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Ma D, Du G, Fang H, Li R, Zhang D. Advances and prospects in microbial production of biotin. Microb Cell Fact 2024; 23:135. [PMID: 38735926 PMCID: PMC11089781 DOI: 10.1186/s12934-024-02413-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/30/2024] [Indexed: 05/14/2024] Open
Abstract
Biotin, serving as a coenzyme in carboxylation reactions, is a vital nutrient crucial for the natural growth, development, and overall well-being of both humans and animals. Consequently, biotin is widely utilized in various industries, including feed, food, and pharmaceuticals. Despite its potential advantages, the chemical synthesis of biotin for commercial production encounters environmental and safety challenges. The burgeoning field of synthetic biology now allows for the creation of microbial cell factories producing bio-based products, offering a cost-effective alternative to chemical synthesis for biotin production. This review outlines the pathway and regulatory mechanism involved in biotin biosynthesis. Then, the strategies to enhance biotin production through both traditional chemical mutagenesis and advanced metabolic engineering are discussed. Finally, the article explores the limitations and future prospects of microbial biotin production. This comprehensive review not only discusses strategies for biotin enhancement but also provides in-depth insights into systematic metabolic engineering approaches aimed at boosting biotin production.
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Affiliation(s)
- Donghan Ma
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Guangqing Du
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Huan Fang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Rong Li
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, China.
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China.
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Rodrigues V, Deusdado S. Meta-learning approach for bacteria classification and identification of informative genes of the Bacillus megaterium: tomato roots tissue interaction. 3 Biotech 2023; 13:271. [PMID: 37449251 PMCID: PMC10335980 DOI: 10.1007/s13205-023-03690-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 06/26/2023] [Indexed: 07/18/2023] Open
Abstract
Plant growth-promoting rhizobacteria (PGPRs) are bacteria that colonize the plant roots. These beneficial bacteria have an influence on plant development through multiple mechanisms, such as nutrient availability, alleviating biotic and abiotic stress, and secrete phytohormones. Therefore, their inoculation constitutes a powerful tool towards sustainable agriculture and crop production. To understand plant-PGPRs interaction we present the classification of PGPR using machine learning and meta-learning classifiers namely Support Vector Machine (SVM), Kernel Logistic Regression (KLR), meta-SVM and meta-KLR to predict the presence of Bacillus megaterium inoculated in tomato root tissues using publicly available transcriptomic data. The original dataset presents 36 significantly differentially expressed genes. As the meta-KLR achieved near-optimal performance considering all the relevant metrics, this meta learner was afterwards used to identify the informative genes (IGs). The outcomes showed 157 IGs, being present all significantly differentially expressed genes previously identified. Among the IGs, 113 were identified as tomato genes, 5 as Bacillus subtilis proteins, 1 as Escherichia coli protein and 6 were unidentified. Then, a functional enrichment analysis of the tomato IGs showed 175 biological processes, 22 molecular functions and 20 KEGG pathways involved in B. megaterium-tomato interaction. Furthermore, the biological networks study of their Arabidopsis thaliana orthologous genes identified the co-expression, predicted interaction, shared protein domains and co-localization networks. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03690-0.
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Affiliation(s)
| | - Sérgio Deusdado
- Instituto Politécnico de Bragança, CIMO—Centro de Investigação de Montanha, 5301-855 Bragança, Portugal
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3
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Fan PH, Geng Y, Romo AJ, Zhong A, Zhang J, Yeh YC, Lee YH, Liu HW. Two Radical SAM Enzymes Are Necessary and Sufficient for the In Vitro Production of the Oxetane Nucleoside Antiviral Agent Albucidin. Angew Chem Int Ed Engl 2022; 61:e202210362. [PMID: 36064953 PMCID: PMC9561071 DOI: 10.1002/anie.202210362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Indexed: 11/09/2022]
Abstract
Oxetanocin A and albucidin are two oxetane natural products. While the biosynthesis of oxetanocin A has been described, less is known about albucidin. In this work, the albucidin biosynthetic gene cluster is identified in Streptomyces. Heterologous expression in a nonproducing strain demonstrates that the genes alsA and alsB are necessary and sufficient for albucidin biosynthesis confirming a previous study (Myronovskyi et al. Microorganisms 2020, 8, 237). A two-step construction of albucidin 4'-phosphate from 2'-deoxyadenosine monophosphate (2'-dAMP) is shown to be catalyzed in vitro by the cobalamin dependent radical S-adenosyl-l-methionine (SAM) enzyme AlsB, which catalyzes a ring contraction, and the radical SAM enzyme AlsA, which catalyzes elimination of a one-carbon fragment. Isotope labelling studies show that AlsB catalysis begins with stereospecific H-atom transfer of the C2'-pro-R hydrogen from 2'-dAMP to 5'-deoxyadenosine, and that the eliminated one-carbon fragment originates from C3' of 2'-dAMP.
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Affiliation(s)
- Po-Hsun Fan
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Yujie Geng
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Anthony J. Romo
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Aoshu Zhong
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jiawei Zhang
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Yu-Cheng Yeh
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Yu-Hsuan Lee
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hung-wen Liu
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
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Fan PH, Geng Y, Romo AJ, Zhong A, Zhang J, Yeh YC, Lee YH, Liu HW. Two Radical SAM Enzymes Are Necessary and Sufficient for the In Vitro Production of the Oxetane Nucleoside Antiviral Agent Albucidin. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202210362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Po-Hsun Fan
- The University of Texas at Austin Chemistry The University of Texas at Austin 78712-1139 Austin UNITED STATES
| | - Yujie Geng
- The University of Texas at Austin College of Pharmacy College of Pharmacy 78712-1139 Austin UNITED STATES
| | - Anthony J Romo
- The University of Texas at Austin College of Pharmacy College of Pharmacy 78712-1139 Austin UNITED STATES
| | - Aoshu Zhong
- The University of Texas at Austin College of Pharmacy College of Pharmacy 78712-1139 Austin UNITED STATES
| | - Jiawei Zhang
- The University of Texas at Austin Chemistry The University of Texas at Austin 78712-1139 Austin UNITED STATES
| | - Yu-Cheng Yeh
- UT Austin: The University of Texas at Austin Chemistry The University of Texas at Austin 78712-1139 Austin UNITED STATES
| | - Yu-Hsuan Lee
- UT Austin: The University of Texas at Austin Chemistry The University of Texas at Austin 78712-1139 Austin UNITED STATES
| | - Hung-wen Liu
- University of Texas at Austin Phar-Med Chem/3.206 1 University Station A1935PHR 3.206B 78712-0128 Austin UNITED STATES
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Monfort B, Want K, Gervason S, D’Autréaux B. Recent Advances in the Elucidation of Frataxin Biochemical Function Open Novel Perspectives for the Treatment of Friedreich’s Ataxia. Front Neurosci 2022; 16:838335. [PMID: 35310092 PMCID: PMC8924461 DOI: 10.3389/fnins.2022.838335] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/28/2022] [Indexed: 12/25/2022] Open
Abstract
Friedreich’s ataxia (FRDA) is the most prevalent autosomic recessive ataxia and is associated with a severe cardiac hypertrophy and less frequently diabetes. It is caused by mutations in the gene encoding frataxin (FXN), a small mitochondrial protein. The primary consequence is a defective expression of FXN, with basal protein levels decreased by 70–98%, which foremost affects the cerebellum, dorsal root ganglia, heart and liver. FXN is a mitochondrial protein involved in iron metabolism but its exact function has remained elusive and highly debated since its discovery. At the cellular level, FRDA is characterized by a general deficit in the biosynthesis of iron-sulfur (Fe-S) clusters and heme, iron accumulation and deposition in mitochondria, and sensitivity to oxidative stress. Based on these phenotypes and the proposed ability of FXN to bind iron, a role as an iron storage protein providing iron for Fe-S cluster and heme biosynthesis was initially proposed. However, this model was challenged by several other studies and it is now widely accepted that FXN functions primarily in Fe-S cluster biosynthesis, with iron accumulation, heme deficiency and oxidative stress sensitivity appearing later on as secondary defects. Nonetheless, the biochemical function of FXN in Fe-S cluster biosynthesis is still debated. Several roles have been proposed for FXN: iron chaperone, gate-keeper of detrimental Fe-S cluster biosynthesis, sulfide production stimulator and sulfur transfer accelerator. A picture is now emerging which points toward a unique function of FXN as an accelerator of a key step of sulfur transfer between two components of the Fe-S cluster biosynthetic complex. These findings should foster the development of new strategies for the treatment of FRDA. We will review here the latest discoveries on the biochemical function of frataxin and the implication for a potential therapeutic treatment of FRDA.
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A novel pneumococcal protein-polysaccharide conjugate vaccine based on biotin-streptavidin. Infect Immun 2021; 90:e0035221. [PMID: 34694917 DOI: 10.1128/iai.00352-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pneumococcal disease is a serious public health problem worldwide and an important cause of morbidity and mortality among children and adults in developing countries. Although vaccination is among the most effective approaches to prevent and control pneumococcal diseases, approved vaccines have limited protective effects. We developed a pneumococcal protein-polysaccharide conjugate vaccine that is mediated by the non-covalent interaction between biotin and streptavidin. Biotinylated type IV capsular polysaccharide was incubated with a fusion protein containing core streptavidin and Streptococcus pneumoniae virulence protein and relying on the non-covalent interaction between biotin and streptavidin to prepare the protein-polysaccharide conjugate vaccine. Analysis of vaccine efficacy revealed that mice immunized with the protein-polysaccharide conjugate vaccine produced antibodies with high potency against virulence proteins and polysaccharide antigens and were able to induce Th1 and Th17 responses. The antibodies identified using an opsonophagocytic assay were capable of activating the complement system and promoting pathogen elimination by phagocytes. Additionally, mice immunized with the protein-polysaccharide conjugate vaccine and then infected with a lethal dose of Streptococcus pneumoniae demonstrated induced protective immunity. The data indicated that the pneumococcal protein-polysaccharide (biotin-streptavidin) conjugate vaccine demonstrated broad-spectrum activity applicable to a wide range of people and ease of direct coupling between protein and polysaccharide. These findings provide further evidence for the application of biotin-streptavidin in S. pneumoniae vaccines.
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Das M, Dewan A, Shee S, Singh A. The Multifaceted Bacterial Cysteine Desulfurases: From Metabolism to Pathogenesis. Antioxidants (Basel) 2021; 10:antiox10070997. [PMID: 34201508 PMCID: PMC8300815 DOI: 10.3390/antiox10070997] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/01/2021] [Accepted: 05/06/2021] [Indexed: 12/02/2022] Open
Abstract
Living cells have developed a relay system to efficiently transfer sulfur (S) from cysteine to various thio-cofactors (iron-sulfur (Fe-S) clusters, thiamine, molybdopterin, lipoic acid, and biotin) and thiolated tRNA. The presence of such a transit route involves multiple protein components that allow the flux of S to be precisely regulated as a function of environmental cues to avoid the unnecessary accumulation of toxic concentrations of soluble sulfide (S2−). The first enzyme in this relay system is cysteine desulfurase (CSD). CSD catalyzes the release of sulfane S from L-cysteine by converting it to L-alanine by forming an enzyme-linked persulfide intermediate on its conserved cysteine residue. The persulfide S is then transferred to diverse acceptor proteins for its incorporation into the thio-cofactors. The thio-cofactor binding-proteins participate in essential and diverse cellular processes, including DNA repair, respiration, intermediary metabolism, gene regulation, and redox sensing. Additionally, CSD modulates pathogenesis, antibiotic susceptibility, metabolism, and survival of several pathogenic microbes within their hosts. In this review, we aim to comprehensively illustrate the impact of CSD on bacterial core metabolic processes and its requirement to combat redox stresses and antibiotics. Targeting CSD in human pathogens can be a potential therapy for better treatment outcomes.
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Francioso A, Baseggio Conrado A, Mosca L, Fontana M. Chemistry and Biochemistry of Sulfur Natural Compounds: Key Intermediates of Metabolism and Redox Biology. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:8294158. [PMID: 33062147 PMCID: PMC7545470 DOI: 10.1155/2020/8294158] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 06/28/2020] [Accepted: 07/29/2020] [Indexed: 12/24/2022]
Abstract
Sulfur contributes significantly to nature chemical diversity and thanks to its particular features allows fundamental biological reactions that no other element allows. Sulfur natural compounds are utilized by all living beings and depending on the function are distributed in the different kingdoms. It is no coincidence that marine organisms are one of the most important sources of sulfur natural products since most of the inorganic sulfur is metabolized in ocean environments where this element is abundant. Terrestrial organisms such as plants and microorganisms are also able to incorporate sulfur in organic molecules to produce primary metabolites (e.g., methionine, cysteine) and more complex unique chemical structures with diverse biological roles. Animals are not able to fix inorganic sulfur into biomolecules and are completely dependent on preformed organic sulfurous compounds to satisfy their sulfur needs. However, some higher species such as humans are able to build new sulfur-containing chemical entities starting especially from plants' organosulfur precursors. Sulfur metabolism in humans is very complicated and plays a central role in redox biochemistry. The chemical properties, the large number of oxidation states, and the versatile reactivity of the oxygen family chalcogens make sulfur ideal for redox biological reactions and electron transfer processes. This review will explore sulfur metabolism related to redox biochemistry and will describe the various classes of sulfur-containing compounds spread all over the natural kingdoms. We will describe the chemistry and the biochemistry of well-known metabolites and also of the unknown and poorly studied sulfur natural products which are still in search for a biological role.
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Affiliation(s)
- Antonio Francioso
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, 00185 Rome, Italy
- Department of Organic Chemistry, Instituto Universitario de Bio-Orgánica Antonio González, University of La Laguna, La Laguna, 38296 Tenerife, Spain
| | - Alessia Baseggio Conrado
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, 00185 Rome, Italy
| | - Luciana Mosca
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, 00185 Rome, Italy
| | - Mario Fontana
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, 00185 Rome, Italy
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Bockman MR, Mishra N, Aldrich CC. The Biotin Biosynthetic Pathway in Mycobacterium tuberculosis is a Validated Target for the Development of Antibacterial Agents. Curr Med Chem 2020; 27:4194-4232. [PMID: 30663561 DOI: 10.2174/0929867326666190119161551] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/14/2018] [Accepted: 01/12/2019] [Indexed: 12/11/2022]
Abstract
Mycobacterium tuberculosis, responsible for Tuberculosis (TB), remains the leading cause of mortality among infectious diseases worldwide from a single infectious agent, with an estimated 1.7 million deaths in 2016. Biotin is an essential cofactor in M. tuberculosis that is required for lipid biosynthesis and gluconeogenesis. M. tuberculosis relies on de novo biotin biosynthesis to obtain this vital cofactor since it cannot scavenge sufficient biotin from a mammalian host. The biotin biosynthetic pathway in M. tuberculosis has been well studied and rigorously genetically validated providing a solid foundation for medicinal chemistry efforts. This review examines the mechanism and structure of the enzymes involved in biotin biosynthesis and ligation, summarizes the reported genetic validation studies of the pathway, and then analyzes the most promising inhibitors and natural products obtained from structure-based drug design and phenotypic screening.
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Affiliation(s)
- Matthew R Bockman
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
| | - Neeraj Mishra
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
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10
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Barth C, Weiss MC, Roettger M, Martin WF, Unden G. Origin and phylogenetic relationships of [4Fe-4S]-containing O 2 sensors of bacteria. Environ Microbiol 2018; 20:4567-4586. [PMID: 30225854 DOI: 10.1111/1462-2920.14411] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/10/2018] [Indexed: 11/28/2022]
Abstract
The advent of environmental O2 about 2.5 billion years ago forced microbes to metabolically adapt and to develop mechanisms for O2 sensing. Sensing of O2 by [4Fe-4S]2+ to [2Fe-2S]2+ cluster conversion represents an ancient mechanism that is used by FNREc (Escherichia coli), FNRBs (Bacillus subtilis), NreBSa (Staphylococcus aureus) and WhiB3Mt (Mycobacterium tuberculosis). The phylogenetic relationship of these sensors was investigated. FNREc homologues are restricted to the proteobacteria and a few representatives from other phyla. Homologues of FNRBs and NreBSa are located within the bacilli, of WhiB3 within the actinobacteria. Archaea contain no homologues. The data reveal no similarity between the FNREc , FNRBs , NreBSa and WhiB3 sensor families on the sequence and structural levels. These O2 sensor families arose independently in phyla that were already present at the time O2 appeared, their members were subsequently distributed by lateral gene transfer. The chemistry of [4Fe-4S] and [2Fe-2S] cluster formation and interconversion appears to be shared by the sensor protein families. The type of signal output is, however, family specific. The homologues of FNREc and NreBSa vary with regard to the number of Cys residues that coordinate the cluster. It is suggested that the variants derive from lateral gene transfer and gained other functions.
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Affiliation(s)
- C Barth
- Microbiology and Wine Research, Institute for Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - M C Weiss
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - M Roettger
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - W F Martin
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - G Unden
- Microbiology and Wine Research, Institute for Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany
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Holliday GL, Akiva E, Meng EC, Brown SD, Calhoun S, Pieper U, Sali A, Booker SJ, Babbitt PC. Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain. Methods Enzymol 2018; 606:1-71. [PMID: 30097089 DOI: 10.1016/bs.mie.2018.06.004] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The radical SAM superfamily contains over 100,000 homologous enzymes that catalyze a remarkably broad range of reactions required for life, including metabolism, nucleic acid modification, and biogenesis of cofactors. While the highly conserved SAM-binding motif responsible for formation of the key 5'-deoxyadenosyl radical intermediate is a key structural feature that simplifies identification of superfamily members, our understanding of their structure-function relationships is complicated by the modular nature of their structures, which exhibit varied and complex domain architectures. To gain new insight about these relationships, we classified the entire set of sequences into similarity-based subgroups that could be visualized using sequence similarity networks. This superfamily-wide analysis reveals important features that had not previously been appreciated from studies focused on one or a few members. Functional information mapped to the networks indicates which members have been experimentally or structurally characterized, their known reaction types, and their phylogenetic distribution. Despite the biological importance of radical SAM chemistry, the vast majority of superfamily members have never been experimentally characterized in any way, suggesting that many new reactions remain to be discovered. In addition to 20 subgroups with at least one known function, we identified additional subgroups made up entirely of sequences of unknown function. Importantly, our results indicate that even general reaction types fail to track well with our sequence similarity-based subgroupings, raising major challenges for function prediction for currently identified and new members that continue to be discovered. Interactive similarity networks and other data from this analysis are available from the Structure-Function Linkage Database.
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Affiliation(s)
- Gemma L Holliday
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States.
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States
| | - Elaine C Meng
- Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, United States
| | - Shoshana D Brown
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States
| | - Sara Calhoun
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States; Graduate Program in Biophysics, University of California, San Francisco, CA, United States
| | - Ursula Pieper
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, United States; Quantitative Biosciences Institute, University of California, San Francisco, CA, United States
| | - Squire J Booker
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States; Department of Chemistry, The Pennsylvania State University, University Park, PA, United States; The Howard Hughes Medical Institute, The Pennsylvania State University, University Park, PA, United States
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, United States; Quantitative Biosciences Institute, University of California, San Francisco, CA, United States.
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12
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Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part I. [4Fe-4S] + [2Fe-2S] iron-sulfur proteins. J Struct Biol 2017; 200:1-19. [DOI: 10.1016/j.jsb.2017.05.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/25/2017] [Indexed: 01/08/2023]
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Abstract
Oxidative cyclizations are important transformations that occur widely during natural product biosynthesis. The transformations from acyclic precursors to cyclized products can afford morphed scaffolds, structural rigidity, and biological activities. Some of the most dramatic structural alterations in natural product biosynthesis occur through oxidative cyclization. In this Review, we examine the different strategies used by nature to create new intra(inter)molecular bonds via redox chemistry. This Review will cover both oxidation- and reduction-enabled cyclization mechanisms, with an emphasis on the former. Radical cyclizations catalyzed by P450, nonheme iron, α-KG-dependent oxygenases, and radical SAM enzymes are discussed to illustrate the use of molecular oxygen and S-adenosylmethionine to forge new bonds at unactivated sites via one-electron manifolds. Nonradical cyclizations catalyzed by flavin-dependent monooxygenases and NAD(P)H-dependent reductases are covered to show the use of two-electron manifolds in initiating cyclization reactions. The oxidative installations of epoxides and halogens into acyclic scaffolds to drive subsequent cyclizations are separately discussed as examples of "disappearing" reactive handles. Last, oxidative rearrangement of rings systems, including contractions and expansions, will be covered.
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Affiliation(s)
- Man-Cheng Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Yi Zou
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, 443 Via Ortega, Stanford, CA 94305
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
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Time-Course Analysis of Gene Expression During the Saccharomyces cerevisiae Hypoxic Response. G3-GENES GENOMES GENETICS 2017; 7:221-231. [PMID: 27883312 PMCID: PMC5217111 DOI: 10.1534/g3.116.034991] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Many cells experience hypoxia, or low oxygen, and respond by dramatically altering gene expression. In the yeast Saccharomyces cerevisiae, genes that respond are required for many oxygen-dependent cellular processes, such as respiration, biosynthesis, and redox regulation. To more fully characterize the global response to hypoxia, we exposed yeast to hypoxic conditions, extracted RNA at different times, and performed RNA sequencing (RNA-seq) analysis. Time-course statistical analysis revealed hundreds of genes that changed expression by up to 550-fold. The genes responded with varying kinetics suggesting that multiple regulatory pathways are involved. We identified most known oxygen-regulated genes and also uncovered new regulated genes. Reverse transcription-quantitative PCR (RT-qPCR) analysis confirmed that the lysine methyltransferase EFM6 and the recombinase DMC1, both conserved in humans, are indeed oxygen-responsive. Looking more broadly, oxygen-regulated genes participate in expected processes like respiration and lipid metabolism, but also in unexpected processes like amino acid and vitamin metabolism. Using principle component analysis, we discovered that the hypoxic response largely occurs during the first 2 hr and then a new steady-state expression state is achieved. Moreover, we show that the oxygen-dependent genes are not part of the previously described environmental stress response (ESR) consisting of genes that respond to diverse types of stress. While hypoxia appears to cause a transient stress, the hypoxic response is mostly characterized by a transition to a new state of gene expression. In summary, our results reveal that hypoxia causes widespread and complex changes in gene expression to prepare the cell to function with little or no oxygen.
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The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part III. {[Fe2S2](Cys)3(X)} (X=Asp, Arg, His) and {[Fe2S2](Cys)2(His)2} proteins. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2015.07.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Abstract
Two vitamins, biotin and lipoic acid, are essential in all three domains of life. Both coenzymes function only when covalently attached to key metabolic enzymes. There they act as "swinging arms" that shuttle intermediates between two active sites (= covalent substrate channeling) of key metabolic enzymes. Although biotin was discovered over 100 years ago and lipoic acid 60 years ago, it was not known how either coenzyme is made until recently. In Escherichia coli the synthetic pathways for both coenzymes have now been worked out for the first time. The late steps of biotin synthesis, those involved in assembling the fused rings, were well described biochemically years ago, although recent progress has been made on the BioB reaction, the last step of the pathway in which the biotin sulfur moiety is inserted. In contrast, the early steps of biotin synthesis, assembly of the fatty acid-like "arm" of biotin were unknown. It has now been demonstrated that the arm is made by using disguised substrates to gain entry into the fatty acid synthesis pathway followed by removal of the disguise when the proper chain length is attained. The BioC methyltransferase is responsible for introducing the disguise, and the BioH esterase is responsible for its removal. In contrast to biotin, which is attached to its cognate proteins as a finished molecule, lipoic acid is assembled on its cognate proteins. An octanoyl moiety is transferred from the octanoyl acyl carrier protein of fatty acid synthesis to a specific lysine residue of a cognate protein by the LipB octanoyltransferase followed by sulfur insertion at carbons C-6 and C-8 by the LipA lipoyl synthetase. Assembly on the cognate proteins regulates the amount of lipoic acid synthesized, and, thus, there is no transcriptional control of the synthetic genes. In contrast, transcriptional control of the biotin synthetic genes is wielded by a remarkably sophisticated, yet simple, system, exerted through BirA, a dual-function protein that both represses biotin operon transcription and ligates biotin to its cognate proteins.
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Abstract
Two vitamins, biotin and lipoic acid, are essential in all three domains of life. Both coenzymes function only when covalently attached to key metabolic enzymes. There they act as "swinging arms" that shuttle intermediates between two active sites (= covalent substrate channeling) of key metabolic enzymes. Although biotin was discovered over 100 years ago and lipoic acid was discovered 60 years ago, it was not known how either coenzyme is made until recently. In Escherichia coli the synthetic pathways for both coenzymes have now been worked out for the first time. The late steps of biotin synthesis, those involved in assembling the fused rings, were well described biochemically years ago, although recent progress has been made on the BioB reaction, the last step of the pathway, in which the biotin sulfur moiety is inserted. In contrast, the early steps of biotin synthesis, assembly of the fatty acid-like "arm" of biotin, were unknown. It has now been demonstrated that the arm is made by using disguised substrates to gain entry into the fatty acid synthesis pathway followed by removal of the disguise when the proper chain length is attained. The BioC methyltransferase is responsible for introducing the disguise and the BioH esterase for its removal. In contrast to biotin, which is attached to its cognate proteins as a finished molecule, lipoic acid is assembled on its cognate proteins. An octanoyl moiety is transferred from the octanoyl-ACP of fatty acid synthesis to a specific lysine residue of a cognate protein by the LipB octanoyl transferase, followed by sulfur insertion at carbons C6 and C8 by the LipA lipoyl synthetase. Assembly on the cognate proteins regulates the amount of lipoic acid synthesized, and thus there is no transcriptional control of the synthetic genes. In contrast, transcriptional control of the biotin synthetic genes is wielded by a remarkably sophisticated, yet simple, system exerted through BirA, a dual-function protein that both represses biotin operon transcription and ligates biotin to its cognate protein.
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Helliwell KE, Wheeler GL, Smith AG. Widespread decay of vitamin-related pathways: coincidence or consequence? Trends Genet 2013; 29:469-78. [DOI: 10.1016/j.tig.2013.03.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 03/09/2013] [Accepted: 03/25/2013] [Indexed: 02/03/2023]
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Feng J, Wu J, Dai N, Lin S, Xu HH, Deng Z, He X. Discovery and characterization of BlsE, a radical S-adenosyl-L-methionine decarboxylase involved in the blasticidin S biosynthetic pathway. PLoS One 2013; 8:e68545. [PMID: 23874663 PMCID: PMC3715490 DOI: 10.1371/journal.pone.0068545] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 05/30/2013] [Indexed: 11/19/2022] Open
Abstract
BlsE, a predicted radical S-adenosyl-L-methionine (SAM) protein, was anaerobically purified and reconstituted in vitro to study its function in the blasticidin S biosynthetic pathway. The putative role of BlsE was elucidated based on bioinformatics analysis, genetic inactivation and biochemical characterization. Biochemical results showed that BlsE is a SAM-dependent radical enzyme that utilizes cytosylglucuronic acid, the accumulated intermediate metabolite in blsE mutant, as substrate and catalyzes decarboxylation at the C5 position of the glucoside residue to yield cytosylarabinopyranose. Additionally, we report the purification and reconstitution of BlsE, characterization of its [4Fe-4S] cluster using UV-vis and electron paramagnetic resonance (EPR) spectroscopic analysis, and investigation of the ability of flavodoxin (Fld), flavodoxin reductase (Fpr) and NADPH to reduce the [4Fe-4S](2+) cluster. Mutagenesis studies demonstrated that Cys31, Cys35, Cys38 in the C×××C×MC motif and Gly73, Gly74, Glu75, Pro76 in the GGEP motif were crucial amino acids for BlsE activity while mutation of Met37 had little effect on its function. Our results indicate that BlsE represents a typical [4Fe-4S]-containing radical SAM enzyme and it catalyzes decarboxylation in blasticidin S biosynthesis.
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Affiliation(s)
- Jun Feng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Wu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Nan Dai
- New England Biolabs, Inc., Research Department, Ipswich, Massachusetts, United States of America
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - H. Howard Xu
- Department of Biological Sciences, California State University Los Angeles, Los Angeles, California, United States of America
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinyi He
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- * E-mail:
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20
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Differential proteome analysis of a selected bacterial strain isolated from a high background radiation area in response to radium stress. J Proteomics 2012; 75:4820-32. [DOI: 10.1016/j.jprot.2012.05.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 04/24/2012] [Accepted: 05/13/2012] [Indexed: 10/28/2022]
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21
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Lin S, Cronan JE. Closing in on complete pathways of biotin biosynthesis. MOLECULAR BIOSYSTEMS 2011; 7:1811-21. [PMID: 21437340 DOI: 10.1039/c1mb05022b] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Biotin is an enzyme cofactor indispensable to metabolic fixation of carbon dioxide in all three domains of life. Although the catalytic and physiological roles of biotin have been well characterized, the biosynthesis of biotin remains to be fully elucidated. Studies in microbes suggest a two-stage biosynthetic pathway in which a pimelate moiety is synthesized and used to begin assembly of the biotin bicyclic ring structure. The enzymes involved in the bicyclic ring assembly have been studied extensively. In contrast the synthesis of pimelate, a seven carbon α,ω-dicarboxylate, has long been an enigma. Support for two different routes of pimelate synthesis has recently been obtained in Escherichia coli and Bacillus subtilis. The E. coli BioC-BioH pathway employs a methylation and demethylation strategy to allow elongation of a temporarily disguised malonate moiety to a pimelate moiety by the fatty acid synthetic enzymes whereas the B. subtilis BioI-BioW pathway utilizes oxidative cleavage of fatty acyl chains. Both pathways produce the pimelate thioester precursor essential for the first step in assembly of the fused rings of biotin. The enzymatic mechanisms and biochemical strategies of these pimelate synthesis models will be discussed in this review.
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Affiliation(s)
- Steven Lin
- Department of Microbiology, University of Illinois, B103 Chemical and Life Sciences Laboratory, 601 S. Goodwin Ave, Urbana, Illinois 61801, USA
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22
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Vey JL, Drennan CL. Structural insights into radical generation by the radical SAM superfamily. Chem Rev 2011; 111:2487-506. [PMID: 21370834 PMCID: PMC5930932 DOI: 10.1021/cr9002616] [Citation(s) in RCA: 183] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jessica L Vey
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Haft DH. Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners. BMC Genomics 2011; 12:21. [PMID: 21223593 PMCID: PMC3023750 DOI: 10.1186/1471-2164-12-21] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 01/11/2011] [Indexed: 11/10/2022] Open
Abstract
Background Enzymes in the radical SAM (rSAM) domain family serve in a wide variety of biological processes, including RNA modification, enzyme activation, bacteriocin core peptide maturation, and cofactor biosynthesis. Evolutionary pressures and relationships to other cellular constituents impose recognizable grammars on each class of rSAM-containing system, shaping patterns in results obtained through various comparative genomics analyses. Results An uncharacterized gene cluster found in many Actinobacteria and sporadically in Firmicutes, Chloroflexi, Deltaproteobacteria, and one Archaeal plasmid contains a PqqE-like rSAM protein family that includes Rv0693 from Mycobacterium tuberculosis. Members occur clustered with a strikingly well-conserved small polypeptide we designate "mycofactocin," similar in size to bacteriocins and PqqA, precursor of pyrroloquinoline quinone (PQQ). Partial Phylogenetic Profiling (PPP) based on the distribution of these markers identifies the mycofactocin cluster, but also a second tier of high-scoring proteins. This tier, strikingly, is filled with up to thirty-one members per genome from three variant subfamilies that occur, one each, in three unrelated classes of nicotinoproteins. The pattern suggests these variant enzymes require not only NAD(P), but also the novel gene cluster. Further study was conducted using SIMBAL, a PPP-like tool, to search these nicotinoproteins for subsequences best correlated across multiple genomes to the presence of mycofactocin. For both the short chain dehydrogenase/reductase (SDR) and iron-containing dehydrogenase families, aligning SIMBAL's top-scoring sequences to homologous solved crystal structures shows signals centered over NAD(P)-binding sites rather than over substrate-binding or active site residues. Previous studies on some of these proteins have revealed a non-exchangeable NAD cofactor, such that enzymatic activity in vitro requires an artificial electron acceptor such as N,N-dimethyl-4-nitrosoaniline (NDMA) for the enzyme to cycle. Conclusions Taken together, these findings suggest that the mycofactocin precursor is modified by the Rv0693 family rSAM protein and other enzymes in its cluster. It becomes an electron carrier molecule that serves in vivo as NDMA and other artificial electron acceptors do in vitro. Subclasses from three different nicotinoprotein families show "only-if" relationships to mycofactocin because they require its presence. This framework suggests a segregated redox pool in which mycofactocin mediates communication among enzymes with non-exchangeable cofactors.
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Affiliation(s)
- Daniel H Haft
- J Craig Venter Institute, 9704 Rockville, MD 20850, USA.
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Delli-Bovi TA, Spalding MD, Prigge ST. Overexpression of biotin synthase and biotin ligase is required for efficient generation of sulfur-35 labeled biotin in E. coli. BMC Biotechnol 2010; 10:73. [PMID: 20937134 PMCID: PMC2964542 DOI: 10.1186/1472-6750-10-73] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 10/11/2010] [Indexed: 12/27/2022] Open
Abstract
Background Biotin is an essential enzyme cofactor that acts as a CO2 carrier in carboxylation and decarboxylation reactions. The E. coli genome encodes a biosynthetic pathway that produces biotin from pimeloyl-CoA in four enzymatic steps. The final step, insertion of sulfur into desthiobiotin to form biotin, is catalyzed by the biotin synthase, BioB. A dedicated biotin ligase (BirA) catalyzes the covalent attachment of biotin to biotin-dependent enzymes. Isotopic labeling has been a valuable tool for probing the details of the biosynthetic process and assaying the activity of biotin-dependent enzymes, however there is currently no established method for 35S labeling of biotin. Results In this study, we produced [35S]-biotin from Na35SO4 and desthiobiotin with a specific activity of 30.7 Ci/mmol, two orders of magnitude higher than previously published methods. The biotinylation domain (PfBCCP-79) from the Plasmodium falciparum acetyl-CoA carboxylase (ACC) was expressed in E. coli as a biotinylation substrate. We found that overexpression of the E. coli biotin synthase, BioB, and biotin ligase, BirA, increased PfBCCP-79 biotinylation 160-fold over basal levels. Biotinylated PfBCCP-79 was purified by affinity chromatography, and free biotin was liberated using acid hydrolysis. We verified that we had produced radiolabeled biologically active [D]-biotin that specifically labels biotinylated proteins through reuptake in E. coli. Conclusions The strategy described in our report provides a simple and effective method for the production of [35S]-biotin in E. coli based on affinity chromatography.
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Affiliation(s)
- Teegan A Delli-Bovi
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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Ballmann J, Dechert S, Demeshko S, Meyer F. Tuning Electronic Properties of Biomimetic [2Fe-2S] Clusters by Ligand Variations. Eur J Inorg Chem 2009. [DOI: 10.1002/ejic.200900101] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Abstract
The radical S-adenosylmethionine (SAM) superfamily currently comprises more than 2800 proteins with the amino acid sequence motif CxxxCxxC unaccompanied by a fourth conserved cysteine. The charcteristic three-cysteine motif nucleates a [4Fe-4S] cluster, which binds SAM as a ligand to the unique Fe not ligated to a cysteine residue. The members participate in more than 40 distinct biochemical transformations, and most members have not been biochemically characterized. A handful of the members of this superfamily have been purified and at least partially characterized. Significant mechanistic and structural information is available for lysine 2,3-aminomutase, pyruvate formate-lyase, coproporphyrinogen III oxidase, and MoaA required for molybdopterin biosynthesis. Biochemical information is available for spore photoproduct lyase, anaerobic ribonucleotide reductase activation subunit, lipoyl synthase, and MiaB involved in methylthiolation of isopentenyladenine-37 in tRNA. The radical SAM enzymes biochemically characterized to date have in common the cleavage of the [4Fe-4S](1 +) -SAM complex to [4Fe-4S](2 +)-Met and the 5' -deoxyadenosyl radical, which abstracts a hydrogen atom from the substrate to initiate a radical mechanism.
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Affiliation(s)
- Perry A Frey
- Department of Biochemistry, University of Madison, Wisconin-Madison, Wisconsin 53726, USA.
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27
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Abdel-Hamid AM, Cronan JE. In vivo resolution of conflicting in vitro results: synthesis of biotin from dethiobiotin does not require pyridoxal phosphate. ACTA ACUST UNITED AC 2008; 14:1215-20. [PMID: 18022560 DOI: 10.1016/j.chembiol.2007.10.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Revised: 10/01/2007] [Accepted: 10/16/2007] [Indexed: 11/30/2022]
Abstract
The source of the biotin sulfur atom remains a contested point in studies of biotin synthase (BioB) in vitro. Recent reports that BioB has an intrinsic pyridoxal phosphate (PLP)-dependent cysteine desulfurase activity were tested by depleting Escherichia coli cells of PLP. The BioB-dependent conversion of dethiobiotin to biotin proceeded in these cells irrespective of the presence or absence of PLP.
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28
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Booker SJ, Cicchillo RM, Grove TL. Self-sacrifice in radical S-adenosylmethionine proteins. Curr Opin Chem Biol 2007; 11:543-52. [PMID: 17936058 DOI: 10.1016/j.cbpa.2007.08.028] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Revised: 08/22/2007] [Accepted: 08/22/2007] [Indexed: 01/10/2023]
Abstract
The radical SAM superfamily of metalloproteins catalyze the reductive cleavage of S-adenosyl-l-methionine to generate a 5'-deoxyadenosyl radical (5'-dA*) intermediate that is obligate for turnover. The 5'-dA* acts as a potent oxidant, initiating turnover by abstracting a hydrogen atom from an appropriate substrate. A special class of these enzymes use this strategy to functionalize unactivated C-H bonds by insertion of sulfur atoms. This review will describe the characterization of three members of this class - biotin synthase, lipoyl synthase, and MiaB protein - each of which has been shown to cannibalize itself during turnover.
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Affiliation(s)
- Squire J Booker
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16803, United States.
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Mitochondrial Iba57p is required for Fe/S cluster formation on aconitase and activation of radical SAM enzymes. Mol Cell Biol 2007; 28:1851-61. [PMID: 18086897 DOI: 10.1128/mcb.01963-07] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
A genome-wide screen for Saccharomyces cerevisiae iron-sulfur (Fe/S) cluster assembly mutants identified the gene IBA57. The encoded protein Iba57p is located in the mitochondrial matrix and is essential for mitochondrial DNA maintenance. The growth phenotypes of an iba57Delta mutant and extensive functional studies in vivo and in vitro indicate a specific role for Iba57p in the maturation of mitochondrial aconitase-type and radical SAM Fe/S proteins (biotin and lipoic acid synthases). Maturation of other Fe/S proteins occurred normally in the absence of Iba57p. These observations identify Iba57p as a novel dedicated maturation factor with specificity for a subset of Fe/S proteins. The Iba57p primary sequence is distinct from any known Fe/S assembly factor but is similar to certain tetrahydrofolate-binding enzymes, adding a surprising new function to this protein family. Iba57p physically interacts with the mitochondrial ISC assembly components Isa1p and Isa2p. Since all three proteins are conserved in eukaryotes and bacteria, the specificity of the Iba57/Isa complex may represent a biosynthetic concept that is universally used in nature. In keeping with this idea, the human IBA57 homolog C1orf69 complements the iba57Delta growth defects, demonstrating its conserved function throughout the eukaryotic kingdom.
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30
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Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BØ. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 2007; 3:121. [PMID: 17593909 PMCID: PMC1911197 DOI: 10.1038/msb4100155] [Citation(s) in RCA: 964] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Accepted: 04/12/2007] [Indexed: 02/04/2023] Open
Abstract
An updated genome-scale reconstruction of the metabolic network in Escherichia coli K-12 MG1655 is presented. This updated metabolic reconstruction includes: (1) an alignment with the latest genome annotation and the metabolic content of EcoCyc leading to the inclusion of the activities of 1260 ORFs, (2) characterization and quantification of the biomass components and maintenance requirements associated with growth of E. coli and (3) thermodynamic information for the included chemical reactions. The conversion of this metabolic network reconstruction into an in silico model is detailed. A new step in the metabolic reconstruction process, termed thermodynamic consistency analysis, is introduced, in which reactions were checked for consistency with thermodynamic reversibility estimates. Applications demonstrating the capabilities of the genome-scale metabolic model to predict high-throughput experimental growth and gene deletion phenotypic screens are presented. The increased scope and computational capability using this new reconstruction is expected to broaden the spectrum of both basic biology and applied systems biology studies of E. coli metabolism.
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Affiliation(s)
- Adam M Feist
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Christopher S Henry
- Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, IL, USA
| | - Jennifer L Reed
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | | | - Andrew R Joyce
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Peter D Karp
- Bioinformatics Research Group, SRI International, Ravenswood, CA, USA
| | - Linda J Broadbelt
- Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, IL, USA
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology, Ecole polytechnique fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Bernhard Ø Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, Mail Code 0412, La Jolla, CA 92093, USA. Tel.: +1 858 534 5668; Fax: +1 858 822 3120;
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Marquet A, Bui BTS, Smith AG, Warren MJ. Iron–sulfur proteins as initiators of radical chemistry. Nat Prod Rep 2007; 24:1027-40. [PMID: 17898896 DOI: 10.1039/b703109m] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Iron-sulfur proteins are very versatile biological entities for which many new functions are continuously being unravelled. This review focus on their role in the initiation of radical chemistry, with special emphasis on radical-SAM enzymes, since several members of the family catalyse key steps in the biosynthetic pathways of cofactors such as biotin, lipoate, thiamine, heme and the molybdenum cofactor. It will also include other examples to show the chemical logic which is emerging from the presently available data on this family of enzymes. The common step in all the (quite different) reactions described here is the monoelectronic reductive cleavage of SAM by a reduced [4Fe-4S](1+) cluster, producing methionine and a highly oxidising deoxyadenosyl radical, which can initiate chemically difficult reactions. This set of enzymes, which represent a means to perform oxidation under reductive conditions, are often present in anaerobic organisms. Some other, non-SAM-dependent, radical reactions obeying the same chemical logic are also covered.
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Affiliation(s)
- Andrée Marquet
- Université Pierre et Marie Curie-Paris 6, CNRS UMR 7613, (Synthèse, Structure et Fonction de Molécules Bioactives), Paris, France.
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Abstract
Many biotransformations of mid- to long chain fatty acyl derivatives are intrinsically interesting because of their high selectivity and novel mechanisms. These include one carbon transfer, hydration, isomerization, hydrogenation, ladderane and hydrocarbon formation, thiolation and various oxidative transformations such as epoxidation, hydroxylation and desaturation. In addition, hydroperoxidation of polyunsaturated fatty acids leads to a diverse array of bioactive compounds. The bioorganic aspects of selected reactions will be highlighted in this review; 210 references are cited.
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Affiliation(s)
- Peter H Buist
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
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Abstract
Sulfur is a functionally important element of living matter. Incorporation into biomolecules occurs by two basic strategies. Sulfide is added to an activated acceptor in the biosynthesis of cysteine, from which methionine, coenzyme A and a number of biologically important thiols can be constructed. By contrast, the biosyntheses of iron sulfur clusters, cofactors such as thiamin, molybdopterin, biotin and lipoic acid, and the thio modification of tRNA require an activated sulfur species termed persulfidic sulfur (R-S-SH) instead of sulfide. Persulfidic sulfur is produced enzymatically with the IscS protein, the SufS protein and rhodanese being the most prominent biocatalysts. This review gives an overview of sulfur incorporation into biomolecules in prokaryotes with a special emphasis on the properties and the enzymatic generation of persulfidic sulfur as well as its use in biosynthetic pathways.
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Affiliation(s)
- Dorothea Kessler
- Biochemiezentrum Heidelberg, Universität Heidelberg, Heidelberg, Germany.
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34
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Affiliation(s)
- Tadhg P Begley
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
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