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Wang L, Chen W, Zhang C, Xie X, Huang F, Chen M, Mao W, Yu N, Wei Q, Ma L, Li Z. Molecular mechanism for target recognition, dimerization, and activation of Pyrococcus furiosus Argonaute. Mol Cell 2024; 84:675-686.e4. [PMID: 38295801 DOI: 10.1016/j.molcel.2024.01.004] [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: 08/03/2023] [Revised: 11/15/2023] [Accepted: 01/05/2024] [Indexed: 02/18/2024]
Abstract
The Argonaute nuclease from the thermophilic archaeon Pyrococcus furiosus (PfAgo) contributes to host defense and represents a promising biotechnology tool. Here, we report the structure of a PfAgo-guide DNA-target DNA ternary complex at the cleavage-compatible state. The ternary complex is predominantly dimerized, and the dimerization is solely mediated by PfAgo at PIWI-MID, PIWI-PIWI, and PAZ-N interfaces. Additionally, PfAgo accommodates a short 14-bp guide-target DNA duplex with a wedge-type N domain and specifically recognizes 5'-phosphorylated guide DNA. In contrast, the PfAgo-guide DNA binary complex is monomeric, and the engagement of target DNA with 14-bp complementarity induces sufficient dimerization and activation of PfAgo, accompanied by movement of PAZ and N domains. A closely related Argonaute from Thermococcus thioreducens adopts a similar dimerization configuration with an additional zinc finger formed at the dimerization interface. Dimerization of both Argonautes stabilizes the catalytic loops, highlighting the important role of Argonaute dimerization in the activation and target cleavage.
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Affiliation(s)
- Longyu Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Wanping Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Chendi Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Xiaochen Xie
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Fuyong Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Miaomiao Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Wuxiang Mao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Na Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Qiang Wei
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.
| | - Zhuang Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.
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Rivett ED, Addis HG, Dietz JV, Carroll-Deaton JA, Gupta S, Foreman KL, Dang MA, Fox JL, Khalimonchuk O, Hegg EL. Evidence that the catalytic mechanism of heme a synthase involves the formation of a carbocation stabilized by a conserved glutamate. Arch Biochem Biophys 2023; 744:109665. [PMID: 37348627 PMCID: PMC10529832 DOI: 10.1016/j.abb.2023.109665] [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: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/24/2023]
Abstract
In eukaryotes and many aerobic prokaryotes, the final step of aerobic respiration is catalyzed by an aa3-type cytochrome c oxidase, which requires a modified heme cofactor, heme a. The conversion of heme b, the prototypical cellular heme, to heme o and ultimately to heme a requires two modifications, the latter of which is conversion of a methyl group to an aldehyde, catalyzed by heme a synthase (HAS). The N- and C-terminal halves of HAS share homology, and each half contains a heme-binding site. Previous reports indicate that the C-terminal site is occupied by a heme b cofactor. The N-terminal site may function as the substrate (heme o) binding site, although this has not been confirmed experimentally. Here, we assess the role of conserved residues from the N- and C-terminal heme-binding sites in HAS from prokaryotic (Shewanella oneidensis) and eukaryotic (Saccharomyces cerevisiae) species - SoHAS/CtaA and ScHAS/Cox15, respectively. A glutamate within the N-terminal site is found to be critical for activity in both types of HAS, consistent with the hypothesis that a carbocation forms transiently during catalysis. In contrast, the residue occupying the analogous C-terminal position is dispensable for enzyme activity. In SoHAS, the C-terminal heme ligands are critical for stability, while in ScHAS, substitutions in either heme-binding site have little effect on global structure. In both species, in vivo accumulation of heme o requires the presence of an inactive HAS variant, highlighting a potential regulatory role for HAS in heme o biosynthesis.
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Affiliation(s)
- Elise D Rivett
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Hannah G Addis
- Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC, 29424, USA
| | - Jonathan V Dietz
- Department of Biochemistry, University of Nebraska, Lincoln, NE, 68588, USA
| | - Jayda A Carroll-Deaton
- Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC, 29424, USA
| | - Shipra Gupta
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Koji L Foreman
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Minh Anh Dang
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Jennifer L Fox
- Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC, 29424, USA.
| | - Oleh Khalimonchuk
- Department of Biochemistry, University of Nebraska, Lincoln, NE, 68588, USA; Nebraska Redox Biology Center, University of Nebraska, Lincoln, NE, 68588, USA; Fred & Pamela Buffett Cancer Center, Omaha, NE, 68198, USA.
| | - Eric L Hegg
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.
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Mass spectrometry of intact membrane proteins: shifting towards a more native-like context. Essays Biochem 2023; 67:201-213. [PMID: 36807530 PMCID: PMC10070488 DOI: 10.1042/ebc20220169] [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: 11/17/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 02/23/2023]
Abstract
Integral membrane proteins are involved in a plethora of biological processes including cellular signalling, molecular transport, and catalysis. Many of these functions are mediated by non-covalent interactions with other proteins, substrates, metabolites, and surrounding lipids. Uncovering such interactions and deciphering their effect on protein activity is essential for understanding the regulatory mechanisms underlying integral membrane protein function. However, the detection of such dynamic complexes has proven to be challenging using traditional approaches in structural biology. Native mass spectrometry has emerged as a powerful technique for the structural characterisation of membrane proteins and their complexes, enabling the detection and identification of protein-binding partners. In this review, we discuss recent native mass spectrometry-based studies that have characterised non-covalent interactions of membrane proteins in the presence of detergents or membrane mimetics. We additionally highlight recent progress towards the study of membrane proteins within native membranes and provide our perspective on how these could be combined with recent developments in instrumentation to investigate increasingly complex biomolecular systems.
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LILBID-MS: using lasers to shed light on biomolecular architectures. Biochem Soc Trans 2022; 50:1057-1067. [PMID: 35695670 PMCID: PMC9317959 DOI: 10.1042/bst20190881] [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: 03/08/2022] [Revised: 05/15/2022] [Accepted: 05/20/2022] [Indexed: 11/17/2022]
Abstract
Structural Biology has moved beyond the aim of simply identifying the components of a cellular subsystem towards analysing the dynamics and interactions of multiple players within a cell. This focal shift comes with additional requirements for the analytical tools used to investigate these systems of increased size and complexity, such as Native Mass Spectrometry, which has always been an important tool for structural biology. Scientific advance and recent developments, such as new ways to mimic a cell membrane for a membrane protein, have caused established methods to struggle to keep up with the increased demands. In this review, we summarize the possibilities, which Laser Induced Liquid Bead Ion Desorption (LILBID) mass spectrometry offers with regard to the challenges of modern structural biology, like increasingly complex sample composition, novel membrane mimics and advanced structural analysis, including next neighbor relations and the dynamics of complex formation.
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Rivett ED, Heo L, Feig M, Hegg EL. Biosynthesis and trafficking of heme o and heme a: new structural insights and their implications for reaction mechanisms and prenylated heme transfer. Crit Rev Biochem Mol Biol 2021; 56:640-668. [PMID: 34428995 DOI: 10.1080/10409238.2021.1957668] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Aerobic respiration is a key energy-producing pathway in many prokaryotes and virtually all eukaryotes. The final step of aerobic respiration is most commonly catalyzed by heme-copper oxidases embedded in the cytoplasmic or mitochondrial membrane. The majority of these terminal oxidases contain a prenylated heme (typically heme a or occasionally heme o) in the active site. In addition, many heme-copper oxidases, including mitochondrial cytochrome c oxidases, possess a second heme a cofactor. Despite the critical role of heme a in the electron transport chain, the details of the mechanism by which heme b, the prototypical cellular heme, is converted to heme o and then to heme a remain poorly understood. Recent structural investigations, however, have helped clarify some elements of heme a biosynthesis. In this review, we discuss the insight gained from these advances. In particular, we present a new structural model of heme o synthase (HOS) based on distance restraints from inferred coevolutionary relationships and refined by molecular dynamics simulations that are in good agreement with the experimentally determined structures of HOS homologs. We also analyze the two structures of heme a synthase (HAS) that have recently been solved by other groups. For both HOS and HAS, we discuss the proposed catalytic mechanisms and highlight how new insights into the heme-binding site locations shed light on previously obtained biochemical data. Finally, we explore the implications of the new structural data in the broader context of heme trafficking in the heme a biosynthetic pathway and heme-copper oxidase assembly.
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Affiliation(s)
- Elise D Rivett
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Lim Heo
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Eric L Hegg
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
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Degli Esposti M, Moya-Beltrán A, Quatrini R, Hederstedt L. Respiratory Heme A-Containing Oxidases Originated in the Ancestors of Iron-Oxidizing Bacteria. Front Microbiol 2021; 12:664216. [PMID: 34211444 PMCID: PMC8239418 DOI: 10.3389/fmicb.2021.664216] [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: 02/04/2021] [Accepted: 05/12/2021] [Indexed: 11/13/2022] Open
Abstract
Respiration is a major trait shaping the biology of many environments. Cytochrome oxidase containing heme A (COX) is a common terminal oxidase in aerobic bacteria and is the only one in mammalian mitochondria. The synthesis of heme A is catalyzed by heme A synthase (CtaA/Cox15), an enzyme that most likely coevolved with COX. The evolutionary origin of COX in bacteria has remained unknown. Using extensive sequence and phylogenetic analysis, we show that the ancestral type of heme A synthases is present in iron-oxidizing Proteobacteria such as Acidithiobacillus spp. These bacteria also contain a deep branching form of the major COX subunit (COX1) and an ancestral variant of CtaG, a protein that is specifically required for COX biogenesis. Our work thus suggests that the ancestors of extant iron-oxidizers were the first to evolve COX. Consistent with this conclusion, acidophilic iron-oxidizing prokaryotes lived on emerged land around the time for which there is the earliest geochemical evidence of aerobic respiration on earth. Hence, ecological niches of iron oxidation have apparently promoted the evolution of aerobic respiration.
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Affiliation(s)
- Mauro Degli Esposti
- Center for Genomic Sciences, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Mexico
| | - Ana Moya-Beltrán
- Fundación Ciencia & Vida, Santiago, Chile
- ANID–Millennium Science Initiative Program–Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile
| | - Raquel Quatrini
- Fundación Ciencia & Vida, Santiago, Chile
- ANID–Millennium Science Initiative Program–Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastian, Santiago, Chile
| | - Lars Hederstedt
- The Microbiology Group, Department of Biology, Lund University, Lund, Sweden
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