSION The plasma membrane H+-ATPase can be considered as a redox-dependent enzyme, because diamide-mediated inhibition of its hydrolytic and transport activities is accompanied by alkalization of the rhizosphere and retardation of root growth. Plasma membranes were isolated from roots of etiolated pea seedlings treated in the presence of an oxidant-diamide and an inhibitor of redox-sensitive protein phosphatase-phenylarsine oxide. Hydrolytic and proton transport activities of H+-ATPase were determined. The effects of diamide appeared in inhibition of both ATP hydrolysis and the proton transport. However, root treatment with phenylarsine oxide only slightly reduced Vmax, but did not affect ATP-dependent proton transport. The thiol groups of cysteines in the proteins can act as molecular targets for both compounds. However, treatment of isolated membranes with diamide or dithiothreitol did not have any effect on the H+ transport. It can be assumed that water-soluble diamide acts indirectly and its effects are not associated with oxidation of H+-ATPase cysteines. Therefore, plasmalemma was subjected to PEGylation-process where reduced cysteines available for PEG maleimide (5 kDa) were alkylated. Detection of such cysteines was carried out by Western blot analysis with anti-ATPase antibodies. It was found that shifts in the apparent molecular weight were detected only for denaturated proteins. These data suggest that available thiols are not localized on the enzyme surfaces. BN-PAGE analysis showed that the molecular weights of the ATPase complexes are almost identical in all samples. Therefore, oligomerization is probably not the reason for the inhibition of ATPase activity. Roots treated with these inhibitors in vivo exhibited stunted growth; however, a strong alkaline zone around the roots was formed only in the presence of diamide. Involvement of H+-ATPase redox regulation in this process is discussed.
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Affiliation(s)
- Nikita K Lapshin
- К.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., Moscow, Russia, 127276
| | - Michail S Piotrovskii
- К.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., Moscow, Russia, 127276
| | - Marina S Trofimova
- К.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., Moscow, Russia, 127276.
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Nguyen TT, Blackburn MR, Sussman MR. Intermolecular and Intramolecular Interactions of the Arabidopsis Plasma Membrane Proton Pump Revealed Using a Mass Spectrometry Cleavable Cross-Linker. Biochemistry 2020; 59:2210-2225. [PMID: 32459472 DOI: 10.1021/acs.biochem.0c00268] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In plants and fungi, the plasma membrane proton pump (H+-ATPase) establishes an electrochemical gradient across the plasma membrane, which serves as the driving force for the secondary transport of ions and nutrients across the cell membrane. This is an essential enzyme that functions in many important processes including stomatal movement, cell elongation, and cellular responses to stimuli from hormones, light, and other environmental conditions. Therefore, understanding how the activity of the H+-ATPase is regulated is important to understand how plants adapt to different growth conditions. The autoinhibitory effect of the C-terminal regulatory domain of H+-ATPase is well-established and is thought to be mediated by interactions with the catalytic domains. Here, using the lysine reactive mass spectrometry cleavable cross-linker DSSO, we found that the C-terminal domain of the Arabidopsis H+-ATPase 2 (AHA2) cross-linked extensively with the actuator, nucleotide-binding, and phosphorylation domains, suggesting that the C-terminal domain regulates the catalytic cycle by modulating the relative positions of these domains. Interestingly, several C-terminal cross-links occurred near a predicted proton binding site (Asp-684 in TM6), suggesting that the C-terminal domain may regulate proton efflux. Additionally, cross-links between the C-terminal domain and other domains of AHA2 were detected in a monomeric protein resolved on SDS-PAGE, suggesting that intramolecular interactions may also be involved in the regulation of enzyme activity. Finally, we observed mixed-isotope cross-linking between the C-terminal domain and other domains of 14N-AHA2 (unlabeled) and 15N-AHA2 (labeled), supporting our model that oligomeric H+-ATPase may autoinhibit the neighboring monomer in a "head-to-tail" configuration.
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Affiliation(s)
- Thao T Nguyen
- University of Wisconsin-Madison, Biochemistry Department and the Center for Genome Science Innovation, Madison, Wisconsin 53706, United States
| | - Matthew R Blackburn
- University of Wisconsin-Madison, Biochemistry Department and the Center for Genome Science Innovation, Madison, Wisconsin 53706, United States
| | - Michael R Sussman
- University of Wisconsin-Madison, Biochemistry Department and the Center for Genome Science Innovation, Madison, Wisconsin 53706, United States
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Dülfer J, Kadek A, Kopicki JD, Krichel B, Uetrecht C. Structural mass spectrometry goes viral. Adv Virus Res 2019; 105:189-238. [PMID: 31522705 DOI: 10.1016/bs.aivir.2019.07.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Over the last 20 years, mass spectrometry (MS), with its ability to analyze small sample amounts with high speed and sensitivity, has more and more entered the field of structural virology, aiming to investigate the structure and dynamics of viral proteins as close to their native environment as possible. The use of non-perturbing labels in hydrogen-deuterium exchange MS allows for the analysis of interactions between viral proteins and host cell factors as well as their dynamic responses to the environment. Cross-linking MS, on the other hand, can analyze interactions in viral protein complexes and identify virus-host interactions in cells. Native MS allows transferring viral proteins, complexes and capsids into the gas phase and has broken boundaries to overcome size limitations, so that now even the analysis of intact virions is possible. Different MS approaches not only inform about size, stability, interactions and dynamics of virus assemblies, but also bridge the gap to other biophysical techniques, providing valuable constraints for integrative structural modeling of viral complex assemblies that are often inaccessible by single technique approaches. In this review, recent advances are highlighted, clearly showing that structural MS approaches in virology are moving towards systems biology and ever more experiments are performed on cellular level.
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Affiliation(s)
- Jasmin Dülfer
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Alan Kadek
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany; European XFEL GmbH, Schenefeld, Germany
| | - Janine-Denise Kopicki
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Boris Krichel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany; European XFEL GmbH, Schenefeld, Germany.
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Yang Y, Wu Y, Ma L, Yang Z, Dong Q, Li Q, Ni X, Kudla J, Song C, Guo Y. The Ca 2+ Sensor SCaBP3/CBL7 Modulates Plasma Membrane H +-ATPase Activity and Promotes Alkali Tolerance in Arabidopsis. THE PLANT CELL 2019; 31:1367-1384. [PMID: 30962395 PMCID: PMC6588306 DOI: 10.1105/tpc.18.00568] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 03/12/2019] [Accepted: 03/31/2019] [Indexed: 05/21/2023]
Abstract
Saline-alkali soil is a major environmental constraint impairing plant growth and crop productivity. In this study, we identified a Ca2+ sensor/kinase/plasma membrane (PM) H+-ATPase module as a central component conferring alkali tolerance in Arabidopsis (Arabidopsis thaliana). We report that the SCaBP3 (SOS3-LIKE CALCIUM BINDING PROTEIN3)/CBL7 (CALCINEURIN B-LIKE7) loss-of-function plants exhibit enhanced stress tolerance associated with increased PM H+-ATPase activity and provide fundamental mechanistic insights into the regulation of PM H+-ATPase activity. Consistent with the genetic evidence, interaction analyses, in vivo reconstitution experiments, and determination of H+-ATPase activity indicate that interaction of the Ca2+ sensor SCaBP3 with the C-terminal Region I domain of the PM H+-ATPase AHA2 (Arabidopsis thaliana PLASMA MEMBRANE PROTON ATPASE2) facilitates the intramolecular interaction of the AHA2 C terminus with the Central loop region of the PM H+-ATPase to promote autoinhibition of H+-ATPase activity. Concurrently, direct interaction of SCaPB3 with the kinase PKS5 (PROTEIN KINASE SOS2-LIKE5) stabilizes the kinase-ATPase interaction and thereby fosters the inhibitory phosphorylation of AHA2 by PKS5. Consistently, yeast reconstitution experiments and genetic analysis indicate that SCaBP3 provides a bifurcated pathway for coordinating intramolecular and intermolecular inhibition of PM H+-ATPase. We propose that alkaline stress-triggered Ca2+ signals induce SCaBP3 dissociation from AHA2 to enhance PM H+-ATPase activity. This work illustrates a versatile signaling module that enables the stress-responsive adjustment of plasma membrane proton fluxes.
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Affiliation(s)
- Yongqing Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yujiao Wu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Liang Ma
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhijia Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Qiuyan Dong
- Institut für Biologie und Biotechnologie der Pflanzen, Universität Münster, 48149 Münster, Germany
| | - Qinpei Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xuping Ni
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jörg Kudla
- Institut für Biologie und Biotechnologie der Pflanzen, Universität Münster, 48149 Münster, Germany
| | - ChunPeng Song
- Collaborative Innovation Center of Crop Stress Biology, Henan Province, Institute of Plant Stress Biology, Henan University, Kaifeng 475001, China
| | - Yan Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
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Miyazaki R, Akiyama Y, Mori H. A photo-cross-linking approach to monitor protein dynamics in living cells. Biochim Biophys Acta Gen Subj 2019; 1864:129317. [PMID: 30851405 DOI: 10.1016/j.bbagen.2019.03.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/26/2019] [Accepted: 03/04/2019] [Indexed: 11/16/2022]
Abstract
BACKGROUND Proteins, which comprise one of the major classes of biomolecules that constitute a cell, interact with other cellular factors during both their biogenesis and functional states. Studying not only static but also transient interactions of proteins is important to understand their physiological roles and regulation mechanisms. However, only a limited number of methods are available to analyze the dynamic behaviors of proteins at the molecular level in a living cell. The site-directed in vivo photo-cross-linking approach is an elegant technique to capture protein interactions with high spatial resolution in a living cell. SCOPE OF REVIEW Here, we review the in vivo photo-cross-linking approach including its recent applications and the potential problems to be considered. We also introduce a new in vivo photo-cross-linking-based technique (PiXie) to study protein dynamics with high spatiotemporal resolution. MAJOR CONCLUSIONS In vivo photo-cross-linking enables us to capture weak/transient protein interactions with high spatial resolution, and allows for identification of interacting factors. Moreover, the PiXie approach can be used to monitor rapid folding/assembly processes of proteins in living cells. GENERAL SIGNIFICANCE In vivo photo-cross-linking is a simple method that has been used to analyze the dynamic interactions of many cellular proteins. Originally developed in Escherichia coli, this system has been extended to studies in various organisms, making it a fundamental technique for investigating dynamic protein interactions in many cellular processes. This article is part of a Special issue entitled "Novel major techniques for visualizing 'live' protein molecules" edited by Dr. Daisuke Kohda.
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Affiliation(s)
- Ryoji Miyazaki
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yoshinori Akiyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Hiroyuki Mori
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.
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