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Vallières C, Benoit O, Guittet O, Huang ME, Lepoivre M, Golinelli-Cohen MP, Vernis L. Iron-sulfur protein odyssey: exploring their cluster functional versatility and challenging identification. Metallomics 2024; 16:mfae025. [PMID: 38744662 PMCID: PMC11138216 DOI: 10.1093/mtomcs/mfae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
Abstract
Iron-sulfur (Fe-S) clusters are an essential and ubiquitous class of protein-bound prosthetic centers that are involved in a broad range of biological processes (e.g. respiration, photosynthesis, DNA replication and repair and gene regulation) performing a wide range of functions including electron transfer, enzyme catalysis, and sensing. In a general manner, Fe-S clusters can gain or lose electrons through redox reactions, and are highly sensitive to oxidation, notably by small molecules such as oxygen and nitric oxide. The [2Fe-2S] and [4Fe-4S] clusters, the most common Fe-S cofactors, are typically coordinated by four amino acid side chains from the protein, usually cysteine thiolates, but other residues (e.g. histidine, aspartic acid) can also be found. While diversity in cluster coordination ensures the functional variety of the Fe-S clusters, the lack of conserved motifs makes new Fe-S protein identification challenging especially when the Fe-S cluster is also shared between two proteins as observed in several dimeric transcriptional regulators and in the mitoribosome. Thanks to the recent development of in cellulo, in vitro, and in silico approaches, new Fe-S proteins are still regularly identified, highlighting the functional diversity of this class of proteins. In this review, we will present three main functions of the Fe-S clusters and explain the difficulties encountered to identify Fe-S proteins and methods that have been employed to overcome these issues.
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Affiliation(s)
- Cindy Vallières
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
| | - Orane Benoit
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
| | - Olivier Guittet
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
| | - Meng-Er Huang
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
| | - Michel Lepoivre
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
| | - Marie-Pierre Golinelli-Cohen
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
| | - Laurence Vernis
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
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Wang Y, Liu W, Dong B, Wang D, Nian Y, Zhou H. Isolation and Identification of Herbicidal Active Compounds from Brassica oleracea L. and Exploration of the Binding Sites of Brassicanate A Sulfoxide. PLANTS (BASEL, SWITZERLAND) 2023; 12:2576. [PMID: 37447136 DOI: 10.3390/plants12132576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023]
Abstract
Brassica oleracea L. has strong allelopathic effects on weeds. However, the allelochemicals with herbicidal activity in B. oleracea L. are still unknown. In this study, we evaluated the activity of allelochemicals isolated from Brassica oleracea L. based on the germination and growth of model plant Lactuca sativa Linn., grass weed Panicum miliaceum, and broadleaf weed Chenopodium album. Additionally, we employed molecular docking to predict the binding of brassicanate A sulfoxide to herbicide targets. The results of this study showed that eight compounds with herbicidal activity were isolated from B. oleracea L., and the predicted results indicated that brassicanate A sulfoxide was stably bound to dihydroxyacid dehydratase, hydroxymethylpyruvate dioxygenase, acetolactate synthase, PYL family proteins and transport inhibitor response 1. This research provides compound sources and a theoretical foundation for the development of natural herbicides.
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Affiliation(s)
- Yu Wang
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot 010020, China
| | - Wanyou Liu
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot 010020, China
| | - Baozhu Dong
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot 010020, China
| | - Dong Wang
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot 010020, China
| | - Yin Nian
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hongyou Zhou
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot 010020, China
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3
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Yang B, Xu C, Cheng Y, Jia T, Hu X. Research progress on the biosynthesis and delivery of iron-sulfur clusters in the plastid. PLANT CELL REPORTS 2023:10.1007/s00299-023-03024-7. [PMID: 37160773 DOI: 10.1007/s00299-023-03024-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/27/2023] [Indexed: 05/11/2023]
Abstract
Iron-sulfur (Fe-S) clusters are ancient protein cofactors ubiquitously exist in organisms. They are involved in many important life processes. Plastids are semi-autonomous organelles with a double membrane and it is believed to originate from a cyanobacterial endosymbiont. By learning form the research in cyanobacteria, a Fe-S cluster biosynthesis and delivery pathway has been proposed and partly demonstrated in plastids, including iron uptake, sulfur mobilization, Fe-S cluster assembly and delivery. Fe-S clusters are essential for the downstream Fe-S proteins to perform their normal biological functions. Because of the importance of Fe-S proteins in plastid, researchers have made a lot of research progress on this pathway in recent years. This review summarizes the detail research progress made in recent years. In addition, the scientific problems remained in this pathway are also discussed.
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Affiliation(s)
- Bing Yang
- International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
- Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China
| | - Chenyun Xu
- International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
- Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China
| | - Yuting Cheng
- International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
- Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China
| | - Ting Jia
- International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
| | - Xueyun Hu
- International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
- Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China.
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4
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Bayaraa T, Lonhienne T, Sutiono S, Melse O, Brück TB, Marcellin E, Bernhardt PV, Boden M, Harmer JR, Sieber V, Guddat LW, Schenk G. Structural and Functional Insight into the Mechanism of the Fe-S Cluster-Dependent Dehydratase from Paralcaligenes ureilyticus. Chemistry 2023; 29:e202203140. [PMID: 36385513 PMCID: PMC10107998 DOI: 10.1002/chem.202203140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/18/2022]
Abstract
Enzyme-catalyzed reaction cascades play an increasingly important role for the sustainable manufacture of diverse chemicals from renewable feedstocks. For instance, dehydratases from the ilvD/EDD superfamily have been embedded into a cascade to convert glucose via pyruvate to isobutanol, a platform chemical for the production of aviation fuels and other valuable materials. These dehydratases depend on the presence of both a Fe-S cluster and a divalent metal ion for their function. However, they also represent the rate-limiting step in the cascade. Here, catalytic parameters and the crystal structure of the dehydratase from Paralcaligenes ureilyticus (PuDHT, both in presence of Mg2+ and Mn2+ ) were investigated. Rate measurements demonstrate that the presence of stoichiometric concentrations Mn2+ promotes higher activity than Mg2+ , but at high concentrations the former inhibits the activity of PuDHT. Molecular dynamics simulations identify the position of a second binding site for the divalent metal ion. Only binding of Mn2+ (not Mg2+ ) to this site affects the ligand environment of the catalytically essential divalent metal binding site, thus providing insight into an inhibitory mechanism of Mn2+ at higher concentrations. Furthermore, in silico docking identified residues that play a role in determining substrate binding and selectivity. The combined data inform engineering approaches to design an optimal dehydratase for the cascade.
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Affiliation(s)
- Tenuun Bayaraa
- School of Chemistry and Molecular Biosciences, The University of Queensland, 4072, Brisbane, Australia
| | - Thierry Lonhienne
- School of Chemistry and Molecular Biosciences, The University of Queensland, 4072, Brisbane, Australia
| | - Samuel Sutiono
- Chair of Chemistry of Biogenic resources, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, 94315, Straubing, Germany
| | - Okke Melse
- Chair of Chemistry of Biogenic resources, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, 94315, Straubing, Germany
| | - Thomas B Brück
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich, 85748, Garching, Germany
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, 4072, Brisbane, Australia
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences, The University of Queensland, 4072, Brisbane, Australia
| | - Mikael Boden
- School of Chemistry and Molecular Biosciences, The University of Queensland, 4072, Brisbane, Australia
| | - Jeffrey R Harmer
- Centre for Advanced Imaging, The University of Queensland, 4072, Brisbane, Australia
| | - Volker Sieber
- School of Chemistry and Molecular Biosciences, The University of Queensland, 4072, Brisbane, Australia.,Chair of Chemistry of Biogenic resources, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, 94315, Straubing, Germany
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, 4072, Brisbane, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, 4072, Brisbane, Australia.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, 4072, Brisbane, Australia.,Sustainable Minerals Institute, The University of Queensland, 4072, Brisbane, Australia
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5
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Bayaraa T, Gaete J, Sutiono S, Kurz J, Lonhienne T, Harmer JR, Bernhardt PV, Sieber V, Guddat L, Schenk G. Dihydroxy‐Acid Dehydratases From Pathogenic Bacteria: Emerging Drug Targets to Combat Antibiotic Resistance. Chemistry 2022; 28:e202200927. [PMID: 35535733 PMCID: PMC9543379 DOI: 10.1002/chem.202200927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Indexed: 11/30/2022]
Abstract
There is an urgent global need for the development of novel therapeutics to combat the rise of various antibiotic‐resistant superbugs. Enzymes of the branched‐chain amino acid (BCAA) biosynthesis pathway are an attractive target for novel anti‐microbial drug development. Dihydroxy‐acid dehydratase (DHAD) is the third enzyme in the BCAA biosynthesis pathway. It relies on an Fe−S cluster for catalytic activity and has recently also gained attention as a catalyst in cell‐free enzyme cascades. Two types of Fe−S clusters have been identified in DHADs, i.e. [2Fe−2S] and [4Fe−4S], with the latter being more prone to degradation in the presence of oxygen. Here, we characterise two DHADs from bacterial human pathogens, Staphylococcus aureus and Campylobacter jejuni (SaDHAD and CjDHAD). Purified SaDHAD and CjDHAD are virtually inactive, but activity could be reversibly reconstituted in vitro (up to ∼19,000‐fold increase with kcat as high as ∼6.7 s−1). Inductively‐coupled plasma‐optical emission spectroscopy (ICP‐OES) measurements are consistent with the presence of [4Fe−4S] clusters in both enzymes. N‐isopropyloxalyl hydroxamate (IpOHA) and aspterric acid are both potent inhibitors for both SaDHAD (Ki=7.8 and 51.6 μM, respectively) and CjDHAD (Ki=32.9 and 35.1 μM, respectively). These compounds thus present suitable starting points for the development of novel anti‐microbial chemotherapeutics.
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Affiliation(s)
- Tenuun Bayaraa
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 Australia
| | - Jose Gaete
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 Australia
| | - Samuel Sutiono
- Chair of Chemistry of Biogenic resources Campus Straubing for Biotechnology and Sustainability Technical University of Munich Schulgasse 16 94315 Straubing Germany
| | - Julia Kurz
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 Australia
| | - Thierry Lonhienne
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 Australia
| | - Jeffrey R. Harmer
- Centre for Advanced Imaging The University of Queensland Brisbane 4072 Australia
| | - Paul V. Bernhardt
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 Australia
| | - Volker Sieber
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 Australia
- Chair of Chemistry of Biogenic resources Campus Straubing for Biotechnology and Sustainability Technical University of Munich Schulgasse 16 94315 Straubing Germany
| | - Luke Guddat
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane 4072 Australia
- Sustainable Minerals Institute The University of Queensland Brisbane 4072 Australia
- Australian Institute for Bioengineering and Nanotechnology The University of Queensland Brisbane 4072 Australia
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6
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Eprintsev AT, Fedorin DN, Anokhina GB, Igamberdiev AU. Effects of light, anoxia and salinity on the expression of dihydroxyacid dehydratase in maize. JOURNAL OF PLANT PHYSIOLOGY 2021; 265:153507. [PMID: 34478919 DOI: 10.1016/j.jplph.2021.153507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/24/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Dihydroxyacid dehydratase (EC 4.2.1.9) participates in metabolism of branched chain amino acids, in CoA biosynthesis and in the conversion of hydroxycitric acid that accumulates in several plants. In maize (Zea mays L.), this enzyme is encoded by the two genes (Dhad1 and Dhad2), having different patterns of their expression during germination. We have demonstrated the inhibition of Dhad1 expression by light and the opposite effect of light on Dhad2. These effects were phytochrome-dependent and involved methylation/demethylation of promoters. Incubation of maize plants in a nitrogen atmosphere resulted in Dhad1 activation peaking at 12 h, which coincided with the decrease in promoter methylation. The gene Dhad2 was activated only during the first 6 h of anoxia, with no correlation with the level of promoter methylation. Salt stress (150 mM NaCl) caused the activation of expression of Dhad2 while the expression of Dhad1 was inhibited in the first hour and then after 12 h incubation with NaCl. We conclude that the expression of two genes encoding dihydroxyacid dehydratase reveals the opposite or different patterns of regulation by light, anoxia and salinity. The mechanisms underlying these modifications involve promoter methylation and result in corresponding changes in the enzymatic activity of the conversion of hydroxycitrate to 2-oxoglutarate.
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Affiliation(s)
- Alexander T Eprintsev
- Department of Biochemistry and Cell Physiology, Voronezh State University, 394018, Voronezh, Russia.
| | - Dmitry N Fedorin
- Department of Biochemistry and Cell Physiology, Voronezh State University, 394018, Voronezh, Russia.
| | - Galina B Anokhina
- Department of Biochemistry and Cell Physiology, Voronezh State University, 394018, Voronezh, Russia.
| | - Abir U Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1B 3X9, Canada.
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7
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Khademian M, Imlay JA. How Microbes Evolved to Tolerate Oxygen. Trends Microbiol 2021; 29:428-440. [PMID: 33109411 PMCID: PMC8043972 DOI: 10.1016/j.tim.2020.10.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/03/2020] [Accepted: 10/05/2020] [Indexed: 12/24/2022]
Abstract
Ancient microbes invented biochemical mechanisms and assembled core metabolic pathways on an anoxic Earth. Molecular oxygen appeared far later, forcing microbes to devise layers of defensive tactics that fend off the destructive actions of both reactive oxygen species (ROS) and oxygen itself. Recent work has pinpointed the enzymes that ROS attack, plus an array of clever protective strategies that abet the well known scavenging systems. Oxygen also directly damages the low-potential metal centers and radical-based mechanisms that optimize anaerobic metabolism; therefore, committed anaerobes have evolved customized tactics that defend these various enzymes from occasional oxygen exposure. Thus a more comprehensive, detailed, and surprising view of oxygen toxicity is coming into view.
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Affiliation(s)
- Maryam Khademian
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA.
| | - James A Imlay
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
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8
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Liang YF, Long ZX, Zhang YJ, Luo CY, Yan LT, Gao WY, Li H. The chemical mechanisms of the enzymes in the branched-chain amino acids biosynthetic pathway and their applications. Biochimie 2021; 184:72-87. [PMID: 33607240 DOI: 10.1016/j.biochi.2021.02.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/04/2021] [Accepted: 02/10/2021] [Indexed: 12/27/2022]
Abstract
l-Valine, l-isoleucine, and l-leucine are three key proteinogenic amino acids, and they are also the essential amino acids required for mammalian growth, possessing important and to some extent, special physiological and biological functions. Because of the branched structures in their carbon chains, they are also named as branched-chain amino acids (BCAAs). This review will highlight the advance in studies of the enzymes involved in the biosynthetic pathway of BCAAs, concentrating on their chemical mechanisms and applications in screening herbicides and antibacterial agents. The uses of some of these enzymes in lab scale organic synthesis are also discussed.
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Affiliation(s)
- Yan-Fei Liang
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China
| | - Zi-Xian Long
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China
| | - Ya-Jian Zhang
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China
| | - Cai-Yun Luo
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China
| | - Le-Tian Yan
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China
| | - Wen-Yun Gao
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China.
| | - Heng Li
- College of Life Sciences, National Engineering Research Center for Miniaturized Detection Systems, Northwest University, Xi'an, 710069, China.
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Abstract
The Embden–Meyerhof–Parnas (EMP) and Entner–Doudoroff (ED) pathways are considered the most abundant catabolic pathways found in microorganisms, and ED enzymes have been shown to also be widespread in cyanobacteria, algae and plants. In a large number of organisms, especially common strains used in molecular biology, these pathways account for the catabolism of glucose. The existence of pathways for other carbohydrates that are relevant to biomass utilization has been recognized as new strains have been characterized among thermophilic bacteria and Archaea that are able to transform simple polysaccharides from biomass to more complex and potentially valuable precursors for industrial microbiology. Many of the variants of the ED pathway have the key dehydratase enzyme involved in the oxidation of sugar derived from different families such as the enolase, IlvD/EDD and xylose-isomerase-like superfamilies. There are the variations in structure of proteins that have the same specificity and generally greater-than-expected substrate promiscuity. Typical biomass lignocellulose has an abundance of xylan, and four different pathways have been described, which include the Weimberg and Dahms pathways initially oxidizing xylose to xylono-gamma-lactone/xylonic acid, as well as the major xylose isomerase pathway. The recent realization that xylan constitutes a large proportion of biomass has generated interest in exploiting the compound for value-added precursors, but few chassis microorganisms can grow on xylose. Arabinose is part of lignocellulose biomass and can be metabolized with similar pathways to xylose, as well as an oxidative pathway. Like enzymes in many non-phosphorylative carbohydrate pathways, enzymes involved in L-arabinose pathways from bacteria and Archaea show metabolic and substrate promiscuity. A similar multiplicity of pathways was observed for other biomass-derived sugars such as L-rhamnose and L-fucose, but D-mannose appears to be distinct in that a non-phosphorylative version of the ED pathway has not been reported. Many bacteria and Archaea are able to grow on mannose but, as with other minor sugars, much of the information has been derived from whole cell studies with additional enzyme proteins being incorporated, and so far, only one synthetic pathway has been described. There appears to be a need for further discovery studies to clarify the general ability of many microorganisms to grow on the rarer sugars, as well as evaluation of the many gene copies displayed by marine bacteria.
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Zhang P, MacTavish BS, Yang G, Chen M, Roh J, Newsome KR, Bruner SD, Ding Y. Cyanobacterial Dihydroxyacid Dehydratases Are a Promising Growth Inhibition Target. ACS Chem Biol 2020; 15:2281-2288. [PMID: 32786290 PMCID: PMC8162731 DOI: 10.1021/acschembio.0c00507] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Microbes are essential to the global ecosystem, but undesirable microbial growth causes issues ranging from food spoilage and infectious diseases to harmful cyanobacterial blooms. The use of chemicals to control microbial growth has achieved significant success, while specific roles for a majority of essential genes in growth control remain unexplored. Here, we show the growth inhibition of cyanobacterial species by targeting an essential enzyme for the biosynthesis of branched-chain amino acids. Specifically, we report the biochemical, genetic, and structural characterization of dihydroxyacid dehydratase from the model cyanobacterium Synechocystis sp. PCC 6803 (SnDHAD). Our studies suggest that SnDHAD is an oxygen-stable enzyme containing a [2Fe-2S] cluster. Furthermore, we demonstrate that SnDHAD is selectively inhibited in vitro and in vivo by the natural product aspterric acid, which also inhibits the growth of representative bloom-forming Microcystis and Anabaena strains but has minimal effects on microbial pathogens with [4Fe-4S] containing DHADs. This study suggests DHADs as a promising target for the precise growth control of microbes and highlights the exploration of other untargeted essential genes for microbial management.
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Affiliation(s)
- Peilan Zhang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, Florida, 32610, United States
| | - Brian S. MacTavish
- Department of Chemistry, University of Florida, Gainesville, Florida, 32611, United States
| | - Guang Yang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, Florida, 32610, United States
| | - Manyun Chen
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, Florida, 32610, United States
| | - Jaehyeok Roh
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, Florida, 32610, United States
| | - Kevin R. Newsome
- Department of Chemistry, University of Florida, Gainesville, Florida, 32611, United States
| | - Steven D. Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida, 32611, United States
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, Florida, 32610, United States
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11
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Khademian M, Imlay JA. Do reactive oxygen species or does oxygen itself confer obligate anaerobiosis? The case of Bacteroides thetaiotaomicron. Mol Microbiol 2020; 114:333-347. [PMID: 32301184 DOI: 10.1111/mmi.14516] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/07/2020] [Accepted: 04/07/2020] [Indexed: 02/06/2023]
Abstract
Bacteroides thetaiotaomicron was examined to determine whether its obligate anaerobiosis is imposed by endogenous reactive oxygen species or by molecular oxygen itself. Previous analyses established that aerated B. thetaiotaomicron loses some enzyme activities due to a high rate of endogenous superoxide formation. However, the present study establishes that another key step in central metabolism is poisoned by molecular oxygen itself. Pyruvate dissimilation was shown to depend upon two enzymes, pyruvate:formate lyase (PFL) and pyruvate:ferredoxin oxidoreductase (PFOR), that lose activity upon aeration. PFL is a glycyl-radical enzyme whose vulnerability to oxygen is already understood. The rate of PFOR damage was unaffected by the level of superoxide or peroxide, showing that molecular oxygen itself is the culprit. The cell cannot repair PFOR, which amplifies the impact of damage. The rates of PFOR and fumarase inactivation are similar, suggesting that superoxide dismutase is calibrated so the oxygen- and superoxide-sensitive enzymes are equally sensitive to aeration. The physiological purpose of PFL and PFOR is to degrade pyruvate without disrupting the redox balance, and they do so using catalytic mechanisms that are intrinsically vulnerable to oxygen. In this way, the anaerobic excellence and oxygen sensitivity of B. thetaiotaomicron are two sides of the same coin.
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Affiliation(s)
- Maryam Khademian
- Department of Microbiology, University of Illinois, Urbana, IL, USA
| | - James A Imlay
- Department of Microbiology, University of Illinois, Urbana, IL, USA
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12
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Bashiri G, Grove TL, Hegde SS, Lagautriere T, Gerfen GJ, Almo SC, Squire CJ, Blanchard JS, Baker EN. The active site of the Mycobacterium tuberculosis branched-chain amino acid biosynthesis enzyme dihydroxyacid dehydratase contains a 2Fe-2S cluster. J Biol Chem 2019; 294:13158-13170. [PMID: 31315931 DOI: 10.1074/jbc.ra119.009498] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/15/2019] [Indexed: 01/17/2023] Open
Abstract
Iron-sulfur clusters are protein cofactors with an ancient evolutionary origin. These clusters are best known for their roles in redox proteins such as ferredoxins, but some iron-sulfur clusters have nonredox roles in the active sites of enzymes. Such clusters are often prone to oxidative degradation, making the enzymes difficult to characterize. Here we report a structural and functional characterization of dihydroxyacid dehydratase (DHAD) from Mycobacterium tuberculosis (Mtb), an essential enzyme in the biosynthesis of branched-chain amino acids. Conducting this analysis under fully anaerobic conditions, we solved the DHAD crystal structure, at 1.88 Å resolution, revealing a 2Fe-2S cluster in which one iron ligand is a potentially exchangeable water molecule or hydroxide. UV and EPR spectroscopy both suggested that the substrate binds directly to the cluster or very close to it. Kinetic analysis implicated two ionizable groups in the catalytic mechanism, which we postulate to be Ser-491 and the iron-bound water/hydroxide. Site-directed mutagenesis showed that Ser-491 is essential for activity, and substrate docking indicated that this residue is perfectly placed for proton abstraction. We found that a bound Mg2+ ion 6.5 Å from the 2Fe-2S cluster plays a key role in substrate binding. We also identified a putative entry channel that enables access to the cluster and show that Mtb-DHAD is inhibited by a recently discovered herbicide, aspterric acid, that, given the essentiality of DHAD for Mtb survival, is a potential lead compound for the design of novel anti-TB drugs.
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Affiliation(s)
- Ghader Bashiri
- Maurice Wilkins Center for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Tyler L Grove
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10805
| | - Subray S Hegde
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10805
| | - Thomas Lagautriere
- Maurice Wilkins Center for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Gary J Gerfen
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10805
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10805
| | - Christopher J Squire
- Maurice Wilkins Center for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - John S Blanchard
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10805
| | - Edward N Baker
- Maurice Wilkins Center for Molecular Biodiscovery and School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand.
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13
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Touraine B, Vignols F, Przybyla-Toscano J, Ischebeck T, Dhalleine T, Wu HC, Magno C, Berger N, Couturier J, Dubos C, Feussner I, Caffarri S, Havaux M, Rouhier N, Gaymard F. Iron-sulfur protein NFU2 is required for branched-chain amino acid synthesis in Arabidopsis roots. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1875-1889. [PMID: 30785184 DOI: 10.1093/jxb/erz050] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 01/25/2019] [Indexed: 05/23/2023]
Abstract
Numerous proteins require a metallic co-factor for their function. In plastids, the maturation of iron-sulfur (Fe-S) proteins necessitates a complex assembly machinery. In this study, we focused on Arabidopsis thaliana NFU1, NFU2, and NFU3, which participate in the final steps of the maturation process. According to the strong photosynthetic defects observed in high chlorophyll fluorescence 101 (hcf101), nfu2, and nfu3 plants, we determined that NFU2 and NFU3, but not NFU1, act immediately upstream of HCF101 for the maturation of [Fe4S4]-containing photosystem I subunits. An additional function of NFU2 in the maturation of the [Fe2S2] cluster of a dihydroxyacid dehydratase was obvious from the accumulation of precursors of the branched-chain amino acid synthesis pathway in roots of nfu2 plants and from the rescue of the primary root growth defect by supplying branched-chain amino acids. The absence of NFU3 in roots precluded any compensation. Overall, unlike their eukaryotic and prokaryotic counterparts, which are specific to [Fe4S4] proteins, NFU2 and NFU3 contribute to the maturation of both [Fe2S2] and [Fe4S4] proteins, either as a relay in conjunction with other proteins such as HCF101 or by directly delivering Fe-S clusters to client proteins. Considering the low number of Fe-S cluster transfer proteins relative to final acceptors, additional targets probably await identification.
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Affiliation(s)
- Brigitte Touraine
- BPMP, CNRS, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Florence Vignols
- BPMP, CNRS, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | | | - Till Ischebeck
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077 Göttingen, Germany
| | | | - Hui-Chen Wu
- BPMP, CNRS, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Cyril Magno
- BPMP, CNRS, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Nathalie Berger
- BPMP, CNRS, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | | | - Christian Dubos
- BPMP, CNRS, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, 37077 Göttingen, Germany
| | - Stefano Caffarri
- Aix-Marseille Université, CEA Cadarache, CNRS UMR 7265, Laboratoire de Génétique et Biophysique des Plantes, 13009 Marseille, France
| | - Michel Havaux
- CEA Cadarache, CNRS UMR 7265, Aix-Marseille Université, Laboratoire d'Ecophysiologie Moléculaire des Plantes, 13108, Saint-Paul-lez-Durance, France
| | | | - Frédéric Gaymard
- BPMP, CNRS, INRA, Montpellier SupAgro, Université de Montpellier, Montpellier, France
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14
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Resistance-gene-directed discovery of a natural-product herbicide with a new mode of action. Nature 2018; 559:415-418. [PMID: 29995859 PMCID: PMC6097235 DOI: 10.1038/s41586-018-0319-4] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 05/22/2018] [Indexed: 01/21/2023]
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15
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Gao H, Azam T, Randeniya S, Couturier J, Rouhier N, Johnson MK. Function and maturation of the Fe-S center in dihydroxyacid dehydratase from Arabidopsis. J Biol Chem 2018; 293:4422-4433. [PMID: 29425096 DOI: 10.1074/jbc.ra117.001592] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/02/2018] [Indexed: 12/26/2022] Open
Abstract
Dihydroxyacid dehydratase (DHAD) is the third enzyme required for branched-chain amino acid biosynthesis in bacteria, fungi, and plants. DHAD enzymes contain two distinct types of active-site Fe-S clusters. The best characterized examples are Escherichia coli DHAD, which contains an oxygen-labile [Fe4S4] cluster, and spinach DHAD, which contains an oxygen-resistant [Fe2S2] cluster. Although the Fe-S cluster is crucial for DHAD function, little is known about the cluster-coordination environment or the mechanism of catalysis and cluster biogenesis. Here, using the combination of UV-visible absorption and circular dichroism and resonance Raman and electron paramagnetic resonance, we spectroscopically characterized the Fe-S center in DHAD from Arabidopsis thaliana (At). Our results indicated that AtDHAD can accommodate [Fe2S2] and [Fe4S4] clusters. However, only the [Fe2S2] cluster-bound form is catalytically active. We found that the [Fe2S2] cluster is coordinated by at least one non-cysteinyl ligand, which can be replaced by the thiol group(s) of dithiothreitol. In vitro cluster transfer and reconstitution reactions revealed that [Fe2S2] cluster-containing NFU2 protein is likely the physiological cluster donor for in vivo maturation of AtDHAD. In summary, AtDHAD binds either one [Fe4S4] or one [Fe2S2] cluster, with only the latter being catalytically competent and capable of substrate and product binding, and NFU2 appears to be the physiological [Fe2S2] cluster donor for DHAD maturation. This work represents the first in vitro characterization of recombinant AtDHAD, providing new insights into the properties, biogenesis, and catalytic role of the active-site Fe-S center in a plant DHAD.
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Affiliation(s)
- Huanyao Gao
- From the Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602 and
| | - Tamanna Azam
- From the Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602 and
| | - Sajini Randeniya
- From the Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602 and
| | - Jérémy Couturier
- the UMR1136 Interactions Arbres-Microorganismes, Université de Lorraine/INRA, Faculté des Sciences et Technologies, 54500 Vandoeuvre-lès-Nancy, France
| | - Nicolas Rouhier
- the UMR1136 Interactions Arbres-Microorganismes, Université de Lorraine/INRA, Faculté des Sciences et Technologies, 54500 Vandoeuvre-lès-Nancy, France
| | - Michael K Johnson
- From the Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602 and
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16
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Przybyla-Toscano J, Roland M, Gaymard F, Couturier J, Rouhier N. Roles and maturation of iron-sulfur proteins in plastids. J Biol Inorg Chem 2018; 23:545-566. [PMID: 29349662 PMCID: PMC6006212 DOI: 10.1007/s00775-018-1532-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 12/14/2017] [Indexed: 12/28/2022]
Abstract
One reason why iron is an essential element for most organisms is its presence in prosthetic groups such as hemes or iron–sulfur (Fe–S) clusters, which are notably required for electron transfer reactions. As an organelle with an intense metabolism in plants, chloroplast relies on many Fe–S proteins. This includes those present in the electron transfer chain which will be, in fact, essential for most other metabolic processes occurring in chloroplasts, e.g., carbon fixation, nitrogen and sulfur assimilation, pigment, amino acid, and vitamin biosynthetic pathways to cite only a few examples. The maturation of these Fe–S proteins requires a complex and specific machinery named SUF (sulfur mobilisation). The assembly process can be split in two major steps, (1) the de novo assembly on scaffold proteins which requires ATP, iron and sulfur atoms, electrons, and thus the concerted action of several proteins forming early acting assembly complexes, and (2) the transfer of the preformed Fe–S cluster to client proteins using a set of late-acting maturation factors. Similar machineries, having in common these basic principles, are present in the cytosol and in mitochondria. This review focuses on the currently known molecular details concerning the assembly and roles of Fe–S proteins in plastids.
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Affiliation(s)
- Jonathan Przybyla-Toscano
- Université de Lorraine, Interactions Arbres-Microorganismes, UMR1136, 54500, Vandoeuvre-lès-Nancy, France
| | - Mélanie Roland
- Université de Lorraine, Interactions Arbres-Microorganismes, UMR1136, 54500, Vandoeuvre-lès-Nancy, France
| | - Frédéric Gaymard
- Biochimie et Physiologie Moléculaire des Plantes, CNRS/INRA/Université Montpellier 2, SupAgro Campus, 34060, Montpellier, France
| | - Jérémy Couturier
- Université de Lorraine, Interactions Arbres-Microorganismes, UMR1136, 54500, Vandoeuvre-lès-Nancy, France
| | - Nicolas Rouhier
- Université de Lorraine, Interactions Arbres-Microorganismes, UMR1136, 54500, Vandoeuvre-lès-Nancy, France.
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17
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Rahman MM, Andberg M, Koivula A, Rouvinen J, Hakulinen N. The crystal structure of D-xylonate dehydratase reveals functional features of enzymes from the Ilv/ED dehydratase family. Sci Rep 2018; 8:865. [PMID: 29339766 PMCID: PMC5770437 DOI: 10.1038/s41598-018-19192-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 12/22/2017] [Indexed: 01/06/2023] Open
Abstract
The Ilv/ED dehydratase protein family includes dihydroxy acid-, gluconate-, 6-phosphogluconate- and pentonate dehydratases. The members of this family are involved in various biosynthetic and carbohydrate metabolic pathways. Here, we describe the first crystal structure of D-xylonate dehydratase from Caulobacter crescentus (CcXyDHT) at 2.7 Å resolution and compare it with other available enzyme structures from the IlvD/EDD protein family. The quaternary structure of CcXyDHT is a tetramer, and each monomer is composed of two domains in which the N-terminal domain forms a binding site for a [2Fe-2S] cluster and a Mg2+ ion. The active site is located at the monomer-monomer interface and contains residues from both the N-terminal recognition helix and the C-terminus of the dimeric counterpart. The active site also contains a conserved Ser490, which probably acts as a base in catalysis. Importantly, the cysteines that participate in the binding and formation of the [2Fe-2S] cluster are not all conserved within the Ilv/ED dehydratase family, which suggests that some members of the IlvD/EDD family may bind different types of [Fe-S] clusters.
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Affiliation(s)
- Mohammad Mubinur Rahman
- Department of Chemistry, University of Eastern Finland, PO Box 111, FIN-80101, Joensuu, Finland
| | - Martina Andberg
- VTT Technical Research Centre of Finland Ltd, PO Box 1000, FIN-02044 VTT, Espoo, Finland
| | - Anu Koivula
- VTT Technical Research Centre of Finland Ltd, PO Box 1000, FIN-02044 VTT, Espoo, Finland
| | - Juha Rouvinen
- Department of Chemistry, University of Eastern Finland, PO Box 111, FIN-80101, Joensuu, Finland
| | - Nina Hakulinen
- Department of Chemistry, University of Eastern Finland, PO Box 111, FIN-80101, Joensuu, Finland.
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18
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Amorim Franco TM, Blanchard JS. Bacterial Branched-Chain Amino Acid Biosynthesis: Structures, Mechanisms, and Drugability. Biochemistry 2017; 56:5849-5865. [PMID: 28977745 DOI: 10.1021/acs.biochem.7b00849] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The eight enzymes responsible for the biosynthesis of the three branched-chain amino acids (l-isoleucine, l-leucine, and l-valine) were identified decades ago using classical genetic approaches based on amino acid auxotrophy. This review will highlight the recent progress in the determination of the three-dimensional structures of these enzymes, their chemical mechanisms, and insights into their suitability as targets for the development of antibacterial agents. Given the enormous rise in bacterial drug resistance to every major class of antibacterial compound, there is a clear and present need for the identification of new antibacterial compounds with nonoverlapping targets to currently used antibacterials that target cell wall, protein, mRNA, and DNA synthesis.
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Affiliation(s)
- Tathyana M Amorim Franco
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10805, United States
| | - John S Blanchard
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10805, United States
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19
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Rahman MM, Andberg M, Thangaraj SK, Parkkinen T, Penttilä M, Jänis J, Koivula A, Rouvinen J, Hakulinen N. The Crystal Structure of a Bacterial l-Arabinonate Dehydratase Contains a [2Fe-2S] Cluster. ACS Chem Biol 2017; 12:1919-1927. [PMID: 28574691 DOI: 10.1021/acschembio.7b00304] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a novel crystal structure of the IlvD/EDD family enzyme, l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii (RlArDHT, EC 4.2.1.25), which catalyzes the conversion of l-arabinonate to 2-dehydro-3-deoxy-l-arabinonate. The enzyme is a tetramer consisting of a dimer of dimers, where each monomer is composed of two domains. The active site contains a catalytically important [2Fe-2S] cluster and Mg2+ ion and is buried between two domains, and also at the dimer interface. The active site Lys129 was found to be carbamylated. Ser480 and Thr482 were shown to be essential residues for catalysis, and the S480A mutant structure showed an unexpected open conformation in which the active site was more accessible for the substrate. This structure showed the partial binding of l-arabinonate, which allowed us to suggest that the alkoxide ion form of the Ser480 side chain functions as a base and the [2Fe-2S] cluster functions as a Lewis acid in the elimination reaction.
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Affiliation(s)
- Mohammad Mubinur Rahman
- Department
of Chemistry, University of Eastern Finland, P.O. Box 111, FIN-80101 Joensuu, Finland
| | - Martina Andberg
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FIN-02044 VTT, Espoo, Finland
| | - Senthil Kumar Thangaraj
- Department
of Chemistry, University of Eastern Finland, P.O. Box 111, FIN-80101 Joensuu, Finland
| | - Tarja Parkkinen
- Department
of Chemistry, University of Eastern Finland, P.O. Box 111, FIN-80101 Joensuu, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FIN-02044 VTT, Espoo, Finland
| | - Janne Jänis
- Department
of Chemistry, University of Eastern Finland, P.O. Box 111, FIN-80101 Joensuu, Finland
| | - Anu Koivula
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FIN-02044 VTT, Espoo, Finland
| | - Juha Rouvinen
- Department
of Chemistry, University of Eastern Finland, P.O. Box 111, FIN-80101 Joensuu, Finland
| | - Nina Hakulinen
- Department
of Chemistry, University of Eastern Finland, P.O. Box 111, FIN-80101 Joensuu, Finland
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20
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Roberts CA, Al-Tameemi HM, Mashruwala AA, Rosario-Cruz Z, Chauhan U, Sause WE, Torres VJ, Belden WJ, Boyd JM. The Suf Iron-Sulfur Cluster Biosynthetic System Is Essential in Staphylococcus aureus, and Decreased Suf Function Results in Global Metabolic Defects and Reduced Survival in Human Neutrophils. Infect Immun 2017; 85:e00100-17. [PMID: 28320837 PMCID: PMC5442634 DOI: 10.1128/iai.00100-17] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 03/16/2017] [Indexed: 01/30/2023] Open
Abstract
Staphylococcus aureus remains a causative agent for morbidity and mortality worldwide. This is in part a result of antimicrobial resistance, highlighting the need to uncover novel antibiotic targets and to discover new therapeutic agents. In the present study, we explored the possibility that iron-sulfur (Fe-S) cluster synthesis is a viable antimicrobial target. RNA interference studies established that Suf (sulfur mobilization)-dependent Fe-S cluster synthesis is essential in S. aureus We found that sufCDSUB were cotranscribed and that suf transcription was positively influenced by sigma factor B. We characterized an S. aureus strain that contained a transposon inserted in the intergenic space between sufC and sufD (sufD*), resulting in decreased transcription of sufSUB Consistent with the transcriptional data, the sufD* strain had multiple phenotypes associated with impaired Fe-S protein maturation. They included decreased activities of Fe-S cluster-dependent enzymes, decreased growth in media lacking metabolites that require Fe-S proteins for synthesis, and decreased flux through the tricarboxylic acid (TCA) cycle. Decreased Fe-S cluster synthesis resulted in sensitivity to reactive oxygen and reactive nitrogen species, as well as increased DNA damage and impaired DNA repair. The sufD* strain also exhibited perturbed intracellular nonchelated Fe pools. Importantly, the sufD* strain did not exhibit altered exoprotein production or altered biofilm formation, but it was attenuated for survival upon challenge by human polymorphonuclear leukocytes. The results presented are consistent with the hypothesis that Fe-S cluster synthesis is a viable target for antimicrobial development.
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Affiliation(s)
- Christina A Roberts
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, State University of New Jersey, New Brunswick, New Jersey, USA
| | - Hassan M Al-Tameemi
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, State University of New Jersey, New Brunswick, New Jersey, USA
| | - Ameya A Mashruwala
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, State University of New Jersey, New Brunswick, New Jersey, USA
| | - Zuelay Rosario-Cruz
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, State University of New Jersey, New Brunswick, New Jersey, USA
| | - Unnati Chauhan
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, State University of New Jersey, New Brunswick, New Jersey, USA
| | - William E Sause
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | - Victor J Torres
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | - William J Belden
- Department of Animal Sciences, School of Environmental and Biological Sciences, Rutgers, State University of New Jersey, New Brunswick, New Jersey, USA
| | - Jeffrey M Boyd
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, State University of New Jersey, New Brunswick, New Jersey, USA
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21
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The Fumarate Reductase of Bacteroides thetaiotaomicron, unlike That of Escherichia coli, Is Configured so that It Does Not Generate Reactive Oxygen Species. mBio 2017; 8:mBio.01873-16. [PMID: 28049145 PMCID: PMC5210497 DOI: 10.1128/mbio.01873-16] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The impact of oxidative stress upon organismal fitness is most apparent in the phenomenon of obligate anaerobiosis. The root cause may be multifaceted, but the intracellular generation of reactive oxygen species (ROS) likely plays a key role. ROS are formed when redox enzymes accidentally transfer electrons to oxygen rather than to their physiological substrates. In this study, we confirm that the predominant intestinal anaerobe Bacteroides thetaiotaomicron generates intracellular ROS at a very high rate when it is aerated. Fumarate reductase (Frd) is a prominent enzyme in the anaerobic metabolism of many bacteria, including B. thetaiotaomicron, and prior studies of Escherichia coli Frd showed that the enzyme is unusually prone to ROS generation. Surprisingly, in this study biochemical analysis demonstrated that the B. thetaiotaomicron Frd does not react with oxygen at all: neither superoxide nor hydrogen peroxide is formed. Subunit-swapping experiments indicated that this difference does not derive from the flavoprotein subunit at which ROS normally arise. Experiments with the related enzyme succinate dehydrogenase discouraged the hypothesis that heme moieties are responsible. Thus, resistance to oxidation may reflect a shift of electron density away from the flavin moiety toward the iron-sulfur clusters. This study shows that the autoxidizability of a redox enzyme can be suppressed by subtle modifications that do not compromise its physiological function. One implication is that selective pressures might enhance the oxygen tolerance of an organism by manipulating the electronic properties of its redox enzymes so they do not generate ROS. IMPORTANCE Whether in sediments or pathogenic biofilms, the structures of microbial communities are configured around the sensitivities of their members to oxygen. Oxygen triggers the intracellular formation of reactive oxygen species (ROS), and the sensitivity of a microbe to oxygen likely depends upon the rates at which ROS are formed inside it. This study supports that idea, as an obligate anaerobe was confirmed to generate ROS very rapidly upon aeration. However, the suspected source of the ROS was disproven, as the fumarate reductase of the anaerobe did not display the high oxidation rate of its E. coli homologue. Evidently, adjustments in its electronic structure can suppress the tendency of an enzyme to generate ROS. Importantly, this outcome suggests that evolutionary pressure may succeed in modifying redox enzymes and thereby diminishing the stress that an organism experiences in oxic environments. The actual source of ROS in the anaerobe remains to be discovered.
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22
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Rahman MM, Andberg M, Koivula A, Rouvinen J, Hakulinen N. Crystallization and X-ray diffraction analysis of an L-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii and a D-xylonate dehydratase from Caulobacter crescentus. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2016; 72:604-8. [PMID: 27487924 PMCID: PMC4973301 DOI: 10.1107/s2053230x16010311] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/25/2016] [Indexed: 11/28/2022]
Abstract
l-Arabinonate dehydratase and d-xylonate dehydratase from the IlvD/EDD family were crystallized by the vapour-diffusion method. Diffraction data sets were collected to resolutions of 2.40 and 2.66 Å from crystals of l-arabinonate dehydratase and d-xylonate dehydratase, respectively. l-Arabinonate dehydratase (EC 4.2.1.25) and d-xylonate dehydratase (EC 4.2.1.82) are two enzymes that are involved in a nonphosphorylative oxidation pathway of pentose sugars. l-Arabinonate dehydratase converts l-arabinonate into 2-dehydro-3-deoxy-l-arabinonate, and d-xylonate dehydratase catalyzes the dehydration of d-xylonate to 2-dehydro-3-deoxy-d-xylonate. l-Arabinonate and d-xylonate dehydratases belong to the IlvD/EDD family, together with 6-phosphogluconate dehydratases and dihydroxyacid dehydratases. No crystal structure of any l-arabinonate or d-xylonate dehydratase is available in the PDB. In this study, recombinant l-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii (RlArDHT) and d-xylonate dehydratase from Caulobacter crescentus (CcXyDHT) were heterologously expressed in Escherichia coli and purified by the use of affinity chromatography followed by gel-filtration chromatography. The purified proteins were crystallized using the hanging-drop vapour-diffusion method at 293 K. Crystals of RlArDHT that diffracted to 2.40 Å resolution were obtained using sodium formate as a precipitating agent. They belonged to space group P21, with unit-cell parameters a = 106.07, b = 208.61, c = 147.09 Å, β = 90.43°. Eight RlArDHT molecules (two tetramers) in the asymmetric unit give a VM value of 3.2 Å3 Da−1 and a solvent content of 62%. Crystals of CcXyDHT that diffracted to 2.66 Å resolution were obtained using sodium formate and polyethylene glycol 3350. They belonged to space group C2, with unit-cell parameters a = 270.42, b = 236.13, c = 65.17 Å, β = 97.38°. Four CcXyDHT molecules (a tetramer) in the asymmetric unit give a VM value of 4.0 Å3 Da−1 and a solvent content of 69%.
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Affiliation(s)
- Mohammad Mubinur Rahman
- Department of Chemistry, University of Eastern Finland, Joensuu Campus, PO Box 111, FIN-80101 Joensuu, Finland
| | - Martina Andberg
- VTT Technical Research Centre of Finland Ltd, PO Box 1000, FIN-02044 VTT Espoo, Finland
| | - Anu Koivula
- VTT Technical Research Centre of Finland Ltd, PO Box 1000, FIN-02044 VTT Espoo, Finland
| | - Juha Rouvinen
- Department of Chemistry, University of Eastern Finland, Joensuu Campus, PO Box 111, FIN-80101 Joensuu, Finland
| | - Nina Hakulinen
- Department of Chemistry, University of Eastern Finland, Joensuu Campus, PO Box 111, FIN-80101 Joensuu, Finland
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Andberg M, Aro-Kärkkäinen N, Carlson P, Oja M, Bozonnet S, Toivari M, Hakulinen N, O'Donohue M, Penttilä M, Koivula A. Characterization and mutagenesis of two novel iron-sulphur cluster pentonate dehydratases. Appl Microbiol Biotechnol 2016; 100:7549-63. [PMID: 27102126 DOI: 10.1007/s00253-016-7530-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/15/2016] [Accepted: 03/29/2016] [Indexed: 10/21/2022]
Abstract
We describe here the identification and characterization of two novel enzymes belonging to the IlvD/EDD protein family, the D-xylonate dehydratase from Caulobacter crescentus, Cc XyDHT, (EC 4.2.1.82), and the L-arabonate dehydratase from Rhizobium leguminosarum bv. trifolii, Rl ArDHT (EC 4.2.1.25), that produce the corresponding 2-keto-3-deoxy-sugar acids. There is only a very limited amount of characterization data available on pentonate dehydratases, even though the enzymes from these oxidative pathways have potential applications with plant biomass pentose sugars. The two bacterial enzymes share 41 % amino acid sequence identity and were expressed and purified from Escherichia coli as homotetrameric proteins. Both dehydratases were shown to accept pentonate and hexonate sugar acids as their substrates and require Mg(2+) for their activity. Cc XyDHT displayed the highest activity on D-xylonate and D-gluconate, while Rl ArDHT functioned best on D-fuconate, L-arabonate and D-galactonate. The configuration of the OH groups at C2 and C3 position of the sugar acid were shown to be critical, and the C4 configuration also contributed substantially to the substrate recognition. The two enzymes were also shown to contain an iron-sulphur [Fe-S] cluster. Our phylogenetic analysis and mutagenesis studies demonstrated that the three conserved cysteine residues in the aldonic acid dehydratase group of IlvD/EDD family members, those of C60, C128 and C201 in Cc XyDHT, and of C59, C127 and C200 in Rl ArDHT, are needed for coordination of the [Fe-S] cluster. The iron-sulphur cluster was shown to be crucial for the catalytic activity (kcat) but not for the substrate binding (Km) of the two pentonate dehydratases.
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Affiliation(s)
- Martina Andberg
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, VTT, FI-02044, Espoo, Finland.
| | - Niina Aro-Kärkkäinen
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, VTT, FI-02044, Espoo, Finland
| | - Paul Carlson
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, VTT, FI-02044, Espoo, Finland
| | - Merja Oja
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, VTT, FI-02044, Espoo, Finland
| | - Sophie Bozonnet
- INSA, UPS, INP; LISBP, Université de Toulouse, 135 Avenue de Rangueil, F-31077, Toulouse, France.,INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400, Toulouse, France.,CNRS, UMR5504, F-31400, Toulouse, France
| | - Mervi Toivari
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, VTT, FI-02044, Espoo, Finland
| | - Nina Hakulinen
- Department of Chemistry, University of Eastern Finland, PO Box 111, FI-80101, Joensuu, Finland
| | - Michael O'Donohue
- INSA, UPS, INP; LISBP, Université de Toulouse, 135 Avenue de Rangueil, F-31077, Toulouse, France.,INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400, Toulouse, France.,CNRS, UMR5504, F-31400, Toulouse, France
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, VTT, FI-02044, Espoo, Finland
| | - Anu Koivula
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, VTT, FI-02044, Espoo, Finland
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Igamberdiev AU, Eprintsev AT. Organic Acids: The Pools of Fixed Carbon Involved in Redox Regulation and Energy Balance in Higher Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:1042. [PMID: 27471516 PMCID: PMC4945632 DOI: 10.3389/fpls.2016.01042] [Citation(s) in RCA: 187] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 07/04/2016] [Indexed: 05/18/2023]
Abstract
Organic acids are synthesized in plants as a result of the incomplete oxidation of photosynthetic products and represent the stored pools of fixed carbon accumulated due to different transient times of conversion of carbon compounds in metabolic pathways. When redox level in the cell increases, e.g., in conditions of active photosynthesis, the tricarboxylic acid (TCA) cycle in mitochondria is transformed to a partial cycle supplying citrate for the synthesis of 2-oxoglutarate and glutamate (citrate valve), while malate is accumulated and participates in the redox balance in different cell compartments (via malate valve). This results in malate and citrate frequently being the most accumulated acids in plants. However, the intensity of reactions linked to the conversion of these compounds can cause preferential accumulation of other organic acids, e.g., fumarate or isocitrate, in higher concentrations than malate and citrate. The secondary reactions, associated with the central metabolic pathways, in particularly with the TCA cycle, result in accumulation of other organic acids that are derived from the intermediates of the cycle. They form the additional pools of fixed carbon and stabilize the TCA cycle. Trans-aconitate is formed from citrate or cis-aconitate, accumulation of hydroxycitrate can be linked to metabolism of 2-oxoglutarate, while 4-hydroxy-2-oxoglutarate can be formed from pyruvate and glyoxylate. Glyoxylate, a product of either glycolate oxidase or isocitrate lyase, can be converted to oxalate. Malonate is accumulated at high concentrations in legume plants. Organic acids play a role in plants in providing redox equilibrium, supporting ionic gradients on membranes, and acidification of the extracellular medium.
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Affiliation(s)
- Abir U. Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John’sNL, Canada
- *Correspondence: Abir U. Igamberdiev,
| | - Alexander T. Eprintsev
- Department of Biochemistry and Cell Physiology, Voronezh State UniversityVoronezh, Russia
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25
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Rosario-Cruz Z, Chahal HK, Mike LA, Skaar EP, Boyd JM. Bacillithiol has a role in Fe-S cluster biogenesis in Staphylococcus aureus. Mol Microbiol 2015; 98:218-42. [PMID: 26135358 DOI: 10.1111/mmi.13115] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2015] [Indexed: 01/20/2023]
Abstract
Staphylococcus aureus does not produce the low-molecular-weight (LMW) thiol glutathione, but it does produce the LMW thiol bacillithiol (BSH). To better understand the roles that BSH plays in staphylococcal metabolism, we constructed and examined strains lacking BSH. Phenotypic analysis found that the BSH-deficient strains cultured either aerobically or anaerobically had growth defects that were alleviated by the addition of exogenous iron (Fe) or the amino acids leucine and isoleucine. The activities of the iron-sulfur (Fe-S) cluster-dependent enzymes LeuCD and IlvD, which are required for the biosynthesis of leucine and isoleucine, were decreased in strains lacking BSH. The BSH-deficient cells also had decreased aconitase and glutamate synthase activities, suggesting a general defect in Fe-S cluster biogenesis. The phenotypes of the BSH-deficient strains were exacerbated in strains lacking the Fe-S cluster carrier Nfu and partially suppressed by multicopy expression of either sufA or nfu, suggesting functional overlap between BSH and Fe-S carrier proteins. Biochemical analysis found that SufA bound and transferred Fe-S clusters to apo-aconitase, verifying that it serves as an Fe-S cluster carrier. The results presented are consistent with the hypothesis that BSH has roles in Fe homeostasis and the carriage of Fe-S clusters to apo-proteins in S. aureus.
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Affiliation(s)
- Zuelay Rosario-Cruz
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Harsimranjit K Chahal
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Laura A Mike
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Eric P Skaar
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Jeffrey M Boyd
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
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26
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Characterization and modification of enzymes in the 2-ketoisovalerate biosynthesis pathway of Ralstonia eutropha H16. Appl Microbiol Biotechnol 2014; 99:761-74. [DOI: 10.1007/s00253-014-5965-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/15/2014] [Accepted: 07/16/2014] [Indexed: 11/27/2022]
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Holmes-Hampton GP, Tong WH, Rouault TA. Biochemical and biophysical methods for studying mitochondrial iron metabolism. Methods Enzymol 2014; 547:275-307. [PMID: 25416363 DOI: 10.1016/b978-0-12-801415-8.00015-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Iron is a heavily utilized element in organisms and numerous mechanisms accordingly regulate the trafficking, metabolism, and storage of iron. Despite the high regulation of iron homeostasis, several diseases and mutations can lead to the misregulation and often accumulation of iron in the cytosol or mitochondria of tissues. To understand the genesis of iron overload, it is necessary to employ various techniques to quantify iron in organisms and mitochondria. This chapter discusses techniques for determining the total iron content of tissue samples, ranging from colorimetric determination of iron concentrations, atomic absorption spectroscopy, inductively coupled plasma-optical emission spectroscopy, and inductively coupled plasma-mass spectrometry. In addition, we discuss in situ techniques for analyzing iron including electron microscopic nonheme iron histochemistry, electron energy loss spectroscopy, synchrotron X-ray fluorescence imaging, and confocal Raman microscopy. Finally, we discuss biophysical methods for studying iron in isolated mitochondria, including ultraviolet-visible, electron paramagnetic resonance, X-ray absorbance, and Mössbauer spectroscopies. This chapter should aid researchers to select and interpret mitochondrial iron quantifications.
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Affiliation(s)
- Gregory P Holmes-Hampton
- Molecular Medicine Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA
| | - Wing-Hang Tong
- Molecular Medicine Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA
| | - Tracey A Rouault
- Molecular Medicine Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA.
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Türker L. A Model Study on the Possible Effects of an External Electrical Field on Enzymes Having Dinuclear Iron Cluster [2Fe-2S]. ScientificWorldJournal 2012; 2012:985958. [PMID: 22629229 PMCID: PMC3353660 DOI: 10.1100/2012/985958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 12/01/2011] [Indexed: 11/17/2022] Open
Abstract
Hydrogenases which catalyze the H2↔ 2H+ + 2e− reaction are metalloenzymes that can be divided into two classes, the NiFe and Fe enzymes, on the basis of their metal content. Iron-sulfur clusters [2Fe-2S] and [4Fe-4S] are common in ironhydrogenases. In the present model study, [2Fe-2S] cluster has been considered to visualize the effect of external electric field on various quantum chemical properties of it. In the model, all the cysteinyl residues are in the amide form. The PM3 type semiempirical calculations have been performed for the geometry optimization of the model structure in the absence and presence of the external field. Then, single point DFT calculations (B3LYP/6-31+G(d)) have been carried out. Depending on the direction of the field, the chemical reactivity of the model enzyme varies which suggests that an external electric field could, under proper conditions, improve the enzymatic hydrogen production.
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Affiliation(s)
- Lemi Türker
- Department of Chemistry, Middle East Technical University, 06531 Ankara, Turkey
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29
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Mühlenhoff U, Richter N, Pines O, Pierik AJ, Lill R. Specialized function of yeast Isa1 and Isa2 proteins in the maturation of mitochondrial [4Fe-4S] proteins. J Biol Chem 2011; 286:41205-41216. [PMID: 21987576 DOI: 10.1074/jbc.m111.296152] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Most eukaryotes contain iron-sulfur cluster (ISC) assembly proteins related to Saccharomyces cerevisiae Isa1 and Isa2. We show here that Isa1 but not Isa2 can be functionally replaced by the bacterial relatives IscA, SufA, and ErpA. The specific function of these "A-type" ISC proteins within the framework of mitochondrial and bacterial Fe/S protein biogenesis is still unresolved. In a comprehensive in vivo analysis, we show that S. cerevisiae Isa1 and Isa2 form a complex that is required for maturation of mitochondrial [4Fe-4S] proteins, including aconitase and homoaconitase. In contrast, Isa1-Isa2 were dispensable for the generation of mitochondrial [2Fe-2S] proteins and cytosolic [4Fe-4S] proteins. Targeting of bacterial [2Fe-2S] and [4Fe-4S] ferredoxins to yeast mitochondria further supported this specificity. Isa1 and Isa2 proteins are shown to bind iron in vivo, yet the Isa1-Isa2-bound iron was not needed as a donor for de novo assembly of the [2Fe-2S] cluster on the general Fe/S scaffold proteins Isu1-Isu2. Upon depletion of the ISC assembly factor Iba57, which specifically interacts with Isa1 and Isa2, or in the absence of the major mitochondrial [4Fe-4S] protein aconitase, iron accumulated on the Isa proteins. These results suggest that the iron bound to the Isa proteins is required for the de novo synthesis of [4Fe-4S] clusters in mitochondria and for their insertion into apoproteins in a reaction mediated by Iba57. Taken together, these findings define Isa1, Isa2, and Iba57 as a specialized, late-acting ISC assembly subsystem that is specifically dedicated to the maturation of mitochondrial [4Fe-4S] proteins.
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Affiliation(s)
- Ulrich Mühlenhoff
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Robert-Koch Strasse 6, 35032 Marburg, Germany
| | - Nadine Richter
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Robert-Koch Strasse 6, 35032 Marburg, Germany
| | - Ophry Pines
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University, Jerusalem 91120, Israel
| | - Antonio J Pierik
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Robert-Koch Strasse 6, 35032 Marburg, Germany
| | - Roland Lill
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Robert-Koch Strasse 6, 35032 Marburg, Germany.
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31
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Watanabe S, Shimada N, Tajima K, Kodaki T, Makino K. Identification and Characterization of l-Arabonate Dehydratase, l-2-Keto-3-deoxyarabonate Dehydratase, and l-Arabinolactonase Involved in an Alternative Pathway of l-Arabinose Metabolism. J Biol Chem 2006; 281:33521-36. [PMID: 16950779 DOI: 10.1074/jbc.m606727200] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Azospirillum brasiliense possesses an alternative pathway of L-arabinose metabolism, different from the known bacterial and fungal pathways. In the preceding articles, we identified and characterized L-arabinose-1-dehydrogenase and alpha-ketoglutaric semialdehyde dehydrogenase, which catalyzes the first and final reaction steps in this pathway, respectively (Watanabe, S., Kodaki, T., and Makino, K. (2006) J. Biol. Chem. 281, 2612-2623 and Watanabe, S., Kodaki, T., and Makino, K. (2006) J. Biol. Chem. 281, 28876-28888). We here report the remaining three enzymes, L-arabonate dehydratase, L-2-keto-3-deoxyarabonate (L-KDA) dehydratase, and L-arabinolactonase. N-terminal amino acid sequences of L-arabonate dehydratase and L-KDA dehydratase purified from A. brasiliense cells corresponded to those of AraC and AraD genes, which form a single transcriptional unit together with the L-arabinose-1-dehydrogenase gene. Furthermore, the L-arabinolactonase gene (AraB) was also identified as a component of the gene cluster. Genetic characterization of the alternative L-arabinose pathway suggested a significant evolutional relationship with the known sugar metabolic pathways, including the Entner-Doudoroff (ED) pathway and the several modified versions. L-arabonate dehydratase belongs to the ILVD/EDD family and spectrophotometric and electron paramagnetic resonance analysis revealed it to contain a [4Fe-4S](2+) cluster. Site-directed mutagenesis identified three cysteine ligands essential for cluster coordination. L-KDA dehydratase was sequentially similar to DHDPS/NAL family proteins. D-2-Keto-3-deoxygluconate aldolase, a member of the DHDPS/NAL family, catalyzes the equivalent reaction to L-KDA aldolase involved in another alternative L-arabinose pathway, probably associating a unique evolutional event between the two alternative L-arabinose pathways by mutation(s) of a common ancestral enzyme. Site-directed mutagenesis revealed a unique catalytic amino acid residue in L-KDA dehydratase, which may be a candidate for such a natural mutation.
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Affiliation(s)
- Seiya Watanabe
- Faculty of Engineering, Kyoto University, Kyotodaigaku-katsura, Saikyo-ku, Kyoto 615-8530, Japan
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McCourt JA, Duggleby RG. Acetohydroxyacid synthase and its role in the biosynthetic pathway for branched-chain amino acids. Amino Acids 2006; 31:173-210. [PMID: 16699828 DOI: 10.1007/s00726-005-0297-3] [Citation(s) in RCA: 171] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2005] [Accepted: 12/09/2005] [Indexed: 11/25/2022]
Abstract
The branched-chain amino acids are synthesized by plants, fungi and microorganisms, but not by animals. Therefore, the enzymes of this pathway are potential target sites for the development of antifungal agents, antimicrobials and herbicides. Most research has focused upon the first enzyme in this biosynthetic pathway, acetohydroxyacid synthase (AHAS) largely because it is the target site for many commercial herbicides. In this review we provide a brief overview of the important properties of each enzyme within the pathway and a detailed summary of the most recent AHAS research, against the perspective of work that has been carried out over the past 50 years.
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Affiliation(s)
- J A McCourt
- School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Australia
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Azevedo RA, Lancien M, Lea PJ. The aspartic acid metabolic pathway, an exciting and essential pathway in plants. Amino Acids 2006; 30:143-62. [PMID: 16525757 DOI: 10.1007/s00726-005-0245-2] [Citation(s) in RCA: 142] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2005] [Accepted: 06/20/2005] [Indexed: 10/24/2022]
Abstract
Aspartate is the common precursor of the essential amino acids lysine, threonine, methionine and isoleucine in higher plants. In addition, aspartate may also be converted to asparagine, in a potentially competing reaction. The latest information on the properties of the enzymes involved in the pathways and the genes that encode them is described. An understanding of the overall regulatory control of the flux through the pathways is undisputedly of great interest, since the nutritive value of all cereal and legume crops is reduced due to low concentrations of at least one of the aspartate-derived amino acids. We have reviewed the recent literature and discussed in this paper possible methods by which the concentrations of the limiting amino acids may be increased in the seeds.
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Affiliation(s)
- R A Azevedo
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, Brazil.
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Kim S, Lee SB. Catalytic Promiscuity in Dihydroxy-Acid Dehydratase from the Thermoacidophilic Archaeon Sulfolobus solfataricus. ACTA ACUST UNITED AC 2006; 139:591-6. [PMID: 16567425 DOI: 10.1093/jb/mvj057] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Dihydroxy-acid dehydratase (DHAD) is one of the key enzymes involved in the biosynthetic pathway of the branched chain amino acids. Although the enzyme has been purified and characterized in various mesophiles, including bacteria and eukarya, the biochemical properties of DHAD from hyperthermophilic archaea have not yet been reported. In this study we cloned, expressed in Escherichia coli, and purified a DHAD homologue from the thermoacidophilic archaeon Sulfolobus solfataricus, which grows optimally at 80 degrees C and pH 3. The recombinant S. solfataricus DHAD (rSso_DHAD) showed the highest activity on 2,3-dihydroxyisovalerate among 17 aldonic acids tested. Interestingly, this enzyme also displayed high activity toward d-gluconate and some other pentonic and hexonic sugar acids. The k(cat)/K(m) values were 140.3 mM(-1) s(-1) for 2,3-dihydroxyisovalerate and 20.0 mM(-1) s(-1) for d-gluconate, respectively. A possible evolutionary explanation for substrate promiscuity was provided through amino acid sequence alignments of DHADs and 6-phosphogluconate dehydratases from archaea, bacteria and eukarya.
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Affiliation(s)
- Seonghun Kim
- School of Environmental Science and Engineering, Pohang University of Science and Technology, San 31, Hyoja-dong, Pohang 790-784, Korea
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36
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Balmer Y, Vensel WH, Cai N, Manieri W, Schürmann P, Hurkman WJ, Buchanan BB. A complete ferredoxin/thioredoxin system regulates fundamental processes in amyloplasts. Proc Natl Acad Sci U S A 2006; 103:2988-93. [PMID: 16481623 PMCID: PMC1413819 DOI: 10.1073/pnas.0511040103] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
A growing number of processes throughout biology are regulated by redox via thiol-disulfide exchange. This mechanism is particularly widespread in plants, where almost 200 proteins have been linked to thioredoxin (Trx), a widely distributed small regulatory disulfide protein. The current study extends regulation by Trx to amyloplasts, organelles prevalent in heterotrophic plant tissues that, among other biosynthetic activities, catalyze the synthesis and storage of copious amounts of starch. Using proteomics and immunological methods, we identified the components of the ferredoxin/Trx system (ferredoxin, ferredoxin-Trx reductase, and Trx), originally described for chloroplasts, in amyloplasts isolated from wheat starchy endosperm. Ferredoxin is reduced not by light, as in chloroplasts, but by metabolically generated NADPH via ferredoxin-NADP reductase. However, once reduced, ferredoxin appears to act as established for chloroplasts, i.e., via ferredoxin-Trx reductase and a Trx (m-type). A proteomics approach in combination with affinity chromatography and a fluorescent thiol probe led to the identification of 42 potential Trx target proteins, 13 not previously recognized, including a major membrane transporter (Brittle-1 or ADP-glucose transporter). The proteins function in a range of processes in addition to starch metabolism: biosynthesis of lipids, amino acids, and nucleotides; protein folding; and several miscellaneous reactions. The results suggest a mechanism whereby light is initially recognized as a thiol signal in chloroplasts, then as a sugar during transit to the sink, where it is converted again to a thiol signal. In this way, amyloplast reactions in the grain can be coordinated with photosynthesis taking place in leaves.
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Affiliation(s)
- Yves Balmer
- *Department of Plant and Biology, University of California, 111 Koshland Hall, Berkeley, CA 94720
| | - William H. Vensel
- Western Regional Research Center, U.S. Department of Agriculture Agricultural Research Service, Albany, CA 94710; and
| | - Nick Cai
- *Department of Plant and Biology, University of California, 111 Koshland Hall, Berkeley, CA 94720
| | - Wanda Manieri
- Laboratoire de Biochimie Végétale, Université de Neuchātel, 2007 Neuchātel, Switzerland
| | - Peter Schürmann
- Laboratoire de Biochimie Végétale, Université de Neuchātel, 2007 Neuchātel, Switzerland
| | - William J. Hurkman
- Western Regional Research Center, U.S. Department of Agriculture Agricultural Research Service, Albany, CA 94710; and
| | - Bob B. Buchanan
- *Department of Plant and Biology, University of California, 111 Koshland Hall, Berkeley, CA 94720
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Ye H, Pilon M, Pilon-Smits EAH. CpNifS-dependent iron-sulfur cluster biogenesis in chloroplasts. THE NEW PHYTOLOGIST 2006; 171:285-92. [PMID: 16866936 DOI: 10.1111/j.1469-8137.2006.01751.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Iron-sulfur (Fe-S) clusters are important prosthetic groups in all organisms. The biosynthesis of Fe-S clusters has been studied extensively in bacteria and yeast. By contrast, much remains to be discovered about Fe-S cluster biogenesis in higher plants. Plant plastids are known to make their own Fe-S clusters. Plastid Fe-S proteins are involved in essential metabolic pathways, such as photosynthesis, nitrogen and sulfur assimilation, protein import, and chlorophyll transformation. This review aims to summarize the roles of Fe-S proteins in essential metabolic pathways and to give an overview of the latest findings on plastidic Fe-S assembly. The plastidic Fe-S biosynthetic machinery contains many homologues of bacterial mobilization of sulfur (SUF) proteins, but there are additional components and properties that may be plant-specific. These additional features could make the plastidic machinery more suitable for assembling Fe-S clusters in the presence of oxygen, and may enable it to be regulated in response to oxidative stress, iron status and light.
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Affiliation(s)
- Hong Ye
- Biology Department, Colorado State University, Fort Collins, CO 80523, USA
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Blank L, Green J, Guest JR. AcnC of Escherichia coli is a 2-methylcitrate dehydratase (PrpD) that can use citrate and isocitrate as substrates. MICROBIOLOGY (READING, ENGLAND) 2002; 148:133-146. [PMID: 11782506 DOI: 10.1099/00221287-148-1-133] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Escherichia coli possesses two well-characterized aconitases (AcnA and AcnB) and a minor activity (designated AcnC) that is retained by acnAB double mutants and represents no more than 5% of total wild-type aconitase activity. Here it is shown that a 2-methylcitrate dehydratase (PrpD) encoded by the prpD gene of the propionate catabolic operon (prpRBCDE) is identical to AcnC. Inactivation of prpD abolished the residual aconitase activity of an AcnAB-null strain, whereas inactivation of ybhJ, an unidentified acnA paralogue, had no significant effect on AcnC activity. Purified PrpD catalysed the dehydration of citrate and isocitrate but was most active with 2-methylcitrate. PrpD also catalysed the dehydration of several other hydroxy acids but failed to hydrate cis-aconitate and related substrates containing double bonds, indicating that PrpD is not a typical aconitase but a dehydratase. Purified PrpD was shown to be a monomeric iron-sulphur protein (M(r) 54000) having one unstable [2Fe-2S] cluster per monomer, which is needed for maximum catalytic activity and can be reconstituted by treatment with Fe(2+) under reducing conditions.
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Affiliation(s)
- Lindsay Blank
- The Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK1
| | - Jeffrey Green
- The Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK1
| | - John R Guest
- The Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK1
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Metzler DE, Metzler CM, Sauke DJ. Transition Metals in Catalysis and Electron Transport. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50019-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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40
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Metzler DE, Metzler CM, Sauke DJ. The Metabolism of Nitrogen and Amino Acids. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50027-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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42
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Guigliarelli B, Bertrand P. Application of EPR Spectroscopy to the Structural and Functional Study of Iron-Sulfur Proteins. ADVANCES IN INORGANIC CHEMISTRY 1999. [DOI: 10.1016/s0898-8838(08)60084-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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43
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Telser J, Huang H, Lee HI, Adams MWW, Hoffman BM. Site Valencies and Spin Coupling in the 3Fe and 4Fe (S = 1/2) Clusters of Pyrococcus furiosus Ferredoxin by 57Fe ENDOR. J Am Chem Soc 1998. [DOI: 10.1021/ja971546x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joshua Telser
- Contribution from the Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and the Department of Biochemistry & Molecular Biology and the Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602-2556
| | - Heshu Huang
- Contribution from the Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and the Department of Biochemistry & Molecular Biology and the Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602-2556
| | - Hong-In Lee
- Contribution from the Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and the Department of Biochemistry & Molecular Biology and the Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602-2556
| | - Michael W. W. Adams
- Contribution from the Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and the Department of Biochemistry & Molecular Biology and the Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602-2556
| | - Brian M. Hoffman
- Contribution from the Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and the Department of Biochemistry & Molecular Biology and the Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602-2556
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Baldet P, Alban C, Douce R. Biotin synthesis in higher plants: purification and characterization of bioB gene product equivalent from Arabidopsis thaliana overexpressed in Escherichia coli and its subcellular localization in pea leaf cells. FEBS Lett 1997; 419:206-10. [PMID: 9428635 DOI: 10.1016/s0014-5793(97)01458-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Biotin synthase catalyses the final step in the biotin biosynthetic pathway and is encoded by the bioB gene in Escherichia coli. To investigate the conversion of dethiobiotin to biotin in the plant kingdom, the cDNA encoding the bioB gene product equivalent from Arabidopsis thaliana was used to construct an E. coli overexpression strain. The purified A. thaliana bioB gene product is a homodimer (100 kDa) with a reddish color and has an absorbance spectrum characteristic of protein with [2Fe-2S] clusters. Its intracellular compartmentation in pea leaves discloses a unique polypeptide of 39 kDa within the matrix of mitochondria.
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Affiliation(s)
- P Baldet
- INRA, Unité de Physiologie Végétale, Villenave d'Ornon, France.
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45
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Azevedo RA, Arruda P, Turner WL, Lea PJ. The biosynthesis and metabolism of the aspartate derived amino acids in higher plants. PHYTOCHEMISTRY 1997; 46:395-419. [PMID: 9332022 DOI: 10.1016/s0031-9422(97)00319-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The essential amino acids lysine, threonine, methionine and isoleucine are synthesised in higher plants via a common pathway starting with aspartate. The regulation of the pathway is discussed in detail, and the properties of the key enzymes described. Recent data obtained from studies of regulation at the gene level and information derived from mutant and transgenic plants are also discussed. The herbicide target enzyme acetohydroxyacid synthase involved in the synthesis of the branched chain amino acids is reviewed.
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Affiliation(s)
- R A Azevedo
- Departamento de Genética, Universidade de São Paulo, Piracicaba, SP, Brasil
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46
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Beinert H, Kennedy MC, Stout CD. Aconitase as Ironminus signSulfur Protein, Enzyme, and Iron-Regulatory Protein. Chem Rev 1996; 96:2335-2374. [PMID: 11848830 DOI: 10.1021/cr950040z] [Citation(s) in RCA: 422] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Helmut Beinert
- Institute for Enzyme Research, Graduate School, and Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin, Madison, Wisconsin 53705, Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, and Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037
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Affiliation(s)
- Dennis H. Flint
- E. I. du Pont de Nemours and Co., Central Research and Development, Experimental Station, P.O. Box 80328, Wilmington, Delaware 19880-0328
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48
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Müh U, Cinkaya I, Albracht SP, Buckel W. 4-Hydroxybutyryl-CoA dehydratase from Clostridium aminobutyricum: characterization of FAD and iron-sulfur clusters involved in an overall non-redox reaction. Biochemistry 1996; 35:11710-8. [PMID: 8794752 DOI: 10.1021/bi9601363] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
4-Hydroxybutyryl-CoA dehydratase catalyzes the reversible dehydration of 4-hydroxybutyryl-CoA to crotonyl-CoA, which involves cleavage of an unactivated beta-C-H bond. The enzyme also catalyzes the apparently irreversible isomerization of vinylacetyl-CoA to crotonyl-CoA. Addition of crotonyl-CoA to the dehydratase, which contains FAD as well as non-heme iron and acid labile sulfur, led to a decrease of the flavin absorbance at 438 nm and an increase in the region from 500 to 800 nm. The protein-bound FAD was easily reduced to the semiquinone (redox equilibration within seconds) and only slowly to the hydroquinone (redox equilibration minutes to hours): the redox potentials were not unusual for flavoproteins (Eox/sq = -140 +/- 15 mV and Esq/red = -240 +/- 15 mV; pH 7.0, 25 degrees C). There was no equilibration of electrons between the flavin and the Fe-S cluster, which was difficult to reduce. After extensive photoreduction, an EPR signal indicative of a [4Fe-4S]+ cluster was detected (g-values: 2.037, 1.895, 1.844). Upon exposure to air at 0 degrees C, the enzyme lost dehydration activity completely within 40 min, but isomerase activity dropped to about 40% of the initial value and persisted for more than a day. The properties of the protein-bound FAD are consistent with a mechanism involving transient one-electron oxidation of the substrate to activate the the beta-C-H bond. The putative [4Fe-4S]2+ cluster could serve a structural role and/or as Lewis acid facilitating the leaving of the hydroxyl group.
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Affiliation(s)
- U Müh
- Laboratorium für Mikrobiologie am Fachbereich Biologie der Philipps Universität Marburg, Germany
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49
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Flint DH, Tuminello JF, Miller TJ. Studies on the synthesis of the Fe-S cluster of dihydroxy-acid dehydratase in escherichia coli crude extract. Isolation of O-acetylserine sulfhydrylases A and B and beta-cystathionase based on their ability to mobilize sulfur from cysteine and to participate in Fe-S cluster synthesis. J Biol Chem 1996; 271:16053-67. [PMID: 8663055 DOI: 10.1074/jbc.271.27.16053] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The apoprotein of Escherichia coli dihydroxy-acid dehydratase, which contains a catalytically essential [4Fe-4S] cluster in its active form, has been used as a substrate to investigate Fe-S cluster synthesis. The inactive apoprotein could be reactivated in vitro by factors present in the crude extract of E. coli and to a much smaller extent in the presence of Fe3+, S2-, and dithiothreitol. This reactivation occurs as a result of Fe-S cluster synthesis. It is anticipated that the Fe-S cluster synthesis observed in crude extracts in vitro may involve some of the components that participate in Fe-S cluster synthesis in vivo. The origin of the sulfur used to form Fe-S clusters was investigated. Four enzymatic activities in the crude extract of E. coli were found that can provide sulfur for Fe-S cluster synthesis in vitro by mobilizing the sulfur from cysteine. The purification of the proteins responsible for three of these activities is reported in this paper. The three proteins have been identified as O-acetylserine sulfhydrylase A, O-acetylserine sulfhydrylase B, and beta-cystathionase. The rate and extent of sulfide mobilization from cysteine in the reaction catalyzed by O-acetylserine sulfhydrylases A and B depend on the presence of nucleophiles that can add to the aminoacrylate formed on the enzyme following the removal of sulfide from cysteine. A new amino acid is formed when the nucleophiles add to the aminoacrylate. Sulfur mobilization by beta-cystathionase does not require a nucleophile, and the reaction is a minor variation on the cleavage of beta-cystathionine, with pyruvate, ammonia, and sulfide being the products. Once sulfur is mobilized by these enzymes, its efficient use in Fe-S cluster synthesis seems to be affected by the presence of yet unidentified factors present in crude extract. In crude extract and partially purified preparations from E. coli where these factors are present, the rapidity with which Fe-S clusters are formed and the efficiency with which sulfur is used imply an orderly controlled formation of Fe-S clusters that is generally typified by enzymatic reactions.
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Affiliation(s)
- D H Flint
- E. I. du Pont de Nemours & Company, Central Research and Development, Experimental Station, Wilmington, Delaware 19880-0328, USA
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50
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Flint DH. Escherichia coli Contains a Protein That Is Homologous in Function and N-terminal Sequence to the Protein Encoded by the nifS Gene of Azotobacter vinelandii and That Can Participate in the Synthesis of the Fe-S Cluster of Dihydroxy-acid Dehydratase. J Biol Chem 1996. [DOI: 10.1016/s0021-9258(18)48580-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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