1
|
Dancis A, Pandey AK, Pain D. Mitochondria function in cytoplasmic FeS protein biogenesis. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119733. [PMID: 38641180 DOI: 10.1016/j.bbamcr.2024.119733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/18/2024] [Accepted: 04/12/2024] [Indexed: 04/21/2024]
Abstract
Iron‑sulfur (FeS) clusters are cofactors of numerous proteins involved in essential cellular functions including respiration, protein translation, DNA synthesis and repair, ribosome maturation, anti-viral responses, and isopropylmalate isomerase activity. Novel FeS proteins are still being discovered due to the widespread use of cryogenic electron microscopy (cryo-EM) and elegant genetic screens targeted at protein discovery. A complex sequence of biochemical reactions mediated by a conserved machinery controls biosynthesis of FeS clusters. In eukaryotes, a remarkable epistasis has been observed: the mitochondrial machinery, termed ISC (Iron-Sulfur Cluster), lies upstream of the cytoplasmic machinery, termed CIA (Cytoplasmic Iron‑sulfur protein Assembly). The basis for this arrangement is the production of a hitherto uncharacterized intermediate, termed X-S or (Fe-S)int, produced in mitochondria by the ISC machinery, exported by the mitochondrial ABC transporter Atm1 (ABCB7 in humans), and then utilized by the CIA machinery for the cytoplasmic/nuclear FeS cluster assembly. Genetic and biochemical findings supporting this sequence of events are herein presented. New structural views of the Atm1 transport phases are reviewed. The key compartmental roles of glutathione in cellular FeS cluster biogenesis are highlighted. Finally, data are presented showing that every one of the ten core components of the mitochondrial ISC machinery and Atm1, when mutated or depleted, displays similar phenotypes: mitochondrial and cytoplasmic FeS clusters are both rendered deficient, consistent with the epistasis noted above.
Collapse
Affiliation(s)
- Andrew Dancis
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA.
| | - Ashutosh K Pandey
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Debkumar Pain
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| |
Collapse
|
2
|
Choi SH, Lee SS, Lee HY, Kim S, Kim JW, Jin MS. Cryo-EM structure of cadmium-bound human ABCB6. Commun Biol 2024; 7:672. [PMID: 38822018 PMCID: PMC11143254 DOI: 10.1038/s42003-024-06377-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 05/23/2024] [Indexed: 06/02/2024] Open
Abstract
ATP-binding cassette transporter B6 (ABCB6), a protein essential for heme biosynthesis in mitochondria, also functions as a heavy metal efflux pump. Here, we present cryo-electron microscopy structures of human ABCB6 bound to a cadmium Cd(II) ion in the presence of antioxidant thiol peptides glutathione (GSH) and phytochelatin 2 (PC2) at resolutions of 3.2 and 3.1 Å, respectively. The overall folding of the two structures resembles the inward-facing apo state but with less separation between the two halves of the transporter. Two GSH molecules are symmetrically bound to the Cd(II) ion in a bent conformation, with the central cysteine protruding towards the metal. The N-terminal glutamate and C-terminal glycine of GSH do not directly interact with Cd(II) but contribute to neutralizing positive charges of the binding cavity by forming hydrogen bonds and van der Waals interactions with nearby residues. In the presence of PC2, Cd(II) binding to ABCB6 is similar to that observed with GSH, except that two cysteine residues of each PC2 molecule participate in Cd(II) coordination to form a tetrathiolate. Structural comparison of human ABCB6 and its homologous Atm-type transporters indicate that their distinct substrate specificity might be attributed to variations in the capping residues situated at the top of the substrate-binding cavity.
Collapse
Affiliation(s)
- Seung Hun Choi
- School of Life Sciences, GIST, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, Republic of Korea
| | - Sang Soo Lee
- School of Life Sciences, GIST, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, Republic of Korea
| | - Hyeon You Lee
- School of Life Sciences, GIST, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, Republic of Korea
| | - Subin Kim
- School of Life Sciences, GIST, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, Republic of Korea
| | - Ji Won Kim
- Department of Life Sciences, POSTECH, 77 Cheongam-Ro, Nam-gu, Pohang, Republic of Korea
| | - Mi Sun Jin
- School of Life Sciences, GIST, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, Republic of Korea.
| |
Collapse
|
3
|
Soong TH, Hotze C, Khandelwal NK, Tomasiak TM. Structural Basis for Oxidized Glutathione Recognition by the Yeast Cadmium Factor 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578287. [PMID: 38352558 PMCID: PMC10862839 DOI: 10.1101/2024.01.31.578287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Transporters from the ABCC family have an essential role in detoxifying electrophilic compounds including metals, drugs, and lipids, often through conjugation with glutathione complexes. The Yeast Cadmium Factor 1 (Ycf1) transports glutathione alone as well as glutathione conjugated to toxic heavy metals including Cd2+, Hg2+, and As3+. To understand the complicated selectivity and promiscuity of heavy metal substrate binding, we determined the cryo-EM structure of Ycf1 bound to the substrate, oxidized glutathione. We systematically tested binding determinants with cellular survival assays against cadmium to determine how the substrate site accommodates different-sized metal complexes. We identify a "flex-pocket" for substrate binding that binds glutathione complexes asymmetrically and flexes to accommodate different size complexes.
Collapse
Affiliation(s)
- Tik Hang Soong
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Clare Hotze
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Nitesh Kumar Khandelwal
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
- Department of Biochemistry and Physics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Thomas M Tomasiak
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| |
Collapse
|
4
|
Tamizhselvan P, Madhavan S, Constan-Aguilar C, Elrefaay ER, Liu J, Pěnčík A, Novák O, Cairó A, Hrtyan M, Geisler M, Tognetti VB. Chloroplast Auxin Efflux Mediated by ABCB28 and ABCB29 Fine-Tunes Salt and Drought Stress Responses in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2023; 13:7. [PMID: 38202315 PMCID: PMC10780339 DOI: 10.3390/plants13010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/26/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024]
Abstract
Photosynthesis is among the first processes negatively affected by environmental cues and its performance directly determines plant cell fitness and ultimately crop yield. Primarily sites of photosynthesis, chloroplasts are unique sites also for the biosynthesis of precursors of the growth regulator auxin and for sensing environmental stress, but their role in intracellular auxin homeostasis, vital for plant growth and survival in changing environments, remains poorly understood. Here, we identified two ATP-binding cassette (ABC) subfamily B transporters, ABCB28 and ABCB29, which export auxin across the chloroplast envelope to the cytosol in a concerted action in vivo. Moreover, we provide evidence for an auxin biosynthesis pathway in Arabidopsis thaliana chloroplasts. The overexpression of ABCB28 and ABCB29 influenced stomatal regulation and resulted in significantly improved water use efficiency and survival rates during salt and drought stresses. Our results suggest that chloroplast auxin production and transport contribute to stomata regulation for conserving water upon salt stress. ABCB28 and ABCB29 integrate photosynthesis and auxin signals and as such hold great potential to improve the adaptation potential of crops to environmental cues.
Collapse
Affiliation(s)
- Prashanth Tamizhselvan
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
| | - Sharmila Madhavan
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
| | - Christian Constan-Aguilar
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
| | - Eman Ryad Elrefaay
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
| | - Jie Liu
- Department of Biology, University of Fribourg, CH-1700 Fribourg, Switzerland; (J.L.); (M.G.)
| | - Aleš Pěnčík
- Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences, & Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic; (A.P.); (O.N.)
| | - Ondřej Novák
- Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences, & Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic; (A.P.); (O.N.)
| | - Albert Cairó
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
| | - Mónika Hrtyan
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
| | - Markus Geisler
- Department of Biology, University of Fribourg, CH-1700 Fribourg, Switzerland; (J.L.); (M.G.)
| | - Vanesa Beatriz Tognetti
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; (P.T.); (S.M.); (C.C.-A.); (E.R.E.); (A.C.); (M.H.)
| |
Collapse
|
5
|
Lee SS, Park JG, Jang E, Choi SH, Kim S, Kim JW, Jin MS. W546 stacking disruption traps the human porphyrin transporter ABCB6 in an outward-facing transient state. Commun Biol 2023; 6:960. [PMID: 37735522 PMCID: PMC10514269 DOI: 10.1038/s42003-023-05339-3] [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: 03/16/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023] Open
Abstract
Human ATP-binding cassette transporter subfamily B6 (ABCB6) is a mitochondrial ATP-driven pump that translocates porphyrins from the cytoplasm into mitochondria for heme biosynthesis. Within the transport pathway, a conserved aromatic residue W546 located in each monomer plays a pivotal role in stabilizing the occluded conformation via π-stacking interactions. Herein, we employed cryo-electron microscopy to investigate the structural consequences of a single W546A mutation in ABCB6, both in detergent micelles and nanodiscs. The results demonstrate that the W546A mutation alters the conformational dynamics of detergent-purified ABCB6, leading to entrapment of the transporter in an outward-facing transient state. However, in the nanodisc system, we observed a direct interaction between the transporter and a phospholipid molecule that compensates for the absence of the W546 residue, thereby facilitating the normal conformational transition of the transporter toward the occluded state following ATP hydrolysis. The findings also reveal that adoption of the outward-facing conformation causes charge repulsion between ABCB6 and the bound substrate, and rearrangement of key interacting residues at the substrate-binding site. Consequently, the affinity for the substrate is significantly reduced, facilitating its release from the transporter.
Collapse
Affiliation(s)
- Sang Soo Lee
- School of Life Sciences, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju, 61005, Republic of Korea
| | - Jun Gyou Park
- School of Life Sciences, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju, 61005, Republic of Korea
| | - Eunhong Jang
- School of Life Sciences, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju, 61005, Republic of Korea
| | - Seung Hun Choi
- School of Life Sciences, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju, 61005, Republic of Korea
| | - Subin Kim
- School of Life Sciences, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju, 61005, Republic of Korea
| | - Ji Won Kim
- Department of Life Sciences, POSTECH, 77 Cheongam-Ro, Nam-gu, Pohang, 37673, Republic of Korea
| | - Mi Sun Jin
- School of Life Sciences, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju, 61005, Republic of Korea.
| |
Collapse
|
6
|
Santos MFA, Pessoa JC. Interaction of Vanadium Complexes with Proteins: Revisiting the Reported Structures in the Protein Data Bank (PDB) since 2015. Molecules 2023; 28:6538. [PMID: 37764313 PMCID: PMC10536487 DOI: 10.3390/molecules28186538] [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: 07/27/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The structural determination and characterization of molecules, namely proteins and enzymes, is crucial to gaining a better understanding of their role in different chemical and biological processes. The continuous technical developments in the experimental and computational resources of X-ray diffraction (XRD) and, more recently, cryogenic Electron Microscopy (cryo-EM) led to an enormous growth in the number of structures deposited in the Protein Data Bank (PDB). Bioinorganic chemistry arose as a relevant discipline in biology and therapeutics, with a massive number of studies reporting the effects of metal complexes on biological systems, with vanadium complexes being one of the relevant systems addressed. In this review, we focus on the interactions of vanadium compounds (VCs) with proteins. Several types of binding are established between VCs and proteins/enzymes. Considering that the V-species that bind may differ from those initially added, the mentioned structural techniques are pivotal to clarifying the nature and variety of interactions of VCs with proteins and to proposing the mechanisms involved either in enzymatic inhibition or catalysis. As such, we provide an account of the available structural information of VCs bound to proteins obtained by both XRD and/or cryo-EM, mainly exploring the more recent structures, particularly those containing organic-based vanadium complexes.
Collapse
Affiliation(s)
- Marino F. A. Santos
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Centro de Química Estrutural, Departamento de Engenharia Química, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - João Costa Pessoa
- Centro de Química Estrutural, Departamento de Engenharia Química, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| |
Collapse
|
7
|
Andersen CG, Bavnhøj L, Pedersen BP. May the proton motive force be with you: A plant transporter review. Curr Opin Struct Biol 2023; 79:102535. [PMID: 36796226 DOI: 10.1016/j.sbi.2023.102535] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/28/2022] [Accepted: 01/03/2023] [Indexed: 02/16/2023]
Abstract
As our ecosystems experience challenges associated with climate change, an improved understanding of the fundamental biochemical processes governing plant physiology is needed. Strikingly, current structural information on plant membrane transporters is severely limited compared to other kingdoms of life, with only 18 unique structures in total. To advance future breakthroughs and insight in plant cell molecular biology, structural knowledge of membrane transporters is indispensable. This review summarizes the current status of structural knowledge in the plant membrane transporter field. Plants utilize the proton motive force (PMF) to drive secondary active transport. We discuss the PMF, how it relates to secondary active transport and provide a classification of PMF driven secondary active transport, discussing recently published structures of symporters, antiporters, and uniporters from plants.
Collapse
Affiliation(s)
| | - Laust Bavnhøj
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark. https://twitter.com/laustbavnhoej
| | | |
Collapse
|
8
|
Li P, Hendricks AL, Wang Y, Villones RLE, Lindkvist-Petersson K, Meloni G, Cowan JA, Wang K, Gourdon P. Structures of Atm1 provide insight into [2Fe-2S] cluster export from mitochondria. Nat Commun 2022; 13:4339. [PMID: 35896548 PMCID: PMC9329353 DOI: 10.1038/s41467-022-32006-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 07/11/2022] [Indexed: 01/22/2023] Open
Abstract
In eukaryotes, iron-sulfur clusters are essential cofactors for numerous physiological processes, but these clusters are primarily biosynthesized in mitochondria. Previous studies suggest mitochondrial ABCB7-type exporters are involved in maturation of cytosolic iron-sulfur proteins. However, the molecular mechanism for how the ABCB7-type exporters participate in this process remains elusive. Here, we report a series of cryo-electron microscopy structures of a eukaryotic homolog of human ABCB7, CtAtm1, determined at average resolutions ranging from 2.8 to 3.2 Å, complemented by functional characterization and molecular docking in silico. We propose that CtAtm1 accepts delivery from glutathione-complexed iron-sulfur clusters. A partially occluded state links cargo-binding to residues at the mitochondrial matrix interface that line a positively charged cavity, while the binding region becomes internalized and is partially divided in an early occluded state. Collectively, our findings substantially increase the understanding of the transport mechanism of eukaryotic ABCB7-type proteins.
Collapse
Affiliation(s)
- Ping Li
- Department of Experimental Medical Science, Lund University, Sölvegatan 19, SE-221 84, Lund, Sweden
| | - Amber L Hendricks
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, 43210, USA
| | - Yong Wang
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, 314400, China
| | - Rhiza Lyne E Villones
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 W Campbell Rd., Richardson, TX, 75080, USA
| | | | - Gabriele Meloni
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 W Campbell Rd., Richardson, TX, 75080, USA
| | - J A Cowan
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, 43210, USA
| | - Kaituo Wang
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark.
| | - Pontus Gourdon
- Department of Experimental Medical Science, Lund University, Sölvegatan 19, SE-221 84, Lund, Sweden.
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark.
| |
Collapse
|