1
|
Doni D, Cavallari E, Noguera ME, Gentili HG, Cavion F, Parisi G, Fornasari MS, Sartori G, Santos J, Bellanda M, Carbonera D, Costantini P, Bortolus M. Searching for Frataxin Function: Exploring the Analogy with Nqo15, the Frataxin-like Protein of Respiratory Complex I from Thermus thermophilus. Int J Mol Sci 2024; 25:1912. [PMID: 38339189 PMCID: PMC10855754 DOI: 10.3390/ijms25031912] [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: 12/23/2023] [Revised: 01/26/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
Nqo15 is a subunit of respiratory complex I of the bacterium Thermus thermophilus, with strong structural similarity to human frataxin (FXN), a protein involved in the mitochondrial disease Friedreich's ataxia (FRDA). Recently, we showed that the expression of recombinant Nqo15 can ameliorate the respiratory phenotype of FRDA patients' cells, and this prompted us to further characterize both the Nqo15 solution's behavior and its potential functional overlap with FXN, using a combination of in silico and in vitro techniques. We studied the analogy of Nqo15 and FXN by performing extensive database searches based on sequence and structure. Nqo15's folding and flexibility were investigated by combining nuclear magnetic resonance (NMR), circular dichroism, and coarse-grained molecular dynamics simulations. Nqo15's iron-binding properties were studied using NMR, fluorescence, and specific assays and its desulfurase activation by biochemical assays. We found that the recombinant Nqo15 isolated from complex I is monomeric, stable, folded in solution, and highly dynamic. Nqo15 does not share the iron-binding properties of FXN or its desulfurase activation function.
Collapse
Affiliation(s)
- Davide Doni
- Department of Biology, University of Padova, 35121 Padova, Italy; (D.D.); (F.C.)
| | - Eva Cavallari
- Department of Biology, University of Padova, 35121 Padova, Italy; (D.D.); (F.C.)
- Grenoble Alpes University, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France
| | - Martin Ezequiel Noguera
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Intendente Güiraldes 2160, Buenos Aires C1428EG, Argentina; (M.E.N.); (H.G.G.); (J.S.)
- Institute of Biological Chemistry and Physical Chemistry, Dr Alejandro Paladini (UBA-CONICET), University of Buenos Aires, Junín 956, Buenos Aires 1113AAD, Argentina
- Department of Science and Technology, National University of Quilmes, Roque Saenz Peña 352, Bernal B1876BXD, Argentina; (G.P.); (M.S.F.)
| | - Hernan Gustavo Gentili
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Intendente Güiraldes 2160, Buenos Aires C1428EG, Argentina; (M.E.N.); (H.G.G.); (J.S.)
| | - Federica Cavion
- Department of Biology, University of Padova, 35121 Padova, Italy; (D.D.); (F.C.)
| | - Gustavo Parisi
- Department of Science and Technology, National University of Quilmes, Roque Saenz Peña 352, Bernal B1876BXD, Argentina; (G.P.); (M.S.F.)
| | - Maria Silvina Fornasari
- Department of Science and Technology, National University of Quilmes, Roque Saenz Peña 352, Bernal B1876BXD, Argentina; (G.P.); (M.S.F.)
| | - Geppo Sartori
- Department of Biomedical Sciences, University of Padova, 35121 Padova, Italy;
| | - Javier Santos
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Intendente Güiraldes 2160, Buenos Aires C1428EG, Argentina; (M.E.N.); (H.G.G.); (J.S.)
| | - Massimo Bellanda
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy; (M.B.); (D.C.)
- Consiglio Nazionale delle Ricerche Institute of Biomolecular Chemistry, 35131 Padova, Italy
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy; (M.B.); (D.C.)
| | - Paola Costantini
- Department of Biology, University of Padova, 35121 Padova, Italy; (D.D.); (F.C.)
| | - Marco Bortolus
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy; (M.B.); (D.C.)
| |
Collapse
|
2
|
Alsohaibani R, Claudel AL, Perchat-Varlet R, Boutserin S, Talfournier F, Boschi-Muller S, Selles B. Rhodanese-Fold Containing Proteins in Humans: Not Just Key Players in Sulfur Trafficking. Antioxidants (Basel) 2023; 12:antiox12040843. [PMID: 37107218 PMCID: PMC10135228 DOI: 10.3390/antiox12040843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/21/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
The Rhodanese-fold is a ubiquitous structural domain present in various protein subfamilies associated with different physiological functions or pathophysiological conditions in humans. Proteins harboring a Rhodanese domain are diverse in terms of domain architecture, with some representatives exhibiting one or several Rhodanese domains, fused or not to other structural domains. The most famous Rhodanese domains are catalytically active, thanks to an active-site loop containing an essential cysteine residue which allows for catalyzing sulfur transfer reactions involved in sulfur trafficking, hydrogen sulfide metabolism, biosynthesis of molybdenum cofactor, thio-modification of tRNAs or protein urmylation. In addition, they also catalyse phosphatase reactions linked to cell cycle regulation, and recent advances proposed a new role into tRNA hydroxylation, illustrating the catalytic versatility of Rhodanese domain. To date, no exhaustive analysis of Rhodanese containing protein equipment from humans is available. In this review, we focus on structural and biochemical properties of human-active Rhodanese-containing proteins, in order to provide a picture of their established or putative key roles in many essential biological functions.
Collapse
|
3
|
Pang Y, Wang J, Gao X, Jiang M, Zhu L, Liang F, Liang M, Wu X, Xu X, Ren X, Xie T, Wang W, Sun Q, Xiong X, Lyu J, Li J, Tan G. Roles of conserved active site residues in the IscS cysteine desulfurase reaction. Front Microbiol 2023; 14:1084205. [PMID: 36876095 PMCID: PMC9978102 DOI: 10.3389/fmicb.2023.1084205] [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: 10/30/2022] [Accepted: 01/31/2023] [Indexed: 02/18/2023] Open
Abstract
Escherichia coli cysteine desulfurase (CD), IscS, modifies basal metabolism by transferring sulphur (S) from L-cysteine to numerous cellular pathways, whereas NFS1, a human CD, is active only in the formation of the [Acp]2:[ISD11]2:[NFS1]2 complex. Despite the accumulation of red-coloured IscS in E. coli cells as a result of the deficiency of accessible iron, as revealed in our previous studies, the mechanism of the potential enzymatic reaction remains unclear. In this study, the N-terminus of IscS was fused with the C-terminus of NFS1, which was reported to be almost fully active as IscS and exhibits a pyridoxal 5'-phosphate (PLP) absorption peak at 395 nm. Moreover, SUMO-EH-IscS exhibited significant growth recovery and NADH-dehydrogenase I activity in the iscS mutant cells. Furthermore, through in vitro and in vivo experiments combined with high-performance liquid chromatography and ultra-performance liquid chromatography-tandem mass spectrometry, it was shown that the new absorption peaks of the IscS H104Q, IscS Q183E, IscS K206A, and IscS K206A&C328S variants at 340 and 350 nm may correspond to the enzyme reaction intermediates, Cys-ketimine and Cys-aldimine, respectively. However, after mutation of the conserved active-site residues, additional absorption peaks at 420 and 430 nm were associated with PLP migration in the active-site pocket. Additionally, the corresponding absorption peaks of Cys-quinonoid, Ala-ketimine, and Ala-aldimine intermediates in IscS were 510, 325, and 345 nm, respectively, as determined by site-directed mutagenesis and substrate/product-binding analyses during the CD reaction process. Notably, red IscS formed in vitro by incubating IscS variants (Q183E and K206A) with excess L-alanine and sulphide under aerobic conditions produced an absorption peak similar to the wild-type IscS, at 510 nm. Interestingly, site-directed mutation of IscS with hydrogen bonds to PLP at Asp180 and Gln183 resulted in a loss of enzymatic activity followed by an absorption peak consistent with NFS1 (420 nm). Furthermore, mutations at Asp180 or Lys206 inhibited the reaction of IscS in vitro with L-cysteine (substrate) and L-alanine (product). These results suggest that the conserved active site residues (His104, Asp180, and Gln183) and their hydrogen bond with PLP in the N-terminus of IscS play a key role in determining whether the L-cysteine substrate can enter the active-site pocket and regulate the enzymatic reaction process. Therefore, our findings provide a framework for evaluating the roles of conserved active-site residues, motifs, and domains in CDs.
Collapse
Affiliation(s)
- Yilin Pang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Hunan Animal Pharmaceutical Company, Hunan Agricultural Group Company, Hunan Agricultural Development & Investment Group Company, Wangcheng Economic and Technological Development Zone, Changsha, Hunan, China
| | - Jing Wang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xueping Gao
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Mengyao Jiang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lifei Zhu
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Feng Liang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Mengxiang Liang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaolin Wu
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xianxian Xu
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaojun Ren
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.,People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Ting Xie
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Wu Wang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qianqian Sun
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaojun Xiong
- Hunan Animal Pharmaceutical Company, Hunan Agricultural Group Company, Hunan Agricultural Development & Investment Group Company, Wangcheng Economic and Technological Development Zone, Changsha, Hunan, China
| | - Jianxin Lyu
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.,People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Jianghui Li
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Guoqiang Tan
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| |
Collapse
|
4
|
Fujihara KM, Zhang BZ, Jackson TD, Ogunkola MO, Nijagal B, Milne JV, Sallman DA, Ang CS, Nikolic I, Kearney CJ, Hogg SJ, Cabalag CS, Sutton VR, Watt S, Fujihara AT, Trapani JA, Simpson KJ, Stojanovski D, Leimkühler S, Haupt S, Phillips WA, Clemons NJ. Eprenetapopt triggers ferroptosis, inhibits NFS1 cysteine desulfurase, and synergizes with serine and glycine dietary restriction. SCIENCE ADVANCES 2022; 8:eabm9427. [PMID: 36103522 PMCID: PMC9473576 DOI: 10.1126/sciadv.abm9427] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The mechanism of action of eprenetapopt (APR-246, PRIMA-1MET) as an anticancer agent remains unresolved, although the clinical development of eprenetapopt focuses on its reported mechanism of action as a mutant-p53 reactivator. Using unbiased approaches, this study demonstrates that eprenetapopt depletes cellular antioxidant glutathione levels by increasing its turnover, triggering a nonapoptotic, iron-dependent form of cell death known as ferroptosis. Deficiency in genes responsible for supplying cancer cells with the substrates for de novo glutathione synthesis (SLC7A11, SHMT2, and MTHFD1L), as well as the enzymes required to synthesize glutathione (GCLC and GCLM), augments the activity of eprenetapopt. Eprenetapopt also inhibits iron-sulfur cluster biogenesis by limiting the cysteine desulfurase activity of NFS1, which potentiates ferroptosis and may restrict cellular proliferation. The combination of eprenetapopt with dietary serine and glycine restriction synergizes to inhibit esophageal xenograft tumor growth. These findings reframe the canonical view of eprenetapopt from a mutant-p53 reactivator to a ferroptosis inducer.
Collapse
Affiliation(s)
- Kenji M. Fujihara
- Gastrointestinal Cancer Program, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
- Corresponding author. (N.J.C.); (K.M.F.)
| | - Bonnie Z. Zhang
- Gastrointestinal Cancer Program, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Thomas D. Jackson
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, Victoria, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Moses O. Ogunkola
- Institute of Biochemistry and Biology Department for Molecular Enzymology, University of Potsdam, Potsdam, Germany
| | - Brunda Nijagal
- Metabolomics Australia, The Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, Victoria, Australia
| | - Julia V. Milne
- Gastrointestinal Cancer Program, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - David A. Sallman
- Malignant Hematology Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Ching-Seng Ang
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Iva Nikolic
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Conor J. Kearney
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
- Translational Hematology Program, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Simon J. Hogg
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
- Translational Hematology Program, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Carlos S. Cabalag
- Gastrointestinal Cancer Program, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
- Department of Surgical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Vivien R. Sutton
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Sally Watt
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Asuka T. Fujihara
- Gastrointestinal Cancer Program, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Joseph A. Trapani
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Kaylene J. Simpson
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Diana Stojanovski
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, Victoria, Australia
| | - Silke Leimkühler
- Institute of Biochemistry and Biology Department for Molecular Enzymology, University of Potsdam, Potsdam, Germany
| | - Sue Haupt
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
- Tumor Suppression and Cancer Sex Disparity Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Wayne A. Phillips
- Gastrointestinal Cancer Program, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
- Department of Surgery (St. Vincent’s Hospital), The University of Melbourne, Parkville, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Nicholas J. Clemons
- Gastrointestinal Cancer Program, Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
- Corresponding author. (N.J.C.); (K.M.F.)
| |
Collapse
|
5
|
Zhang W, Foo M, Eren AM, Pan T. tRNA modification dynamics from individual organisms to metaepitranscriptomics of microbiomes. Mol Cell 2022; 82:891-906. [PMID: 35032425 PMCID: PMC8897278 DOI: 10.1016/j.molcel.2021.12.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/17/2022]
Abstract
tRNA is the most extensively modified RNA in cells. On average, a bacterial tRNA contains 8 modifications per molecule and a eukaryotic tRNA contains 13 modifications per molecule. Recent studies reveal that tRNA modifications are highly dynamic and respond extensively to environmental conditions. Functions of tRNA modification dynamics include enhanced, on-demand decoding of specific codons in response genes and regulation of tRNA fragment biogenesis. This review summarizes recent advances in the studies of tRNA modification dynamics in biological processes, tRNA modification erasers, and human-associated bacteria. Furthermore, we use the term "metaepitranscriptomics" to describe the potential and approach of tRNA modification studies in natural biological communities such as microbiomes. tRNA is highly modified in cells, and tRNA modifications respond extensively to environmental conditions to enhance translation of specific genes and produce tRNA fragments on demand. We review recent advances in tRNA sequencing methods, tRNA modification dynamics in biological processes, and tRNA modification studies in natural communities such as the microbiomes.
Collapse
Affiliation(s)
- Wen Zhang
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Marcus Foo
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
| | - A. Murat Eren
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA;,Department of Medicine, University of Chicago, Chicago, IL 60637, USA;,Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Tao Pan
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60637, USA; Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA.
| |
Collapse
|
6
|
Selles B, Moseler A, Caubrière D, Sun SK, Ziesel M, Dhalleine T, Hériché M, Wirtz M, Rouhier N, Couturier J. The cytosolic Arabidopsis thaliana cysteine desulfurase ABA3 delivers sulfur to the sulfurtransferase STR18. J Biol Chem 2022; 298:101749. [PMID: 35189141 PMCID: PMC8931425 DOI: 10.1016/j.jbc.2022.101749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 11/23/2022] Open
Abstract
The biosynthesis of many sulfur-containing molecules depends on cysteine as a sulfur source. Both the cysteine desulfurase (CD) and rhodanese (Rhd) domain–containing protein families participate in the trafficking of sulfur for various metabolic pathways in bacteria and human, but their connection is not yet described in plants. The existence of natural chimeric proteins containing both CD and Rhd domains in specific bacterial genera, however, suggests a general interaction between these proteins. We report here the biochemical relationships between two cytosolic proteins from Arabidopsis thaliana, a Rhd domain–containing protein, the sulfurtransferase 18 (STR18), and a CD isoform referred to as ABA3, and compare these biochemical features to those of a natural CD–Rhd fusion protein from the bacterium Pseudorhodoferax sp. We observed that the bacterial enzyme is bifunctional exhibiting both CD and STR activities using l-cysteine and thiosulfate as sulfur donors but preferentially using l-cysteine to catalyze transpersulfidation reactions. In vitro activity assays and mass spectrometry analyses revealed that STR18 stimulates the CD activity of ABA3 by reducing the intermediate persulfide on its catalytic cysteine, thereby accelerating the overall transfer reaction. We also show that both proteins interact in planta and form an efficient sulfur relay system, whereby STR18 catalyzes transpersulfidation reactions from ABA3 to the model acceptor protein roGFP2. In conclusion, the ABA3–STR18 couple likely represents an uncharacterized pathway of sulfur trafficking in the cytosol of plant cells, independent of ABA3 function in molybdenum cofactor maturation.
Collapse
Affiliation(s)
| | - Anna Moseler
- Université de Lorraine, INRAE, IAM, Nancy, France
| | | | - Sheng-Kai Sun
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | | | | | | | - Markus Wirtz
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | | | - Jérémy Couturier
- Université de Lorraine, INRAE, IAM, Nancy, France; Institut Universitaire de France, France.
| |
Collapse
|
7
|
Maio N, Rouault TA. Mammalian iron sulfur cluster biogenesis: From assembly to delivery to recipient proteins with a focus on novel targets of the chaperone and co‐chaperone proteins. IUBMB Life 2022; 74:684-704. [PMID: 35080107 PMCID: PMC10118776 DOI: 10.1002/iub.2593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/05/2021] [Accepted: 12/23/2021] [Indexed: 12/17/2022]
Affiliation(s)
- Nunziata Maio
- Molecular Medicine Branch Eunice Kennedy Shriver National Institute of Child Health and Human Development Bethesda Maryland USA
| | - Tracey A. Rouault
- Molecular Medicine Branch Eunice Kennedy Shriver National Institute of Child Health and Human Development Bethesda Maryland USA
| |
Collapse
|
8
|
Berry T, Abohamza E, Moustafa AA. Treatment-resistant schizophrenia: focus on the transsulfuration pathway. Rev Neurosci 2021; 31:219-232. [PMID: 31714892 DOI: 10.1515/revneuro-2019-0057] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 07/19/2019] [Indexed: 12/12/2022]
Abstract
Treatment-resistant schizophrenia (TRS) is a severe form of schizophrenia. The severity of illness is positively related to homocysteine levels, with high homocysteine levels due to the low activity of the transsulfuration pathway, which metabolizes homocysteine in synthesizing L-cysteine. Glutathione levels are low in schizophrenia, which indicates shortages of L-cysteine and low activity of the transsulfuration pathway. Hydrogen sulfide (H2S) levels are low in schizophrenia. H2S is synthesized by cystathionine β-synthase and cystathionine γ-lyase, which are the two enzymes in the transsulfuration pathway. Iron-sulfur proteins obtain sulfur from L-cysteine. The oxidative phosphorylation (OXPHOS) pathway has various iron-sulfur proteins. With low levels of L-cysteine, iron-sulfur cluster formation will be dysregulated leading to deficits in OXPHOS in schizophrenia. Molybdenum cofactor (MoCo) synthesis requires sulfur, which is obtained from L-cysteine. With low levels of MoCo synthesis, molybdenum-dependent sulfite oxidase (SUOX) will not be synthesized at appropriate levels. SUOX detoxifies sulfite from sulfur-containing amino acids. If sulfites are not detoxified, there can be sulfite toxicity. The transsulfuration pathway metabolizes selenomethionine, whereby selenium from selenomethionine can be used for selenoprotein synthesis. The low activity of the transsulfuration pathway decreases selenoprotein synthesis. Glutathione peroxidase (GPX), with various GPXs being selenoprotein, is low in schizophrenia. The dysregulations of selenoproteins would lead to oxidant stress, which would increase the methylation of genes and histones leading to epigenetic changes in TRS. An add-on treatment to mainline antipsychotics is proposed for TRS that targets the dysregulations of the transsulfuration pathway and the dysregulations of other pathways stemming from the transsulfuration pathway being dysregulated.
Collapse
Affiliation(s)
- Thomas Berry
- School of Social Sciences and Psychology, Western Sydney University, Sydney 2751, New South Wales, Australia
| | - Eid Abohamza
- Department of Social Sciences, College of Arts and Sciences, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Ahmed A Moustafa
- School of Social Sciences and Psychology, Western Sydney University, Sydney 2751, New South Wales, Australia.,Marcs Institute for Brain and Behaviour, Western Sydney University, Sydney 2751, New South Wales, Australia
| |
Collapse
|
9
|
Pang Y, Tan G, Yang X, Lin Y, Chen Y, Zhang J, Xie T, Zhou H, Fang J, Zhao Q, Ren X, Li J, Lyu J, Wang Z. Iron-sulphur cluster biogenesis factor LYRM4 is a novel prognostic biomarker associated with immune infiltrates in hepatocellular carcinoma. Cancer Cell Int 2021; 21:463. [PMID: 34488769 PMCID: PMC8419973 DOI: 10.1186/s12935-021-02131-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/31/2021] [Indexed: 12/11/2022] Open
Abstract
Background LYRM4 is necessary to maintain the stability and activity of the human cysteine desulfurase complex NFS1-LYRM4-ACP. The existing experimental results indicate that cancer cells rely on the high expression of NFS1. However, the role of LYRM4 in liver hepatocellular carcinoma (LIHC) remains unclear. Methods In this study, we combined bioinformatics analysis and clinical specimens to evaluate the mRNA, protein expression, and gene regulatory network of LYRM4 in LIHC. Furthermore, we detected the activity of several classical iron-sulphur proteins in LIHC cell lines through UV-vis spectrophotometry. Results The mRNA and protein levels of LYRM4 were upregulated in LIHC. Subsequent analysis revealed that the LYRM4 mRNA expression was related to various clinical stratifications, prognosis, and survival of LIHC patients. In addition, the mRNA expression of LYRM4 was significantly associated with ALT, tumour thrombus, and encapsulation of HBV-related LIHC patients. IHC results confirmed that LYRM4 was highly expressed in LIHC tissues and showed that the expression of LYRM4 protein in LIHC was significantly correlated with age and serum low-density lipoprotein (LDL) and triglyceride (TG) content. In particular, the mRNA expression of key iron- sulphur proteins POLD1 and PRIM2 was significantly overexpressed and correlated with poor prognosis in LIHC patients. Compared with hepatocytes, the activities of mitochondrial complex I and aconitate hydratase (ACO2) in LIHC cell lines were significantly increased. These results indicated that the iron-sulphur cluster (ISC) biosynthesis was significantly elevated in LIHC, leading to ISC-dependent metabolic reprogramming. Changes in the activity of ISC-dependent proteins may also occur in paracancerous tissues. Further analysis of the biological interaction and gene regulation networks of LYRM4 suggested that these genes were mainly involved in the citric acid cycle and oxidative phosphorylation. Finally, LYRM4 expression in LIHC was significantly positively correlated with the infiltrating levels of six immune cell types, and both factors were strongly associated with prognosis. Conclusion LYRM4 could be a novel prognostic biomarker and molecular target for LIHC therapy. In particular, the potential regulatory networks of LYRM4 overexpression in LIHC provide a scientific basis for future research on the role of the ISC assembly mechanism and LYRM4-mediated sulphur transfer routes in carcinogenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02131-3.
Collapse
Affiliation(s)
- Yilin Pang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, Hunan, China.,Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Guoqiang Tan
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Xunjun Yang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.,Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Yuanshan Lin
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Yao Chen
- Department of Pathology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jinping Zhang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Ting Xie
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Huaibin Zhou
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Jun Fang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Qiongya Zhao
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Xiaojun Ren
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Jianghui Li
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Jianxin Lyu
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China. .,People's Hospital of Hangzhou Medical College, Hangzhou, 310014, China.
| | - Zheng Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, Hunan, China.
| |
Collapse
|
10
|
Maio N, Zhang DL, Ghosh MC, Jain A, SantaMaria AM, Rouault TA. Mechanisms of cellular iron sensing, regulation of erythropoiesis and mitochondrial iron utilization. Semin Hematol 2021; 58:161-174. [PMID: 34389108 DOI: 10.1053/j.seminhematol.2021.06.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/08/2021] [Accepted: 06/10/2021] [Indexed: 12/11/2022]
Abstract
To maintain an adequate iron supply for hemoglobin synthesis and essential metabolic functions while counteracting iron toxicity, humans and other vertebrates have evolved effective mechanisms to conserve and finely regulate iron concentration, storage, and distribution to tissues. At the systemic level, the iron-regulatory hormone hepcidin is secreted by the liver in response to serum iron levels and inflammation. Hepcidin regulates the expression of the sole known mammalian iron exporter, ferroportin, to control dietary absorption, storage and tissue distribution of iron. At the cellular level, iron regulatory proteins 1 and 2 (IRP1 and IRP2) register cytosolic iron concentrations and post-transcriptionally regulate the expression of iron metabolism genes to optimize iron availability for essential cellular processes, including heme biosynthesis and iron-sulfur cluster biogenesis. Genetic malfunctions affecting the iron sensing mechanisms or the main pathways that utilize iron in the cell cause a broad range of human diseases, some of which are characterized by mitochondrial iron accumulation. This review will discuss the mechanisms of systemic and cellular iron sensing with a focus on the main iron utilization pathways in the cell, and on human conditions that arise from compromised function of the regulatory axes that control iron homeostasis.
Collapse
Affiliation(s)
- Nunziata Maio
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - De-Liang Zhang
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Manik C Ghosh
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Anshika Jain
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Anna M SantaMaria
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Tracey A Rouault
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD.
| |
Collapse
|
11
|
Mohammad Sadik, Mohammad Afsar, Ramachandran R, Habib S. [Fe-S] biogenesis and unusual assembly of the ISC scaffold complex in the Plasmodium falciparum mitochondrion. Mol Microbiol 2021; 116:606-623. [PMID: 34032321 DOI: 10.1111/mmi.14735] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 05/06/2021] [Accepted: 05/06/2021] [Indexed: 12/16/2022]
Abstract
The malaria parasite harbors two [Fe-S] biogenesis pathways of prokaryotic origin-the SUF and ISC systems in the apicoplast and mitochondrion, respectively. While the SUF machinery has been delineated, there is little experimental evidence on the ISC pathway. We confirmed mitochondrial targeting of Plasmodium falciparum ISC proteins followed by analyses of cysteine desulfurase, scaffold, and [Fe-S]-carrier components. PfIscU functioned as the scaffold in complex with the PfIscS-PfIsd11 cysteine desulfurase and could directly assemble [4Fe-4S] without prior [2Fe-2S] formation seen in other homologs. Small angle X-ray scattering and spectral studies showed that PfIscU, a trimer, bound one [4Fe-4S]. In a deviation from reported complexes from other organisms, the P. falciparum desulfurase-scaffold complex assembled around a PfIscS tetramer instead of a dimer, resulting in a symmetric hetero-hexamer [2× (2PfIscS-2PfIsd11-2PfIscU)]. PfIscU directly transferred [4Fe-4S] to the apo-protein aconitase B thus abrogating the requirement of intermediary proteins for conversion of [2Fe-2S] to [4Fe-4S] before transfer to [4Fe-4S]-recipients. Among the putative cluster-carriers, PfIscA2 was more efficient than PfNifU-like protein; PfIscA1 primarily bound iron, suggesting its potential role as a Fe2+ carrier/donor. Our results identify the core P. falciparum ISC machinery and reveal unique features compared with those in bacteria or yeast and human mitochondria.
Collapse
Affiliation(s)
- Mohammad Sadik
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Mohammad Afsar
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Ravishankar Ramachandran
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Saman Habib
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| |
Collapse
|
12
|
Perli T, van der Vorm DNA, Wassink M, van den Broek M, Pronk JT, Daran JM. Engineering heterologous molybdenum-cofactor-biosynthesis and nitrate-assimilation pathways enables nitrate utilization by Saccharomyces cerevisiae. Metab Eng 2021; 65:11-29. [PMID: 33617956 DOI: 10.1016/j.ymben.2021.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/28/2021] [Accepted: 02/15/2021] [Indexed: 02/06/2023]
Abstract
Metabolic capabilities of cells are not only defined by their repertoire of enzymes and metabolites, but also by availability of enzyme cofactors. The molybdenum cofactor (Moco) is widespread among eukaryotes but absent from the industrial yeast Saccharomyces cerevisiae. No less than 50 Moco-dependent enzymes covering over 30 catalytic activities have been described to date, introduction of a functional Moco synthesis pathway offers interesting options to further broaden the biocatalytic repertoire of S. cerevisiae. In this study, we identified seven Moco biosynthesis genes in the non-conventional yeast Ogataea parapolymorpha by SpyCas9-mediated mutational analysis and expressed them in S. cerevisiae. Functionality of the heterologously expressed Moco biosynthesis pathway in S. cerevisiae was assessed by co-expressing O. parapolymorpha nitrate-assimilation enzymes, including the Moco-dependent nitrate reductase. Following two-weeks of incubation, growth of the engineered S. cerevisiae strain was observed on nitrate as sole nitrogen source. Relative to the rationally engineered strain, the evolved derivatives showed increased copy numbers of the heterologous genes, increased levels of the encoded proteins and a 5-fold higher nitrate-reductase activity in cell extracts. Growth at nM molybdate concentrations was enabled by co-expression of a Chlamydomonas reinhardtii high-affinity molybdate transporter. In serial batch cultures on nitrate-containing medium, a non-engineered S. cerevisiae strain was rapidly outcompeted by the spoilage yeast Brettanomyces bruxellensis. In contrast, an engineered and evolved nitrate-assimilating S. cerevisiae strain persisted during 35 generations of co-cultivation. This result indicates that the ability of engineered strains to use nitrate may be applicable to improve competitiveness of baker's yeast in industrial processes upon contamination with spoilage yeasts.
Collapse
Affiliation(s)
- Thomas Perli
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands.
| | - Daan N A van der Vorm
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands.
| | - Mats Wassink
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands.
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands.
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands.
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands.
| |
Collapse
|
13
|
Termathe M, Leidel SA. Urm1: A Non-Canonical UBL. Biomolecules 2021; 11:biom11020139. [PMID: 33499055 PMCID: PMC7911844 DOI: 10.3390/biom11020139] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 01/10/2023] Open
Abstract
Urm1 (ubiquitin related modifier 1) is a molecular fossil in the class of ubiquitin-like proteins (UBLs). It encompasses characteristics of classical UBLs, such as ubiquitin or SUMO (small ubiquitin-related modifier), but also of bacterial sulfur-carrier proteins (SCP). Since its main function is to modify tRNA, Urm1 acts in a non-canonical manner. Uba4, the activating enzyme of Urm1, contains two domains: a classical E1-like domain (AD), which activates Urm1, and a rhodanese homology domain (RHD). This sulfurtransferase domain catalyzes the formation of a C-terminal thiocarboxylate on Urm1. Thiocarboxylated Urm1 is the sulfur donor for 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U), a chemical nucleotide modification at the wobble position in tRNA. This thio-modification is conserved in all domains of life and optimizes translation. The absence of Urm1 increases stress sensitivity in yeast triggered by defects in protein homeostasis, a hallmark of neurological defects in higher organisms. In contrast, elevated levels of tRNA modifying enzymes promote the appearance of certain types of cancer and the formation of metastasis. Here, we summarize recent findings on the unique features that place Urm1 at the intersection of UBL and SCP and make Urm1 an excellent model for studying the evolution of protein conjugation and sulfur-carrier systems.
Collapse
Affiliation(s)
- Martin Termathe
- Institute of Biochemistry, Protein Biochemistry and Photobiocatalysis, University of Greifswald, Felix-Hausdorff-Strasse 4, 17489 Greifswald, Germany;
| | - Sebastian A. Leidel
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
- Correspondence:
| |
Collapse
|
14
|
Abstract
Iron–sulfur (Fe–S) clusters are protein cofactors of a multitude of enzymes performing essential biological functions. Specialized multi-protein machineries present in all types of organisms support their biosynthesis. These machineries encompass a scaffold protein on which Fe–S clusters are assembled and a cysteine desulfurase that provides sulfur in the form of a persulfide. The sulfide ions are produced by reductive cleavage of the persulfide, which involves specific reductase systems. Several other components are required for Fe–S biosynthesis, including frataxin, a key protein of controversial function and accessory components for insertion of Fe–S clusters in client proteins. Fe–S cluster biosynthesis is thought to rely on concerted and carefully orchestrated processes. However, the elucidation of the mechanisms of their assembly has remained a challenging task due to the biochemical versatility of iron and sulfur and the relative instability of Fe–S clusters. Nonetheless, significant progresses have been achieved in the past years, using biochemical, spectroscopic and structural approaches with reconstituted system in vitro. In this paper, we review the most recent advances on the mechanism of assembly for the founding member of the Fe–S cluster family, the [2Fe2S] cluster that is the building block of all other Fe–S clusters. The aim is to provide a survey of the mechanisms of iron and sulfur insertion in the scaffold proteins by examining how these processes are coordinated, how sulfide is produced and how the dinuclear [2Fe2S] cluster is formed, keeping in mind the question of the physiological relevance of the reconstituted systems. We also cover the latest outcomes on the functional role of the controversial frataxin protein in Fe–S cluster biosynthesis.
Collapse
|
15
|
Mayr SJ, Mendel RR, Schwarz G. Molybdenum cofactor biology, evolution and deficiency. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118883. [PMID: 33017596 DOI: 10.1016/j.bbamcr.2020.118883] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/21/2020] [Accepted: 09/24/2020] [Indexed: 12/14/2022]
Abstract
The molybdenum cofactor (Moco) represents an ancient metal‑sulfur cofactor, which participates as catalyst in carbon, nitrogen and sulfur cycles, both on individual and global scale. Given the diversity of biological processes dependent on Moco and their evolutionary age, Moco is traced back to the last universal common ancestor (LUCA), while Moco biosynthetic genes underwent significant changes through evolution and acquired additional functions. In this review, focused on eukaryotic Moco biology, we elucidate the benefits of gene fusions on Moco biosynthesis and beyond. While originally the gene fusions were driven by biosynthetic advantages such as coordinated expression of functionally related proteins and product/substrate channeling, they also served as origin for the development of novel functions. Today, Moco biosynthetic genes are involved in a multitude of cellular processes and loss of the according gene products result in severe disorders, both related to Moco biosynthesis and secondary enzyme functions.
Collapse
Affiliation(s)
- Simon J Mayr
- Institute of Biochemistry, Department of Chemistry, Center for Molecular Medicine, University of Cologne, Zuelpicher Str. 47, 50674 Koeln, Germany
| | - Ralf-R Mendel
- Institute of Plant Biology, Braunschweig University of Technology, Humboldtstr. 1, 38106 Braunschweig, Germany
| | - Guenter Schwarz
- Institute of Biochemistry, Department of Chemistry, Center for Molecular Medicine, University of Cologne, Zuelpicher Str. 47, 50674 Koeln, Germany.
| |
Collapse
|
16
|
The Requirement of Inorganic Fe-S Clusters for the Biosynthesis of the Organometallic Molybdenum Cofactor. INORGANICS 2020. [DOI: 10.3390/inorganics8070043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Iron-sulfur (Fe-S) clusters are essential protein cofactors. In enzymes, they are present either in the rhombic [2Fe-2S] or the cubic [4Fe-4S] form, where they are involved in catalysis and electron transfer and in the biosynthesis of metal-containing prosthetic groups like the molybdenum cofactor (Moco). Here, we give an overview of the assembly of Fe-S clusters in bacteria and humans and present their connection to the Moco biosynthesis pathway. In all organisms, Fe-S cluster assembly starts with the abstraction of sulfur from l-cysteine and its transfer to a scaffold protein. After formation, Fe-S clusters are transferred to carrier proteins that insert them into recipient apo-proteins. In eukaryotes like humans and plants, Fe-S cluster assembly takes place both in mitochondria and in the cytosol. Both Moco biosynthesis and Fe-S cluster assembly are highly conserved among all kingdoms of life. Moco is a tricyclic pterin compound with molybdenum coordinated through its unique dithiolene group. Moco biosynthesis begins in the mitochondria in a Fe-S cluster dependent step involving radical/S-adenosylmethionine (SAM) chemistry. An intermediate is transferred to the cytosol where the dithiolene group is formed, to which molybdenum is finally added. Further connections between Fe-S cluster assembly and Moco biosynthesis are discussed in detail.
Collapse
|
17
|
Purroy R, Medina-Carbonero M, Ros J, Tamarit J. Frataxin-deficient cardiomyocytes present an altered thiol-redox state which targets actin and pyruvate dehydrogenase. Redox Biol 2020; 32:101520. [PMID: 32279039 PMCID: PMC7152683 DOI: 10.1016/j.redox.2020.101520] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/10/2020] [Accepted: 03/21/2020] [Indexed: 01/11/2023] Open
Abstract
Friedreich ataxia (FA) is a cardioneurodegenerative disease caused by deficient frataxin expression. This mitochondrial protein has been related to iron homeostasis, energy metabolism, and oxidative stress. Previously, we set up a cardiac cellular model of FA based on neonatal rat cardiac myocytes (NRVM) and lentivirus-mediated frataxin RNA interference. These frataxin-deficient NRVMs presented lipid droplet accumulation, mitochondrial swelling and signs of oxidative stress. Therefore, we decided to explore the presence of protein thiol modifications in this model. With this purpose, reduced glutathione (GSH) levels were measured and the presence of glutathionylated proteins was analyzed. We observed decreased GSH content and increased presence of glutahionylated actin in frataxin-deficient NRVMs. Moreover, the presence of oxidized cysteine residues was investigated using the thiol-reactive fluorescent probe iodoacetamide-Bodipy and 2D-gel electrophoresis. With this approach, we identified two proteins with altered redox status in frataxin-deficient NRVMs: electron transfer flavoprotein-ubiquinone oxidoreductase and dihydrolipoyl dehydrogenase (DLDH). As DLDH is involved in protein-bound lipoic acid redox cycling, we analyzed the redox state of this cofactor and we observed that lipoic acid from pyruvate dehydrogenase was more oxidized in frataxin-deficient cells. Also, by targeted proteomics, we observed a decreased content on the PDH A1 subunit from pyruvate dehydrogenase. Finally, we analyzed the consequences of supplementing frataxin-deficient NRVMs with the PDH cofactors thiamine and lipoic acid, the PDH activator dichloroacetate and the antioxidants N-acetyl cysteine and Tiron. Both dichloroacetate and Tiron were able to partially prevent lipid droplet accumulation in these cells. Overall, these results indicate that frataxin-deficient NRVMs present an altered thiol-redox state which could contribute to the cardiac pathology.
Collapse
Affiliation(s)
- Rosa Purroy
- Dept. Ciències Mèdiques Bàsiques, Fac. Medicina, IRBLLeida, Universitat de Lleida, Lleida, Spain
| | - Marta Medina-Carbonero
- Dept. Ciències Mèdiques Bàsiques, Fac. Medicina, IRBLLeida, Universitat de Lleida, Lleida, Spain
| | - Joaquim Ros
- Dept. Ciències Mèdiques Bàsiques, Fac. Medicina, IRBLLeida, Universitat de Lleida, Lleida, Spain
| | - Jordi Tamarit
- Dept. Ciències Mèdiques Bàsiques, Fac. Medicina, IRBLLeida, Universitat de Lleida, Lleida, Spain.
| |
Collapse
|
18
|
Berry T, Abohamza E, Moustafa AA. A disease-modifying treatment for Alzheimer's disease: focus on the trans-sulfuration pathway. Rev Neurosci 2020; 31:319-334. [PMID: 31751299 DOI: 10.1515/revneuro-2019-0076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 08/31/2019] [Indexed: 12/16/2022]
Abstract
High homocysteine levels in Alzheimer's disease (AD) result from low activity of the trans-sulfuration pathway. Glutathione levels are also low in AD. L-cysteine is required for the synthesis of glutathione. The synthesis of coenzyme A (CoA) requires L-cysteine, which is synthesized via the trans-sulfuration pathway. CoA is required for the synthesis of acetylcholine and appropriate cholinergic neurotransmission. L-cysteine is required for the synthesis of molybdenum-containing proteins. Sulfite oxidase (SUOX), which is a molybdenum-containing protein, could be dysregulated in AD. SUOX detoxifies the sulfites. Glutaminergic neurotransmission could be dysregulated in AD due to low levels of SUOX and high levels of sulfites. L-cysteine provides sulfur for iron-sulfur clusters. Oxidative phosphorylation (OXPHOS) is heavily dependent on iron-sulfur proteins. The decrease in OXPHOS seen in AD could be due to dysregulations of the trans-sulfuration pathway. There is a decrease in aconitase 1 (ACO1) in AD. ACO1 is an iron-sulfur enzyme in the citric acid cycle that upon loss of an iron-sulfur cluster converts to iron regulatory protein 1 (IRP1). With the dysregulation of iron-sulfur cluster formation ACO1 will convert to IRP1 which will decrease the 2-oxglutarate synthesis dysregulating the citric acid cycle and also dysregulating iron metabolism. Selenomethionine is also metabolized by the trans-sulfuration pathway. With the low activity of the trans-sulfuration pathway in AD selenoproteins will be dysregulated in AD. Dysregulation of selenoproteins could lead to oxidant stress in AD. In this article, we propose a novel treatment for AD that addresses dysregulations resulting from low activity of the trans-sulfuration pathway and low L-cysteine.
Collapse
Affiliation(s)
- Thomas Berry
- School of Social Sciences and Psychology, Western Sydney University, 2 Bullecourt Ave, Milperra, 2214 Sydney, New South Wales, Australia
| | - Eid Abohamza
- Department of Social Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Ahmed A Moustafa
- School of Social Sciences and Psychology, Western Sydney University, 2 Bullecourt Ave, Milperra, 2214 Sydney, New South Wales, Australia
| |
Collapse
|
19
|
Maio N, Jain A, Rouault TA. Mammalian iron-sulfur cluster biogenesis: Recent insights into the roles of frataxin, acyl carrier protein and ATPase-mediated transfer to recipient proteins. Curr Opin Chem Biol 2020; 55:34-44. [PMID: 31918395 PMCID: PMC7237328 DOI: 10.1016/j.cbpa.2019.11.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 11/20/2019] [Accepted: 11/30/2019] [Indexed: 12/31/2022]
Abstract
The recently solved crystal structures of the human cysteine desulfurase NFS1, in complex with the LYR protein ISD11, the acyl carrier protein ACP, and the main scaffold ISCU, have shed light on the molecular interactions that govern initial cluster assembly on ISCU. Here, we aim to highlight recent insights into iron-sulfur (Fe-S) cluster (ISC) biogenesis in mammalian cells that have arisen from the crystal structures of the core ISC assembly complex. We will also discuss how ISCs are delivered to recipient proteins and the challenges that remain in dissecting the pathways that deliver clusters to numerous Fe-S recipient proteins in both the mitochondrial matrix and cytosolic compartments of mammalian cells.
Collapse
Affiliation(s)
- Nunziata Maio
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Anshika Jain
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Tracey A Rouault
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 9000 Rockville Pike, Bethesda, MD 20892, USA.
| |
Collapse
|
20
|
Outlining the Complex Pathway of Mammalian Fe-S Cluster Biogenesis. Trends Biochem Sci 2020; 45:411-426. [PMID: 32311335 DOI: 10.1016/j.tibs.2020.02.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/27/2020] [Accepted: 02/04/2020] [Indexed: 12/14/2022]
Abstract
Iron-sulfur (Fe-S) clusters (ISCs) are ubiquitous cofactors essential to numerous fundamental cellular processes. Assembly of ISCs and their insertion into apoproteins involves the function of complex cellular machineries that operate in parallel in the mitochondrial and cytosolic/nuclear compartments of mammalian cells. The spectrum of diseases caused by inherited defects in genes that encode the Fe-S assembly proteins has recently expanded to include multiple rare human diseases, which manifest distinctive combinations and severities of global and tissue-specific impairments. In this review, we provide an overview of our understanding of ISC biogenesis in mammalian cells, discuss recent work that has shed light on the molecular interactions that govern ISC assembly, and focus on human diseases caused by failures of the biogenesis pathway.
Collapse
|
21
|
Feng S, Hou S, Cui Y, Tong Y, Yang H. Metabolic transcriptional analysis on copper tolerance in moderate thermophilic bioleaching microorganism Acidithiobacillus caldus. J Ind Microbiol Biotechnol 2019; 47:21-33. [PMID: 31758413 DOI: 10.1007/s10295-019-02247-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/05/2019] [Indexed: 01/06/2023]
Abstract
Bioleaching, an alternative environmental smelting technology, typically uses high concentrations of heavy metal ions, especially in the subsequent phase, due to metal ion accumulation from the mineral. In this study, we analyzed the overall response of the bioleaching microorganism Acidithiobacillus caldus to copper stress through physiological and transcriptomic analyses. Scanning electron microscopy results showed higher extracellular polymeric substances secretion and cell aggregation under copper stress. Intracellular levels of glutamic acid, glycine and cysteine increased, favoring the synthesis of glutathione for maintenance of the oxidation-reduction state. GSH, during copper stress conditions, the activity of GSH-PX and CAT increased, resulting in reduced oxidative damage while maintaining stable intracellular pH. Higher unsaturated and cyclopropane fatty acid levels resulted in increased membrane fluidity and compactness and decreased ATP levels to support the energy requirements for stress resistance. Initially, H+-ATPase activity increased to provide energy for proton output and decreased later at higher copper ion stress. From transcriptome analysis, 140 genes were differentially expressed under low copper stress (1 g/L), while 250 genes exhibited altered transcriptional levels at higher copper stress (3 g/L). These differentially expressed genes were involved primarily in metabolic pathways such as energy metabolism, two-component systems, amino acid metabolism, and signal transduction. The Sox family cluster gene cluster involved in the conversion of thiosulfate to sulfate was upregulated in the sulfur metabolism pathway. In the oxidative phosphorylation pathway, genes participating in the synthesis of NADH oxidoreductase and cytochrome c oxidase, nuoL, cyoABD (cyoA, cyoB and cyoD) and cydAB (cydA and cydB), were downregulated. The TCS element ompR, closely associated with the osmotic pressure, exhibited active response, while Cu2+ efflux system gene cusRS was upregulated. In the amino acid metabolism, the glnA involved in nitrogen fixation was upregulated and promoted the synthesis of glutamine synthetase for reducing excessive oxidative stress. This study provides new insights into the mechanism underlying A. caldus response to heavy-metal ion stress under harsh bioleaching conditions.
Collapse
Affiliation(s)
- Shoushuai Feng
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, Wuxi, People's Republic of China.,Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, People's Republic of China
| | - Shaoxiang Hou
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, Wuxi, People's Republic of China.,Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, People's Republic of China
| | - Yaquan Cui
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China.,The Key Laboratory of Industrial Biotechnology, Ministry of Education, Wuxi, People's Republic of China.,Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, People's Republic of China
| | - Yanjun Tong
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China. .,School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China.
| | - Hailin Yang
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, People's Republic of China. .,The Key Laboratory of Industrial Biotechnology, Ministry of Education, Wuxi, People's Republic of China. .,Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, People's Republic of China.
| |
Collapse
|
22
|
Bellanda M, Maso L, Doni D, Bortolus M, De Rosa E, Lunardi F, Alfonsi A, Noguera ME, Herrera MG, Santos J, Carbonera D, Costantini P. Exploring iron-binding to human frataxin and to selected Friedreich ataxia mutants by means of NMR and EPR spectroscopies. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2019; 1867:140254. [PMID: 31344531 DOI: 10.1016/j.bbapap.2019.07.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/12/2019] [Accepted: 07/18/2019] [Indexed: 11/23/2022]
Abstract
The neurodegenerative disease Friedreich ataxia results from a deficiency of frataxin, a mitochondrial protein. Most patients have a GAA expansion in the first intron of both alleles of frataxin gene, whereas a minority of them are heterozygous for the expansion and contain a mutation in the other allele. Frataxin has been claimed to participate in iron homeostasis and biosynthesis of FeS clusters, however its role in both pathways is not unequivocally defined. In this work we combined different advanced spectroscopic analyses to explore the iron-binding properties of human frataxin, as isolated and at the FeS clusters assembly machinery. For the first time we used EPR spectroscopy to address this key issue providing clear evidence of the formation of a complex with a low symmetry coordination of the metal ion. By 2D NMR, we confirmed that iron can be bound in both oxidation states, a controversial issue, and, in addition, we were able to point out a transient interaction of frataxin with a N-terminal 6his-tagged variant of ISCU, the scaffold protein of the FeS clusters assembly machinery. To obtain insights on structure/function relationships relevant to understand the disease molecular mechanism(s), we extended our studies to four clinical frataxin mutants. All variants showed a moderate to strong impairment in their ability to activate the FeS cluster assembly machinery in vitro, while keeping the same iron-binding features of the wild type protein. This supports the multifunctional nature of frataxin and the complex biochemical consequences of its mutations.
Collapse
Affiliation(s)
- Massimo Bellanda
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy
| | - Lorenzo Maso
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy
| | - Davide Doni
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy
| | - Marco Bortolus
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy
| | - Edith De Rosa
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy; Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy
| | - Federica Lunardi
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy
| | - Arianna Alfonsi
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy
| | - Martín Ezequiel Noguera
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Universidad de Buenos Aires, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Intendente Güiraldes 2160 - Ciudad Universitaria, 1428EGA C.A.B.A., Argentina; Intituto de Química y Fisicoquímica Biológicas, Dr. Alejandro Paladini, Universidad de Buenos Aires, CONICET, Junín 956, 1113AAD C.A.B.A., Argentina
| | - Maria Georgina Herrera
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Universidad de Buenos Aires, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Intendente Güiraldes 2160 - Ciudad Universitaria, 1428EGA C.A.B.A., Argentina; Intituto de Química y Fisicoquímica Biológicas, Dr. Alejandro Paladini, Universidad de Buenos Aires, CONICET, Junín 956, 1113AAD C.A.B.A., Argentina
| | - Javier Santos
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencia Exactas y Naturales, Universidad de Buenos Aires, Instituto de Biociencias, Biotecnología y Biomedicina (iB3), Intendente Güiraldes 2160 - Ciudad Universitaria, 1428EGA C.A.B.A., Argentina; Intituto de Química y Fisicoquímica Biológicas, Dr. Alejandro Paladini, Universidad de Buenos Aires, CONICET, Junín 956, 1113AAD C.A.B.A., Argentina
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova, Via F. Marzolo 1, 35131 Padova, Italy.
| | - Paola Costantini
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy.
| |
Collapse
|
23
|
Wang J, Guo X, Li H, Qi H, Qian J, Yan S, Shi J, Niu W. Hydrogen Sulfide From Cysteine Desulfurase, Not 3-Mercaptopyruvate Sulfurtransferase, Contributes to Sustaining Cell Growth and Bioenergetics in E. coli Under Anaerobic Conditions. Front Microbiol 2019; 10:2357. [PMID: 31681220 PMCID: PMC6797615 DOI: 10.3389/fmicb.2019.02357] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 09/27/2019] [Indexed: 01/09/2023] Open
Abstract
Endogenous hydrogen sulfide (H2S), which is primarily generated by 3-mercaptopyruvate sulfurtransferase (3-MST) in Escherichia coli (E. coli) under aerobic conditions, renders bacteria highly resistant to oxidative stress. However, the biosynthetic pathway and physiological role of this gas under anaerobic conditions remains largely unknown. In the present study, we demonstrate that cysteine desulfurase (IscS), not 3-MST, is the primary source of endogenous H2S in E. coli under anaerobic conditions. A significant decrease in H2S production under anaerobic conditions was observed in E. coli upon deletion of IscS, but not in 3-MST-deficient bacteria (ΔmstA). Furthermore, the H2S-producing activity of recombinant IscS using L-cysteine as a substrate exhibited an approximately 2.6-fold increase in the presence of dithiothreitol (DTT), indicating that H2S production catalyzed by IscS was greatly increased under reducing conditions. The activity of IscS was regulated under the different redox conditions and the midpoint redox potential was determined to be −329 ± 1.6 mV. Moreover, in E. coli cells H2S production from IscS is regulated under oxidative and reductive stress. A mutant E. coli (ΔiscS) strain lacking a chromosomal copy of the IscS-encoding gene iscS showed significant growth defects and low levels of ATP under both aerobic and anaerobic conditions. The growth defects could be fully restored after addition of 500 μM Na2S (an H2S donor) under anaerobic conditions, but not by the addition of cysteine, sodium sulfite or sodium sulfate. We also showed that the addition of 500 μM Na2S to culture medium stimulates ATP synthesis in the mutant E. coli (ΔiscS) strain in the logarithmic growth phase but suppresses ATP synthesis in wild-type E. coli. Our results reveal a new H2S-producing pathway in E. coli under anaerobic conditions and show that hydrogen sulfide from IscS contributes to sustaining cell growth and bioenergetics under oxygen-deficient conditions.
Collapse
Affiliation(s)
- Jun Wang
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Xin Guo
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Heng Li
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Haizhen Qi
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Jing Qian
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Shasha Yan
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Junling Shi
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Weining Niu
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| |
Collapse
|
24
|
Patra S, Barondeau DP. Mechanism of activation of the human cysteine desulfurase complex by frataxin. Proc Natl Acad Sci U S A 2019; 116:19421-19430. [PMID: 31511419 PMCID: PMC6765240 DOI: 10.1073/pnas.1909535116] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The function of frataxin (FXN) has garnered great scientific interest since its depletion was linked to the incurable neurodegenerative disease Friedreich's ataxia (FRDA). FXN has been shown to be necessary for iron-sulfur (Fe-S) cluster biosynthesis and proper mitochondrial function. The structural and functional core of the Fe-S cluster assembly complex is a low-activity pyridoxal 5'-phosphate (PLP)-dependent cysteine desulfurase enzyme that consists of catalytic (NFS1), LYRM protein (ISD11), and acyl carrier protein (ACP) subunits. Although previous studies show that FXN stimulates the activity of this assembly complex, the mechanism of FXN activation is poorly understood. Here, we develop a radiolabeling assay and use stopped-flow kinetics to establish that FXN is functionally linked to the mobile S-transfer loop cysteine of NFS1. Our results support key roles for this essential cysteine residue in substrate binding, as a general acid to advance the Cys-quinonoid PLP intermediate, as a nucleophile to form an NFS1 persulfide, and as a sulfur delivery agent to generate a persulfide species on the Fe-S scaffold protein ISCU2. FXN specifically accelerates each of these individual steps in the mechanism. Our resulting architectural switch model explains why the human Fe-S assembly system has low inherent activity and requires activation, the connection between the functional mobile S-transfer loop cysteine and FXN binding, and why the prokaryotic system does not require a similar FXN-based activation. Together, these results provide mechanistic insights into the allosteric-activator role of FXN and suggest new strategies to replace FXN function in the treatment of FRDA.
Collapse
Affiliation(s)
- Shachin Patra
- Department of Chemistry, Texas A&M University, College Station, TX 77842
| | - David P Barondeau
- Department of Chemistry, Texas A&M University, College Station, TX 77842
| |
Collapse
|
25
|
Wang L, Cai X, Xing J, Liu C, Hendy A, Chen XL. URM1-Mediated Ubiquitin-Like Modification Is Required for Oxidative Stress Adaptation During Infection of the Rice Blast Fungus. Front Microbiol 2019; 10:2039. [PMID: 31551975 PMCID: PMC6746893 DOI: 10.3389/fmicb.2019.02039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 08/19/2019] [Indexed: 12/17/2022] Open
Abstract
Ubiquitin is a small modifier protein which is usually conjugated to substrate proteins for degradation. In recent years, a number of ubiquitin-like proteins have been identified; however, their roles in eukaryotes are largely unknown. Here, we describe a ubiquitin-like protein URM1, and found it plays important roles in the development and infection process of the rice blast fungus, Magnaporthe oryzae. Targeted deletion of URM1 in M. oryzae resulted in slight reduction in vegetative growth and significant decrease in conidiation. More importantly, the Δurm1 mutant also showed evident reduction in virulence to host plants. Infection process observation demonstrated that the mutant was arrested in invasive growth and resulted in accumulation of massive host reactive oxygen species (ROS). Further, we found the Δurm1 mutant was sensitive to the cell wall disturbing reagents, thiol oxidizing agent diamide and rapamycin. We also showed that URM1-mediated modification was responsive to oxidative stresses, and the thioredoxin peroxidase Ahp1 was one of the important urmylation targets. These results suggested that URM1-mediated urmylation plays important roles in detoxification of host oxidative stress to facilitate invasive growth in M. oryzae.
Collapse
Affiliation(s)
- Luyang Wang
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xuan Cai
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Junjie Xing
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
| | - Caiyun Liu
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ahmed Hendy
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,Department of Agricultural Botany, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, Egypt
| | - Xiao-Lin Chen
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
| |
Collapse
|
26
|
Selles B, Moseler A, Rouhier N, Couturier J. Rhodanese domain-containing sulfurtransferases: multifaceted proteins involved in sulfur trafficking in plants. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4139-4154. [PMID: 31055601 DOI: 10.1093/jxb/erz213] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 04/29/2019] [Indexed: 05/25/2023]
Abstract
Sulfur is an essential element for the growth and development of plants, which synthesize cysteine and methionine from the reductive assimilation of sulfate. Besides its incorporation into proteins, cysteine is the building block for the biosynthesis of numerous sulfur-containing molecules and cofactors. The required sulfur atoms are extracted either directly from cysteine by cysteine desulfurases or indirectly after its catabolic transformation to 3-mercaptopyruvate, a substrate for sulfurtransferases (STRs). Both enzymes are transiently persulfidated in their reaction cycle, i.e. the abstracted sulfur atom is bound to a reactive cysteine residue in the form of a persulfide group. Trans-persulfidation reactions occur when sulfur atoms are transferred to nucleophilic acceptors such as glutathione, proteins, or small metabolites. STRs form a ubiquitous, multigenic protein family. They are characterized by the presence of at least one rhodanese homology domain (Rhd), which usually contains the catalytic, persulfidated cysteine. In this review, we focus on Arabidopsis STRs, presenting the sequence characteristics of all family members as well as their biochemical and structural features. The physiological functions of particular STRs in the biosynthesis of molybdenum cofactor, thio-modification of cytosolic tRNAs, arsenate tolerance, cysteine catabolism, and hydrogen sulfide formation are also discussed.
Collapse
Affiliation(s)
| | - Anna Moseler
- Université de Lorraine, Inra, IAM, Nancy, France
| | | | | |
Collapse
|
27
|
Das D, Patra S, Bridwell-Rabb J, Barondeau DP. Mechanism of frataxin "bypass" in human iron-sulfur cluster biosynthesis with implications for Friedreich's ataxia. J Biol Chem 2019; 294:9276-9284. [PMID: 30975898 PMCID: PMC6556584 DOI: 10.1074/jbc.ra119.007716] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/10/2019] [Indexed: 11/06/2022] Open
Abstract
In humans, mitochondrial iron-sulfur cluster biosynthesis is an essential biochemical process mediated by the assembly complex consisting of cysteine desulfurase (NFS1), LYR protein (ISD11), acyl-carrier protein (ACP), and the iron-sulfur cluster assembly scaffold protein (ISCU2). The protein frataxin (FXN) is an allosteric activator that binds the assembly complex and stimulates the cysteine desulfurase and iron-sulfur cluster assembly activities. FXN depletion causes loss of activity of iron-sulfur-dependent enzymes and the development of the neurodegenerative disease Friedreich's ataxia. Recently, a mutation that suppressed the loss of the FXN homolog in Saccharomyces cerevisiae was identified that encodes an amino acid substitution equivalent to the human variant ISCU2 M140I. Here, we developed iron-sulfur cluster synthesis and transfer functional assays and determined that the human ISCU2 M140I variant can substitute for FXN in accelerating the rate of iron-sulfur cluster formation on the monothiol glutaredoxin (GRX5) acceptor protein. Incorporation of both FXN and the M140I substitution had an additive effect, suggesting an acceleration of distinct steps in iron-sulfur cluster biogenesis. In contrast to the canonical role of FXN in stimulating the formation of [2Fe-2S]-ISCU2 intermediates, we found here that the M140I substitution in ISCU2 promotes the transfer of iron-sulfur clusters to GRX5. Together, these results reveal an unexpected mechanism that replaces FXN-based stimulation of the iron-sulfur cluster biosynthetic pathway and suggest new strategies to overcome the loss of cellular FXN that may be relevant to the development of therapeutics for Friedreich's ataxia.
Collapse
Affiliation(s)
- Deepika Das
- From the Department of Chemistry, Texas A & M University, College Station, Texas 77842
| | - Shachin Patra
- From the Department of Chemistry, Texas A & M University, College Station, Texas 77842
| | | | - David P Barondeau
- From the Department of Chemistry, Texas A & M University, College Station, Texas 77842
| |
Collapse
|
28
|
Rouault TA. The indispensable role of mammalian iron sulfur proteins in function and regulation of multiple diverse metabolic pathways. Biometals 2019; 32:343-353. [PMID: 30923992 PMCID: PMC6584224 DOI: 10.1007/s10534-019-00191-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 03/18/2019] [Indexed: 02/07/2023]
Abstract
In recent years, iron sulfur (Fe–S) proteins have been identified as key players in mammalian metabolism, ranging from long-known roles in the respiratory complexes and the citric acid cycle, to more recently recognized roles in RNA and DNA metabolism. Fe–S cofactors have often been missed because of their intrinsic lability and oxygen sensitivity. More Fe–S proteins have now been identified owing to detection of their direct interactions with components of the Fe–S biogenesis machinery, and through use of informatics to detect a motif that binds the co-chaperone responsible for transferring nascent Fe–S clusters to domains of recipient proteins. Dissection of the molecular steps involved in Fe–S transfer to Fe–S proteins has revealed that direct and shielded transfer occurs through highly conserved pathways that operate in parallel in the mitochondrial matrix and in the cytosolic/nuclear compartments of eukaryotic cells. Because Fe–S clusters have the unusual ability to accept or donate single electrons in chemical reactions, their presence renders complex chemical reactions possible. In addition, Fe–S clusters may function as sensors that interconnect activity of metabolic pathways with cellular redox status. Presence in pathways that control growth and division may enable cells to regulate their growth according to sufficiency of energy stores represented by redox capacity, and oxidation of such proteins could diminish anabolic activities to give cells an opportunity to restore energy supplies. This review will discuss mechanisms of Fe–S biogenesis and delivery, and methods that will likely reveal important roles of Fe–S proteins in proteins not yet recognized as Fe–S proteins.
Collapse
|
29
|
Neukranz Y, Kotter A, Beilschmidt L, Marelja Z, Helm M, Gräf R, Leimkühler S. Analysis of the Cellular Roles of MOCS3 Identifies a MOCS3-Independent Localization of NFS1 at the Tips of the Centrosome. Biochemistry 2019; 58:1786-1798. [PMID: 30817134 DOI: 10.1021/acs.biochem.8b01160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The deficiency of the molybdenum cofactor (Moco) is an autosomal recessive disease, which leads to the loss of activity of all molybdoenzymes in humans with sulfite oxidase being the essential protein. Moco deficiency generally results in death in early childhood. Moco is a sulfur-containing cofactor synthesized in the cytosol with the sulfur being provided by a sulfur relay system composed of the l-cysteine desulfurase NFS1, MOCS3, and MOCS2A. Human MOCS3 is a dual-function protein that was shown to play an important role in Moco biosynthesis and in the mcm5s2U thio modifications of nucleosides in cytosolic tRNAs for Lys, Gln, and Glu. In this study, we constructed a homozygous MOCS3 knockout in HEK293T cells using the CRISPR/Cas9 system. The effects caused by the absence of MOCS3 were analyzed in detail. We show that sulfite oxidase activity was almost completely abolished, on the basis of the absence of Moco in these cells. In addition, mcm5s2U thio-modified tRNAs were not detectable. Because the l-cysteine desulfurase NFS1 was shown to act as a sulfur donor for MOCS3 in the cytosol, we additionally investigated the impact of a MOCS3 knockout on the cellular localization of NFS1. By different methods, we identified a MOCS3-independent novel localization of NFS1 at the centrosome.
Collapse
Affiliation(s)
| | - Annika Kotter
- Institute of Pharmacy and Biochemistry , Johannes Gutenberg-Universität Mainz , 55128 Mainz , Germany
| | | | | | - Mark Helm
- Institute of Pharmacy and Biochemistry , Johannes Gutenberg-Universität Mainz , 55128 Mainz , Germany
| | | | | |
Collapse
|
30
|
Rasheed M, Jamshidiha M, Puglisi R, Yan R, Cota E, Pastore A. Structural and functional characterization of a frataxin from a thermophilic organism. FEBS J 2019; 286:495-506. [PMID: 30636112 PMCID: PMC6506826 DOI: 10.1111/febs.14750] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/03/2018] [Accepted: 01/10/2019] [Indexed: 01/07/2023]
Abstract
Frataxins form an interesting family of iron-binding proteins with an almost unique fold and are highly conserved from bacteria to primates. They have a pivotal role in iron-sulfur cluster biogenesis as regulators of the rates of cluster formation, as it is testified by the fact that frataxin absence is incompatible with life and reduced levels of the protein lead to the recessive neurodegenerative disease Friedreich's ataxia. Despite its importance, the structure of frataxin has been solved only from relatively few species. Here, we discuss the X-ray structure of frataxin from the thermophilic fungus Chaetomium thermophilum, and the characterization of its interactions and dynamics in solution. We show that this eukaryotic frataxin has an unusual variation in the classical frataxin fold: the last helix is shorter than in other frataxins which results in a less symmetrical and compact structure. The stability of this protein is comparable to that of human frataxin, currently the most stable among the frataxin orthologues. We also characterized the iron-binding mode of Ct frataxin and demonstrated that it binds it through a semiconserved negatively charged ridge on the first helix and beta-strand. Moreover, this frataxin is also able to bind the bacterial ortholog of the desulfurase, which is central in iron-sulfur cluster synthesis, and act as its inhibitor.
Collapse
Affiliation(s)
- Masooma Rasheed
- King's College LondonUK
- UK Dementia Research Institute at King's College LondonUK
| | | | - Rita Puglisi
- King's College LondonUK
- UK Dementia Research Institute at King's College LondonUK
| | - Robert Yan
- King's College LondonUK
- UK Dementia Research Institute at King's College LondonUK
| | - Ernesto Cota
- Department of Life SciencesImperial CollegeLondonSouth KensingtonUK
| | - Annalisa Pastore
- King's College LondonUK
- UK Dementia Research Institute at King's College LondonUK
- University of PaviaItaly
| |
Collapse
|
31
|
Kim KS, Maio N, Singh A, Rouault TA. Cytosolic HSC20 integrates de novo iron-sulfur cluster biogenesis with the CIAO1-mediated transfer to recipients. Hum Mol Genet 2019; 27:837-852. [PMID: 29309586 DOI: 10.1093/hmg/ddy004] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/29/2017] [Indexed: 12/29/2022] Open
Abstract
Iron-sulfur (Fe-S) clusters are cofactors in hundreds of proteins involved in multiple cellular processes, including mitochondrial respiration, the maintenance of genome stability, ribosome biogenesis and translation. Fe-S cluster biogenesis is performed by multiple enzymes that are highly conserved throughout evolution, and mutations in numerous biogenesis factors are now recognized to cause a wide range of previously uncategorized rare human diseases. Recently, a complex formed of components of the cytoplasmic Fe-S cluster assembly (CIA) machinery, consisting of CIAO1, FAM96B and MMS19, was found to deliver Fe-S clusters to a subset of proteins involved in DNA metabolism, but it was unclear how this complex acquired its fully synthesized Fe-S clusters, because Fe-S clusters have been alleged to be assembled de novo solely in the mitochondrial matrix. Here, we investigated the potential role of the human cochaperone HSC20 in cytosolic Fe-S assembly and found that HSC20 assists Fe-S cluster delivery to cytosolic and nuclear Fe-S proteins. Cytosolic HSC20 (C-HSC20) mediated complex formation between components of the cytosolic Fe-S biogenesis pathway (ISC), including the primary scaffold, ISCU1, and the cysteine desulfurase, NFS1, and the CIA targeting complex, consisting of CIAO1, FAM96B and MMS19, to facilitate Fe-S cluster insertion into cytoplasmic and nuclear Fe-S recipients. Thus, C-HSC20 integrates initial Fe-S biosynthesis with the transfer activities of the CIA targeting system. Our studies demonstrate that a novel cytosolic pathway functions in parallel to the mitochondrial ISC to perform de novo Fe-S biogenesis, and to escort Fe-S clusters to cytoplasmic and nuclear proteins.
Collapse
Affiliation(s)
- Ki Soon Kim
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Nunziata Maio
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Anamika Singh
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Tracey A Rouault
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| |
Collapse
|
32
|
Roles of Elongator Dependent tRNA Modification Pathways in Neurodegeneration and Cancer. Genes (Basel) 2018; 10:genes10010019. [PMID: 30597914 PMCID: PMC6356722 DOI: 10.3390/genes10010019] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 12/18/2018] [Accepted: 12/20/2018] [Indexed: 02/07/2023] Open
Abstract
Transfer RNA (tRNA) is subject to a multitude of posttranscriptional modifications which can profoundly impact its functionality as the essential adaptor molecule in messenger RNA (mRNA) translation. Therefore, dynamic regulation of tRNA modification in response to environmental changes can tune the efficiency of gene expression in concert with the emerging epitranscriptomic mRNA regulators. Several of the tRNA modifications are required to prevent human diseases and are particularly important for proper development and generation of neurons. In addition to the positive role of different tRNA modifications in prevention of neurodegeneration, certain cancer types upregulate tRNA modification genes to sustain cancer cell gene expression and metastasis. Multiple associations of defects in genes encoding subunits of the tRNA modifier complex Elongator with human disease highlight the importance of proper anticodon wobble uridine modifications (xm⁵U34) for health. Elongator functionality requires communication with accessory proteins and dynamic phosphorylation, providing regulatory control of its function. Here, we summarized recent insights into molecular functions of the complex and the role of Elongator dependent tRNA modification in human disease.
Collapse
|
33
|
Fox NG, Martelli A, Nabhan JF, Janz J, Borkowska O, Bulawa C, Yue WW. Zinc(II) binding on human wild-type ISCU and Met140 variants modulates NFS1 desulfurase activity. Biochimie 2018; 152:211-218. [PMID: 30031876 PMCID: PMC6098246 DOI: 10.1016/j.biochi.2018.07.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/18/2018] [Indexed: 12/01/2022]
Abstract
Human de novo iron-sulfur (Fe-S) assembly complex consists of cysteine desulfurase NFS1, accessory protein ISD11, acyl carrier protein ACP, scaffold protein ISCU, and allosteric activator frataxin (FXN). FXN binds the NFS1-ISD11-ACP-ISCU complex (SDAU), to activate the desulfurase activity and Fe-S cluster biosynthesis. In the absence of FXN, the NFS1-ISD11-ACP (SDA) complex was reportedly inhibited by binding of recombinant ISCU. Recent studies also reported a substitution at position Met141 on the yeast ISCU orthologue Isu, to Ile, Leu, Val, or Cys, could bypass the requirement of FXN for Fe-S cluster biosynthesis and cell viability. Here, we show that recombinant human ISCU binds zinc(II) ion, as previously demonstrated with the E. coli orthologue IscU. Surprisingly, the relative proportion between zinc-bound and zinc-depleted forms varies among purification batches. Importantly the presence of zinc in ISCU impacts SDAU desulfurase activity. Indeed, removal of zinc(II) ion from ISCU causes a moderate but significant increase in activity compared to SDA alone, and FXN can activate both zinc-depleted and zinc-bound forms of ISCU complexed to SDA. Taking into consideration the inhibition of desulfurase activity by zinc-bound ISCU, we characterized wild type ISCU and the M140I, M140L, and M140V variants under both zinc-bound and zinc-depleted conditions, and did not observe significant differences in the biochemical and biophysical properties between wild-type and variants. Importantly, in the absence of FXN, ISCU variants behaved like wild-type and did not stimulate the desulfurase activity of the SDA complex. This study therefore identifies an important regulatory role for zinc-bound ISCU in modulation of the human Fe-S assembly system in vitro and reports no 'FXN bypass' effect on mutations at position Met140 in human ISCU. Furthermore, this study also calls for caution in interpreting studies involving recombinant ISCU by taking into consideration the influence of the bound zinc(II) ion on SDAU complex activity.
Collapse
Affiliation(s)
- Nicholas G Fox
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7DQ, UK
| | - Alain Martelli
- Pfizer Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., 610 Main Street, Cambridge, MA, 02139, United States
| | - Joseph F Nabhan
- Pfizer Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., 610 Main Street, Cambridge, MA, 02139, United States
| | - Jay Janz
- Pfizer Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., 610 Main Street, Cambridge, MA, 02139, United States
| | - Oktawia Borkowska
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7DQ, UK
| | - Christine Bulawa
- Pfizer Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., 610 Main Street, Cambridge, MA, 02139, United States.
| | - Wyatt W Yue
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7DQ, UK.
| |
Collapse
|
34
|
Li J, Han Q, Zhang T, Du J, Sun Q, Pang Y. Expression of soluble native protein in Escherichia coli using a cold-shock SUMO tag-fused expression vector. ACTA ACUST UNITED AC 2018; 19:e00261. [PMID: 30009138 PMCID: PMC6042314 DOI: 10.1016/j.btre.2018.e00261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 05/27/2018] [Accepted: 05/28/2018] [Indexed: 02/01/2023]
Abstract
Construction of a simple and efficient cloning vector namely, pWMU-19T based on seamless cloning method. The novel pCold-SUMOa vector is suitable for expression of soluble native heterologous proteins. The pCold-SUMOa expression vector can dramatically enhance the stability and activity of target proteins.
At present, approximately 30% of eukaryotic proteins can be expressed in a soluble form in Escherichia coli. In this study, a pCold-SUMOa plasmid was constructed in order to express heterologous proteins fused with SUMO by a cold-shock expression vector. The human cysteine desulfurase NFS1 and a chimeric cysteine desulfurase namely, EH-IscS were successfully expressed in E. coli. The proteins were particularly difficult to be produced functionally, due to their readily sequestered nature. The recombinant cysteine desulfurases that were generated by pCold-SUMOa exhibited higher activity, solubility and stability compared with the well-known plasmid pCold I. In contrast to the pCold TF plasmid, the SUMO tag conferred no biological activity with regard to the conformation of the cysteine desulfurases. Furthermore, the SUMO protease 1 can efficiently recognize the tertiary structure of SUMO and cleave it. The data indicate that the pCold-SUMOa vector is a promising tool for native eukaryotic protein production.
Collapse
Affiliation(s)
- Jianghui Li
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Institute of Enzyme Engineering and Medical Diagnosis, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Qinxia Han
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Institute of Enzyme Engineering and Medical Diagnosis, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Tao Zhang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Institute of Enzyme Engineering and Medical Diagnosis, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Jing Du
- People's Hospital of Hangzhou Medical College, Hangzhou 310014, China
| | - Qianqian Sun
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Institute of Enzyme Engineering and Medical Diagnosis, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Yilin Pang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Institute of Enzyme Engineering and Medical Diagnosis, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| |
Collapse
|
35
|
Marelja Z, Leimkühler S, Missirlis F. Iron Sulfur and Molybdenum Cofactor Enzymes Regulate the Drosophila Life Cycle by Controlling Cell Metabolism. Front Physiol 2018; 9:50. [PMID: 29491838 PMCID: PMC5817353 DOI: 10.3389/fphys.2018.00050] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/16/2018] [Indexed: 12/20/2022] Open
Abstract
Iron sulfur (Fe-S) clusters and the molybdenum cofactor (Moco) are present at enzyme sites, where the active metal facilitates electron transfer. Such enzyme systems are soluble in the mitochondrial matrix, cytosol and nucleus, or embedded in the inner mitochondrial membrane, but virtually absent from the cell secretory pathway. They are of ancient evolutionary origin supporting respiration, DNA replication, transcription, translation, the biosynthesis of steroids, heme, catabolism of purines, hydroxylation of xenobiotics, and cellular sulfur metabolism. Here, Fe-S cluster and Moco biosynthesis in Drosophila melanogaster is reviewed and the multiple biochemical and physiological functions of known Fe-S and Moco enzymes are described. We show that RNA interference of Mocs3 disrupts Moco biosynthesis and the circadian clock. Fe-S-dependent mitochondrial respiration is discussed in the context of germ line and somatic development, stem cell differentiation and aging. The subcellular compartmentalization of the Fe-S and Moco assembly machinery components and their connections to iron sensing mechanisms and intermediary metabolism are emphasized. A biochemically active Fe-S core complex of heterologously expressed fly Nfs1, Isd11, IscU, and human frataxin is presented. Based on the recent demonstration that copper displaces the Fe-S cluster of yeast and human ferredoxin, an explanation for why high dietary copper leads to cytoplasmic iron deficiency in flies is proposed. Another proposal that exosomes contribute to the transport of xanthine dehydrogenase from peripheral tissues to the eye pigment cells is put forward, where the Vps16a subunit of the HOPS complex may have a specialized role in concentrating this enzyme within pigment granules. Finally, we formulate a hypothesis that (i) mitochondrial superoxide mobilizes iron from the Fe-S clusters in aconitase and succinate dehydrogenase; (ii) increased iron transiently displaces manganese on superoxide dismutase, which may function as a mitochondrial iron sensor since it is inactivated by iron; (iii) with the Krebs cycle thus disrupted, citrate is exported to the cytosol for fatty acid synthesis, while succinyl-CoA and the iron are used for heme biosynthesis; (iv) as iron is used for heme biosynthesis its concentration in the matrix drops allowing for manganese to reactivate superoxide dismutase and Fe-S cluster biosynthesis to reestablish the Krebs cycle.
Collapse
Affiliation(s)
- Zvonimir Marelja
- Imagine Institute, Université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Silke Leimkühler
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Fanis Missirlis
- Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| |
Collapse
|
36
|
Genetic dissection of cyclic pyranopterin monophosphate biosynthesis in plant mitochondria. Biochem J 2018; 475:495-509. [PMID: 29247140 PMCID: PMC5791162 DOI: 10.1042/bcj20170559] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 12/07/2017] [Accepted: 12/14/2017] [Indexed: 01/04/2023]
Abstract
Mitochondria play a key role in the biosynthesis of two metal cofactors, iron–sulfur (FeS) clusters and molybdenum cofactor (Moco). The two pathways intersect at several points, but a scarcity of mutants has hindered studies to better understand these links. We screened a collection of sirtinol-resistant Arabidopsis thaliana mutants for lines with decreased activities of cytosolic FeS enzymes and Moco enzymes. We identified a new mutant allele of ATM3 (ABC transporter of the mitochondria 3), encoding the ATP-binding cassette transporter of the mitochondria 3 (systematic name ABCB25), confirming the previously reported role of ATM3 in both FeS cluster and Moco biosynthesis. We also identified a mutant allele in CNX2, cofactor of nitrate reductase and xanthine dehydrogenase 2, encoding GTP 3′,8-cyclase, the first step in Moco biosynthesis which is localized in the mitochondria. A single-nucleotide polymorphism in cnx2-2 leads to substitution of Arg88 with Gln in the N-terminal FeS cluster-binding motif. cnx2-2 plants are small and chlorotic, with severely decreased Moco enzyme activities, but they performed better than a cnx2-1 knockout mutant, which could only survive with ammonia as a nitrogen source. Measurement of cyclic pyranopterin monophosphate (cPMP) levels by LC–MS/MS showed that this Moco intermediate was below the limit of detection in both cnx2-1 and cnx2-2, and accumulated more than 10-fold in seedlings mutated in the downstream gene CNX5. Interestingly, atm3-1 mutants had less cPMP than wild type, correlating with previous reports of a similar decrease in nitrate reductase activity. Taken together, our data functionally characterize CNX2 and suggest that ATM3 is indirectly required for cPMP synthesis.
Collapse
|
37
|
Castro IH, Ferrari A, Herrera MG, Noguera ME, Maso L, Benini M, Rufini A, Testi R, Costantini P, Santos J. Biophysical characterisation of the recombinant human frataxin precursor. FEBS Open Bio 2018; 8:390-405. [PMID: 29511616 PMCID: PMC5832983 DOI: 10.1002/2211-5463.12376] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/25/2017] [Accepted: 12/27/2017] [Indexed: 11/10/2022] Open
Abstract
Friedreich's ataxia is a disease caused by a decrease in the levels of expression or loss of functionality of the mitochondrial protein frataxin (FXN). The development of an active and stable recombinant variant of FXN is important for protein replacement therapy. Although valuable data about the mature form FXN81-210 has been collected, not enough information is available about the conformation of the frataxin precursor (FXN1-210). We investigated the conformation, stability and function of a recombinant precursor variant (His6-TAT-FXN1-210), which includes a TAT peptide in the N-terminal region to assist with transport across cell membranes. His6-TAT-FXN1-210 was expressed in Escherichia coli and conditions were found for purifying folded protein free of aggregation, oxidation or degradation, even after freezing and thawing. The protein was found to be stable and monomeric, with the N-terminal stretch (residues 1-89) mostly unstructured and the C-terminal domain properly folded. The experimental data suggest a complex picture for the folding process of full-length frataxin in vitro: the presence of the N-terminal region increased the tendency of FXN to aggregate at high temperatures but this could be avoided by the addition of low concentrations of GdmCl. The purified precursor was translocated through cell membranes. In addition, immune response against His6-TAT-FXN1-210 was measured, suggesting that the C-terminal fragment was not immunogenic at the assayed protein concentrations. Finally, the recognition of recombinant FXN by cellular proteins was studied to evaluate its functionality. In this regard, cysteine desulfurase NFS1/ISD11/ISCU was activated in vitro by His6-TAT-FXN1-210. Moreover, the results showed that His6-TAT-FXN1-210 can be ubiquitinated in vitro by the recently identified frataxin E3 ligase RNF126, in a similar way as the FXN1-210, suggesting that the His6-TAT extension does not interfere with the ubiquitination machinery.
Collapse
Affiliation(s)
- Ignacio Hugo Castro
- Institute of Biological Chemistry and Physicochemistry Dr Alejandro Paladini (UBA-CONICET) University of Buenos Aires Argentina
| | - Alejandro Ferrari
- Institute of Biological Chemistry and Physicochemistry Dr Alejandro Paladini (UBA-CONICET) University of Buenos Aires Argentina
| | - María Georgina Herrera
- Institute of Biological Chemistry and Physicochemistry Dr Alejandro Paladini (UBA-CONICET) University of Buenos Aires Argentina
| | - Martín Ezequiel Noguera
- Institute of Biological Chemistry and Physicochemistry Dr Alejandro Paladini (UBA-CONICET) University of Buenos Aires Argentina
| | - Lorenzo Maso
- Department of Biology University of Padova Italy
| | - Monica Benini
- Laboratory of Signal Transduction Department of Biomedicine and Prevention University of Rome ''Tor Vergata'' Italy.,Fratagene Therapeutics srl Rome Italy
| | - Alessandra Rufini
- Laboratory of Signal Transduction Department of Biomedicine and Prevention University of Rome ''Tor Vergata'' Italy.,Fratagene Therapeutics srl Rome Italy
| | - Roberto Testi
- Laboratory of Signal Transduction Department of Biomedicine and Prevention University of Rome ''Tor Vergata'' Italy.,Fratagene Therapeutics srl Rome Italy
| | | | - Javier Santos
- Institute of Biological Chemistry and Physicochemistry Dr Alejandro Paladini (UBA-CONICET) University of Buenos Aires Argentina
| |
Collapse
|
38
|
Noguera ME, Aran M, Smal C, Vazquez DS, Herrera MG, Roman EA, Alaimo N, Gallo M, Santos J. Insights on the conformational dynamics of human frataxin through modifications of loop-1. Arch Biochem Biophys 2017; 636:123-137. [PMID: 29097312 DOI: 10.1016/j.abb.2017.10.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 10/20/2017] [Accepted: 10/28/2017] [Indexed: 02/07/2023]
Abstract
Human frataxin (FXN) is a highly conserved mitochondrial protein involved in iron homeostasis and activation of the iron-sulfur cluster assembly. FXN deficiency causes the neurodegenerative disease Friedreich's Ataxia. Here, we investigated the effect of alterations in loop-1, a stretch presumably essential for FXN function, on the conformational stability and dynamics of the native state. We generated four loop-1 variants, carrying substitutions, insertions and deletions. All of them were stable and well-folded proteins. Fast local motions (ps-ns) and slower long-range conformational dynamics (μs-ms) were altered in some mutants as judged by NMR. Particularly, loop-1 modifications impact on the dynamics of a distant region that includes residues from the β-sheet, helix α1 and the C-terminal. Remarkably, all the mutants retain the ability to activate cysteine desulfurase, even when two of them exhibit a strong decrease in iron binding, revealing a differential sensitivity of these functional features to loop-1 perturbation. Consequently, we found that even for a small and relatively rigid protein, engineering a loop segment enables to alter conformational dynamics through a long-range effect, preserving the native-state structure and important aspects of function.
Collapse
Affiliation(s)
- Martín E Noguera
- Instituto de Química y Físico-Química Biológicas, University of Buenos Aires, Junín 956, 1113AAD, Buenos Aires, Argentina
| | - Martín Aran
- The Leloir Institute Foundation and IIBBA-CONICET, Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Clara Smal
- The Leloir Institute Foundation and IIBBA-CONICET, Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Diego S Vazquez
- Instituto de Química y Físico-Química Biológicas, University of Buenos Aires, Junín 956, 1113AAD, Buenos Aires, Argentina
| | - María Georgina Herrera
- Instituto de Química y Físico-Química Biológicas, University of Buenos Aires, Junín 956, 1113AAD, Buenos Aires, Argentina
| | - Ernesto A Roman
- Instituto de Química y Físico-Química Biológicas, University of Buenos Aires, Junín 956, 1113AAD, Buenos Aires, Argentina
| | - Nadine Alaimo
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome "Tor Vergata", Via della Ricerca Scientifica snc, 00133 Roma, Italy
| | - Mariana Gallo
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome "Tor Vergata", Via della Ricerca Scientifica snc, 00133 Roma, Italy; IRBM Science Park S.p.A., Via Pontina km 30,600., 00071 Pomezia (RM), Italy.
| | - Javier Santos
- Instituto de Química y Físico-Química Biológicas, University of Buenos Aires, Junín 956, 1113AAD, Buenos Aires, Argentina.
| |
Collapse
|
39
|
Alvarez SW, Sviderskiy VO, Terzi EM, Papagiannakopoulos T, Moreira AL, Adams S, Sabatini DM, Birsoy K, Possemato R. NFS1 undergoes positive selection in lung tumours and protects cells from ferroptosis. Nature 2017; 551:639-643. [PMID: 29168506 PMCID: PMC5808442 DOI: 10.1038/nature24637] [Citation(s) in RCA: 455] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 10/10/2017] [Indexed: 12/16/2022]
Abstract
Environmental nutrient levels impact cancer cell metabolism, resulting in context-dependent gene essentiality. Here, using loss-of-function screening based on RNA interference, we show that environmental oxygen levels are a major driver of differential essentiality between in vitro model systems and in vivo tumours. Above the 3-8% oxygen concentration typical of most tissues, we find that cancer cells depend on high levels of the iron-sulfur cluster biosynthetic enzyme NFS1. Mammary or subcutaneous tumours grow despite suppression of NFS1, whereas metastatic or primary lung tumours do not. Consistent with a role in surviving the high oxygen environment of incipient lung tumours, NFS1 lies in a region of genomic amplification present in lung adenocarcinoma and is most highly expressed in well-differentiated adenocarcinomas. NFS1 activity is particularly important for maintaining the iron-sulfur co-factors present in multiple cell-essential proteins upon exposure to oxygen compared to other forms of oxidative damage. Furthermore, insufficient iron-sulfur cluster maintenance robustly activates the iron-starvation response and, in combination with inhibition of glutathione biosynthesis, triggers ferroptosis, a non-apoptotic form of cell death. Suppression of NFS1 cooperates with inhibition of cysteine transport to trigger ferroptosis in vitro and slow tumour growth. Therefore, lung adenocarcinomas select for expression of a pathway that confers resistance to high oxygen tension and protects cells from undergoing ferroptosis in response to oxidative damage.
Collapse
Affiliation(s)
- Samantha W Alvarez
- Department of Pathology, New York University School of Medicine, New York, New York 10016, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, New York 10016, USA
| | - Vladislav O Sviderskiy
- Department of Pathology, New York University School of Medicine, New York, New York 10016, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, New York 10016, USA
| | - Erdem M Terzi
- Department of Pathology, New York University School of Medicine, New York, New York 10016, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, New York 10016, USA
| | - Thales Papagiannakopoulos
- Department of Pathology, New York University School of Medicine, New York, New York 10016, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, New York 10016, USA
| | - Andre L Moreira
- Department of Pathology, New York University School of Medicine, New York, New York 10016, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, New York 10016, USA
| | - Sylvia Adams
- Department of Pathology, New York University School of Medicine, New York, New York 10016, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, New York 10016, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- The David H. Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Seven Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Kıvanç Birsoy
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- The David H. Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Seven Cambridge Center, Cambridge, Massachusetts 02142, USA
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, 1230 York Avenue, New York 10065, USA
| | - Richard Possemato
- Department of Pathology, New York University School of Medicine, New York, New York 10016, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, New York 10016, USA
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- The David H. Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Seven Cambridge Center, Cambridge, Massachusetts 02142, USA
| |
Collapse
|
40
|
|
41
|
Gakh O, Ranatunga W, Galeano BK, Smith DS, Thompson JR, Isaya G. Defining the Architecture of the Core Machinery for the Assembly of Fe-S Clusters in Human Mitochondria. Methods Enzymol 2017; 595:107-160. [PMID: 28882199 DOI: 10.1016/bs.mie.2017.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Although Fe-S clusters may assemble spontaneously from elemental iron and sulfur in protein-free systems, the potential toxicity of free Fe2+, Fe3+, and S2- ions in aerobic environments underscores the requirement for specialized proteins to oversee the safe assembly of Fe-S clusters in living cells. Prokaryotes first developed multiprotein systems for Fe-S cluster assembly, from which mitochondria later derived their own system and became the main Fe-S cluster suppliers for eukaryotic cells. Early studies in yeast and human mitochondria indicated that Fe-S cluster assembly in eukaryotes is centered around highly conserved Fe-S proteins (human ISCU) that serve as scaffolds upon which new Fe-S clusters are assembled from (i) elemental sulfur, provided by a pyridoxal phosphate-dependent cysteine desulfurase (human NFS1) and its stabilizing-binding partner (human ISD11), and (ii) elemental iron, provided by an iron-binding protein of the frataxin family (human FXN). Further studies revealed that all of these proteins could form stable complexes that could reach molecular masses of megadaltons. However, the protein-protein interaction surfaces, catalytic mechanisms, and overall architecture of these macromolecular machines remained undefined for quite some time. The delay was due to difficulties inherent in reconstituting these very large multiprotein complexes in vitro or isolating them from cells in sufficient quantities to enable biochemical and structural studies. Here, we describe approaches we developed to reconstitute the human Fe-S cluster assembly machinery in Escherichia coli and to define its remarkable architecture.
Collapse
Affiliation(s)
| | | | - Belinda K Galeano
- Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN, United States
| | | | | | - Grazia Isaya
- Mayo Clinic, Rochester, MN, United States; Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN, United States; Mayo Clinic Children's Research Center, Rochester, MN, United States.
| |
Collapse
|
42
|
Bühning M, Friemel M, Leimkühler S. Functional Complementation Studies Reveal Different Interaction Partners of Escherichia coli IscS and Human NFS1. Biochemistry 2017; 56:4592-4605. [PMID: 28766335 DOI: 10.1021/acs.biochem.7b00627] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The trafficking and delivery of sulfur to cofactors and nucleosides is a highly regulated and conserved process among all organisms. All sulfur transfer pathways generally have an l-cysteine desulfurase as an initial sulfur-mobilizing enzyme in common, which serves as a sulfur donor for the biosynthesis of sulfur-containing biomolecules like iron-sulfur (Fe-S) clusters, thiamine, biotin, lipoic acid, the molybdenum cofactor (Moco), and thiolated nucleosides in tRNA. The human l-cysteine desulfurase NFS1 and the Escherichia coli homologue IscS share a level of amino acid sequence identity of ∼60%. While E. coli IscS has a versatile role in the cell and was shown to have numerous interaction partners, NFS1 is mainly localized in mitochondria with a crucial role in the biosynthesis of Fe-S clusters. Additionally, NFS1 is also located in smaller amounts in the cytosol with a role in Moco biosynthesis and mcm5s2U34 thio modifications of nucleosides in tRNA. NFS1 and IscS were conclusively shown to have different interaction partners in their respective organisms. Here, we used functional complementation studies of an E. coli iscS deletion strain with human NFS1 to dissect their conserved roles in the transfer of sulfur to a specific target protein. Our results show that human NFS1 and E. coli IscS share conserved binding sites for proteins involved in Fe-S cluster assembly like IscU, but not with proteins for tRNA thio modifications or Moco biosynthesis. In addition, we show that human NFS1 was almost fully able to complement the role of IscS in Moco biosynthesis when its specific interaction partner protein MOCS3 from humans was also present.
Collapse
Affiliation(s)
- Martin Bühning
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam , D-14476 Potsdam, Germany
| | - Martin Friemel
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam , D-14476 Potsdam, Germany
| | - Silke Leimkühler
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam , D-14476 Potsdam, Germany
| |
Collapse
|
43
|
Leimkühler S. Shared function and moonlighting proteins in molybdenum cofactor biosynthesis. Biol Chem 2017; 398:1009-1026. [PMID: 28284029 DOI: 10.1515/hsz-2017-0110] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/03/2017] [Indexed: 11/15/2022]
Abstract
The biosynthesis of the molybdenum cofactor (Moco) is a highly conserved pathway in bacteria, archaea and eukaryotes. The molybdenum atom in Moco-containing enzymes is coordinated to the dithiolene group of a tricyclic pyranopterin monophosphate cofactor. The biosynthesis of Moco can be divided into three conserved steps, with a fourth present only in bacteria and archaea: (1) formation of cyclic pyranopterin monophosphate, (2) formation of molybdopterin (MPT), (3) insertion of molybdenum into MPT to form Mo-MPT, and (4) additional modification of Mo-MPT in bacteria with the attachment of a GMP or CMP nucleotide, forming the dinucleotide variants of Moco. While the proteins involved in the catalytic reaction of each step of Moco biosynthesis are highly conserved among the Phyla, a surprising link to other cellular pathways has been identified by recent discoveries. In particular, the pathways for FeS cluster assembly and thio-modifications of tRNA are connected to Moco biosynthesis by sharing the same protein components. Further, proteins involved in Moco biosynthesis are not only shared with other pathways, but additionally have moonlighting roles. This review gives an overview of Moco biosynthesis in bacteria and humans and highlights the shared function and moonlighting roles of the participating proteins.
Collapse
|
44
|
Cory SA, Van Vranken JG, Brignole EJ, Patra S, Winge DR, Drennan CL, Rutter J, Barondeau DP. Structure of human Fe-S assembly subcomplex reveals unexpected cysteine desulfurase architecture and acyl-ACP-ISD11 interactions. Proc Natl Acad Sci U S A 2017; 114:E5325-E5334. [PMID: 28634302 PMCID: PMC5502623 DOI: 10.1073/pnas.1702849114] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In eukaryotes, sulfur is mobilized for incorporation into multiple biosynthetic pathways by a cysteine desulfurase complex that consists of a catalytic subunit (NFS1), LYR protein (ISD11), and acyl carrier protein (ACP). This NFS1-ISD11-ACP (SDA) complex forms the core of the iron-sulfur (Fe-S) assembly complex and associates with assembly proteins ISCU2, frataxin (FXN), and ferredoxin to synthesize Fe-S clusters. Here we present crystallographic and electron microscopic structures of the SDA complex coupled to enzyme kinetic and cell-based studies to provide structure-function properties of a mitochondrial cysteine desulfurase. Unlike prokaryotic cysteine desulfurases, the SDA structure adopts an unexpected architecture in which a pair of ISD11 subunits form the dimeric core of the SDA complex, which clarifies the critical role of ISD11 in eukaryotic assemblies. The different quaternary structure results in an incompletely formed substrate channel and solvent-exposed pyridoxal 5'-phosphate cofactor and provides a rationale for the allosteric activator function of FXN in eukaryotic systems. The structure also reveals the 4'-phosphopantetheine-conjugated acyl-group of ACP occupies the hydrophobic core of ISD11, explaining the basis of ACP stabilization. The unexpected architecture for the SDA complex provides a framework for understanding interactions with acceptor proteins for sulfur-containing biosynthetic pathways, elucidating mechanistic details of eukaryotic Fe-S cluster biosynthesis, and clarifying how defects in Fe-S cluster assembly lead to diseases such as Friedreich's ataxia. Moreover, our results support a lock-and-key model in which LYR proteins associate with acyl-ACP as a mechanism for fatty acid biosynthesis to coordinate the expression, Fe-S cofactor maturation, and activity of the respiratory complexes.
Collapse
Affiliation(s)
- Seth A Cory
- Department of Chemistry, Texas A&M University, College Station, TX 77842
| | - Jonathan G Van Vranken
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Edward J Brignole
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Shachin Patra
- Department of Chemistry, Texas A&M University, College Station, TX 77842
| | - Dennis R Winge
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
- Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT 84132
| | - Catherine L Drennan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jared Rutter
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84132
| | - David P Barondeau
- Department of Chemistry, Texas A&M University, College Station, TX 77842;
| |
Collapse
|
45
|
Galeano BK, Ranatunga W, Gakh O, Smith DY, Thompson JR, Isaya G. Zinc and the iron donor frataxin regulate oligomerization of the scaffold protein to form new Fe-S cluster assembly centers. Metallomics 2017; 9:773-801. [PMID: 28548666 PMCID: PMC5552075 DOI: 10.1039/c7mt00089h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/02/2017] [Indexed: 02/06/2023]
Abstract
Early studies of the bacterial Fe-S cluster assembly system provided structural details for how the scaffold protein and the cysteine desulfurase interact. This work and additional work on the yeast and human systems elucidated a conserved mechanism for sulfur donation but did not provide any conclusive insights into the mechanism for iron delivery from the iron donor, frataxin, to the scaffold. We previously showed that oligomerization is a mechanism by which yeast frataxin (Yfh1) can promote assembly of the core machinery for Fe-S cluster synthesis both in vitro and in cells, in such a manner that the scaffold protein, Isu1, can bind to Yfh1 independent of the presence of the cysteine desulfurase, Nfs1. Here, in the absence of Yfh1, Isu1 was found to exist in two forms, one mostly monomeric with limited tendency to dimerize, and one with a strong propensity to oligomerize. Whereas the monomeric form is stabilized by zinc, the loss of zinc promotes formation of dimer and higher order oligomers. However, upon binding to oligomeric Yfh1, both forms take on a similar symmetrical trimeric configuration that places the Fe-S cluster coordinating residues of Isu1 in close proximity of iron-binding residues of Yfh1. This configuration is suitable for docking of Nfs1 in a manner that provides a structural context for coordinate iron and sulfur donation to the scaffold. Moreover, distinct structural features suggest that in physiological conditions the zinc-regulated abundance of monomeric vs. oligomeric Isu1 yields [Yfh1]·[Isu1] complexes with different Isu1 configurations that afford unique functional properties for Fe-S cluster assembly and delivery.
Collapse
Affiliation(s)
- B. K. Galeano
- Department of Pediatric & Adolescent Medicine , Mayo Clinic , Rochester , Minnesota , USA . ;
- Department of Biochemistry & Molecular Biology , Mayo Clinic , Rochester , Minnesota , USA
- Mayo Clinic Graduate School of Biomedical Sciences , Rochester , Minnesota , USA
| | - W. Ranatunga
- Department of Pediatric & Adolescent Medicine , Mayo Clinic , Rochester , Minnesota , USA . ;
- Mayo Clinic Children's Research Center , Rochester , Minnesota , USA
| | - O. Gakh
- Department of Pediatric & Adolescent Medicine , Mayo Clinic , Rochester , Minnesota , USA . ;
- Mayo Clinic Children's Research Center , Rochester , Minnesota , USA
| | - D. Y. Smith
- Department of Pediatric & Adolescent Medicine , Mayo Clinic , Rochester , Minnesota , USA . ;
- Mayo Clinic Children's Research Center , Rochester , Minnesota , USA
| | - J. R. Thompson
- Department of Biochemistry & Molecular Biology , Mayo Clinic , Rochester , Minnesota , USA
| | - G. Isaya
- Department of Pediatric & Adolescent Medicine , Mayo Clinic , Rochester , Minnesota , USA . ;
- Department of Biochemistry & Molecular Biology , Mayo Clinic , Rochester , Minnesota , USA
- Mayo Clinic Children's Research Center , Rochester , Minnesota , USA
| |
Collapse
|
46
|
Cai K, Frederick RO, Tonelli M, Markley JL. Mitochondrial Cysteine Desulfurase and ISD11 Coexpressed in Escherichia coli Yield Complex Containing Acyl Carrier Protein. ACS Chem Biol 2017; 12:918-921. [PMID: 28233492 PMCID: PMC5404276 DOI: 10.1021/acschembio.6b01005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Mitochondrial
cysteine desulfurase is an essential component of
the machinery for iron–sulfur cluster biosynthesis. It has
been known that human cysteine desulfurase that is catalytically active in vitro can be prepared by overexpressing in Escherichia
coli cells two protein components of this system, the cysteine
desulfurase protein NFS1 and the auxiliary protein ISD11. We report
here that this active preparation contains, in addition, the holo-form
of E. coli acyl carrier protein (Acp). We have determined
the stoichiometry of the complex to be [Acp]2:[ISD11]2:[NFS1]2. Acyl carrier protein recently has been
found to be an essential component of the iron–sulfur protein
biosynthesis machinery in mitochondria; thus, because of the activity
of [Acp]2:[ISD11]2:[NFS1]2 in supporting
iron–sulfur cluster assembly in vitro, it
appears that E. coli Acp can substitute for its human
homologue.
Collapse
Affiliation(s)
- Kai Cai
- Biochemistry Department, University of Wisconsin—Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Ronnie O. Frederick
- Biochemistry Department, University of Wisconsin—Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Marco Tonelli
- Biochemistry Department, University of Wisconsin—Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - John L. Markley
- Biochemistry Department, University of Wisconsin—Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| |
Collapse
|
47
|
Friemel M, Marelja Z, Li K, Leimkühler S. The N-Terminus of Iron-Sulfur Cluster Assembly Factor ISD11 Is Crucial for Subcellular Targeting and Interaction with l-Cysteine Desulfurase NFS1. Biochemistry 2017; 56:1797-1808. [PMID: 28271877 DOI: 10.1021/acs.biochem.6b01239] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Assembly of iron-sulfur (FeS) clusters is an important process in living cells. The initial sulfur mobilization step for FeS cluster biosynthesis is catalyzed by l-cysteine desulfurase NFS1, a reaction that is localized in mitochondria in humans. In humans, the function of NFS1 depends on the ISD11 protein, which is required to stabilize its structure. The NFS1/ISD11 complex further interacts with scaffold protein ISCU and regulator protein frataxin, thereby forming a quaternary complex for FeS cluster formation. It has been suggested that the role of ISD11 is not restricted to its role in stabilizing the structure of NFS1, because studies of single-amino acid variants of ISD11 additionally demonstrated its importance for the correct assembly of the quaternary complex. In this study, we are focusing on the N-terminal region of ISD11 to determine the role of N-terminal amino acids in the formation of the complex with NFS1 and to reveal the mitochondrial targeting sequence for subcellular localization. Our in vitro studies with the purified proteins and in vivo studies in a cellular system show that the first 10 N-terminal amino acids of ISD11 are indispensable for the activity of NFS1 and especially the conserved "LYR" motif is essential for the role of ISD11 in forming a stable and active complex with NFS1.
Collapse
Affiliation(s)
- Martin Friemel
- Institut für Biochemie und Biologie, Molekulare Enzymologie, Universität Potsdam , Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Zvonimir Marelja
- Imagine Institute, Université Paris Descartes, Sorbonne Paris Cité , 75015 Paris, France
| | - Kuanyu Li
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University , Nanjing, China
| | - Silke Leimkühler
- Institut für Biochemie und Biologie, Molekulare Enzymologie, Universität Potsdam , Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| |
Collapse
|
48
|
Sulfur Modifications of the Wobble U 34 in tRNAs and their Intracellular Localization in Eukaryotic Cells. Biomolecules 2017; 7:biom7010017. [PMID: 28218716 PMCID: PMC5372729 DOI: 10.3390/biom7010017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 02/08/2017] [Accepted: 02/08/2017] [Indexed: 12/21/2022] Open
Abstract
The wobble uridine (U34) of transfer RNAs (tRNAs) for two-box codon recognition, i.e., tRNALysUUU, tRNAGluUUC, and tRNAGlnUUG, harbor a sulfur- (thio-) and a methyl-derivative structure at the second and fifth positions of U34, respectively. Both modifications are necessary to construct the proper anticodon loop structure and to enable them to exert their functions in translation. Thio-modification of U34 (s2U34) is found in both cytosolic tRNAs (cy-tRNAs) and mitochondrial tRNAs (mt-tRNAs). Although l-cysteine desulfurase is required in both cases, subsequent sulfur transfer pathways to cy-tRNAs and mt-tRNAs are different due to their distinct intracellular locations. The s2U34 formation in cy-tRNAs involves a sulfur delivery system required for the biosynthesis of iron-sulfur (Fe/S) clusters and certain resultant Fe/S proteins. This review addresses presumed sulfur delivery pathways for the s2U34 formation in distinct intracellular locations, especially that for cy-tRNAs in comparison with that for mt-tRNAs.
Collapse
|
49
|
Leimkühler S, Bühning M, Beilschmidt L. Shared Sulfur Mobilization Routes for tRNA Thiolation and Molybdenum Cofactor Biosynthesis in Prokaryotes and Eukaryotes. Biomolecules 2017; 7:biom7010005. [PMID: 28098827 PMCID: PMC5372717 DOI: 10.3390/biom7010005] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 01/04/2017] [Accepted: 01/09/2017] [Indexed: 11/18/2022] Open
Abstract
Modifications of transfer RNA (tRNA) have been shown to play critical roles in the biogenesis, metabolism, structural stability and function of RNA molecules, and the specific modifications of nucleobases with sulfur atoms in tRNA are present in pro- and eukaryotes. Here, especially the thiomodifications xm5s2U at the wobble position 34 in tRNAs for Lys, Gln and Glu, were suggested to have an important role during the translation process by ensuring accurate deciphering of the genetic code and by stabilization of the tRNA structure. The trafficking and delivery of sulfur nucleosides is a complex process carried out by sulfur relay systems involving numerous proteins, which not only deliver sulfur to the specific tRNAs but also to other sulfur-containing molecules including iron–sulfur clusters, thiamin, biotin, lipoic acid and molybdopterin (MPT). Among the biosynthesis of these sulfur-containing molecules, the biosynthesis of the molybdenum cofactor (Moco) and the synthesis of thio-modified tRNAs in particular show a surprising link by sharing protein components for sulfur mobilization in pro- and eukaryotes.
Collapse
Affiliation(s)
- Silke Leimkühler
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany.
| | - Martin Bühning
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany.
| | - Lena Beilschmidt
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany.
| |
Collapse
|
50
|
Jüdes A, Bruch A, Klassen R, Helm M, Schaffrath R. Sulfur transfer and activation by ubiquitin-like modifier system Uba4•Urm1 link protein urmylation and tRNA thiolation in yeast. MICROBIAL CELL (GRAZ, AUSTRIA) 2016; 3:554-564. [PMID: 28357324 PMCID: PMC5349211 DOI: 10.15698/mic2016.11.539] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 09/19/2016] [Indexed: 01/03/2023]
Abstract
Urm1 is a unique dual-function member of the ubiquitin protein family and conserved from yeast to man. It acts both as a protein modifier in ubiquitin-like urmylation and as a sulfur donor for tRNA thiolation, which in concert with the Elongator pathway forms 5-methoxy-carbonyl-methyl-2-thio (mcm5s2) modified wobble uridines (U34) in anticodons. Using Saccharomyces cerevisiae as a model to study a relationship between these two functions, we examined whether cultivation temperature and sulfur supply previously implicated in the tRNA thiolation branch of the URM1 pathway also contribute to proper urmylation. Monitoring Urm1 conjugation, we found urmylation of the peroxiredoxin Ahp1 is suppressed either at elevated cultivation temperatures or under sulfur starvation. In line with this, mutants with sulfur transfer defects that are linked to enzymes (Tum1, Uba4) required for Urm1 activation by thiocarboxylation (Urm1-COSH) were found to maintain drastically reduced levels of Ahp1 urmylation and mcm5s2U34 modification. Moreover, as revealed by site specific mutagenesis, the S-transfer rhodanese domain (RHD) in the E1-like activator (Uba4) crucial for Urm1-COSH formation is critical but not essential for protein urmylation and tRNA thiolation. In sum, sulfur supply, transfer and activation chemically link protein urmylation and tRNA thiolation. These are features that distinguish the ubiquitin-like modifier system Uba4•Urm1 from canonical ubiquitin family members and will help elucidate whether, in addition to their mechanistic links, the protein and tRNA modification branches of the URM1 pathway may also relate in function to one another.
Collapse
Affiliation(s)
- André Jüdes
- Universität Kassel, Institut für Biologie, FG Mikrobiologie,
Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Alexander Bruch
- Universität Kassel, Institut für Biologie, FG Mikrobiologie,
Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Roland Klassen
- Universität Kassel, Institut für Biologie, FG Mikrobiologie,
Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Mark Helm
- Johannes Gutenberg Universität Mainz, Institut für Pharmazie und
Biochemie, Staudinger Weg 5, 55128 Mainz, Germany
| | - Raffael Schaffrath
- Universität Kassel, Institut für Biologie, FG Mikrobiologie,
Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| |
Collapse
|