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Cronan JE. Lipoic acid attachment to proteins: stimulating new developments. Microbiol Mol Biol Rev 2024; 88:e0000524. [PMID: 38624243 PMCID: PMC11332335 DOI: 10.1128/mmbr.00005-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024] Open
Abstract
SUMMARYLipoic acid-modified proteins are essential for central metabolism and pathogenesis. In recent years, the Escherichia coli and Bacillus subtilis lipoyl assembly pathways have been modified and extended to archaea and diverse eukaryotes including humans. These extensions include a new pathway to insert the key sulfur atoms of lipoate, several new pathways of lipoate salvage, and a novel use of lipoic acid in sulfur-oxidizing bacteria. Other advances are the modification of E. coli LplA for studies of protein localization and protein-protein interactions in cell biology and in enzymatic removal of lipoate from lipoyl proteins. Finally, scenarios have been put forth for the evolution of lipoate assembly in archaea.
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Affiliation(s)
- John E. Cronan
- Department of Microbiology, University of Illinois, Urbana, Illinois, USA
- Department of Biochemistry, University of Illinois, Urbana, Illinois, USA
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2
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Scattolini A, Grammatoglou K, Nikitjuka A, Jirgensons A, Mansilla MC, Windshügel B. Substrate Analogues Entering the Lipoic Acid Salvage Pathway via Lipoate-Protein Ligase 2 Interfere with Staphylococcus aureus Virulence. ACS Infect Dis 2024; 10:2172-2182. [PMID: 38724014 PMCID: PMC11184557 DOI: 10.1021/acsinfecdis.4c00148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 06/15/2024]
Abstract
Lipoic acid (LA) is an essential cofactor in prokaryotic and eukaryotic organisms, required for the function of several multienzyme complexes such as oxoacid dehydrogenases. Prokaryotes either synthesize LA or salvage it from the environment. The salvage pathway in Staphylococcus aureus includes two lipoate-protein ligases, LplA1 and LplA2, as well as the amidotransferase LipL. In this study, we intended to hijack the salvage pathway by LA analogues that are transferred via LplA2 and LipL to the E2 subunits of various dehydrogenases, thereby resulting in nonfunctional enzymes that eventually impair viability of the bacterium. Initially, a virtual screening campaign was carried out to identify potential LA analogues that bind to LplA2. Three selected compounds affected S. aureus USA300 growth in minimal medium at concentrations ranging from 2.5 to 10 μg/mL. Further analysis of the most potent compound (Lpl-004) revealed its transfer to E2 subunits of dehydrogenase complexes and a negative impact on its functionality. Growth impairment caused by Lpl-004 treatment was restored by adding products of the lipoate-dependent enzyme complexes. In addition, Caenorhabditis elegans infected with LpL-004-treated USA300 demonstrated a significantly expanded lifespan compared to worms infected with untreated bacteria. Our results provide evidence that LA analogues exploiting the LA salvage pathway represent an innovative strategy for the development of novel antimicrobial substances.
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Affiliation(s)
- Albertina Scattolini
- Instituto
de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas
y Técnicas, Ocampo y Esmeralda, S2000FHQ Rosario, Argentina
- Departamento
de Microbiología, Facultad de Ciencias Bioquímicas y
Farmacéuticas, Universidad Nacional
de Rosario, 2000 Rosario, Argentina
| | | | - Anna Nikitjuka
- Latvian
Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia
| | - Aigars Jirgensons
- Latvian
Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia
| | - María Cecilia Mansilla
- Instituto
de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas
y Técnicas, Ocampo y Esmeralda, S2000FHQ Rosario, Argentina
- Departamento
de Microbiología, Facultad de Ciencias Bioquímicas y
Farmacéuticas, Universidad Nacional
de Rosario, 2000 Rosario, Argentina
| | - Björn Windshügel
- Fraunhofer
Institute for Translational Medicine and Pharmacology ITMP, Discovery
Research ScreeningPort, Schnackenburgallee 114, 22525 Hamburg, Germany
- School
of Science, Constructor University, Campus Ring 1, 28759 Bremen, Germany
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3
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Xue J, Ye C. The role of lipoylation in mitochondrial adaptation to methionine restriction. Bioessays 2024; 46:e2300218. [PMID: 38616332 DOI: 10.1002/bies.202300218] [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: 11/11/2023] [Revised: 03/12/2024] [Accepted: 04/02/2024] [Indexed: 04/16/2024]
Abstract
Dietary methionine restriction (MR) is associated with a spectrum of health-promoting benefits. Being conducive to prevention of chronic diseases and extension of life span, MR can activate integrated responses at metabolic, transcriptional, and physiological levels. However, how the mitochondria of MR influence metabolic phenotypes remains elusive. Here, we provide a summary of cellular functions of methionine metabolism and an overview of the current understanding of effector mechanisms of MR, with a focus on the aspect of mitochondria-mediated responses. We propose that mitochondria can sense and respond to MR through a modulatory role of lipoylation, a mitochondrial protein modification sensitized by MR.
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Affiliation(s)
- Jingyuan Xue
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Cunqi Ye
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Sanya, China
- National R&D Center for Freshwater Fish Processing, Jiangxi Normal University, Nanchang, China
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4
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Kümpel C, Grosser M, Tanabe TS, Dahl C. Fe/S proteins in microbial sulfur oxidation. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119732. [PMID: 38631440 DOI: 10.1016/j.bbamcr.2024.119732] [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: 11/14/2023] [Revised: 02/26/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024]
Abstract
Iron-sulfur clusters serve as indispensable cofactors within proteins across all three domains of life. Fe/S clusters emerged early during the evolution of life on our planet and the biogeochemical cycle of sulfur is one of the most ancient and important element cycles. It is therefore no surprise that Fe/S proteins have crucial roles in the multiple steps of microbial sulfur metabolism. During dissimilatory sulfur oxidation in prokaryotes, Fe/S proteins not only serve as electron carriers in several steps, but also perform catalytic roles, including unprecedented reactions. Two cytoplasmic enzyme systems that oxidize sulfane sulfur to sulfite are of particular interest in this context: The rDsr pathway employs the reverse acting dissimilatory sulfite reductase rDsrAB as its key enzyme, while the sHdr pathway utilizes polypeptides resembling the HdrA, HdrB and HdrC subunits of heterodisulfide reductase from methanogenic archaea. Both pathways involve components predicted to bind unusual noncubane Fe/S clusters acting as catalysts for the formation of disulfide or sulfite. Mapping of Fe/S cluster machineries on the sulfur-oxidizing prokaryote tree reveals that ISC, SUF, MIS and SMS are all sufficient to meet the Fe/S cluster maturation requirements for operation of the sHdr or rDsr pathways. The sHdr pathway is dependent on lipoate-binding proteins that are assembled by a novel pathway, involving two Radical SAM proteins, namely LipS1 and LipS2. These proteins coordinate sulfur-donating auxiliary Fe/S clusters in atypical patterns by three cysteines and one histidine and act as lipoyl synthases by jointly inserting two sulfur atoms to an octanoyl residue. This article is part of a Special Issue entitled: Biogenesis and Function of Fe/S proteins.
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Affiliation(s)
- Carolin Kümpel
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Martina Grosser
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Tomohisa Sebastian Tanabe
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.
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5
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Dieckmann CL. A hub for regulation of mitochondrial metabolism: Fatty acid and lipoic acid biosynthesis. IUBMB Life 2024; 76:332-344. [PMID: 38088214 DOI: 10.1002/iub.2802] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/21/2023] [Indexed: 05/28/2024]
Abstract
Having evolved from a prokaryotic origin, mitochondria retain pathways required for the catabolism of energy-rich molecules and for the biosynthesis of molecules that aid catabolism and/or participate in other cellular processes essential for life of the cell. Reviewed here are details of the mitochondrial fatty acid biosynthetic pathway (FAS II) and its role in building both the octanoic acid precursor for lipoic acid biosynthesis (LAS) and longer-chain fatty acids functioning in chaperoning the assembly of mitochondrial multisubunit complexes. Also covered are the details of mitochondrial lipoic acid biosynthesis, which is distinct from that of prokaryotes, and the attachment of lipoic acid to subunits of pyruvate dehydrogenase, α-ketoglutarate dehydrogenase, and glycine cleavage system complexes. Special emphasis has been placed on presenting what is currently known about the interconnected paths and loops linking the FAS II-LAS pathway and two other mitochondrial realms, the organellar translation machinery and Fe-S cluster biosynthesis and function.
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Affiliation(s)
- Carol L Dieckmann
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
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6
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Ahator SD, Hegstad K, Lentz CS, Johannessen M. Deciphering Staphylococcus aureus-host dynamics using dual activity-based protein profiling of ATP-interacting proteins. mSystems 2024; 9:e0017924. [PMID: 38656122 PMCID: PMC11097646 DOI: 10.1128/msystems.00179-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
The utilization of ATP within cells plays a fundamental role in cellular processes that are essential for the regulation of host-pathogen dynamics and the subsequent immune response. This study focuses on ATP-binding proteins to dissect the complex interplay between Staphylococcus aureus and human cells, particularly macrophages (THP-1) and keratinocytes (HaCaT), during an intracellular infection. A snapshot of the various protein activity and function is provided using a desthiobiotin-ATP probe, which targets ATP-interacting proteins. In S. aureus, we observe enrichment in pathways required for nutrient acquisition, biosynthesis and metabolism of amino acids, and energy metabolism when located inside human cells. Additionally, the direct profiling of the protein activity revealed specific adaptations of S. aureus to the keratinocytes and macrophages. Mapping the differentially activated proteins to biochemical pathways in the human cells with intracellular bacteria revealed cell-type-specific adaptations to bacterial challenges where THP-1 cells prioritized immune defenses, autophagic cell death, and inflammation. In contrast, HaCaT cells emphasized barrier integrity and immune activation. We also observe bacterial modulation of host processes and metabolic shifts. These findings offer valuable insights into the dynamics of S. aureus-host cell interactions, shedding light on modulating host immune responses to S. aureus, which could involve developing immunomodulatory therapies. IMPORTANCE This study uses a chemoproteomic approach to target active ATP-interacting proteins and examines the dynamic proteomic interactions between Staphylococcus aureus and human cell lines THP-1 and HaCaT. It uncovers the distinct responses of macrophages and keratinocytes during bacterial infection. S. aureus demonstrated a tailored response to the intracellular environment of each cell type and adaptation during exposure to professional and non-professional phagocytes. It also highlights strategies employed by S. aureus to persist within host cells. This study offers significant insights into the human cell response to S. aureus infection, illuminating the complex proteomic shifts that underlie the defense mechanisms of macrophages and keratinocytes. Notably, the study underscores the nuanced interplay between the host's metabolic reprogramming and immune strategy, suggesting potential therapeutic targets for enhancing host defense and inhibiting bacterial survival. The findings enhance our understanding of host-pathogen interactions and can inform the development of targeted therapies against S. aureus infections.
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Affiliation(s)
- Stephen Dela Ahator
- Centre for New Antibacterial Strategies (CANS) & Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, Tromsø, Norway
| | - Kristin Hegstad
- Centre for New Antibacterial Strategies (CANS) & Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Christian S. Lentz
- Centre for New Antibacterial Strategies (CANS) & Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, Tromsø, Norway
| | - Mona Johannessen
- Centre for New Antibacterial Strategies (CANS) & Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT–The Arctic University of Norway, Tromsø, Norway
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7
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Huang Y, Wan X, Su Q, Zhao C, Cao J, Yue Y, Li S, Chen X, Yin J, Deng Y, Zhang X, Wu T, Zhou Z, Wang D. Ultrasound-activated piezo-hot carriers trigger tandem catalysis coordinating cuproptosis-like bacterial death against implant infections. Nat Commun 2024; 15:1643. [PMID: 38388555 PMCID: PMC10884398 DOI: 10.1038/s41467-024-45619-y] [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: 08/17/2023] [Accepted: 01/30/2024] [Indexed: 02/24/2024] Open
Abstract
Implant-associated infections due to the formation of bacterial biofilms pose a serious threat in medical healthcare, which needs effective therapeutic methods. Here, we propose a multifunctional nanoreactor by spatiotemporal ultrasound-driven tandem catalysis to amplify the efficacy of sonodynamic and chemodynamic therapy. By combining piezoelectric barium titanate with polydopamine and copper, the ultrasound-activated piezo-hot carriers transfer easily to copper by polydopamine. It boosts reactive oxygen species production by piezoelectrics, and facilitates the interconversion between Cu2+ and Cu+ to promote hydroxyl radical generation via Cu+ -catalyzed chemodynamic reactions. Finally, the elevated reactive oxygen species cause bacterial membrane structure loosening and DNA damage. Transcriptomics and metabolomics analysis reveal that intracellular copper overload restricts the tricarboxylic acid cycle, promoting bacterial cuproptosis-like death. Therefore, the polyetherketoneketone scaffold engineered with the designed nanoreactor shows excellent antibacterial performance with ultrasound stimulation and promotes angiogenesis and osteogenesis on-demand in vivo.
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Affiliation(s)
- Yanli Huang
- Key Laboratory of Opto-Electronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Photonics Technology, College of Photonic and Electronic Engineering, Fujian Normal University, Fuzhou, 350117, China
| | - Xufeng Wan
- Orthopaedic Research Institute, Department of Orthopaedics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qiang Su
- Department of Orthopedics, The Third Hospital of Mianyang, Sichuan Mental Health Center, Mianyang, 621000, China
| | - Chunlin Zhao
- College of Materials Science and Engineering, Fuzhou University, Fuzhou, 350108, China
| | - Jian Cao
- Orthopaedic Research Institute, Department of Orthopaedics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yan Yue
- Orthopaedic Research Institute, Department of Orthopaedics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Shuoyuan Li
- Orthopaedic Research Institute, Department of Orthopaedics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaoting Chen
- Animal Experimental Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jie Yin
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research, Singapore, 138634, Singapore
| | - Yi Deng
- College of Biomedical Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Xianzeng Zhang
- Key Laboratory of Opto-Electronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Photonics Technology, College of Photonic and Electronic Engineering, Fujian Normal University, Fuzhou, 350117, China.
| | - Tianmin Wu
- Key Laboratory of Opto-Electronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Photonics Technology, College of Photonic and Electronic Engineering, Fujian Normal University, Fuzhou, 350117, China.
| | - Zongke Zhou
- Orthopaedic Research Institute, Department of Orthopaedics, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Duan Wang
- Orthopaedic Research Institute, Department of Orthopaedics, West China Hospital, Sichuan University, Chengdu, 610041, China.
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8
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Schoenmakers LLJ, Reydon TAC, Kirschning A. Evolution at the Origins of Life? Life (Basel) 2024; 14:175. [PMID: 38398684 PMCID: PMC10890241 DOI: 10.3390/life14020175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
The role of evolutionary theory at the origin of life is an extensively debated topic. The origin and early development of life is usually separated into a prebiotic phase and a protocellular phase, ultimately leading to the Last Universal Common Ancestor. Most likely, the Last Universal Common Ancestor was subject to Darwinian evolution, but the question remains to what extent Darwinian evolution applies to the prebiotic and protocellular phases. In this review, we reflect on the current status of evolutionary theory in origins of life research by bringing together philosophy of science, evolutionary biology, and empirical research in the origins field. We explore the various ways in which evolutionary theory has been extended beyond biology; we look at how these extensions apply to the prebiotic development of (proto)metabolism; and we investigate how the terminology from evolutionary theory is currently being employed in state-of-the-art origins of life research. In doing so, we identify some of the current obstacles to an evolutionary account of the origins of life, as well as open up new avenues of research.
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Affiliation(s)
- Ludo L. J. Schoenmakers
- Konrad Lorenz Institute for Evolution and Cognition Research (KLI), 3400 Klosterneuburg, Austria
| | - Thomas A. C. Reydon
- Institute of Philosophy, Centre for Ethics and Law in the Life Sciences (CELLS), Leibniz University Hannover, 30159 Hannover, Germany;
| | - Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, 30167 Hannover, Germany;
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9
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Chakraborty S, Choudhuri A, Mishra A, Bhattacharyya C, Billiar TR, Stoyanovsky DA, Sengupta R. Nitric oxide and thioredoxin modulate the activity of caspase 9 in HepG2 cells. Biochim Biophys Acta Gen Subj 2023; 1867:130452. [PMID: 37652366 PMCID: PMC10592080 DOI: 10.1016/j.bbagen.2023.130452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
The interdependent and finely tuned balance between the well-established redox-based modification, S-nitrosylation, and its counteractive mechanism of S-nitrosothiol degradation, i.e., S-denitrosylation of biological protein or non-protein thiols defines the cellular fate in the context of redox homeostasis. S-nitrosylation of cysteine residues by S-nitrosoglutathione, S-nitroso-L-cysteine-like physiological and S-nitroso-L-cysteine ethyl ester-like synthetic NO donors inactivate Caspase-3, 8, and 9, thereby hindering their apoptotic activity. However, spontaneous restoration of their activity upon S-denitrosylation of S-nitrosocaspases into their reduced, free thiol active states, aided by the members of the ubiquitous cellular redoxin (thioredoxin/ thioredoxin reductase/ NADPH) and low molecular weight dithiol (lipoic acid/ lipoamide dehydrogenase/ dihydrolipoic acid/ NADPH) systems imply a direct relevance to their proteolytic activities and further downstream signaling cascades. Additionally, our previous and current findings offer crucial insight into the concept of redundancy between thioredoxin and lipoic acid systems, and the redox-modulated control of the apoptotic and proteolytic activity of caspases, triggering their cyto- and neurotoxic effects in response to nitro-oxidative stress. Thus, this might lay the foundation for the exogenous introduction of precise and efficient NO or related donor drug delivery systems that can directly participate in catering to the S-(de)-nitrosylation-mediated functional outcomes of the cysteinyl proteases in pathophysiological settings.
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Affiliation(s)
- Surupa Chakraborty
- Amity Institute of Biotechnology, Amity University, Kolkata 700135, West Bengal, India
| | - Ankita Choudhuri
- Amity Institute of Biotechnology, Amity University, Kolkata 700135, West Bengal, India
| | - Akansha Mishra
- Amity Institute of Biotechnology, Amity University, Kolkata 700135, West Bengal, India
| | - Camelia Bhattacharyya
- Amity Institute of Biotechnology, Amity University, Kolkata 700135, West Bengal, India
| | - Timothy R Billiar
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | | | - Rajib Sengupta
- Amity Institute of Biotechnology, Amity University, Kolkata 700135, West Bengal, India; Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA.
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Acosta IC, Alonzo F. The Intersection between Bacterial Metabolism and Innate Immunity. J Innate Immun 2023; 15:782-803. [PMID: 37899025 PMCID: PMC10663042 DOI: 10.1159/000534872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/25/2023] [Indexed: 10/31/2023] Open
Abstract
BACKGROUND The innate immune system is the first line of defense against microbial pathogens and is essential for maintaining good health. If pathogens breach innate barriers, the likelihood of infection is significantly increased. Many bacterial pathogens pose a threat to human health on account of their ability to evade innate immunity and survive in growth-restricted environments. These pathogens have evolved sophisticated strategies to obtain nutrients as well as manipulate innate immune responses, resulting in disease or chronic infection. SUMMARY The relationship between bacterial metabolism and innate immunity is complex. Although aspects of bacterial metabolism can be beneficial to the host, particularly those related to the microbiota and barrier integrity, others can be harmful. Several bacterial pathogens harness metabolism to evade immune responses and persist during infection. The study of these adaptive traits provides insight into the roles of microbial metabolism in pathogenesis that extend beyond energy balance. This review considers recent studies on bacterial metabolic pathways that promote infection by circumventing several facets of the innate immune system. We also discuss relationships between innate immunity and antibiotics and highlight future directions for research in this field. KEY MESSAGES Pathogenic bacteria have a remarkable capacity to harness metabolism to manipulate immune responses and promote pathogenesis. While we are beginning to understand the multifaceted and complex metabolic adaptations that occur during infection, there is still much to uncover with future research.
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Affiliation(s)
- Ivan C Acosta
- Department of Microbiology and Immunology, University of Illinois at Chicago - College of Medicine, Chicago, Illinois, USA
| | - Francis Alonzo
- Department of Microbiology and Immunology, University of Illinois at Chicago - College of Medicine, Chicago, Illinois, USA
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11
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Zuber P, Kreth J. Aspects of oral streptococcal metabolic diversity: Imagining the landscape beneath the fog. Mol Microbiol 2023; 120:508-524. [PMID: 37329112 DOI: 10.1111/mmi.15106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 06/18/2023]
Abstract
It is widely acknowledged that the human-associated microbial community influences host physiology, systemic health, disease progression, and even behavior. There is currently an increased interest in the oral microbiome, which occupies the entryway to much of what the human initially encounters from the environment. In addition to the dental pathology that results from a dysbiotic microbiome, microbial activity within the oral cavity exerts significant systemic effects. The composition and activity of the oral microbiome is influenced by (1) host-microbial interactions, (2) the emergence of niche-specific microbial "ecotypes," and (3) numerous microbe-microbe interactions, shaping the underlying microbial metabolic landscape. The oral streptococci are central players in the microbial activity ongoing in the oral cavity, due to their abundance and prevalence in the oral environment and the many interspecies interactions in which they participate. Streptococci are major determinants of a healthy homeostatic oral environment. The metabolic activities of oral Streptococci, particularly the metabolism involved in energy generation and regeneration of oxidative resources vary among the species and are important factors in niche-specific adaptations and intra-microbiome interactions. Here we summarize key differences among streptococcal central metabolic networks and species-specific differences in how the key glycolytic intermediates are utilized.
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Affiliation(s)
- Peter Zuber
- Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, Oregon, USA
| | - Jens Kreth
- School of Dentistry, Oregon Health & Science University, Portland, Oregon, USA
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12
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Álvarez-Córdoba M, Talaverón-Rey M, Povea-Cabello S, Cilleros-Holgado P, Gómez-Fernández D, Piñero-Pérez R, Reche-López D, Munuera-Cabeza M, Suárez-Carrillo A, Romero-González A, Romero-Domínguez JM, López-Cabrera A, Armengol JÁ, Sánchez-Alcázar JA. Patient-Derived Cellular Models for Polytarget Precision Medicine in Pantothenate Kinase-Associated Neurodegeneration. Pharmaceuticals (Basel) 2023; 16:1359. [PMID: 37895830 PMCID: PMC10609847 DOI: 10.3390/ph16101359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/21/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
The term neurodegeneration with brain iron accumulation (NBIA) brings together a broad set of progressive and disabling neurological genetic disorders in which iron is deposited preferentially in certain areas of the brain. Among NBIA disorders, the most frequent subtype is pantothenate kinase-associated neurodegeneration (PKAN) caused by pathologic variants in the PANK2 gene codifying the enzyme pantothenate kinase 2 (PANK2). To date, there are no effective treatments to stop the progression of these diseases. This review discusses the utility of patient-derived cell models as a valuable tool for the identification of pharmacological or natural compounds for implementing polytarget precision medicine in PKAN. Recently, several studies have described that PKAN patient-derived fibroblasts present the main pathological features associated with the disease including intracellular iron overload. Interestingly, treatment of mutant cell cultures with various supplements such as pantothenate, pantethine, vitamin E, omega 3, α-lipoic acid L-carnitine or thiamine, improved all pathophysiological alterations in PKAN fibroblasts with residual expression of the PANK2 enzyme. The information provided by pharmacological screenings in patient-derived cellular models can help optimize therapeutic strategies in individual PKAN patients.
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Affiliation(s)
- Mónica Álvarez-Córdoba
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Marta Talaverón-Rey
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Suleva Povea-Cabello
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Paula Cilleros-Holgado
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - David Gómez-Fernández
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Rocío Piñero-Pérez
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Diana Reche-López
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Manuel Munuera-Cabeza
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Alejandra Suárez-Carrillo
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Ana Romero-González
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Jose Manuel Romero-Domínguez
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Alejandra López-Cabrera
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - José Ángel Armengol
- Department of Physiology, Anatomy and Cellular Biology, Pablo de Olavide University, 41013 Seville, Spain;
| | - José Antonio Sánchez-Alcázar
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
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13
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Kieft B, Finke N, McLaughlin RJ, Nallan AN, Krzywinski M, Crowe SA, Hallam SJ. Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater. Nat Commun 2023; 14:5380. [PMID: 37666802 PMCID: PMC10477309 DOI: 10.1038/s41467-023-40907-5] [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: 05/12/2023] [Accepted: 08/15/2023] [Indexed: 09/06/2023] Open
Abstract
Anaerobic digestion of municipal mixed sludge produces methane that can be converted into renewable natural gas. To improve economics of this microbial mediated process, metabolic interactions catalyzing biomass conversion to energy need to be identified. Here, we present a two-year time series associating microbial metabolism and physicochemistry in a full-scale wastewater treatment plant. By creating a co-occurrence network with thousands of time-resolved microbial populations from over 100 samples spanning four operating configurations, known and novel microbial consortia with potential to drive methane production were identified. Interactions between these populations were further resolved in relation to specific process configurations by mapping metagenome assembled genomes and cognate gene expression data onto the network. Prominent interactions included transcriptionally active Methanolinea methanogens and syntrophic benzoate oxidizing Syntrophorhabdus, as well as a Methanoregulaceae population and putative syntrophic acetate oxidizing bacteria affiliated with Bateroidetes (Tenuifilaceae) expressing the glycine cleavage bypass of the Wood-Ljungdahl pathway.
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Affiliation(s)
- Brandon Kieft
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Niko Finke
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Ryan J McLaughlin
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Aditi N Nallan
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Martin Krzywinski
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Sean A Crowe
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada.
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- Genome Science and Technology Program, University of British Columbia, 2329 West Mall, Vancouver, BC, V6T 1Z4, Canada.
- Bradshaw Research Institute for Minerals and Mining (BRIMM), University of British Columbia, Vancouver, BC, V6T1Z4, Canada.
- Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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14
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Palmieri EM, Holewinski R, McGinity CL, Pierri CL, Maio N, Weiss JM, Tragni V, Miranda KM, Rouault TA, Andresson T, Wink DA, McVicar DW. Pyruvate dehydrogenase operates as an intramolecular nitroxyl generator during macrophage metabolic reprogramming. Nat Commun 2023; 14:5114. [PMID: 37607904 PMCID: PMC10444860 DOI: 10.1038/s41467-023-40738-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 08/04/2023] [Indexed: 08/24/2023] Open
Abstract
M1 macrophages enter a glycolytic state when endogenous nitric oxide (NO) reprograms mitochondrial metabolism by limiting aconitase 2 and pyruvate dehydrogenase (PDH) activity. Here, we provide evidence that NO targets the PDH complex by using lipoate to generate nitroxyl (HNO). PDH E2-associated lipoate is modified in NO-rich macrophages while the PDH E3 enzyme, also known as dihydrolipoamide dehydrogenase (DLD), is irreversibly inhibited. Mechanistically, we show that lipoate facilitates NO-mediated production of HNO, which interacts with thiols forming irreversible modifications including sulfinamide. In addition, we reveal a macrophage signature of proteins with reduction-resistant modifications, including in DLD, and identify potential HNO targets. Consistently, DLD enzyme is modified in an HNO-dependent manner at Cys477 and Cys484, and molecular modeling and mutagenesis show these modifications impair the formation of DLD homodimers. In conclusion, our work demonstrates that HNO is produced physiologically. Moreover, the production of HNO is dependent on the lipoate-rich PDH complex facilitating irreversible modifications that are critical to NO-dependent metabolic rewiring.
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Affiliation(s)
- Erika M Palmieri
- Cancer Innovation Laboratory, NCI-Frederick, Frederick, MD, 21702, USA
| | - Ronald Holewinski
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | | | - Ciro L Pierri
- Laboratory of Biochemistry, Molecular and Structural Biology, Department of Pharmacy-Pharmaceutical Sciences, University of Bari, Via E. Orabona, 4, Bari, 70125, Italy
| | - Nunziata Maio
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Jonathan M Weiss
- Cancer Innovation Laboratory, NCI-Frederick, Frederick, MD, 21702, USA
| | - Vincenzo Tragni
- Laboratory of Biochemistry, Molecular and Structural Biology, Department of Pharmacy-Pharmaceutical Sciences, University of Bari, Via E. Orabona, 4, Bari, 70125, Italy
| | - Katrina M Miranda
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Tracey A Rouault
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - David A Wink
- Cancer Innovation Laboratory, NCI-Frederick, Frederick, MD, 21702, USA
| | - Daniel W McVicar
- Cancer Innovation Laboratory, NCI-Frederick, Frederick, MD, 21702, USA.
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15
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Dienemann JN, Chen SY, Hitzenberger M, Sievert ML, Hacker SM, Prigge ST, Zacharias M, Groll M, Sieber SA. A Chemical Proteomic Strategy Reveals Inhibitors of Lipoate Salvage in Bacteria and Parasites. Angew Chem Int Ed Engl 2023; 62:e202304533. [PMID: 37249408 PMCID: PMC10896624 DOI: 10.1002/anie.202304533] [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: 04/03/2023] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 05/31/2023]
Abstract
The development of novel anti-infectives requires unprecedented strategies targeting pathways which are solely present in pathogens but absent in humans. Following this principle, we developed inhibitors of lipoic acid (LA) salvage, a crucial pathway for the survival of LA auxotrophic bacteria and parasites but non-essential in human cells. An LA-based probe was selectively transferred onto substrate proteins via lipoate protein ligase (LPL) in intact cells, and their binding sites were determined by mass spectrometry. Probe labeling served as a proxy of LPL activity, enabling in situ screenings for cell-permeable LPL inhibitors. Profiling a focused compound library revealed two substrate analogs (LAMe and C3) as inhibitors, which were further validated by binding studies and co-crystallography. Importantly, LAMe exhibited low toxicity in human cells and achieved killing of Plasmodium falciparum in erythrocytes with an EC50 value of 15 μM, making it the most effective LPL inhibitor reported to date.
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Affiliation(s)
- Jan-Niklas Dienemann
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer Strasse 8, 85748, Garching bei München, Germany
| | - Shu-Yu Chen
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer Strasse 8, 85748, Garching bei München, Germany
| | - Manuel Hitzenberger
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer Strasse 8, 85748, Garching bei München, Germany
| | - Montana L Sievert
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, 615N. Wolfe Street, E5132, MD 21205, Baltimore, USA
| | - Stephan M Hacker
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | - Sean T Prigge
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, 615N. Wolfe Street, E5132, MD 21205, Baltimore, USA
| | - Martin Zacharias
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer Strasse 8, 85748, Garching bei München, Germany
| | - Michael Groll
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer Strasse 8, 85748, Garching bei München, Germany
| | - Stephan A Sieber
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer Strasse 8, 85748, Garching bei München, Germany
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16
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Tanabe TS, Grosser M, Hahn L, Kümpel C, Hartenfels H, Vtulkin E, Flegler W, Dahl C. Identification of a novel lipoic acid biosynthesis pathway reveals the complex evolution of lipoate assembly in prokaryotes. PLoS Biol 2023; 21:e3002177. [PMID: 37368881 DOI: 10.1371/journal.pbio.3002177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
Lipoic acid is an essential biomolecule found in all domains of life and is involved in central carbon metabolism and dissimilatory sulfur oxidation. The machineries for lipoate assembly in mitochondria and chloroplasts of higher eukaryotes, as well as in the apicoplasts of some protozoa, are all of prokaryotic origin. Here, we provide experimental evidence for a novel lipoate assembly pathway in bacteria based on a sLpl(AB) lipoate:protein ligase, which attaches octanoate or lipoate to apo-proteins, and 2 radical SAM proteins, LipS1 and LipS2, which work together as lipoyl synthase and insert 2 sulfur atoms. Extensive homology searches combined with genomic context analyses allowed us to precisely distinguish between the new and established pathways and map them on the tree of life. This not only revealed a much wider distribution of lipoate biogenesis systems than expected, in particular, the novel sLpl(AB)-LipS1/S2 pathway, and indicated a highly modular nature of the enzymes involved, with unforeseen combinations, but also provided a new framework for the evolution of lipoate assembly. Our results show that dedicated machineries for both de novo lipoate biogenesis and scavenging from the environment were implemented early in evolution and that their distribution in the 2 prokaryotic domains was shaped by a complex network of horizontal gene transfers, acquisition of additional genes, fusions, and losses. Our large-scale phylogenetic analyses identify the bipartite archaeal LplAB ligase as the ancestor of the bacterial sLpl(AB) proteins, which were obtained by horizontal gene transfer. LipS1/S2 have a more complex evolutionary history with multiple of such events but probably also originated in the domain archaea.
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Affiliation(s)
- Tomohisa Sebastian Tanabe
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Martina Grosser
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Lea Hahn
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Carolin Kümpel
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Hanna Hartenfels
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Evelyn Vtulkin
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Wanda Flegler
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
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17
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Tran TH, Roberts AQ, Escapa IF, Gao W, Segre JA, Kong HH, Conlan S, Kelly MS, Lemon KP. Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543719. [PMID: 37333201 PMCID: PMC10274666 DOI: 10.1101/2023.06.05.543719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Corynebacterium species are globally ubiquitous in human nasal microbiota across the lifespan. Moreover, nasal microbiota profiles typified by higher relative abundances of Corynebacterium are often positively associated with health. Among the most common human nasal Corynebacterium species are C. propinquum, C. pseudodiphtheriticum, C. accolens, and C. tuberculostearicum. Based on the prevalence of these species, at least two likely coexist in the nasal microbiota of 82% of adults. To gain insight into the functions of these four species, we identified genomic, phylogenomic, and pangenomic properties and estimated the functional protein repertoire and metabolic capabilities of 87 distinct human nasal Corynebacterium strain genomes: 31 from Botswana and 56 from the U.S. C. pseudodiphtheriticum had geographically distinct clades consistent with localized strain circulation, whereas some strains from the other species had wide geographic distribution across Africa and North America. All four species had similar genomic and pangenomic structures. Gene clusters assigned to all COG metabolic categories were overrepresented in the persistent (core) compared to the accessory genome of each species indicating limited strain-level variability in metabolic capacity. Moreover, core metabolic capabilities were highly conserved among the four species indicating limited species-level metabolic variation. Strikingly, strains in the U.S. clade of C. pseudodiphtheriticum lacked genes for assimilatory sulfate reduction present in the Botswanan clade and in the other studied species, indicating a recent, geographically related loss of assimilatory sulfate reduction. Overall, the minimal species and strain variability in metabolic capacity implies coexisting strains might have limited ability to occupy distinct metabolic niches.
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Affiliation(s)
- Tommy H. Tran
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Ari Q. Roberts
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Isabel F. Escapa
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Wei Gao
- The Forsyth Institute (Microbiology), Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Julie A. Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Heidi H. Kong
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Matthew S. Kelly
- Division of Pediatric Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
| | - Katherine P. Lemon
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Division of Infectious Diseases, Texas Children’s Hospital, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
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18
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Seim GL, John SV, Arp NL, Fang Z, Pagliarini DJ, Fan J. Nitric oxide-driven modifications of lipoic arm inhibit α-ketoacid dehydrogenases. Nat Chem Biol 2023; 19:265-274. [PMID: 36266351 PMCID: PMC9974485 DOI: 10.1038/s41589-022-01153-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 08/31/2022] [Indexed: 12/30/2022]
Abstract
Pyruvate dehydrogenase complex (PDHC) and oxoglutarate dehydrogenase complex (OGDC), which belong to the mitochondrial α-ketoacid dehydrogenase family, play crucial roles in cellular metabolism. These multi-subunit enzyme complexes use lipoic arms covalently attached to their E2 subunits to transfer an acyl group to coenzyme A (CoA). Here, we report a novel mechanism capable of substantially inhibiting PDHC and OGDC: reactive nitrogen species (RNS) can covalently modify the thiols on their lipoic arms, generating a series of adducts that block catalytic activity. S-Nitroso-CoA, a product between RNS and the E2 subunit's natural substrate, CoA, can efficiently deliver these modifications onto the lipoic arm. We found RNS-mediated inhibition of PDHC and OGDC occurs during classical macrophage activation, driving significant rewiring of cellular metabolism over time. This work provides a new mechanistic link between RNS and mitochondrial metabolism with potential relevance for numerous physiological and pathological conditions in which RNS accumulate.
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Affiliation(s)
- Gretchen L Seim
- Morgridge Institute for Research, Madison, WI, USA
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Steven V John
- Morgridge Institute for Research, Madison, WI, USA
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Nicholas L Arp
- Morgridge Institute for Research, Madison, WI, USA
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Zixiang Fang
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - David J Pagliarini
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Jing Fan
- Morgridge Institute for Research, Madison, WI, USA.
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA.
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA.
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19
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Lennox-Hvenekilde D, Bali AP, Gronenberg LS, Acevedo-Rocha C, Sommer MOA, Genee HJ. Metabolic engineering of Escherichia coli for high-level production of free lipoic acid. Metab Eng 2023; 76:39-49. [PMID: 36639019 DOI: 10.1016/j.ymben.2023.01.004] [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: 09/26/2022] [Revised: 01/04/2023] [Accepted: 01/07/2023] [Indexed: 01/12/2023]
Abstract
L-Lipoic acid (LA) is an important antioxidant with various industrial applications as a nutraceutical and therapeutic. Currently, LA is produced by chemical synthesis. Cell factory development is complex as LA and its direct precursors only occur naturally in protein-bound forms. Here we report a rationally engineered LA cell factory and demonstrate de novo free LA production from glucose for the first time in E. coli. The pathway represents a significant challenge as the three key enzymes, native Octanoyltransferase (LipB) and Lipoyl Synthase (LipA), and heterologous Lipoamidase (LpA), are all toxic to overexpress in E. coli. To overcome the toxicity of LipB, functional metagenomic selection was used to identify a highly active and non-toxic LipB and LipA from S. liquefaciens. Using high throughput screening, we balanced translation initiation rates and dual, orthogonal induction systems for the toxic genes, LipA and LpA. The optimized strain yielded 2.5 mg free LA per gram of glucose in minimal media, expressing carefully balanced LipB and LipA, Enterococcus faecalis LpA, and a truncated, native, Dihydrolipoyllysine-residue acetyltransferase (AceF) lipoylation domain. When the optimized cell factory strain was cultivated in a fed-batch fermentation, a titer of 87 mg/L free LA in the supernatant was reached after 48 h. This titer is ∼3000-fold higher than previously reported free LA titer and ∼8-fold higher than the previous best total, protein-bound LA titer. The strategies presented here could be helpful in designing, constructing and balancing biosynthetic pathways that harbor toxic enzymes with protein-bound intermediates or products.
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Affiliation(s)
- David Lennox-Hvenekilde
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark; Biosyntia ApS, Fruebjergvej 3, 2100, Oesterbro, Denmark
| | - Anne P Bali
- Biosyntia ApS, Fruebjergvej 3, 2100, Oesterbro, Denmark
| | | | | | - Morten O A Sommer
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark
| | - Hans J Genee
- Biosyntia ApS, Fruebjergvej 3, 2100, Oesterbro, Denmark.
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20
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Lund T, Kulkova MY, Jersie-Christensen R, Atlung T. Essentiality of the Escherichia coli YgfZ Protein for the In Vivo Thiomethylation of Ribosomal Protein S12 by the RimO Enzyme. Int J Mol Sci 2023; 24:ijms24054728. [PMID: 36902159 PMCID: PMC10002905 DOI: 10.3390/ijms24054728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/16/2023] [Accepted: 02/22/2023] [Indexed: 03/05/2023] Open
Abstract
Enzymes carrying Iron-Sulfur (Fe-S) clusters perform many important cellular functions and their biogenesis require complex protein machinery. In mitochondria, the IBA57 protein is essential and promotes assembly of [4Fe-4S] clusters and their insertion into acceptor proteins. YgfZ is the bacterial homologue of IBA57 but its precise role in Fe-S cluster metabolism is uncharacterized. YgfZ is needed for activity of the radical S-adenosyl methionine [4Fe-4S] cluster enzyme MiaB which thiomethylates some tRNAs. The growth of cells lacking YgfZ is compromised especially at low temperature. The RimO enzyme is homologous to MiaB and thiomethylates a conserved aspartic acid in ribosomal protein S12. To quantitate thiomethylation by RimO, we developed a bottom-up LC-MS2 analysis of total cell extracts. We show here that the in vivo activity of RimO is very low in the absence of YgfZ and independent of growth temperature. We discuss these results in relation to the hypotheses relating to the role of the auxiliary 4Fe-4S cluster in the Radical SAM enzymes that make Carbon-Sulfur bonds.
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21
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Schulz V, Basu S, Freibert SA, Webert H, Boss L, Mühlenhoff U, Pierrel F, Essen LO, Warui DM, Booker SJ, Stehling O, Lill R. Functional spectrum and specificity of mitochondrial ferredoxins FDX1 and FDX2. Nat Chem Biol 2023; 19:206-217. [PMID: 36280795 PMCID: PMC10873809 DOI: 10.1038/s41589-022-01159-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 09/01/2022] [Indexed: 02/04/2023]
Abstract
Ferredoxins comprise a large family of iron-sulfur (Fe-S) proteins that shuttle electrons in diverse biological processes. Human mitochondria contain two isoforms of [2Fe-2S] ferredoxins, FDX1 (aka adrenodoxin) and FDX2, with known functions in cytochrome P450-dependent steroid transformations and Fe-S protein biogenesis. Here, we show that only FDX2, but not FDX1, is involved in Fe-S protein maturation. Vice versa, FDX1 is specific not only for steroidogenesis, but also for heme a and lipoyl cofactor biosyntheses. In the latter pathway, FDX1 provides electrons to kickstart the radical chain reaction catalyzed by lipoyl synthase. We also identified lipoylation as a target of the toxic antitumor copper ionophore elesclomol. Finally, the striking target specificity of each ferredoxin was assigned to small conserved sequence motifs. Swapping these motifs changed the target specificity of these electron donors. Together, our findings identify new biochemical tasks of mitochondrial ferredoxins and provide structural insights into their functional specificity.
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Affiliation(s)
- Vinzent Schulz
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany
| | - Somsuvro Basu
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany
- Freelance Medical Communications Consultant, Brno, Czech Republic
| | - Sven-A Freibert
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany
| | - Holger Webert
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany
| | - Linda Boss
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany
| | - Ulrich Mühlenhoff
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany
| | - Fabien Pierrel
- Univ. of Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, Grenoble, France
| | - Lars-O Essen
- Department of Biochemistry, Faculty of Chemistry, Philipps University of Marburg, Marburg, Germany
| | - Douglas M Warui
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Squire J Booker
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
- The Howard Hughes Medical Institute, The Pennsylvania State University, University Park, PA, USA
| | - Oliver Stehling
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany.
- Centre for Synthetic Microbiology, Synmikro, Marburg, Germany.
| | - Roland Lill
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany.
- Centre for Synthetic Microbiology, Synmikro, Marburg, Germany.
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22
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Schulz V, Freibert SA, Boss L, Mühlenhoff U, Stehling O, Lill R. Mitochondrial [2Fe-2S] ferredoxins: new functions for old dogs. FEBS Lett 2023; 597:102-121. [PMID: 36443530 DOI: 10.1002/1873-3468.14546] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 12/02/2022]
Abstract
Ferredoxins (FDXs) comprise a large family of iron-sulfur proteins that shuttle electrons from NADPH and FDX reductases into diverse biological processes. This review focuses on the structure, function and specificity of mitochondrial [2Fe-2S] FDXs that are related to bacterial FDXs due to their endosymbiotic inheritance. Their classical function in cytochrome P450-dependent steroid transformations was identified around 1960, and is exemplified by mammalian FDX1 (aka adrenodoxin). Thirty years later the essential function in cellular Fe/S protein biogenesis was discovered for the yeast mitochondrial FDX Yah1 that is additionally crucial for the formation of haem a and ubiquinone CoQ6 . In mammals, Fe/S protein biogenesis is exclusively performed by the FDX1 paralog FDX2, despite the high structural similarity of both proteins. Recently, additional and specific roles of human FDX1 in haem a and lipoyl cofactor biosyntheses were described. For lipoyl synthesis, FDX1 transfers electrons to the radical S-adenosyl methionine-dependent lipoyl synthase to kickstart its radical chain reaction. The high target specificity of the two mammalian FDXs is contained within small conserved sequence motifs, that upon swapping change the target selection of these electron donors.
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Affiliation(s)
- Vinzent Schulz
- Institut für Zytobiologie, Philipps-Universität Marburg, Germany.,Zentrum für Synthetische Mikrobiologie Synmikro, Marburg, Germany
| | - Sven-A Freibert
- Institut für Zytobiologie, Philipps-Universität Marburg, Germany.,Zentrum für Synthetische Mikrobiologie Synmikro, Marburg, Germany
| | - Linda Boss
- Institut für Zytobiologie, Philipps-Universität Marburg, Germany.,Zentrum für Synthetische Mikrobiologie Synmikro, Marburg, Germany
| | - Ulrich Mühlenhoff
- Institut für Zytobiologie, Philipps-Universität Marburg, Germany.,Zentrum für Synthetische Mikrobiologie Synmikro, Marburg, Germany
| | - Oliver Stehling
- Institut für Zytobiologie, Philipps-Universität Marburg, Germany.,Zentrum für Synthetische Mikrobiologie Synmikro, Marburg, Germany
| | - Roland Lill
- Institut für Zytobiologie, Philipps-Universität Marburg, Germany.,Zentrum für Synthetische Mikrobiologie Synmikro, Marburg, Germany
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23
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Bauwe H. Photorespiration - Rubisco's repair crew. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153899. [PMID: 36566670 DOI: 10.1016/j.jplph.2022.153899] [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: 11/15/2022] [Revised: 12/11/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
The photorespiratory repair pathway (photorespiration in short) was set up from ancient metabolic modules about three billion years ago in cyanobacteria, the later ancestors of chloroplasts. These prokaryotes developed the capacity for oxygenic photosynthesis, i.e. the use of water as a source of electrons and protons (with O2 as a by-product) for the sunlight-driven synthesis of ATP and NADPH for CO2 fixation in the Calvin cycle. However, the CO2-binding enzyme, ribulose 1,5-bisphosphate carboxylase (known under the acronym Rubisco), is not absolutely selective for CO2 and can also use O2 in a side reaction. It then produces 2-phosphoglycolate (2PG), the accumulation of which would inhibit and potentially stop the Calvin cycle and subsequently photosynthetic electron transport. Photorespiration removes the 2-PG and in this way prevents oxygenic photosynthesis from poisoning itself. In plants, the core of photorespiration consists of ten enzymes distributed over three different types of organelles, requiring interorganellar transport and interaction with several auxiliary enzymes. It goes together with the release and to some extent loss of freshly fixed CO2. This disadvantageous feature can be suppressed by CO2-concentrating mechanisms, such as those that evolved in C4 plants thirty million years ago, which enhance CO2 fixation and reduce 2PG synthesis. Photorespiration itself provided a pioneer variant of such mechanisms in the predecessors of C4 plants, C3-C4 intermediate plants. This article is a review and update particularly on the enzyme components of plant photorespiration and their catalytic mechanisms, on the interaction of photorespiration with other metabolism and on its impact on the evolution of photosynthesis. This focus was chosen because a better knowledge of the enzymes involved and how they are embedded in overall plant metabolism can facilitate the targeted use of the now highly advanced methods of metabolic network modelling and flux analysis. Understanding photorespiration more than before as a process that enables, rather than reduces, plant photosynthesis, will help develop rational strategies for crop improvement.
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Affiliation(s)
- Hermann Bauwe
- University of Rostock, Plant Physiology, Albert-Einstein-Straße 3, D-18051, Rostock, Germany.
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24
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Pantothenate and L-Carnitine Supplementation Improves Pathological Alterations in Cellular Models of KAT6A Syndrome. Genes (Basel) 2022; 13:genes13122300. [PMID: 36553567 PMCID: PMC9778406 DOI: 10.3390/genes13122300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/28/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
Mutations in several genes involved in the epigenetic regulation of gene expression have been considered risk alterations to different intellectual disability (ID) syndromes associated with features of autism spectrum disorder (ASD). Among them are the pathogenic variants of the lysine-acetyltransferase 6A (KAT6A) gene, which causes KAT6A syndrome. The KAT6A enzyme participates in a wide range of critical cellular functions, such as chromatin remodeling, gene expression, protein synthesis, cell metabolism, and replication. In this manuscript, we examined the pathophysiological alterations in fibroblasts derived from three patients harboring KAT6A mutations. We addressed survival in a stress medium, histone acetylation, protein expression patterns, and transcriptome analysis, as well as cell bioenergetics. In addition, we evaluated the therapeutic effectiveness of epigenetic modulators and mitochondrial boosting agents, such as pantothenate and L-carnitine, in correcting the mutant phenotype. Pantothenate and L-carnitine treatment increased histone acetylation and partially corrected protein and transcriptomic expression patterns in mutant KAT6A cells. Furthermore, the cell bioenergetics of mutant cells was significantly improved. Our results suggest that pantothenate and L-carnitine can significantly improve the mutant phenotype in cellular models of KAT6A syndrome.
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25
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Warui D, Sil D, Lee KH, Neti SS, Esakova OA, Knox HL, Krebs C, Booker SJ. In Vitro Demonstration of Human Lipoyl Synthase Catalytic Activity in the Presence of NFU1. ACS BIO & MED CHEM AU 2022; 2:456-468. [PMID: 36281303 PMCID: PMC9585516 DOI: 10.1021/acsbiomedchemau.2c00020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lipoyl synthase (LS) catalyzes the last step in the biosynthesis of the lipoyl cofactor, which is the attachment of sulfur atoms at C6 and C8 of an n-octanoyllysyl side chain of a lipoyl carrier protein (LCP). The protein is a member of the radical S-adenosylmethionine (SAM) superfamily of enzymes, which use SAM as a precursor to a 5'-deoxyadenosyl 5'-radical (5'-dA·). The role of the 5'-dA· in the LS reaction is to abstract hydrogen atoms from C6 and C8 of the octanoyl moiety of the substrate to initiate subsequent sulfur attachment. All radical SAM enzymes have at least one [4Fe-4S] cluster that is used in the reductive cleavage of SAM to generate the 5'-dA·; however, LSs contain an additional auxiliary [4Fe-4S] cluster from which sulfur atoms are extracted during turnover, leading to degradation of the cluster. Therefore, these enzymes catalyze only 1 turnover in the absence of a system that restores the auxiliary cluster. In Escherichia coli, the auxiliary cluster of LS can be regenerated by the iron-sulfur (Fe-S) cluster carrier protein NfuA as fast as catalysis takes place, and less efficiently by IscU. NFU1 is the human ortholog of E. coli NfuA and has been shown to interact directly with human LS (i.e., LIAS) in yeast two-hybrid analyses. Herein, we show that NFU1 and LIAS form a tight complex in vitro and that NFU1 can efficiently restore the auxiliary cluster of LIAS during turnover. We also show that BOLA3, previously identified as being critical in the biosynthesis of the lipoyl cofactor in humans and Saccharomyces cerevisiae, has no direct effect on Fe-S cluster transfer from NFU1 or GLRX5 to LIAS. Further, we show that ISCA1 and ISCA2 can enhance LIAS turnover, but only slightly.
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Affiliation(s)
- Douglas
M. Warui
- Department
of Chemistry and Biochemistry and Molecular Biology and the Howard Hughes
Medical Institute, The Pennsylvania State
University, University
Park, Pennsylvania 16802, United States
| | - Debangsu Sil
- Department
of Chemistry and Biochemistry and Molecular Biology and the Howard Hughes
Medical Institute, The Pennsylvania State
University, University
Park, Pennsylvania 16802, United States
| | - Kyung-Hoon Lee
- Department
of Chemistry and Biochemistry and Molecular Biology and the Howard Hughes
Medical Institute, The Pennsylvania State
University, University
Park, Pennsylvania 16802, United States
| | - Syam Sundar Neti
- Department
of Chemistry and Biochemistry and Molecular Biology and the Howard Hughes
Medical Institute, The Pennsylvania State
University, University
Park, Pennsylvania 16802, United States
| | - Olga A. Esakova
- Department
of Chemistry and Biochemistry and Molecular Biology and the Howard Hughes
Medical Institute, The Pennsylvania State
University, University
Park, Pennsylvania 16802, United States
| | - Hayley L. Knox
- Department
of Chemistry and Biochemistry and Molecular Biology and the Howard Hughes
Medical Institute, The Pennsylvania State
University, University
Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department
of Chemistry and Biochemistry and Molecular Biology and the Howard Hughes
Medical Institute, The Pennsylvania State
University, University
Park, Pennsylvania 16802, United States
| | - Squire J. Booker
- Department
of Chemistry and Biochemistry and Molecular Biology and the Howard Hughes
Medical Institute, The Pennsylvania State
University, University
Park, Pennsylvania 16802, United States
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26
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Neti SS, Sil D, Warui DM, Esakova OA, Solinski AE, Serrano DA, Krebs C, Booker SJ. Characterization of LipS1 and LipS2 from Thermococcus kodakarensis: Proteins Annotated as Biotin Synthases, which Together Catalyze Formation of the Lipoyl Cofactor. ACS BIO & MED CHEM AU 2022; 2:509-520. [PMID: 36281299 PMCID: PMC9585515 DOI: 10.1021/acsbiomedchemau.2c00018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 11/28/2022]
Abstract
Lipoic acid is an eight-carbon sulfur-containing biomolecule that functions primarily as a cofactor in several multienzyme complexes. It is biosynthesized as an attachment to a specific lysyl residue on one of the subunits of these multienzyme complexes. In Escherichia coli and many other organisms, this biosynthetic pathway involves two dedicated proteins: octanoyltransferase (LipB) and lipoyl synthase (LipA). LipB transfers an n-octanoyl chain from the octanoyl-acyl carrier protein to the target lysyl residue, and then, LipA attaches two sulfur atoms (one at C6 and one at C8) to give the final lipoyl cofactor. All classical lipoyl synthases (LSs) are radical S-adenosylmethionine (SAM) enzymes, which use an [Fe4S4] cluster to reductively cleave SAM to generate a 5'-deoxyadenosyl 5'-radical. Classical LSs also contain a second [Fe4S4] cluster that serves as the source of both appended sulfur atoms. Recently, a novel pathway for generating the lipoyl cofactor was reported. This pathway replaces the canonical LS with two proteins, LipS1 and LipS2, which act together to catalyze formation of the lipoyl cofactor. In this work, we further characterize LipS1 and LipS2 biochemically and spectroscopically. Although LipS1 and LipS2 were previously annotated as biotin synthases, we show that both proteins, unlike E. coli biotin synthase, contain two [Fe4S4] clusters. We identify the cluster ligands to both iron-sulfur clusters in both proteins and show that LipS2 acts only on an octanoyl-containing substrate, while LipS1 acts only on an 8-mercaptooctanoyl-containing substrate. Therefore, similarly to E. coli biotin synthase and in contrast to E. coli LipA, sulfur attachment takes place initially at the terminal carbon (C8) and then at the C6 methylene carbon.
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Affiliation(s)
- Syam Sundar Neti
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Debangsu Sil
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Douglas M. Warui
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Olga A. Esakova
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Amy E. Solinski
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Dante A. Serrano
- Department
of Biochemistry and Molecular Biology, The
Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department
of Biochemistry and Molecular Biology, The
Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Squire J. Booker
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department
of Biochemistry and Molecular Biology, The
Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Howard
Hughes
Medical Institute, The Pennsylvania State
University, University
Park, Pennsylvania 16802, United States
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27
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Chatterjee S, Hausinger RP. Sulfur incorporation into biomolecules: recent advances. Crit Rev Biochem Mol Biol 2022; 57:461-476. [PMID: 36403141 PMCID: PMC10192010 DOI: 10.1080/10409238.2022.2141678] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/05/2022] [Accepted: 10/26/2022] [Indexed: 11/21/2022]
Abstract
Sulfur is an essential element for a variety of cellular constituents in all living organisms and adds considerable functionality to a wide range of biomolecules. The pathways for incorporating sulfur into central metabolites of the cell such as cysteine, methionine, cystathionine, and homocysteine have long been established. Furthermore, the importance of persulfide intermediates during the biosynthesis of thionucleotide-containing tRNAs, iron-sulfur clusters, thiamin diphosphate, and the molybdenum cofactor are well known. This review briefly surveys these topics while emphasizing more recent aspects of sulfur metabolism that involve unconventional biosynthetic pathways. Sacrificial sulfur transfers from protein cysteinyl side chains to precursors of thiamin and the nickel-pincer nucleotide (NPN) cofactor are described. Newer aspects of synthesis for lipoic acid, biotin, and other compounds are summarized, focusing on the requisite iron-sulfur cluster destruction. Sulfur transfers by using a noncore sulfide ligand bound to a [4Fe-4S] cluster are highlighted for generating certain thioamides and for alternative biosynthetic pathways of thionucleotides and the NPN cofactor. Thioamide formation by activating an amide oxygen atom via phosphorylation also is illustrated. The discussion of these topics stresses the chemical reaction mechanisms of the transformations and generally avoids comments on the gene/protein nomenclature or the sources of the enzymes. This work sets the stage for future efforts to decipher the diverse mechanisms of sulfur incorporation into biological molecules.
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Affiliation(s)
- Shramana Chatterjee
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Robert P. Hausinger
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA
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28
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Abstract
Covering: up to 2022The report provides a broad approach to deciphering the evolution of coenzyme biosynthetic pathways. Here, these various pathways are analyzed with respect to the coenzymes required for this purpose. Coenzymes whose biosynthesis relies on a large number of coenzyme-mediated reactions probably appeared on the scene at a later stage of biological evolution, whereas the biosyntheses of pyridoxal phosphate (PLP) and nicotinamide (NAD+) require little additional coenzymatic support and are therefore most likely very ancient biosynthetic pathways.
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Affiliation(s)
- Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, D-30167 Hannover, Germany.
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29
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A Lipoate-Protein Ligase Is Required for De Novo Lipoyl-Protein Biosynthesis in the Hyperthermophilic Archaeon Thermococcus kodakarensis. Appl Environ Microbiol 2022; 88:e0064422. [PMID: 35736229 PMCID: PMC9275244 DOI: 10.1128/aem.00644-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Lipoic acid is an organosulfur cofactor essential for several key enzyme complexes in oxidative and one-carbon metabolism. It is covalently bound to the lipoyl domain of the E2 subunit in some 2-oxoacid dehydrogenase complexes and the H-protein in the glycine cleavage system. Lipoate-protein ligase (Lpl) is involved in the salvage of exogenous lipoate and attaches free lipoate to the E2 subunit or the H-protein in an ATP-dependent manner. In the hyperthermophilic archaeon Thermococcus kodakarensis, TK1234 and TK1908 are predicted to encode the N- and C-terminal regions of Lpl, respectively. TK1908 and TK1234 recombinant proteins form a heterodimer and together displayed significant ligase activity toward octanoate in addition to lipoate when a chemically synthesized octapeptide was used as the acceptor. The proteins also displayed activity toward other fatty acids, indicating broad fatty acid specificity. On the other hand, lipoyl synthase from T. kodakarensis only recognized octanoyl-peptide as a substrate. Examination of individual proteins indicated that the TK1908 protein alone was able to catalyze the ligase reaction although with a much lower activity. Gene disruption of TK1908 led to lipoate/serine auxotrophy, whereas TK1234 gene deletion did not. Acyl carrier protein homologs are not found on the archaeal genomes, and the TK1908/TK1234 protein complex did not utilize octanoyl-CoA, raising the possibility that the substrate of the ligase reaction is octanoic acid itself. Although Lpl has been considered as an enzyme involved in lipoate salvage, the results imply that in T. kodakarensis, the TK1908 and TK1234 proteins function in de novo lipoyl-protein biosynthesis. IMPORTANCE Based on previous studies in bacteria and eukaryotes, lipoate-protein ligases (Lpls) have been considered to be involved exclusively in lipoate salvage. The genetic analyses in this study on the lipoate-protein ligase in T. kodakarensis, however, suggest otherwise and that the enzyme is additionally involved in de novo protein lipoylation. We also provide biochemical evidence that the lipoate-protein ligase displays broad substrate specificity and is capable of ligating acyl groups of various chain-lengths to the peptide substrate. We show that this apparent ambiguity in Lpl is resolved by the strict substrate specificity of the lipoyl synthase LipS in this organism, which only recognizes octanoyl-peptide. The results provide relevant physiological insight into archaeal protein lipoylation.
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30
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Martins-Noguerol R, Acket S, Troncoso-Ponce MA, Garcés R, Venegas-Calerón M, Salas JJ, Martínez-Force E, Moreno-Pérez AJ. Characterization and impact of sunflower plastidial octanoyltransferases (Helianthus annuus L.) on oil composition. JOURNAL OF PLANT PHYSIOLOGY 2022; 274:153730. [PMID: 35623270 DOI: 10.1016/j.jplph.2022.153730] [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: 03/24/2022] [Revised: 05/11/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Prosthetic lipoyl groups are essential for the metabolic activity of several multienzyme complexes in most organisms. In plants, octanoyltransferase (LIP2) and lipoyl synthase (LIP1) enzymes in the mitochondria and plastids participate in the de novo synthesis of lipoic acid, and in the attachment of the lipoyl cofactors to their specific targets. In plastids, the lipoylated pyruvate dehydrogenase complex catalyzes the synthesis of the acetyl-CoA that is required for de novo fatty acid synthesis. Since lipoic acid transport across plastid membranes has not been demonstrated, these organelles require specific plastidial LIP1 and LIP2 activities for the in situ synthesis of this cofactor. Previously, one essential LIP1 enzyme and two redundant LIP2 enzymes have been identified within Arabidopsis chloroplasts. In this study, two plastidial sunflower (Helianthus annuus L.) LIP2 genes (HaLIP2p1 and HaLIP2p2) were identified, cloned and characterized. The expression of these genes in different tissues was studied and the tertiary structure of the peptides they encode was modeled by protein docking. These genes were overexpressed in Escherichia coli and their impact on bacterial fatty acid synthesis was studied. Finally, transgenic Arabidopsis plants overexpressing HaLIP2p1 were generated and their seed lipid profiles analyzed. The lipid composition of the transgenic seeds, particularly their TAG species, differed from that of wild-type plants, revealing a relationship between lipoic acid synthesis and the accumulation of storage lipids in Arabidopsis seeds.
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Affiliation(s)
- Raquel Martins-Noguerol
- Instituto de la Grasa-CSIC, Building 46, UPO Campus, Ctra. de Utrera km 1, 41013, Seville, Spain; Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Sebastien Acket
- Université de Technologie de Compiègne, Génie Enzymatique et Cellulaire (GEC), UMR-CNRS 7025, CS 60319, 60203, Compiègne Cedex, France
| | - Manuel Adrián Troncoso-Ponce
- Université de Technologie de Compiègne, Génie Enzymatique et Cellulaire (GEC), UMR-CNRS 7025, CS 60319, 60203, Compiègne Cedex, France
| | - Rafael Garcés
- Instituto de la Grasa-CSIC, Building 46, UPO Campus, Ctra. de Utrera km 1, 41013, Seville, Spain
| | - Mónica Venegas-Calerón
- Instituto de la Grasa-CSIC, Building 46, UPO Campus, Ctra. de Utrera km 1, 41013, Seville, Spain
| | - Joaquín J Salas
- Instituto de la Grasa-CSIC, Building 46, UPO Campus, Ctra. de Utrera km 1, 41013, Seville, Spain
| | - Enrique Martínez-Force
- Instituto de la Grasa-CSIC, Building 46, UPO Campus, Ctra. de Utrera km 1, 41013, Seville, Spain
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31
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Lipoate protein ligase B primarily recognizes the C 8-phosphopantetheine arm of its donor substrate and weakly binds the acyl carrier protein. J Biol Chem 2022; 298:102203. [PMID: 35764173 PMCID: PMC9307952 DOI: 10.1016/j.jbc.2022.102203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/22/2022] [Accepted: 06/22/2022] [Indexed: 11/22/2022] Open
Abstract
Lipoic acid is a sulfur containing cofactor indispensable for the function of several metabolic enzymes. In microorganisms, lipoic acid can be salvaged from the surroundings by Lipoate protein ligase A (LplA), an ATP-dependent enzyme. Alternatively, it can be synthesized by the sequential actions of Lipoate protein ligase B (LipB) and Lipoyl synthase (LipA). LipB takes up the octanoyl chain from C8-acyl carrier protein (C8-ACP), a byproduct of the type II fatty acid synthesis pathway, and transfers it to a conserved lysine of the lipoyl domain of a dehydrogenase. However, the molecular basis of its substrate recognition is still not fully understood. Using E. coli LipB as a model enzyme, we show here that the octanoyl-transferase mainly recognizes the 4'-phosphopantetheine-tethered acyl-chain of its donor substrate and weakly binds the apo-acyl carrier protein. We demonstrate LipB can accept octanoate from its own ACP and noncognate ACPs, as well as C8-CoA. Furthermore, our 1H STD and 31P NMR studies demonstrate the binding of adenosine, as well as the phosphopantetheine arm of CoA to LipB, akin to binding to LplA. Finally, we show a conserved 71RGG73 loop, analogous to the lipoate binding loop of LplA, is required for full LipB activity. Collectively, our studies highlight commonalities between LipB and LplA in their mechanism of substrate recognition. This knowledge could be of significance in the treatment of mitochondrial fatty acid synthesis related disorders.
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Jo HG, Adidjaja JJ, Kim DK, Park BS, Lee N, Cho BK, Kim HU, Oh MK. Comparative genomic analysis of Streptomyces rapamycinicus NRRL 5491 and its mutant overproducing rapamycin. Sci Rep 2022; 12:10302. [PMID: 35717543 PMCID: PMC9206652 DOI: 10.1038/s41598-022-14199-6] [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: 01/02/2022] [Accepted: 06/02/2022] [Indexed: 12/04/2022] Open
Abstract
Streptomyces rapamycinicus NRRL 5491 is a well-known producer of rapamycin, a secondary metabolite with useful bioactivities, including antifungal, antitumor, and immunosuppressive functions. For the enhanced rapamycin production, a rapamycin-overproducing strain SRMK07 was previously obtained as a result of random mutagenesis. To identify genomic changes that allowed the SRMK07 strain’s enhanced rapamycin production, genomes of the NRRL 5491 and SRMK07 strains were newly sequenced in this study. The resulting genome sequences of the wild-type and SRMK07 strains showed the size of 12.47 Mbp and 9.56 Mbp, respectively. Large deletions were observed at both end regions of the SRMK07 strain’s genome, which cover 17 biosynthetic gene clusters (BGCs) encoding secondary metabolites. Also, genes in a genomic region containing the rapamycin BGC were shown to be duplicated. Finally, comparative metabolic network analysis using these two strains’ genome-scale metabolic models revealed biochemical reactions with different metabolic fluxes, which were all associated with NADPH generation. Taken together, the genomic and computational approaches undertaken in this study suggest biological clues for the enhanced rapamycin production of the SRMK07 strain. These clues can also serve as a basis for systematic engineering of a production host for further enhanced rapamycin production.
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Affiliation(s)
- Hee-Geun Jo
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Joshua Julio Adidjaja
- Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Do-Kyung Kim
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Bu-Soo Park
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Namil Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering (BK21 Four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
| | - Min-Kyu Oh
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea.
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Meireles DA, da Silva Neto JF, Domingos RM, Alegria TGP, Santos LCM, Netto LES. Ohr - OhrR, a neglected and highly efficient antioxidant system: Structure, catalysis, phylogeny, regulation, and physiological roles. Free Radic Biol Med 2022; 185:6-24. [PMID: 35452809 DOI: 10.1016/j.freeradbiomed.2022.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 03/09/2022] [Accepted: 04/02/2022] [Indexed: 12/24/2022]
Abstract
Ohrs (organic hydroperoxide resistance proteins) are antioxidant enzymes that play central roles in the response of microorganisms to organic peroxides. Here, we describe recent advances in the structure, catalysis, phylogeny, regulation, and physiological roles of Ohr proteins and of its transcriptional regulator, OhrR, highlighting their unique features. Ohr is extremely efficient in reducing fatty acid peroxides and peroxynitrite, two oxidants relevant in host-pathogen interactions. The highly reactive Cys residue of Ohr, named peroxidatic Cys (Cp), composes together with an arginine and a glutamate the catalytic triad. The catalytic cycle of Ohrs involves a condensation between a sulfenic acid (Cp-SOH) and the thiol of the second conserved Cys, leading to the formation of an intra-subunit disulfide bond, which is then reduced by dihydrolipoamide or lipoylated proteins. A structural switch takes place during catalysis, with the opening and closure of the active site by the so-called Arg-loop. Ohr is part of the Ohr/OsmC super-family that also comprises OsmC and Ohr-like proteins. Members of the Ohr, OsmC and Ohr-like subgroups present low sequence similarities among themselves, but share a high structural conservation, presenting two Cys residues in their active site. The pattern of gene expression is also distinct among members of the Ohr/OsmC subfamilies. The expression of ohr genes increases upon organic hydroperoxides treatment, whereas the signals for the upregulation of osmC are entry into the stationary phase and/or osmotic stress. For many ohr genes, the upregulation by organic hydroperoxides is mediated by OhrR, a Cys-based transcriptional regulator that only binds to its target DNAs in its reduced state. Since Ohrs and OhrRs are involved in virulence of some microorganisms and are absent in vertebrate and vascular plants, they may represent targets for novel therapeutic approaches based on the disruption of this key bacterial organic peroxide defense system.
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Affiliation(s)
- Diogo A Meireles
- Laboratório de Fisiologia e Bioquímica de Microrganismos (LFBM) da Universidade Estadual do Norte Fluminense Darcy Ribeiro, Brazil
| | - José F da Silva Neto
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos da Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo (FMRP-USP), Brazil
| | | | - Thiago G P Alegria
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Brazil
| | - Lene Clara M Santos
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Brazil
| | - Luis Eduardo S Netto
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Brazil.
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Jeyachandran VR, Boal AK. Structural insights into auxiliary cofactor usage by radical S-adenosylmethionine enzymes. Curr Opin Chem Biol 2022; 68:102153. [PMID: 35512465 DOI: 10.1016/j.cbpa.2022.102153] [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: 12/31/2021] [Revised: 03/22/2022] [Accepted: 03/28/2022] [Indexed: 11/03/2022]
Abstract
Radical S-adenosylmethionine (SAM) enzymes use a common catalytic core for diverse transformations. While all radical SAM enzymes bind a Fe4S4 cluster via a characteristic tri-cysteine motif, many bind additional metal cofactors. Recently reported structures of radical SAM enzymes that use methylcobalamin or additional iron-sulfur clusters as cosubstrates show that these auxiliary units are anchored by N- and C-terminal domains that vary significantly in size and topology. Despite this architectural diversity, all use a common surface for auxiliary cofactor docking. In the sulfur insertion and metallocofactor assembly systems evaluated here, interaction with iron-sulfur cluster assembly proteins or downstream scaffold proteins is an important component of catalysis. Structures of these complexes represent important new frontiers in structural analysis of radical SAM enzymes.
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Affiliation(s)
- Vivian Robert Jeyachandran
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Amie K Boal
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA; Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.
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Scattolini A, Lavatelli A, Vacchina P, Lambruschi DA, Mansilla MC, Uttaro AD. Functional characterization of the first lipoyl-relay pathway from a parasitic protozoan. Mol Microbiol 2022; 117:1352-1365. [PMID: 35484915 DOI: 10.1111/mmi.14913] [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: 06/28/2021] [Revised: 04/25/2022] [Accepted: 04/25/2022] [Indexed: 11/30/2022]
Abstract
Lipoic acid (LA) is a sulfur-containing cofactor covalently attached to key enzymes of central metabolism in prokaryotes and eukaryotes. LA can be acquired by scavenging, mediated by a lipoate ligase, or de novo synthesized by a pathway requiring an octanoyltransferase and a lipoate synthase. A more complex pathway, referred to as "lipoyl-relay", requires two additional proteins, GcvH, the glycine cleavage system H subunit, and an amidotransferase. This route was described so far in Bacillus subtilis and related Gram positive bacteria, Saccharomyces cerevisiae, Homo sapiens and Caenorhabditis elegans. Using collections of S. cerevisiae and B. subtilis mutants, defective in LA metabolism, we gathered evidence that allow us to propose for the first time that lipoyl-relay pathways are also present in parasitic protozoa. By a reverse genetic approach, we assigned octanoyltransferase and amidotransferase activity to the products of Tb927.11.9390 (TblipT) and Tb927.8.630 (TblipL) genes of Trypanosoma brucei, respectively. The B. subtilis model allowed us to identify the parasite amidotransferase as the target of lipoate analogues like 8-bromo octanoic acid, explaining the complete loss of protein lipoylation and growth impairment caused by this compound in T. cruzi. This model could be instrumental for the screening of selective and more efficient chemotherapies against trypanosomiases.
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Affiliation(s)
- Albertina Scattolini
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas.,Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario. Ocampo y Esmeralda, Predio CONICET (S2000FHQ) Rosario, Argentina
| | - Antonela Lavatelli
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas.,Consejo Superior de Investigaciones Científicas, Centre for Research in Agricultural Genomics
| | - Paola Vacchina
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas
| | - Daniel A Lambruschi
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas
| | - María C Mansilla
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas.,Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario. Ocampo y Esmeralda, Predio CONICET (S2000FHQ) Rosario, Argentina
| | - Antonio D Uttaro
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas.,Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario. Ocampo y Esmeralda, Predio CONICET (S2000FHQ) Rosario, Argentina
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Chang LC, Chiang SK, Chen SE, Hung MC. Targeting 2-oxoglutarate dehydrogenase for cancer treatment. Am J Cancer Res 2022; 12:1436-1455. [PMID: 35530286 PMCID: PMC9077069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/02/2022] [Indexed: 06/14/2023] Open
Abstract
Tricarboxylic acid (TCA) cycle, also called Krebs cycle or citric acid cycle, is an amphoteric pathway, contributing to catabolic degradation and anaplerotic reactions to supply precursors for macromolecule biosynthesis. Oxoglutarate dehydrogenase complex (OGDHc, also called α-ketoglutarate dehydrogenase) a highly regulated enzyme in TCA cycle, converts α-ketoglutarate (αKG) to succinyl-Coenzyme A in accompany with NADH generation for ATP generation through oxidative phosphorylation. The step collaborates with glutaminolysis at an intersectional point to govern αKG levels for energy production, nucleotide and amino acid syntheses, and the resources for macromolecule synthesis in cancer cells with rapid proliferation. Despite being a flavoenzyme susceptible to electron leakage contributing to mitochondrial reactive oxygen species (ROS) production, OGDHc is highly sensitive to peroxides such as HNE (4-hydroxy-2-nonenal) and moreover, its activity mediates the activation of several antioxidant pathways. The characteristics endow OGDHc as a critical redox sensor in mitochondria. Accumulating evidences suggest that dysregulation of OGDHc impairs cellular redox homeostasis and disturbs substrate fluxes, leading to a buildup of oncometabolites along the pathogenesis and development of cancers. In this review, we describe molecular interactions, regulation of OGDHc expression and activity and its relationships with diseases, specifically focusing on cancers. In the end, we discuss the potential of OGDHs as a therapeutic target for cancer treatment.
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Affiliation(s)
- Ling-Chu Chang
- Center for Molecular Medicine, China Medical University Hospital, China Medical UniversityTaichung 404, Taiwan
| | - Shih-Kai Chiang
- Department of Animal Science, National Chung Hsing UniversityTaichung 40227, Taiwan
| | - Shuen-Ei Chen
- Department of Animal Science, National Chung Hsing UniversityTaichung 40227, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing UniversityTaichung 40227, Taiwan
- Innovation and Development Center of Sustainable Agriculture (IDCSA), National Chung Hsing UniversityTaiwan
- Research Center for Sustainable Energy and Nanotechnology, National Chung Hsing UniversityTaichung 40227, Taiwan
| | - Mien-Chie Hung
- Center for Molecular Medicine, China Medical University Hospital, China Medical UniversityTaichung 404, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical UniversityTaichung 404, Taiwan
- Deparment of Biotechnology, Asia UniversityTaichung 413, Taiwan
- Research Center for Cancer Biology, China Medical UniversityTaichung 404, Taiwan
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Przybyla-Toscano J, Maclean AE, Franceschetti M, Liebsch D, Vignols F, Keech O, Rouhier N, Balk J. Protein lipoylation in mitochondria requires Fe-S cluster assembly factors NFU4 and NFU5. PLANT PHYSIOLOGY 2022; 188:997-1013. [PMID: 34718778 PMCID: PMC8825329 DOI: 10.1093/plphys/kiab501] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 09/30/2021] [Indexed: 05/27/2023]
Abstract
Plants have evolutionarily conserved NifU (NFU)-domain proteins that are targeted to plastids or mitochondria. "Plastid-type" NFU1, NFU2, and NFU3 in Arabidopsis (Arabidopsis thaliana) play a role in iron-sulfur (Fe-S) cluster assembly in this organelle, whereas the type-II NFU4 and NFU5 proteins have not been subjected to mutant studies in any plant species to determine their biological role. Here, we confirmed that NFU4 and NFU5 are targeted to the mitochondria. The proteins were constitutively produced in all parts of the plant, suggesting a housekeeping function. Double nfu4 nfu5 knockout mutants were embryonic lethal, and depletion of NFU4 and NFU5 proteins led to growth arrest of young seedlings. Biochemical analyses revealed that NFU4 and NFU5 are required for lipoylation of the H proteins of the glycine decarboxylase complex and the E2 subunits of other mitochondrial dehydrogenases, with little impact on Fe-S cluster-containing respiratory complexes or aconitase. Consequently, the Gly-to-Ser ratio was increased in mutant seedlings and early growth improved with elevated CO2 treatment. In addition, pyruvate, 2-oxoglutarate, and branched-chain amino acids accumulated in nfu4 nfu5 mutants, further supporting defects in the other three mitochondrial lipoate-dependent enzyme complexes. NFU4 and NFU5 interacted with mitochondrial lipoyl synthase (LIP1) in yeast 2-hybrid and bimolecular fluorescence complementation assays. These data indicate that NFU4 and NFU5 have a more specific function than previously thought, most likely providing Fe-S clusters to lipoyl synthase.
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Affiliation(s)
| | - Andrew E Maclean
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, UK
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | | | - Daniela Liebsch
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umeå, Sweden
| | - Florence Vignols
- BPMP, Université de Montpellier, CNRS, INRAE, SupAgro, F-34060 Montpellier, France
| | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, S-90187 Umeå, Sweden
| | | | - Janneke Balk
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, UK
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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Disruption of the adh (acetoin dehydrogenase) operon has wide-ranging effects on Streptococcus mutans growth and stress response. J Bacteriol 2022; 204:e0057821. [PMID: 35007154 DOI: 10.1128/jb.00578-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The agent largely responsible for initiating dental caries, Streptococcus mutans produces acetoin dehydrogenase that is encoded by the adh operon. The operon consists of the adhA and B genes (E1 dehydrogenase), adhC (E2 lipoylated transacetylase), adhD (E3 dihydrolipoamide dehydrogenase), and lplA (lipoyl ligase). Evidence is presented that AdhC interacts with SpxA2, a redox-sensitive transcription factor functioning in cell wall and oxidative stress responses. In-frame deletion mutations of adh genes conferred oxygen-dependent sensitivity to slightly alkaline pH (pH 7.2-7.6), within the range of values observed in human saliva. Growth defects were also observed when glucose or sucrose served as major carbon sources. A deletion of the adhC orthologous gene, acoC gene of Streptococcus gordonii, did not result in pH sensitivity or defective growth in glucose and sucrose. The defects observed in adh mutants were partially reversed by addition of pyruvate. Unlike most 2-oxoacid dehydrogenases, the E3 AdhD subunit bears an N-terminal lipoylation domain nearly identical to that of E2 AdhC. Changing the lipoyl domains of AdhC and AdhD by replacing the lipoate attachment residue, lysine to arginine, caused no significant reduction in pH sensitivity but the adhDK43R mutation eliminating the lipoylation site resulted in an observable growth defect in glucose medium. The adh mutations were partially suppressed by a deletion of rex, encoding an NAD+/NADH-sensing transcription factor that represses genes functioning in fermentation. spxA2 adh double mutants show synthetic growth restriction at elevated pH and upon ampicillin treatment. These results suggest a role for Adh in stress management in S. mutans. IMPORTANCE Dental caries is often initiated by Streptococcus mutans, which establishes a biofilm and a low pH environment on tooth enamel surfaces. The current study has uncovered vulnerabilities of S. mutans mutant strains that are unable to produce the enzyme complex, acetoin dehydrogenase (Adh). Such mutants are sensitive to modest increases in pH to 7.2-7.6, within the range of human saliva, while a mutant of a commensal Streptococcal species is resistant. The S. mutans adh strains are also defective in carbohydrate utilization and are hypersensitive to a cell wall-acting antibiotic. The studies suggest that Adh could be a potential target for interfering with S. mutans colonization of the oral environment.
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Understanding and Engineering Glycine Cleavage System and Related Metabolic Pathways for C1-Based Biosynthesis. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2022; 180:273-298. [DOI: 10.1007/10_2021_186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Martins-Noguerol R, Acket S, Troncoso-Ponce MA, Garcés R, Thomasset B, Venegas-Calerón M, Salas JJ, Martínez-Force E, Moreno-Pérez AJ. Characterization of Helianthus annuus Lipoic Acid Biosynthesis: The Mitochondrial Octanoyltransferase and Lipoyl Synthase Enzyme System. FRONTIERS IN PLANT SCIENCE 2021; 12:781917. [PMID: 34868183 PMCID: PMC8639206 DOI: 10.3389/fpls.2021.781917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/26/2021] [Indexed: 05/03/2023]
Abstract
Lipoic acid (LA, 6,8-dithiooctanoic acid) is a sulfur containing coenzyme essential for the activity of several key enzymes involved in oxidative and single carbon metabolism in most bacteria and eukaryotes. LA is synthetized by the concerted activity of the octanoyltransferase (LIP2, EC 2.3.1.181) and lipoyl synthase (LIP1, EC 2.8.1.8) enzymes. In plants, pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase or glycine decarboxylase are essential complexes that need to be lipoylated. These lipoylated enzymes and complexes are located in the mitochondria, while PDH is also present in plastids where it provides acetyl-CoA for de novo fatty acid biosynthesis. As such, lipoylation of PDH could regulate fatty acid synthesis in both these organelles. In the present work, the sunflower LIP1 and LIP2 genes (HaLIP1m and HaLIP2m) were isolated sequenced, cloned, and characterized, evaluating their putative mitochondrial location. The expression of these genes was studied in different tissues and protein docking was modeled. The genes were also expressed in Escherichia coli and Arabidopsis thaliana, where their impact on fatty acid and glycerolipid composition was assessed. Lipidomic studies in Arabidopsis revealed lipid remodeling in lines overexpressing these enzymes and the involvement of both sunflower proteins in the phenotypes observed is discussed in the light of the results obtained.
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Affiliation(s)
- Raquel Martins-Noguerol
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Sébastien Acket
- UPJV, UMR CNRS 7025, Enzyme and Cell Engineering, Centre de Recherche Royallieu, Université de Technologie de Compiègne, Compiègne, France
| | - M. Adrián Troncoso-Ponce
- UPJV, UMR CNRS 7025, Enzyme and Cell Engineering, Centre de Recherche Royallieu, Université de Technologie de Compiègne, Compiègne, France
| | | | - Brigitte Thomasset
- UPJV, UMR CNRS 7025, Enzyme and Cell Engineering, Centre de Recherche Royallieu, Université de Technologie de Compiègne, Compiègne, France
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Mishra A, Gupta J, Kumari T, Pal R, Thakur IS. Unravelling the attributes of novel cyanobacteria Jacksonvillea sp. ISTCYN1 by draft genome sequencing. BIORESOURCE TECHNOLOGY 2021; 337:125473. [PMID: 34320753 DOI: 10.1016/j.biortech.2021.125473] [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: 05/16/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Filamentous cyanobacteria, Jacksonvillea sp. ISTCYN1 was isolated from agriculture field and cultured in BG-11 medium. This study, report the genome sequence of cyanobacteria Jacksonvillea thatto the best of our knowledgeis the firstgenome sequenceof thisgenus. The 5.7 MB draft genome sequence of this cyanobacterium contains 5134 protein-coding genes. The phylogenetic tree was constructed based on genome and Desertifilum sp. IPPAS B-1220 validated the closest relationship with Jacksonvillea sp. ISTCYN1. The growth of strain ISTCYN1 has been reported in the presence of different types of plastic when used as a sole carbon source. SEM analysis revealed biofilm formation by cyanobacterial strain ISTCYN1 on the surface of high and low-density polyethylene and polypropylene. In the presence of these plastics, EPS production has also been reported by this strain. Whole genome sequence analysis reveals the presence of many genes involved in biofilm formation. The presence of key enzymes responsible for plastic degradation laccase, esterase, lipase, thioesterase, and peroxidase have been predicted in the genome analysis. Genome analysis also provides insight into the genes involved in biotin biosynthetic pathways. Furthermore, the presence of many selenoproteins reveals the selenium acquisition by this cyanobacterium.
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Affiliation(s)
- Arti Mishra
- Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Sector-125, Noida 201303, India
| | - Juhi Gupta
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Taruna Kumari
- Department of Statistics, University of Delhi, New Delhi 110007, India
| | - Ruchita Pal
- Advanced Instrumentation Research Facility, Jawaharlal Nehru University, New Delhi 110067, India
| | - I S Thakur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India.
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Theodosis-Nobelos P, Papagiouvannis G, Tziona P, Rekka EA. Lipoic acid. Kinetics and pluripotent biological properties and derivatives. Mol Biol Rep 2021; 48:6539-6550. [PMID: 34420148 DOI: 10.1007/s11033-021-06643-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/10/2021] [Indexed: 12/14/2022]
Abstract
Lipoic acid (LA) is globally known and its supplements are widely used. Despite its importance for the organism it is not considered a vitamin any more. The multiple metabolic forms and the differences in kinetics (absorption, distribution and excretion), as well as the actions of its enantiomers are analysed in the present article together with its biosynthetic path. The proteins involved in the transfer, biotransformation and activity of LA are mentioned. Furthermore, the safety and the toxicological profile of the compound are commented, together with its stability issues. Mechanisms of lipoic acid intervention in the human body are analysed considering the antioxidant and non-antioxidant characteristics of the compound. The chelating properties, the regenerative ability of other antioxidants, the co-enzyme activity and the signal transduction by the implication in various pathways will be discussed in order to be elucidated the pleiotropic effects of LA. Finally, lipoic acid integrating analogues are mentioned under the scope of the multiple pharmacological actions they acquire towards degenerative conditions.
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Affiliation(s)
| | - Georgios Papagiouvannis
- Department of Pharmacy, School of Health Sciences, Frederick University, 1036, Nicosia, Cyprus
| | - Paraskevi Tziona
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotelian University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Eleni A Rekka
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotelian University of Thessaloniki, 54124, Thessaloniki, Greece
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Biochemical Approaches to Probe the Role of the Auxiliary Iron-Sulfur Cluster of Lipoyl Synthase from Mycobacterium Tuberculosis. Methods Mol Biol 2021. [PMID: 34292556 DOI: 10.1007/978-1-0716-1605-5_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Lipoic acid is an essential sulfur-containing cofactor used by several multienzyme complexes involved in energy metabolism and the breakdown of certain amino acids. It is composed of n-octanoic acid with sulfur atoms appended at C6 and C8. Lipoic acid is biosynthesized de novo in its cofactor form, in which it is covalently bound in an amide linkage to a target lysyl residue on a lipoyl carrier protein (LCP). The n-octanoyl moiety of the cofactor is derived from type 2 fatty acid biosynthesis and is transferred to an LCP to afford an octanoyllysyl amino acid. Next, lipoyl synthase (LipA in bacteria) catalyzes the attachment of the two sulfur atoms to afford the intact cofactor. LipA is a radical S-adenosylmethionine (SAM) enzyme that contains two [4Fe-4S] clusters. One [4Fe-4S] cluster is used to facilitate a reductive cleavage of SAM to render the highly oxidizing 5'-deoxyadenosyl 5'-radical needed to abstract C6 and C8 hydrogen atoms to allow for sulfur attachment. By contrast, the second cluster is the sulfur source, necessitating its destruction during turnover. In Escherichia coli, this auxiliary cluster can be restored after each turnover by NfuA or IscU, which are two iron-sulfur cluster carrier proteins that are implicated in iron-sulfur cluster biogenesis. In this chapter, we describe methods for purifying and characterizing LipA and NfuA from Mycobacterium tuberculosis, a human pathogen for which endogenously synthesized lipoic acid is essential. These studies provide the foundation for assessing lipoic acid biosynthesis as a potential target for the design of novel antituberculosis agents.
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Das M, Dewan A, Shee S, Singh A. The Multifaceted Bacterial Cysteine Desulfurases: From Metabolism to Pathogenesis. Antioxidants (Basel) 2021; 10:997. [PMID: 34201508 PMCID: PMC8300815 DOI: 10.3390/antiox10070997] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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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Affiliation(s)
| | | | | | - Amit Singh
- Centre for Infectious Disease Research, Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India; (M.D.); (A.D.); (S.S.)
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Álvarez-Córdoba M, Talaverón-Rey M, Villalón-García I, Povea-Cabello S, Suárez-Rivero JM, Suárez-Carrillo A, Munuera-Cabeza M, Salas JJ, Sánchez-Alcázar JA. Down regulation of the expression of mitochondrial phosphopantetheinyl-proteins in pantothenate kinase-associated neurodegeneration: pathophysiological consequences and therapeutic perspectives. Orphanet J Rare Dis 2021; 16:201. [PMID: 33952316 PMCID: PMC8101147 DOI: 10.1186/s13023-021-01823-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/20/2021] [Indexed: 02/06/2023] Open
Abstract
Background Neurodegeneration with brain iron accumulation (NBIA) is a group of genetic neurological disorders frequently associated with iron accumulation in the basal nuclei of the brain characterized by progressive spasticity, dystonia, muscle rigidity, neuropsychiatric symptoms, and retinal degeneration or optic nerve atrophy. Pantothenate kinase-associated neurodegeneration (PKAN) is the most widespread NBIA disorder. It is caused by mutations in the gene of pantothenate kinase 2 (PANK2) which catalyzes the first reaction of coenzyme A (CoA) biosynthesis. Thus, altered PANK2 activity is expected to induce CoA deficiency as well as low levels of essential metabolic intermediates such as 4′-phosphopantetheine which is a necessary cofactor for critical proteins involved in cytosolic and mitochondrial pathways such as fatty acid biosynthesis, mitochondrial respiratory complex I assembly and lysine and tetrahydrofolate metabolism, among other metabolic processes. Methods In this manuscript, we examined the effect of PANK2 mutations on the expression levels of proteins with phosphopantetheine cofactors in fibroblast derived from PKAN patients. These proteins include cytosolic acyl carrier protein (ACP), which is integrated within the multifunctional polypeptide chain of the fatty acid synthase involved in cytosolic fatty acid biosynthesis type I (FASI); mitochondrial ACP (mtACP) associated with mitocondrial fatty acid biosynthesis type II (FASII); mitochondrial alpha-aminoadipic semialdehyde synthase (AASS); and 10-formyltetrahydrofolate dehydrogenases (cytosolic, ALD1L1, and mitochondrial, ALD1L2). Results In PKAN fibroblasts the expression levels of cytosolic FAS and ALD1L1 were not affected while the expression levels of mtACP, AASS and ALD1L2 were markedly reduced, suggesting that 4′-phosphopantetheinylation of mitochondrial but no cytosolic proteins were markedly affected in PKAN patients. Furthermore, the correction of PANK2 expression levels by treatment with pantothenate in selected mutations with residual enzyme content was able to correct the expression levels of mitochondrial phosphopantetheinyl-proteins and restore the affected pathways. The positive effects of pantothenate in particular mutations were also corroborated in induced neurons obtained by direct reprograming of mutant PANK2 fibroblasts. Conclusions Our results suggest that the expression levels of mitochondrial phosphopantetheinyl-proteins are severely reduced in PKAN cells and that in selected mutations pantothenate increases the expression levels of both PANK2 and mitochondrial phosphopantetheinyl-proteins associated with remarkable improvement of cell pathophysiology. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-021-01823-3.
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Affiliation(s)
- Mónica Álvarez-Córdoba
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Carretera de Utrera Km 1, 41013, Sevilla, Spain.,Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain
| | - Marta Talaverón-Rey
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Carretera de Utrera Km 1, 41013, Sevilla, Spain.,Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain
| | - Irene Villalón-García
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Carretera de Utrera Km 1, 41013, Sevilla, Spain.,Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain
| | - Suleva Povea-Cabello
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Carretera de Utrera Km 1, 41013, Sevilla, Spain.,Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain
| | - Juan M Suárez-Rivero
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Carretera de Utrera Km 1, 41013, Sevilla, Spain.,Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain
| | - Alejandra Suárez-Carrillo
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Carretera de Utrera Km 1, 41013, Sevilla, Spain.,Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain
| | - Manuel Munuera-Cabeza
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Carretera de Utrera Km 1, 41013, Sevilla, Spain.,Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain
| | - Joaquín J Salas
- Departamento de Bioquímica Y Biología Molecular de Productos Vegetales, Instituto de La Grasa (CSIC), Sevilla, Spain
| | - José A Sánchez-Alcázar
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Carretera de Utrera Km 1, 41013, Sevilla, Spain. .,Centro de Investigación Biomédica en Red: Enfermedades Raras, Instituto de Salud Carlos III, 41013, Sevilla, Spain.
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Bouvenot T, Dewitte A, Bennaceur N, Pradel E, Pierre F, Bontemps-Gallo S, Sebbane F. Interplay between Yersinia pestis and its flea vector in lipoate metabolism. THE ISME JOURNAL 2021; 15:1136-1149. [PMID: 33479491 PMCID: PMC8182812 DOI: 10.1038/s41396-020-00839-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 10/22/2020] [Accepted: 11/11/2020] [Indexed: 01/29/2023]
Abstract
To thrive, vector-borne pathogens must survive in the vector's gut. How these pathogens successfully exploit this environment in time and space has not been extensively characterized. Using Yersinia pestis (the plague bacillus) and its flea vector, we developed a bioluminescence-based approach and employed it to investigate the mechanisms of pathogenesis at an unprecedented level of detail. Remarkably, lipoylation of metabolic enzymes, via the biosynthesis and salvage of lipoate, increases the Y. pestis transmission rate by fleas. Interestingly, the salvage pathway's lipoate/octanoate ligase LplA enhances the first step in lipoate biosynthesis during foregut colonization but not during midgut colonization. Lastly, Y. pestis primarily uses lipoate provided by digestive proteolysis (presumably as lipoyl peptides) rather than free lipoate in blood, which is quickly depleted by the vector. Thus, spatial and temporal factors dictate the bacterium's lipoylation strategies during an infection, and replenishment of lipoate by digestive proteolysis in the vector might constitute an Achilles' heel that is exploited by pathogens.
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Affiliation(s)
- Typhanie Bouvenot
- grid.503422.20000 0001 2242 6780Univ. Lille, Inserm, CNRS, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 – CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Amélie Dewitte
- grid.503422.20000 0001 2242 6780Univ. Lille, Inserm, CNRS, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 – CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Nadia Bennaceur
- grid.503422.20000 0001 2242 6780Univ. Lille, Inserm, CNRS, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 – CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Elizabeth Pradel
- grid.503422.20000 0001 2242 6780Univ. Lille, Inserm, CNRS, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 – CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - François Pierre
- grid.503422.20000 0001 2242 6780Univ. Lille, Inserm, CNRS, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 – CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Sébastien Bontemps-Gallo
- grid.503422.20000 0001 2242 6780Univ. Lille, Inserm, CNRS, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 – CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Florent Sebbane
- grid.503422.20000 0001 2242 6780Univ. Lille, Inserm, CNRS, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 – CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
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Staphylococcus aureus adapts to the host nutritional landscape to overcome tissue-specific branched-chain fatty acid requirement. Proc Natl Acad Sci U S A 2021; 118:2022720118. [PMID: 33753501 DOI: 10.1073/pnas.2022720118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
During infection, pathogenic microbes adapt to the nutritional milieu of the host through metabolic reprogramming and nutrient scavenging. For the bacterial pathogen Staphylococcus aureus, virulence in diverse infection sites is driven by the ability to scavenge myriad host nutrients, including lipoic acid, a cofactor required for the function of several critical metabolic enzyme complexes. S. aureus shuttles lipoic acid between these enzyme complexes via the amidotransferase, LipL. Here, we find that acquisition of lipoic acid, or its attachment via LipL to enzyme complexes required for the generation of acetyl-CoA and branched-chain fatty acids, is essential for bacteremia, yet dispensable for skin infection in mice. A lipL mutant is auxotrophic for carboxylic acid precursors required for synthesis of branched-chain fatty acids, an essential component of staphylococcal membrane lipids and the agent of membrane fluidity. However, the skin is devoid of branched-chain fatty acids. We showed that S. aureus instead scavenges host-derived unsaturated fatty acids from the skin using the secreted lipase, Geh, and the unsaturated fatty acid-binding protein, FakB2. Moreover, murine infections demonstrated the relevance of host lipid assimilation to staphylococcal survival. Altogether, these studies provide insight into an adaptive trait that bypasses de novo lipid synthesis to facilitate S. aureus persistence during superficial infection. The findings also reinforce the inherent challenges associated with targeting bacterial lipogenesis as an antibacterial strategy and support simultaneous inhibition of host fatty acid salvage during treatment.
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Current knowledge and recent advances in understanding metabolism of the model cyanobacterium Synechocystis sp. PCC 6803. Biosci Rep 2021; 40:222317. [PMID: 32149336 PMCID: PMC7133116 DOI: 10.1042/bsr20193325] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/05/2020] [Accepted: 03/06/2020] [Indexed: 02/06/2023] Open
Abstract
Cyanobacteria are key organisms in the global ecosystem, useful models for studying metabolic and physiological processes conserved in photosynthetic organisms, and potential renewable platforms for production of chemicals. Characterizing cyanobacterial metabolism and physiology is key to understanding their role in the environment and unlocking their potential for biotechnology applications. Many aspects of cyanobacterial biology differ from heterotrophic bacteria. For example, most cyanobacteria incorporate a series of internal thylakoid membranes where both oxygenic photosynthesis and respiration occur, while CO2 fixation takes place in specialized compartments termed carboxysomes. In this review, we provide a comprehensive summary of our knowledge on cyanobacterial physiology and the pathways in Synechocystis sp. PCC 6803 (Synechocystis) involved in biosynthesis of sugar-based metabolites, amino acids, nucleotides, lipids, cofactors, vitamins, isoprenoids, pigments and cell wall components, in addition to the proteins involved in metabolite transport. While some pathways are conserved between model cyanobacteria, such as Synechocystis, and model heterotrophic bacteria like Escherichia coli, many enzymes and/or pathways involved in the biosynthesis of key metabolites in cyanobacteria have not been completely characterized. These include pathways required for biosynthesis of chorismate and membrane lipids, nucleotides, several amino acids, vitamins and cofactors, and isoprenoids such as plastoquinone, carotenoids, and tocopherols. Moreover, our understanding of photorespiration, lipopolysaccharide assembly and transport, and degradation of lipids, sucrose, most vitamins and amino acids, and haem, is incomplete. We discuss tools that may aid our understanding of cyanobacterial metabolism, notably CyanoSource, a barcoded library of targeted Synechocystis mutants, which will significantly accelerate characterization of individual proteins.
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Przybyla-Toscano J, Christ L, Keech O, Rouhier N. Iron-sulfur proteins in plant mitochondria: roles and maturation. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2014-2044. [PMID: 33301571 DOI: 10.1093/jxb/eraa578] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 12/05/2020] [Indexed: 05/22/2023]
Abstract
Iron-sulfur (Fe-S) clusters are prosthetic groups ensuring electron transfer reactions, activating substrates for catalytic reactions, providing sulfur atoms for the biosynthesis of vitamins or other cofactors, or having protein-stabilizing effects. Hence, metalloproteins containing these cofactors are essential for numerous and diverse metabolic pathways and cellular processes occurring in the cytoplasm. Mitochondria are organelles where the Fe-S cluster demand is high, notably because the activity of the respiratory chain complexes I, II, and III relies on the correct assembly and functioning of Fe-S proteins. Several other proteins or complexes present in the matrix require Fe-S clusters as well, or depend either on Fe-S proteins such as ferredoxins or on cofactors such as lipoic acid or biotin whose synthesis relies on Fe-S proteins. In this review, we have listed and discussed the Fe-S-dependent enzymes or pathways in plant mitochondria including some potentially novel Fe-S proteins identified based on in silico analysis or on recent evidence obtained in non-plant organisms. We also provide information about recent developments concerning the molecular mechanisms involved in Fe-S cluster synthesis and trafficking steps of these cofactors from maturation factors to client apoproteins.
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Affiliation(s)
- Jonathan Przybyla-Toscano
- Université de Lorraine, INRAE, IAM, Nancy, France
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Loïck Christ
- Université de Lorraine, INRAE, IAM, Nancy, France
| | - Olivier Keech
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
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