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López-Domene R, Manteca A, Rodriguez-Abetxuko A, Beloqui A, Cortajarena AL. In vitro Production of Hemin-Based Artificial Metalloenzymes. Chemistry 2024; 30:e202303254. [PMID: 38145337 DOI: 10.1002/chem.202303254] [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: 10/04/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 12/26/2023]
Abstract
Developing enzyme alternatives is pivotal to improving and enabling new processes in biotechnology and industry. Artificial metalloenzymes (ArMs) are combinations of protein scaffolds with metal elements, such as metal nanoclusters or metal-containing molecules with specific catalytic properties, which can be customized. Here, we engineered an ArM based on the consensus tetratricopeptide repeat (CTPR) scaffold by introducing a unique histidine residue to coordinate the hemin cofactor. Our results show that this engineered system exhibits robust peroxidase-like catalytic activity driven by the hemin. The expression of the scaffold and subsequent coordination of hemin was achieved by recombinant expression in bulk and through in vitro transcription and translation systems in water-in-oil drops. The ability to synthesize this system in emulsio paves the way to improve its properties by means of droplet microfluidic screenings, facilitating the exploration of the protein combinatorial space to discover improved or novel catalytic activities.
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Affiliation(s)
- Rocío López-Domene
- Centre for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, E-20014, Spain
- POLYMAT and Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country UPV/EHU, Donostia-San Sebastián, E-20018, Spain
| | - Aitor Manteca
- Centre for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, E-20014, Spain
| | - Andoni Rodriguez-Abetxuko
- POLYMAT and Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country UPV/EHU, Donostia-San Sebastián, E-20018, Spain
| | - Ana Beloqui
- POLYMAT and Department of Applied Chemistry, Faculty of Chemistry, University of the Basque Country UPV/EHU, Donostia-San Sebastián, E-20018, Spain
- IKERBASQUE, Basque Foundation for Science, Plaza Euskadi 5, E-48009, Bilbao, Spain
| | - Aitziber L Cortajarena
- Centre for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, E-20014, Spain
- IKERBASQUE, Basque Foundation for Science, Plaza Euskadi 5, E-48009, Bilbao, Spain
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2
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Dominic IM, Willoughby MM, Freer AK, Moore CM, Donegan RK, Martinez-Guzman O, Hanna DA, Reddi AR. Fluorometric Methods to Measure Bioavailable and Total Heme. Methods Mol Biol 2024; 2839:151-194. [PMID: 39008253 DOI: 10.1007/978-1-0716-4043-2_9] [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] [Indexed: 07/16/2024]
Abstract
Heme b (iron protoporphyrin IX) is an essential but potentially cytotoxic cofactor, signaling molecule, and nutritional source of iron. Its importance in cell biology and metabolism is underscored by the fact that numerous diseases, including various cancers, neurodegenerative disorders, infectious diseases, anemias, and porphyrias, are associated with the dysregulation of heme synthesis, degradation, trafficking, and/or transport. Consequently, methods to measure, image, and quantify heme in cells are required to better understand the physiology and pathophysiology of heme. Herein, we describe fluorescence-based protocols to probe heme bioavailability and trafficking dynamics using genetically encoded fluorescent heme sensors in combination with various modalities, such as confocal microscopy, flow cytometry, and microplate readers. Additionally, we describe a protocol for measuring total heme and its precursor protoporphyrin IX using a fluorometric assay that exploits porphyrin fluorescence. Together, the methods described enable the monitoring of total and bioavailable heme to study heme homeostatic mechanisms in virtually any cell type and organism.
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Affiliation(s)
- Iramofu M Dominic
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Parker Petit Institute for Bioengineering and Biosciences, Atlanta, GA, USA
| | - Mathilda M Willoughby
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Parker Petit Institute for Bioengineering and Biosciences, Atlanta, GA, USA
| | - Abigail K Freer
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Parker Petit Institute for Bioengineering and Biosciences, Atlanta, GA, USA
| | - Courtney M Moore
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Parker Petit Institute for Bioengineering and Biosciences, Atlanta, GA, USA
| | | | - Osiris Martinez-Guzman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Parker Petit Institute for Bioengineering and Biosciences, Atlanta, GA, USA
| | - David A Hanna
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Parker Petit Institute for Bioengineering and Biosciences, Atlanta, GA, USA
| | - Amit R Reddi
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.
- Parker Petit Institute for Bioengineering and Biosciences, Atlanta, GA, USA.
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3
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Mo Y, Zhou H, Xu J, Chen X, Li L, Zhang S. Genetically encoded fluorescence lifetime biosensors: overview, advances, and opportunities. Analyst 2023; 148:4939-4953. [PMID: 37721109 DOI: 10.1039/d3an01201h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Genetically encoded biosensors based on fluorescent proteins (FPs) are powerful tools for tracking analytes and cellular events with high spatial and temporal resolution in living cells and organisms. Compared with intensiometric readout and ratiometric readout, fluorescence lifetime readout provides absolute measurements, independent of the biosensor expression level and instruments. Thus, genetically encoded fluorescence lifetime biosensors play a vital role in facilitating accurate quantitative assessments within intricate biological systems. In this review, we first provide a concise description of the categorization and working mechanism of genetically encoded fluorescence lifetime biosensors. Subsequently, we elaborate on the combination of the fluorescence lifetime imaging technique and lifetime analysis methods with fluorescence lifetime biosensors, followed by their application in monitoring the dynamics of environment parameters, analytes and cellular events. Finally, we discuss worthwhile considerations for the design, optimization and development of fluorescence lifetime-based biosensors from three representative cases.
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Affiliation(s)
- Yidan Mo
- State Key Laboratory of Precision Spectroscopy, East China Normal University, No. 500, Dongchuan Rd, Shanghai 200241, China
| | - Huangmei Zhou
- State Key Laboratory of Precision Spectroscopy, East China Normal University, No. 500, Dongchuan Rd, Shanghai 200241, China
| | - Jinming Xu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, No. 500, Dongchuan Rd, Shanghai 200241, China
| | - Xihang Chen
- State Key Laboratory of Precision Spectroscopy, East China Normal University, No. 500, Dongchuan Rd, Shanghai 200241, China
| | - Lei Li
- School of Science, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, China.
| | - Sanjun Zhang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, No. 500, Dongchuan Rd, Shanghai 200241, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
- NYU-ECNU Institute of Physics at NYU Shanghai, No. 3663, North Zhongshan Rd, Shanghai 200062, China.
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4
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Han S, Guo K, Wang W, Tao YJ, Gao H. Bacterial TANGO2 homologs are heme-trafficking proteins that facilitate biosynthesis of cytochromes c. mBio 2023; 14:e0132023. [PMID: 37462360 PMCID: PMC10470608 DOI: 10.1128/mbio.01320-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 06/05/2023] [Indexed: 09/02/2023] Open
Abstract
Heme, an essential molecule for virtually all living organisms, acts primarily as a cofactor in a large number of proteins. However, how heme is mobilized from the site of synthesis to the locations where hemoproteins are assembled remains largely unknown in cells, especially bacterial ones. In this study, with Shewanella oneidensis as the model, we identified HtpA (SO0126) as a heme-trafficking protein and homolog of TANGO2 proteins found in eukaryotes. We showed that HtpA homologs are widely distributed in all domains of living organisms and have undergone parallel evolution. In its absence, the cytochrome (cyt) c content and catalase activity decreased significantly. We further showed that both HtpA and representative TANGO2 proteins bind heme with 1:1 stoichiometry and a relatively low dissociation constant. Protein interaction analyses substantiated that HtpA directly interacts with the cytochrome c maturation system. Our findings shed light on cross-membrane transport of heme in bacteria and extend the understanding of TANGO2 proteins. IMPORTANCE The intracellular trafficking of heme, an essential cofactor for hemoproteins, remains underexplored even in eukaryotes, let alone bacteria. Here we developed a high-throughput method by which HtpA, a homolog of eukaryotic TANGO2 proteins, was identified to be a heme-binding protein that enhances cytochrome c biosynthesis and catalase activity in Shewanella oneidensis. HtpA interacts with the cytochrome c biosynthesis system directly, supporting that this protein, like TANGO2, functions in intracellular heme trafficking. HtpA homologs are widely distributed, but a large majority of them were found to be non-exchangeable, likely a result of parallel evolution. By substantiating the heme-trafficking nature of HtpA and its eukaryotic homologs, our findings provide general insight into the heme-trafficking process and highlight the functional conservation along evolution in all living organisms.
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Affiliation(s)
- Sirui Han
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Kailun Guo
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wei Wang
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yizhi J. Tao
- Department of BioSciences, Rice University, Houston, Texas, USA
| | - Haichun Gao
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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5
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Tsiftsoglou SA. Heme Interactions as Regulators of the Alternative Pathway Complement Responses and Implications for Heme-Associated Pathologies. Curr Issues Mol Biol 2023; 45:5198-5214. [PMID: 37367079 DOI: 10.3390/cimb45060330] [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: 05/07/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/28/2023] Open
Abstract
Heme (Fe2+-protoporphyrin IX) is a pigment of life, and as a prosthetic group in several hemoproteins, it contributes to diverse critical cellular processes. While its intracellular levels are tightly regulated by networks of heme-binding proteins (HeBPs), labile heme can be hazardous through oxidative processes. In blood plasma, heme is scavenged by hemopexin (HPX), albumin and several other proteins, while it also interacts directly with complement components C1q, C3 and factor I. These direct interactions block the classical pathway (CP) and distort the alternative pathway (AP). Errors or flaws in heme metabolism, causing uncontrolled intracellular oxidative stress, can lead to several severe hematological disorders. Direct interactions of extracellular heme with alternative pathway complement components (APCCs) may be implicated molecularly in diverse conditions at sites of abnormal cell damage and vascular injury. In such disorders, a deregulated AP could be associated with the heme-mediated disruption of the physiological heparan sulphate-CFH coat of stressed cells and the induction of local hemostatic responses. Within this conceptual frame, a computational evaluation of HBMs (heme-binding motifs) aimed to determine how heme interacts with APCCs and whether these interactions are affected by genetic variation within putative HBMs. Combined computational analysis and database mining identified putative HBMs in all of the 16 APCCs examined, with 10 exhibiting disease-associated genetic (SNPs) and/or epigenetic variation (PTMs). Overall, this article indicates that among the pleiotropic roles of heme reviewed, the interactions of heme with APCCs could induce differential AP-mediated hemostasis-driven pathologies in certain individuals.
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Affiliation(s)
- Stefanos A Tsiftsoglou
- Laboratory of Pharmacology, School of Pharmacy, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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6
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Su H, Chen X, Chen S, Guo M, Liu H. Applications of the Whole-Cell System in the Efficient Biosynthesis of Heme. Int J Mol Sci 2023; 24:ijms24098384. [PMID: 37176091 PMCID: PMC10179345 DOI: 10.3390/ijms24098384] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/22/2023] [Accepted: 04/30/2023] [Indexed: 05/15/2023] Open
Abstract
Heme has a variety of functions, from electronic reactions to binding gases, which makes it useful in medical treatments, dietary supplements, and food processing. In recent years, whole-cell system-based heme biosynthesis methods have been continuously explored and optimized as an alternative to the low-yield, lasting, and adverse ecological environment of chemical synthesis methods. This method relies on two biosynthetic pathways of microbial precursor 5-aminolevulinic acid (C4, C5) and three known downstream biosynthetic pathways of heme. This paper reviews the genetic and metabolic engineering strategies for heme production in recent years by optimizing culture conditions and techniques from different microorganisms. Specifically, we summarized and analyzed the possibility of using biosensors to explore new strategies for the biosynthesis of heme from the perspective of synthetic biology, providing a new direction for future exploration.
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Affiliation(s)
- Hongfei Su
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, China
| | - Xiaolin Chen
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, China
| | - Shijing Chen
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, China
| | - Mingzhang Guo
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, China
| | - Huilin Liu
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, China
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7
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Abstract
Osteosarcoma (OS) is the most common primary solid malignant tumour of bone, with rapid progression and a very poor prognosis. Iron is an essential nutrient that makes it an important player in cellular activities due to its inherent ability to exchange electrons, and its metabolic abnormalities are associated with a variety of diseases. The body tightly regulates iron content at the systemic and cellular levels through various mechanisms to prevent iron deficiency and overload from damaging the body. OS cells regulate various mechanisms to increase the intracellular iron concentration to accelerate proliferation, and some studies have revealed the hidden link between iron metabolism and the occurrence and development of OS. This article briefly describes the process of normal iron metabolism, and focuses on the research progress of abnormal iron metabolism in OS from the systemic and cellular levels.
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Affiliation(s)
- Xiaowei Ma
- Department of Orthopedics, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Nanli, Panjiayuan, Chaoyang District, Beijing, 100021, People's Republic of China
- Department of Orthopedics, The Fourth Hospital of Hebei Medical University, 12 Health Road, Hebei Province, Shijiazhuang, 050011, People's Republic of China
| | - Jiazheng Zhao
- Department of Orthopedics, The Fourth Hospital of Hebei Medical University, 12 Health Road, Hebei Province, Shijiazhuang, 050011, People's Republic of China
| | - Helin Feng
- Department of Orthopedics, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Nanli, Panjiayuan, Chaoyang District, Beijing, 100021, People's Republic of China.
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8
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Kim H, Moore CM, Mestre-Fos S, Hanna DA, Williams LD, Reddi AR, Torres MP. Depletion assisted hemin affinity (DAsHA) proteomics reveals an expanded landscape of heme-binding proteins in the human proteome. Metallomics 2023; 15:6994529. [PMID: 36669767 PMCID: PMC10022665 DOI: 10.1093/mtomcs/mfad004] [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: 08/26/2022] [Accepted: 01/19/2023] [Indexed: 01/22/2023]
Abstract
Heme b (iron protoporphyrin IX) plays important roles in biology as a metallocofactor and signaling molecule. However, the targets of heme signaling and the network of proteins that mediate the exchange of heme from sites of synthesis or uptake to heme dependent or regulated proteins are poorly understood. Herein, we describe a quantitative mass spectrometry (MS)-based chemoproteomics strategy to identify exchange labile hemoproteins in human embryonic kidney HEK293 cells that may be relevant to heme signaling and trafficking. The strategy involves depleting endogenous heme with the heme biosynthetic inhibitor succinylacetone (SA), leaving putative heme-binding proteins in their apo-state, followed by the capture of those proteins using hemin-agarose resin, and finally elution and identification by MS. By identifying only those proteins that interact with high specificity to hemin-agarose relative to control beaded agarose in an SA-dependent manner, we have expanded the number of proteins and ontologies that may be involved in binding and buffering labile heme or are targets of heme signaling. Notably, these include proteins involved in chromatin remodeling, DNA damage response, RNA splicing, cytoskeletal organization, and vesicular trafficking, many of which have been associated with heme through complementary studies published recently. Taken together, these results provide support for the emerging role of heme in an expanded set of cellular processes from genome integrity to protein trafficking and beyond.
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Affiliation(s)
- Hyojung Kim
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Courtney M Moore
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Santi Mestre-Fos
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - David A Hanna
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Amit R Reddi
- Correspondence: Amit R. Reddi, School of Chemistry and Biochemistry, Georgia Institute of Technology, 950 Atlantic Dr. Atlanta, GA 30033. E-mail:
| | - Matthew P Torres
- Correspondence: Matthew P. Torres, School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr. Atlanta, GA 30033. E-mail:
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9
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XUE P, SÁNCHEZ-LEÓN E, DAMOO D, HU G, JUNG WH, KRONSTAD JW. Heme sensing and trafficking in fungi. FUNGAL BIOL REV 2023; 43:100286. [PMID: 37781717 PMCID: PMC10540271 DOI: 10.1016/j.fbr.2022.09.002] [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] [Indexed: 11/04/2022]
Abstract
Fungal pathogens cause life-threatening diseases in humans, and the increasing prevalence of these diseases emphasizes the need for new targets for therapeutic intervention. Nutrient acquisition during infection is a promising target, and recent studies highlight the contributions of endomembrane trafficking, mitochondria, and vacuoles in the sensing and acquisition of heme by fungi. These studies have been facilitated by genetically encoded biosensors and other tools to quantitate heme in subcellular compartments and to investigate the dynamics of trafficking in living cells. In particular, the applications of biosensors in fungi have been extended beyond the detection of metabolites, cofactors, pH, and redox status to include the detection of heme. Here, we focus on studies that make use of biosensors to examine mechanisms of heme uptake and degradation, with guidance from the model fungus Saccharomyces cerevisiae and an emphasis on the pathogenic fungi Candida albicans and Cryptococcus neoformans that threaten human health. These studies emphasize a role for endocytosis in heme uptake, and highlight membrane contact sites involving mitochondria, the endoplasmic reticulum and vacuoles as mediators of intracellular iron and heme trafficking.
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Affiliation(s)
- Peng XUE
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eddy SÁNCHEZ-LEÓN
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Djihane DAMOO
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Guanggan HU
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Won Hee JUNG
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Korea
| | - James W. KRONSTAD
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
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10
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Stuehr DJ, Dai Y, Biswas P, Sweeny EA, Ghosh A. New roles for GAPDH, Hsp90, and NO in regulating heme allocation and hemeprotein function in mammals. Biol Chem 2022; 403:1005-1015. [PMID: 36152339 PMCID: PMC10184026 DOI: 10.1515/hsz-2022-0197] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/17/2022] [Indexed: 12/23/2022]
Abstract
The intracellular trafficking of mitochondrial heme presents a fundamental challenge to animal cells. This article provides some background on heme allocation, discusses some of the concepts, and then reviews research done over the last decade, much in the author's laboratory, that is uncovering unexpected and important roles for glyceraldehyde 3-phosphate dehydrogenase (GAPDH), heat shock protein 90 (hsp90), and nitric oxide (NO) in enabling and regulating the allocation of mitochondrial heme to hemeproteins that mature and function outside of the mitochondria. A model for how hemeprotein functions can be regulated in cells through the coordinate participation of GAPDH, hsp90, and NO in allocating cellular heme is presented.
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Affiliation(s)
- Dennis J Stuehr
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Yue Dai
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Pranjal Biswas
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Elizabeth A Sweeny
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Arnab Ghosh
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
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11
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Intracellular hemin is a potent inhibitor of the voltage-gated potassium channel Kv10.1. Sci Rep 2022; 12:14645. [PMID: 36030326 PMCID: PMC9420133 DOI: 10.1038/s41598-022-18975-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/23/2022] [Indexed: 11/08/2022] Open
Abstract
Heme, an iron-protoporphyrin IX complex, is a cofactor bound to various hemoproteins and supports a broad range of functions, such as electron transfer, oxygen transport, signal transduction, and drug metabolism. In recent years, there has been a growing recognition of heme as a non-genomic modulator of ion channel functions. Here, we show that intracellular free heme and hemin modulate human ether à go-go (hEAG1, Kv10.1) voltage-gated potassium channels. Application of hemin to the intracellular side potently inhibits Kv10.1 channels with an IC50 of about 4 nM under ambient and 63 nM under reducing conditions in a weakly voltage-dependent manner, favoring inhibition at resting potential. Functional studies on channel mutants and biochemical analysis of synthetic and recombinant channel fragments identified a heme-binding motif CxHx8H in the C-linker region of the Kv10.1 C terminus, with cysteine 541 and histidines 543 and 552 being important for hemin binding. Binding of hemin to the C linker may induce a conformational constraint that interferes with channel gating. Our results demonstrate that heme and hemin are endogenous modulators of Kv10.1 channels and could be exploited to modulate Kv10.1-mediated cellular functions.
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12
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Homan RA, Jadhav AM, Conway LP, Parker CG. A Chemical Proteomic Map of Heme-Protein Interactions. J Am Chem Soc 2022; 144:15013-15019. [PMID: 35960875 PMCID: PMC9811995 DOI: 10.1021/jacs.2c06104] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Heme is an essential cofactor for many human proteins as well as the primary transporter of oxygen in blood. Recent studies have also established heme as a signaling molecule, imparting its effects through binding with protein partners rather than through reactivity of its metal center. However, the comprehensive annotation of such heme-binding proteins in the human proteome remains incomplete. Here, we describe a strategy which utilizes a heme-based photoaffinity probe integrated with quantitative proteomics to map heme-protein interactions across the proteome. In these studies, we identified 350+ unique heme-protein interactions, the vast majority of which were heretofore unknown and consist of targets from diverse functional classes, including transporters, receptors, enzymes, transcription factors, and chaperones. Among these proteins is the immune-related interleukin receptor-associated kinase 1 (IRAK1), where we provide preliminary evidence that heme agonizes its catalytic activity. Our findings should improve the current understanding of heme's regulation as well as its signaling functions and facilitate new insights of its roles in human disease.
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Affiliation(s)
- Rick A. Homan
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Appaso M. Jadhav
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Louis P. Conway
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Christopher G. Parker
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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13
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Fleischhacker AS, Sarkar A, Liu L, Ragsdale SW. Regulation of protein function and degradation by heme, heme responsive motifs, and CO. Crit Rev Biochem Mol Biol 2022; 57:16-47. [PMID: 34517731 PMCID: PMC8966953 DOI: 10.1080/10409238.2021.1961674] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Heme is an essential biomolecule and cofactor involved in a myriad of biological processes. In this review, we focus on how heme binding to heme regulatory motifs (HRMs), catalytic sites, and gas signaling molecules as well as how changes in the heme redox state regulate protein structure, function, and degradation. We also relate these heme-dependent changes to the affected metabolic processes. We center our discussion on two HRM-containing proteins: human heme oxygenase-2, a protein that binds and degrades heme (releasing Fe2+ and CO) in its catalytic core and binds Fe3+-heme at HRMs located within an unstructured region of the enzyme, and the transcriptional regulator Rev-erbβ, a protein that binds Fe3+-heme at an HRM and is involved in CO sensing. We will discuss these and other proteins as they relate to cellular heme composition, homeostasis, and trafficking. In addition, we will discuss the HRM-containing family of proteins and how the stability and activity of these proteins are regulated in a dependent manner through the HRMs. Then, after reviewing CO-mediated protein regulation of heme proteins, we turn our attention to the involvement of heme, HRMs, and CO in circadian rhythms. In sum, we stress the importance of understanding the various roles of heme and the distribution of the different heme pools as they relate to the heme redox state, CO, and heme binding affinities.
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Affiliation(s)
- Angela S. Fleischhacker
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Anindita Sarkar
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Liu Liu
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Stephen W. Ragsdale
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
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Lall D, Miscevic D, Bruder M, Westbrook A, Aucoin M, Moo-Young M, Perry Chou C. Strain engineering and bioprocessing strategies for biobased production of porphobilinogen in Escherichia coli. BIORESOUR BIOPROCESS 2022; 8:122. [PMID: 34970474 PMCID: PMC8668860 DOI: 10.1186/s40643-021-00482-3] [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: 09/03/2021] [Accepted: 12/04/2021] [Indexed: 11/10/2022] Open
Abstract
Strain engineering and bioprocessing strategies were applied for biobased production of porphobilinogen (PBG) using Escherichia coli as the cell factory. The non-native Shemin/C4 pathway was first implemented by heterologous expression of hemA from Rhodopseudomonas spheroids to supply carbon flux from the natural tricarboxylic acid (TCA) pathways for PBG biosynthesis via succinyl-CoA. Metabolic strategies were then applied for carbon flux direction from the TCA pathways to the C4 pathway. To promote PBG stability and accumulation, Clustered Regularly Interspersed Short Palindromic Repeats interference (CRISPRi) was applied to repress hemC expression and, therefore, reduce carbon flowthrough toward porphyrin biosynthesis with minimal impact to cell physiology. To further enhance PBG biosynthesis and accumulation under the hemC-repressed genetic background, we further heterologously expressed native E. coli hemB. Using these engineered E. coli strains for bioreactor cultivation based on ~ 30 g L−1 glycerol, we achieved high PBG titers up to 209 mg L−1, representing 1.73% of the theoretical PBG yield, with improved PBG stability and accumulation. Potential biochemical, genetic, and metabolic factors limiting PBG production were systematically identified for characterization.
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Affiliation(s)
- Davinder Lall
- Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1 Canada
| | - Dragan Miscevic
- Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1 Canada
| | - Mark Bruder
- Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1 Canada
| | - Adam Westbrook
- Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1 Canada
| | - Marc Aucoin
- Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1 Canada
| | - Murray Moo-Young
- Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1 Canada
| | - C Perry Chou
- Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1 Canada
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Hanna DA, Moore CM, Liu L, Yuan X, Dominic IM, Fleischhacker AS, Hamza I, Ragsdale SW, Reddi AR. Heme oxygenase-2 (HO-2) binds and buffers labile ferric heme in human embryonic kidney cells. J Biol Chem 2021; 298:101549. [PMID: 34973332 PMCID: PMC8808069 DOI: 10.1016/j.jbc.2021.101549] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 01/13/2023] Open
Abstract
Heme oxygenases (HOs) detoxify heme by oxidatively degrading it into carbon monoxide, iron, and biliverdin, which is reduced to bilirubin and excreted. Humans express two isoforms of HO: the inducible HO-1, which is upregulated in response to excess heme and other stressors, and the constitutive HO-2. Much is known about the regulation and physiological function of HO-1, whereas comparatively little is known about the role of HO-2 in regulating heme homeostasis. The biochemical necessity for expressing constitutive HO-2 is dependent on whether heme is sufficiently abundant and accessible as a substrate under conditions in which HO-1 is not induced. By measuring labile heme, total heme, and bilirubin in human embryonic kidney HEK293 cells with silenced or overexpressed HO-2, as well as various HO-2 mutant alleles, we found that endogenous heme is too limiting a substrate to observe HO-2-dependent heme degradation. Rather, we discovered a novel role for HO-2 in the binding and buffering of heme. Taken together, in the absence of excess heme, we propose that HO-2 regulates heme homeostasis by acting as a heme buffering factor that controls heme bioavailability. When heme is in excess, HO-1 is induced, and both HO-2 and HO-1 can provide protection from heme toxicity via enzymatic degradation. Our results explain why catalytically inactive mutants of HO-2 are cytoprotective against oxidative stress. Moreover, the change in bioavailable heme due to HO-2 overexpression, which selectively binds ferric over ferrous heme, is consistent with labile heme being oxidized, thereby providing new insights into heme trafficking and signaling.
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Affiliation(s)
- David A. Hanna
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Courtney M. Moore
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Liu Liu
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Xiaojing Yuan
- Department of Animal and Avian Sciences, Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Iramofu M. Dominic
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | | | - Iqbal Hamza
- Department of Animal and Avian Sciences, Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Stephen W. Ragsdale
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Amit R. Reddi
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA,School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA,Parker Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA,For correspondence: Amit R. Reddi
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16
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Gallio A, Fung SSP, Cammack-Najera A, Hudson AJ, Raven EL. Understanding the Logistics for the Distribution of Heme in Cells. JACS AU 2021; 1:1541-1555. [PMID: 34723258 PMCID: PMC8549057 DOI: 10.1021/jacsau.1c00288] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Indexed: 05/03/2023]
Abstract
Heme is essential for the survival of virtually all living systems-from bacteria, fungi, and yeast, through plants to animals. No eukaryote has been identified that can survive without heme. There are thousands of different proteins that require heme in order to function properly, and these are responsible for processes such as oxygen transport, electron transfer, oxidative stress response, respiration, and catalysis. Further to this, in the past few years, heme has been shown to have an important regulatory role in cells, in processes such as transcription, regulation of the circadian clock, and the gating of ion channels. To act in a regulatory capacity, heme needs to move from its place of synthesis (in mitochondria) to other locations in cells. But while there is detailed information on how the heme lifecycle begins (heme synthesis), and how it ends (heme degradation), what happens in between is largely a mystery. Here we summarize recent information on the quantification of heme in cells, and we present a discussion of a mechanistic framework that could meet the logistical challenge of heme distribution.
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Affiliation(s)
- Andrea
E. Gallio
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
| | - Simon S.-P. Fung
- Department
of Chemistry and Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Ana Cammack-Najera
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
| | - Andrew J. Hudson
- Department
of Chemistry and Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Emma L. Raven
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
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