1
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Key J, Gispert S, Koepf G, Steinhoff-Wagner J, Reichlmeir M, Auburger G. Translation Fidelity and Respiration Deficits in CLPP-Deficient Tissues: Mechanistic Insights from Mitochondrial Complexome Profiling. Int J Mol Sci 2023; 24:17503. [PMID: 38139332 PMCID: PMC10743472 DOI: 10.3390/ijms242417503] [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: 11/13/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The mitochondrial matrix peptidase CLPP is crucial during cell stress. Its loss causes Perrault syndrome type 3 (PRLTS3) with infertility, neurodegeneration, and a growth deficit. Its target proteins are disaggregated by CLPX, which also regulates heme biosynthesis via unfolding ALAS enzymes, providing access for pyridoxal-5'-phosphate (PLP). Despite efforts in diverse organisms with multiple techniques, CLPXP substrates remain controversial. Here, avoiding recombinant overexpression, we employed complexomics in mitochondria from three mouse tissues to identify endogenous targets. A CLPP absence caused the accumulation and dispersion of CLPX-VWA8 as AAA+ unfoldases, and of PLPBP. Similar changes and CLPX-VWA8 co-migration were evident for mitoribosomal central protuberance clusters, translation factors like GFM1-HARS2, the RNA granule components LRPPRC-SLIRP, and enzymes OAT-ALDH18A1. Mitochondrially translated proteins in testes showed reductions to <30% for MTCO1-3, the mis-assembly of the complex IV supercomplex, and accumulated metal-binding assembly factors COX15-SFXN4. Indeed, heavy metal levels were increased for iron, molybdenum, cobalt, and manganese. RT-qPCR showed compensatory downregulation only for Clpx mRNA; most accumulated proteins appeared transcriptionally upregulated. Immunoblots validated VWA8, MRPL38, MRPL18, GFM1, and OAT accumulation. Co-immunoprecipitation confirmed CLPX binding to MRPL38, GFM1, and OAT, so excess CLPX and PLP may affect their activity. Our data mechanistically elucidate the mitochondrial translation fidelity deficits which underlie progressive hearing impairment in PRLTS3.
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Affiliation(s)
- Jana Key
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Suzana Gispert
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Gabriele Koepf
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Julia Steinhoff-Wagner
- TUM School of Life Sciences, Animal Nutrition and Metabolism, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising-Weihenstephan, Germany;
| | - Marina Reichlmeir
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
| | - Georg Auburger
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (S.G.); (M.R.); (G.A.)
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2
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Shvarev D, Scholz AI, Moeller A. Conformational variability of cyanobacterial ChlI, the AAA+ motor of magnesium chelatase involved in chlorophyll biosynthesis. mBio 2023; 14:e0189323. [PMID: 37737632 PMCID: PMC10653834 DOI: 10.1128/mbio.01893-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 08/02/2023] [Indexed: 09/23/2023] Open
Abstract
IMPORTANCE Photosynthesis is an essential life process that relies on chlorophyll. In photosynthetic organisms, chlorophyll synthesis involves multiple steps and depends on magnesium chelatase. This enzyme complex is responsible for inserting magnesium into the chlorophyll precursor, but the molecular mechanism of this process is not fully understood. By using cryogenic electron microscopy and conducting functional analyses, we have discovered that the motor subunit ChlI of magnesium chelatase undergoes conformational changes in the presence of ATP. Our findings offer new insights into how energy is transferred from ChlI to the other components of magnesium chelatase. This information significantly contributes to our understanding of the initial step in chlorophyll biosynthesis and lays the foundation for future studies on the entire process of chlorophyll production.
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Affiliation(s)
- Dmitry Shvarev
- Structural Biology Section, Department of Biology/Chemistry, Osnabrück University, Osnabrück, Lower Saxony, Germany
| | - Alischa Ira Scholz
- Structural Biology Section, Department of Biology/Chemistry, Osnabrück University, Osnabrück, Lower Saxony, Germany
| | - Arne Moeller
- Structural Biology Section, Department of Biology/Chemistry, Osnabrück University, Osnabrück, Lower Saxony, Germany
- Center of Cellular Nanoanalytics Osnabrück (CellNanOs), Osnabrück University, Osnabrück, Germany
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3
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Bhandari V, Reichheld SE, Houliston S, Lemak A, Arrowsmith CH, Sharpe S, Houry WA. The RavA-ViaA chaperone complex modulates bacterial persistence through its association with the fumarate reductase enzyme. J Biol Chem 2023; 299:105199. [PMID: 37660904 PMCID: PMC10585395 DOI: 10.1016/j.jbc.2023.105199] [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: 06/28/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023] Open
Abstract
Regulatory ATPase variant A (RavA) is a MoxR AAA+ protein that functions together with a partner protein termed von Willebrand factor type A interacting with AAA+ ATPase (ViaA). RavA-ViaA are functionally associated with anaerobic respiration in Escherichia coli through interactions with the fumarate reductase (Frd) electron transport complex. Through this association, RavA and ViaA modulate the activity of the Frd complex and, hence, are proposed to have chaperone-like activity. However, the functional role of RavA-ViaA in the cell is not yet well established. We had demonstrated that RavA-ViaA can sensitize E. coli cells to sublethal concentrations of the aminoglycoside class of antibiotics. Since Frd has been associated with bacterial persistence against antibiotics, the relationship of RavA-ViaA and Frd was explored within this context. Experiments performed here reveal a function of RavA-ViaA in bacterial persistence upon treatment with antibiotics through the association of the chaperone complex with Frd. As part of this work, the NMR structure of the N-terminal domain of ViaA was solved. The structure reveals a novel alpha helical fold, which we name the VAN fold, that has not been observed before. We show that this domain is required for the function of the chaperone complex. We propose that modulating the levels of RavA-ViaA could enhance the susceptibility of Gram-negative bacteria to antibiotics.
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Affiliation(s)
- Vaibhav Bhandari
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Sean E Reichheld
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Scott Houliston
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Alexander Lemak
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Structural Genomics Consortium, Toronto, Ontario, Canada
| | - Simon Sharpe
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.
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4
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Kahle M, Appelgren S, Elofsson A, Carroni M, Ädelroth P. Insights into the structure-function relationship of the NorQ/NorD chaperones from Paracoccus denitrificans reveal shared principles of interacting MoxR AAA+/VWA domain proteins. BMC Biol 2023; 21:47. [PMID: 36855050 PMCID: PMC9976466 DOI: 10.1186/s12915-023-01546-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 02/15/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND NorQ, a member of the MoxR-class of AAA+ ATPases, and NorD, a protein containing a Von Willebrand Factor Type A (VWA) domain, are essential for non-heme iron (FeB) cofactor insertion into cytochrome c-dependent nitric oxide reductase (cNOR). cNOR catalyzes NO reduction, a key step of bacterial denitrification. This work aimed at elucidating the specific mechanism of NorQD-catalyzed FeB insertion, and the general mechanism of the MoxR/VWA interacting protein families. RESULTS We show that NorQ-catalyzed ATP hydrolysis, an intact VWA domain in NorD, and specific surface carboxylates on cNOR are all features required for cNOR activation. Supported by BN-PAGE, low-resolution cryo-EM structures of NorQ and the NorQD complex show that NorQ forms a circular hexamer with a monomer of NorD binding both to the side and to the central pore of the NorQ ring. Guided by AlphaFold predictions, we assign the density that "plugs" the NorQ ring pore to the VWA domain of NorD with a protruding "finger" inserting through the pore and suggest this binding mode to be general for MoxR/VWA couples. CONCLUSIONS Based on our results, we present a tentative model for the mechanism of NorQD-catalyzed cNOR remodeling and suggest many of its features to be applicable to the whole MoxR/VWA family.
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Affiliation(s)
- Maximilian Kahle
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden. .,Present Address: Department of Biochemistry, University of Potsdam, 14476, Potsdam, Germany.
| | - Sofia Appelgren
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Arne Elofsson
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden.,Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Marta Carroni
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden. .,Swedish Cryo-EM Facility, Science for Life Laboratory Stockholm University, Solna, Sweden.
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden.
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5
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Waheeda K, Kitchel H, Wang Q, Chiu PL. Molecular mechanism of Rubisco activase: Dynamic assembly and Rubisco remodeling. Front Mol Biosci 2023; 10:1125922. [PMID: 36845545 PMCID: PMC9951593 DOI: 10.3389/fmolb.2023.1125922] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 01/31/2023] [Indexed: 02/12/2023] Open
Abstract
Ribulose-1,5-bisphosphate (RuBP) carboxylase-oxygenase (Rubisco) enzyme is the limiting step of photosynthetic carbon fixation, and its activation is regulated by its co-evolved chaperone, Rubisco activase (Rca). Rca removes the intrinsic sugar phosphate inhibitors occupying the Rubisco active site, allowing RuBP to split into two 3-phosphoglycerate (3PGA) molecules. This review summarizes the evolution, structure, and function of Rca and describes the recent findings regarding the mechanistic model of Rubisco activation by Rca. New knowledge in these areas can significantly enhance crop engineering techniques used to improve crop productivity.
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Affiliation(s)
- Kazi Waheeda
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States,Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, United States
| | - Heidi Kitchel
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States,Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, United States
| | - Quan Wang
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Po-Lin Chiu
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States,Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, United States,*Correspondence: Po-Lin Chiu,
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6
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Oh ZG, Askey B, Gunn LH. Red Rubiscos and opportunities for engineering green plants. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:520-542. [PMID: 36055563 PMCID: PMC9833100 DOI: 10.1093/jxb/erac349] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
Nature's vital, but notoriously inefficient, CO2-fixing enzyme Rubisco often limits the growth of photosynthetic organisms including crop species. Form I Rubiscos comprise eight catalytic large subunits and eight auxiliary small subunits and can be classified into two distinct lineages-'red' and 'green'. While red-type Rubiscos (Form IC and ID) are found in rhodophytes, their secondary symbionts, and certain proteobacteria, green-type Rubiscos (Form IA and IB) exist in terrestrial plants, chlorophytes, cyanobacteria, and other proteobacteria. Eukaryotic red-type Rubiscos exhibit desirable kinetic properties, namely high specificity and high catalytic efficiency, with certain isoforms outperforming green-type Rubiscos. However, it is not yet possible to functionally express a high-performing red-type Rubisco in chloroplasts to boost photosynthetic carbon assimilation in green plants. Understanding the molecular and evolutionary basis for divergence between red- and green-type Rubiscos could help us to harness the superior CO2-fixing power of red-type Rubiscos. Here we review our current understanding about red-type Rubisco distribution, biogenesis, and sequence-structure, and present opportunities and challenges for utilizing red-type Rubisco kinetics towards crop improvements.
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Affiliation(s)
- Zhen Guo Oh
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Bryce Askey
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
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7
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Felix J, Bumba L, Liesche C, Fraudeau A, Rébeillé F, El Khoury JY, Huard K, Gallet B, Moriscot C, Kleman JP, Duhoo Y, Jessop M, Kandiah E, Barras F, Jouhet J, Gutsche I. The AAA+ ATPase RavA and its binding partner ViaA modulate E. coli aminoglycoside sensitivity through interaction with the inner membrane. Nat Commun 2022; 13:5502. [PMID: 36127320 PMCID: PMC9489729 DOI: 10.1038/s41467-022-32992-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/26/2022] [Indexed: 11/09/2022] Open
Abstract
Enteric bacteria have to adapt to environmental stresses in the human gastrointestinal tract such as acid and nutrient stress, oxygen limitation and exposure to antibiotics. Membrane lipid composition has recently emerged as a key factor for stress adaptation. The E. coli ravA-viaA operon is essential for aminoglycoside bactericidal activity under anaerobiosis but its mechanism of action is unclear. Here we characterise the VWA domain-protein ViaA and its interaction with the AAA+ ATPase RavA, and find that both proteins localise at the inner cell membrane. We demonstrate that RavA and ViaA target specific phospholipids and subsequently identify their lipid-binding sites. We further show that mutations abolishing interaction with lipids restore induced changes in cell membrane morphology and lipid composition. Finally we reveal that these mutations render E. coli gentamicin-resistant under fumarate respiration conditions. Our work thus uncovers a ravA-viaA-based pathway which is mobilised in response to aminoglycosides under anaerobiosis and engaged in cell membrane regulation.
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Affiliation(s)
- Jan Felix
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Ladislav Bumba
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
- Institute of Microbiology, The Academy of Sciences of the Czech Republic, Videnska, 1083, Prague, Czech Republic
| | - Clarissa Liesche
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
| | - Angélique Fraudeau
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
- EMBL Grenoble, 71 Avenue des martyrs, Grenoble, France
| | - Fabrice Rébeillé
- Laboratoire de Physiologie Cellulaire Végétale, Univ Grenoble Alpes, CEA, CNRS, INRAE, IRIG, 17 Avenue des martyrs, Grenoble, France
| | - Jessica Y El Khoury
- Institut Pasteur, Université de Paris, CNRS UMR6047, Stress Adaptation and Metabolism Unit, Department of Microbiology, Paris, France
| | - Karine Huard
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
| | - Benoit Gallet
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
| | - Christine Moriscot
- Univ Grenoble Alpes, CEA, CNRS, ISBG, 71 Avenue des martyrs, Grenoble, France
| | - Jean-Philippe Kleman
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
| | - Yoan Duhoo
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
| | - Matthew Jessop
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
| | - Eaazhisai Kandiah
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France
- European Synchrotron Radiation Facility, 71 Avenue des martyrs, Grenoble, France
| | - Frédéric Barras
- Institut Pasteur, Université de Paris, CNRS UMR6047, Stress Adaptation and Metabolism Unit, Department of Microbiology, Paris, France
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire Végétale, Univ Grenoble Alpes, CEA, CNRS, INRAE, IRIG, 17 Avenue des martyrs, Grenoble, France
| | - Irina Gutsche
- Institut de Biologie Structurale, Univ Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, Grenoble, France.
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8
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Bhandari V, Van Ommen DAJ, Wong KS, Houry WA. Analysis of the Evolution of the MoxR ATPases. J Phys Chem A 2022; 126:4734-4746. [PMID: 35852937 DOI: 10.1021/acs.jpca.2c02554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
MoxR proteins comprise a family of ATPases Associated with diverse cellular Activities (AAA+). These proteins are widespread and found across the diversity of prokaryotic species. Despite their ubiquity, members of the group remain poorly characterized. Only a few examples of MoxR proteins have been associated with cellular roles, where they have been shown to perform chaperone-like functions. A characteristic feature of MoxR proteins is their association with proteins containing the von Willebrand factor type A (VWA) domain. In an effort to understand the spread and diversity of the MoxR family, an evolutionary approach was undertaken. Phylogenetic techniques were used to define nine major subfamilies within the MoxR family. A combination of phylogenetic and genomic approaches was utilized to explore the extent of the partnership between the MoxR and VWA domain containing proteins (VWA proteins). These analyses led to the clarification of genetic linkages between MoxR and VWA proteins. A significant partnership is described here, as seven of nine MoxR subfamilies were found to be linked to VWA proteins. Available genomic data were also used to assess the intraprotein diversification of MoxR and VWA protein sequences. Data clearly indicated that, in MoxR proteins, the ATPase domain is maintained with high conservation while the remaining protein sequence evolves at a faster rate; a similar pattern was observed for the VWA domain in VWA proteins. Overall, our data present insights into the modular evolution of MoxR ATPases.
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Affiliation(s)
- Vaibhav Bhandari
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - David A J Van Ommen
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Keith S Wong
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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9
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Abstract
Carboxysomes are anabolic bacterial microcompartments that play an essential role in carbon fixation in cyanobacteria and some chemoautotrophs. This self-assembling organelle encapsulates the key CO2-fixing enzymes, Rubisco, and carbonic anhydrase using a polyhedral protein shell that is constructed by hundreds of shell protein paralogs. The α-carboxysome from the chemoautotroph Halothiobacillus neapolitanus serves as a model system in fundamental studies and synthetic engineering of carboxysomes. In this study, we adopted a QconCAT-based quantitative mass spectrometry approach to determine the stoichiometric composition of native α-carboxysomes from H. neapolitanus. We further performed an in-depth comparison of the protein stoichiometry of native α-carboxysomes and their recombinant counterparts heterologously generated in Escherichia coli to evaluate the structural variability and remodeling of α-carboxysomes. Our results provide insight into the molecular principles that mediate carboxysome assembly, which may aid in rational design and reprogramming of carboxysomes in new contexts for biotechnological applications. IMPORTANCE A wide range of bacteria use special protein-based organelles, termed bacterial microcompartments, to encase enzymes and reactions to increase the efficiency of biological processes. As a model bacterial microcompartment, the carboxysome contains a protein shell filled with the primary carbon fixation enzyme Rubisco. The self-assembling organelle is generated by hundreds of proteins and plays important roles in converting carbon dioxide to sugar, a process known as carbon fixation. In this study, we uncovered the exact stoichiometry of all building components and the structural plasticity of the functional α-carboxysome, using newly developed quantitative mass spectrometry together with biochemistry, electron microscopy, and enzymatic assay. The study advances our understanding of the architecture and modularity of natural carboxysomes. The knowledge learned from natural carboxysomes will suggest feasible ways to produce functional carboxysomes in other hosts, such as crop plants, with the overwhelming goal of boosting cell metabolism and crop yields.
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10
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Mickolajczyk KJ, Olinares PDB, Chait BT, Liu S, Kapoor TM. The MIDAS domain of AAA mechanoenzyme Mdn1 forms catch bonds with two different substrates. eLife 2022; 11:73534. [PMID: 35147499 PMCID: PMC8837202 DOI: 10.7554/elife.73534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/19/2022] [Indexed: 12/21/2022] Open
Abstract
Catch bonds are a form of mechanoregulation wherein protein-ligand interactions are strengthened by the application of dissociative tension. Currently, the best-characterized examples of catch bonds are between single protein-ligand pairs. The essential AAA (ATPase associated with diverse cellular activities) mechanoenzyme Mdn1 drives at least two separate steps in ribosome biogenesis, using its MIDAS domain to extract the ubiquitin-like (UBL) domain-containing proteins Rsa4 and Ytm1 from ribosomal precursors. However, it must subsequently release these assembly factors to reinitiate the enzymatic cycle. The mechanism underlying the switching of the MIDAS-UBL interaction between strongly and weakly bound states is unknown. Here, we use optical tweezers to investigate the force dependence of MIDAS-UBL binding. Parallel experiments with Rsa4 and Ytm1 show that forces up to ~4 pN, matching the magnitude of force produced by AAA proteins similar to Mdn1, enhance the MIDAS domain binding lifetime up to 10-fold, and higher forces accelerate dissociation. Together, our studies indicate that Mdn1's MIDAS domain can form catch bonds with more than one UBL substrate, and provide insights into how mechanoregulation may contribute to the Mdn1 enzymatic cycle during ribosome biogenesis.
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Affiliation(s)
- Keith J Mickolajczyk
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, United States
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, United States
| | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, United States
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11
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Chen T, Fang Y, Jiang Q, Dykes GF, Lin Y, Price GD, Long BM, Liu LN. Incorporation of Functional Rubisco Activases into Engineered Carboxysomes to Enhance Carbon Fixation. ACS Synth Biol 2022; 11:154-161. [PMID: 34664944 PMCID: PMC8787814 DOI: 10.1021/acssynbio.1c00311] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
The carboxysome is
a versatile paradigm of prokaryotic organelles
and is a proteinaceous self-assembling microcompartment that plays
essential roles in carbon fixation in all cyanobacteria and some chemoautotrophs.
The carboxysome encapsulates
the central CO2-fixing enzyme, ribulose-1,5-bisphosphate
carboxylase/oxygenase (Rubisco), using a polyhedral protein shell
that is selectively permeable to specific metabolites in favor of
Rubisco carboxylation. There is tremendous interest in repurposing
carboxysomes to boost carbon fixation in heterologous organisms. Here,
we develop the design and engineering of α-carboxysomes by coexpressing
the Rubisco activase components CbbQ and CbbO with α-carboxysomes
in Escherichia coli. Our results show
that CbbQ and CbbO could assemble into the reconstituted α-carboxysome
as intrinsic components. Incorporation of both CbbQ and CbbO within
the carboxysome promotes activation of Rubisco and enhances the CO2-fixation activities of recombinant carboxysomes. We also
show that the structural composition of these carboxysomes could be
modified in different expression systems, representing the plasticity
of the carboxysome architecture. In translational terms, our study
informs strategies for engineering and modulating carboxysomes in
diverse biotechnological applications.
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Affiliation(s)
- Taiyu Chen
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Yi Fang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
| | - Qiuyao Jiang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
| | - Gregory F. Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - G. Dean Price
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory 2601, Australia
| | - Benedict M. Long
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory 2601, Australia
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
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12
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Yan XF, Yang C, Wang M, Yong Y, Deng Y, Gao YG. Structural analyses of the AAA+ ATPase domain of the transcriptional regulator GtrR in the BDSF quorum-sensing system in Burkholderia cenocepacia. FEBS Lett 2022; 596:71-80. [PMID: 34837384 DOI: 10.1002/1873-3468.14244] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/08/2021] [Accepted: 11/23/2021] [Indexed: 11/11/2022]
Abstract
Global transcriptional regulator downstream RpfR (GtrR) is a key downstream regulator for quorum-sensing signaling molecule cis-2-dodecenoic acid (BDSF). As a bacterial enhancer-binding protein (bEBP), GtrR is composed of an N-terminal receiver domain, a central ATPases associated with diverse cellular activities (AAA+) ATPase σ54 -interaction domain, and a C-terminal helix-turn-helix DNA-binding domain. In this work, we solved its AAA+ ATPase domain in both apo and GTP-bound forms. The structure revealed how GtrR specifically recognizes GTP. In addition, we also revealed that GtrR has moderate GTPase activity in vitro in the absence of its activation signal. Finally, we found the residues K170, D236, R311, and R357 in GtrR that are crucial to its biological function, any single mutation leading to completely abolishing GtrR activity.
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Affiliation(s)
- Xin-Fu Yan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Chunxi Yang
- Jiangxi provincial People's Hospital Affiliated to Nanchang University, Nanchang, China
| | - Mingfang Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Yonlada Yong
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yinyue Deng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Yong-Gui Gao
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
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13
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Ting SY, LaCourse KD, Ledvina HE, Zhang R, Radey MC, Kulasekara HD, Somavanshi R, Bertolli SK, Gallagher LA, Kim J, Penewit KM, Salipante SJ, Xu L, Peterson SB, Mougous JD. Discovery of coordinately regulated pathways that provide innate protection against interbacterial antagonism. eLife 2022; 11:74658. [PMID: 35175195 PMCID: PMC8926400 DOI: 10.7554/elife.74658] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 02/16/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial survival is fraught with antagonism, including that deriving from viruses and competing bacterial cells. It is now appreciated that bacteria mount complex antiviral responses; however, whether a coordinated defense against bacterial threats is undertaken is not well understood. Previously, we showed that Pseudomonas aeruginosa possess a danger-sensing pathway that is a critical fitness determinant during competition against other bacteria. Here, we conducted genome-wide screens in P. aeruginosa that reveal three conserved and widespread interbacterial antagonism resistance clusters (arc1-3). We find that although arc1-3 are coordinately activated by the Gac/Rsm danger-sensing system, they function independently and provide idiosyncratic defense capabilities, distinguishing them from general stress response pathways. Our findings demonstrate that Arc3 family proteins provide specific protection against phospholipase toxins by preventing the accumulation of lysophospholipids in a manner distinct from previously characterized membrane repair systems. These findings liken the response of P. aeruginosa to bacterial threats to that of eukaryotic innate immunity, wherein threat detection leads to the activation of specialized defense systems.
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Affiliation(s)
- See-Yeun Ting
- Department of Microbiology, University of Washington School of MedicineSeattleUnited States
| | - Kaitlyn D LaCourse
- Department of Microbiology, University of Washington School of MedicineSeattleUnited States
| | - Hannah E Ledvina
- Department of Microbiology, University of Washington School of MedicineSeattleUnited States
| | - Rutan Zhang
- Department of Medicinal Chemistry, University of Washington School of PharmacySeattleUnited States
| | - Matthew C Radey
- Department of Microbiology, University of Washington School of MedicineSeattleUnited States
| | - Hemantha D Kulasekara
- Department of Microbiology, University of Washington School of MedicineSeattleUnited States
| | - Rahul Somavanshi
- Department of Microbiology, University of Washington School of MedicineSeattleUnited States
| | - Savannah K Bertolli
- Department of Microbiology, University of Washington School of MedicineSeattleUnited States
| | - Larry A Gallagher
- Department of Microbiology, University of Washington School of MedicineSeattleUnited States
| | - Jennifer Kim
- Department of Microbiology, University of Washington School of MedicineSeattleUnited States
| | - Kelsi M Penewit
- Department of Laboratory Medicine and Pathology, University of Washington School of MedicineSeattleUnited States
| | - Stephen J Salipante
- Department of Laboratory Medicine and Pathology, University of Washington School of MedicineSeattleUnited States
| | - Libin Xu
- Department of Medicinal Chemistry, University of Washington School of PharmacySeattleUnited States
| | - S Brook Peterson
- Department of Microbiology, University of Washington School of MedicineSeattleUnited States
| | - Joseph D Mougous
- Department of Microbiology, University of Washington School of MedicineSeattleUnited States,Department of Biochemistry, University of Washington School of MedicineSeattleUnited States,Howard Hughes Medical Institute, University of WashingtonSeattleUnited States
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14
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The CbbQO-type rubisco activases encoded in carboxysome gene clusters can activate carboxysomal form IA rubiscos. J Biol Chem 2021; 298:101476. [PMID: 34890642 PMCID: PMC8718961 DOI: 10.1016/j.jbc.2021.101476] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 01/15/2023] Open
Abstract
The CO2-fixing enzyme rubisco is responsible for almost all carbon fixation. This process frequently requires rubisco activase (Rca) machinery, which couples ATP hydrolysis to the removal of inhibitory sugar phosphates, including the rubisco substrate ribulose 1,5-bisphosphate (RuBP). Rubisco is sometimes compartmentalized in carboxysomes, bacterial microcompartments that enable a carbon dioxide concentrating mechanism (CCM). Characterized carboxysomal rubiscos, however, are not prone to inhibition, and often no activase machinery is associated with these enzymes. Here, we characterize two carboxysomal rubiscos of the form IAC clade that are associated with CbbQO-type Rcas. These enzymes release RuBP at a much lower rate than the canonical carboxysomal rubisco from Synechococcus PCC6301. We found that CbbQO-type Rcas encoded in carboxysome gene clusters can remove RuBP and the tight-binding transition state analog carboxy-arabinitol 1,5-bisphosphate from cognate rubiscos. The Acidithiobacillus ferrooxidans genome encodes two form IA rubiscos associated with two sets of cbbQ and cbbO genes. We show that the two CbbQO activase systems display specificity for the rubisco enzyme encoded in the same gene cluster, and this property can be switched by substituting the C-terminal three residues of the large subunit. Our findings indicate that the kinetic and inhibitory properties of proteobacterial form IA rubiscos are diverse and predict that Rcas may be necessary for some α-carboxysomal CCMs. These findings will have implications for efforts aiming to introduce biophysical CCMs into plants and other hosts for improvement of carbon fixation of crops.
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15
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Liu LN. Advances in the bacterial organelles for CO 2 fixation. Trends Microbiol 2021; 30:567-580. [PMID: 34802870 DOI: 10.1016/j.tim.2021.10.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 02/08/2023]
Abstract
Carboxysomes are a family of bacterial microcompartments (BMCs), present in all cyanobacteria and some proteobacteria, which encapsulate the primary CO2-fixing enzyme, Rubisco, within a virus-like polyhedral protein shell. Carboxysomes provide significantly elevated levels of CO2 around Rubisco to maximize carboxylation and reduce wasteful photorespiration, thus functioning as the central CO2-fixation organelles of bacterial CO2-concentration mechanisms. Their intriguing architectural features allow carboxysomes to make a vast contribution to carbon assimilation on a global scale. In this review, we discuss recent research progress that provides new insights into the mechanisms of how carboxysomes are assembled and functionally maintained in bacteria and recent advances in synthetic biology to repurpose the metabolic module in diverse applications.
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Affiliation(s)
- Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK; College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 266003 Qingdao, China.
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16
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Khan YA, White KI, Brunger AT. The AAA+ superfamily: a review of the structural and mechanistic principles of these molecular machines. Crit Rev Biochem Mol Biol 2021; 57:156-187. [PMID: 34632886 DOI: 10.1080/10409238.2021.1979460] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
ATPases associated with diverse cellular activities (AAA+ proteins) are a superfamily of proteins found throughout all domains of life. The hallmark of this family is a conserved AAA+ domain responsible for a diverse range of cellular activities. Typically, AAA+ proteins transduce chemical energy from the hydrolysis of ATP into mechanical energy through conformational change, which can drive a variety of biological processes. AAA+ proteins operate in a variety of cellular contexts with diverse functions including disassembly of SNARE proteins, protein quality control, DNA replication, ribosome assembly, and viral replication. This breadth of function illustrates both the importance of AAA+ proteins in health and disease and emphasizes the importance of understanding conserved mechanisms of chemo-mechanical energy transduction. This review is divided into three major portions. First, the core AAA+ fold is presented. Next, the seven different clades of AAA+ proteins and structural details and reclassification pertaining to proteins in each clade are described. Finally, two well-known AAA+ proteins, NSF and its close relative p97, are reviewed in detail.
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Affiliation(s)
- Yousuf A Khan
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.,Department of Structural Biology, Stanford University, Stanford, CA, USA.,Department of Photon Science, Stanford University, Stanford, CA, USA.,Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA
| | - K Ian White
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.,Department of Structural Biology, Stanford University, Stanford, CA, USA.,Department of Photon Science, Stanford University, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.,Department of Structural Biology, Stanford University, Stanford, CA, USA.,Department of Photon Science, Stanford University, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
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17
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Borden JS, Savage DF. New discoveries expand possibilities for carboxysome engineering. Curr Opin Microbiol 2021; 61:58-66. [PMID: 33798818 DOI: 10.1016/j.mib.2021.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/06/2021] [Accepted: 03/11/2021] [Indexed: 12/19/2022]
Abstract
Carboxysomes are CO2-fixing protein compartments present in all cyanobacteria and some proteobacteria. These structures are attractive candidates for carbon assimilation bioengineering because they concentrate carbon, allowing the fixation reaction to occur near its maximum rate, and because they self-assemble in diverse organisms with a set of standard biological parts. Recent discoveries have expanded our understanding of how the carboxysome assembles, distributes itself, and sustains its metabolism. These studies have already led to substantial advances in engineering the carboxysome and carbon concentrating mechanism into recombinant organisms, with an eye towards establishing the system in industrial microbes and plants. Future studies may also consider the potential of in vitro carboxysomes for both discovery and applied science.
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Affiliation(s)
- Julia S Borden
- Department of Molecular & Cellular Biology, UC Berkeley, Berkeley, CA 94720, USA
| | - David F Savage
- Department of Molecular & Cellular Biology, UC Berkeley, Berkeley, CA 94720, USA.
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18
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Jessop M, Felix J, Gutsche I. AAA+ ATPases: structural insertions under the magnifying glass. Curr Opin Struct Biol 2021; 66:119-128. [PMID: 33246198 PMCID: PMC7973254 DOI: 10.1016/j.sbi.2020.10.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/19/2020] [Accepted: 10/27/2020] [Indexed: 11/29/2022]
Abstract
AAA+ ATPases are a diverse protein superfamily which power a vast number of cellular processes, from protein degradation to genome replication and ribosome biogenesis. The latest advances in cryo-EM have resulted in a spectacular increase in the number and quality of AAA+ ATPase structures. This abundance of new information enables closer examination of different types of structural insertions into the conserved core, revealing discrepancies in the current classification of AAA+ modules into clades. Additionally, combined with biochemical data, it has allowed rapid progress in our understanding of structure-functional relationships and provided arguments both in favour and against the existence of a unifying molecular mechanism for the ATPase activity and action on substrates, stimulating further intensive research.
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Affiliation(s)
- Matthew Jessop
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044 Grenoble, France.
| | - Jan Felix
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044 Grenoble, France
| | - Irina Gutsche
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044 Grenoble, France.
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19
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The Novel Halovirus Hardycor1, and the Presence of Active (Induced) Proviruses in Four Haloarchaea. Genes (Basel) 2021; 12:genes12020149. [PMID: 33498646 PMCID: PMC7911831 DOI: 10.3390/genes12020149] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 12/15/2022] Open
Abstract
The virus Hardycor1 was isolated in 1998 and infects the haloarchaeon Halorubrum coriense. DNA from a frozen stock (HC1) was sequenced and the viral genome found to be 45,142 bp of dsDNA, probably having redundant, circularly permuted termini. The genome showed little similarity (BLASTn) to known viruses. Only twenty-two of the 53 (41%) predicted proteins were significantly similar to sequences in the NCBI nr protein database (E-value ≤ 10-15). Six caudovirus-like proteins were encoded, including large subunit terminase (TerL), major capsid protein (Mcp) and tape measure protein (Tmp). Hardycor1 was predicted to be a siphovirus (VIRFAM). No close relationship to other viruses was found using phylogenetic tree reconstructions based on TerL and Mcp. Unexpectedly, the sequenced virus stock HC1 also revealed two induced proviruses of the host: a siphovirus (Humcor1) and a pleolipovirus (Humcor2). A re-examination of other similarly sequenced, archival virus stocks revealed induced proviruses of Haloferax volcanii, Haloferax gibbonsii and Haloarcula hispanica, three of which were pleolipoviruses. One provirus (Halfvol2) of Hfx. volcanii showed little similarity (BLASTn) to known viruses and probably represents a novel virus group. The attP sequences of many pleolipoproviruses were found to be embedded in a newly detected coding sequence, split in the provirus state, that spans between genes for integrase and a downstream CxxC-motif protein. This gene might play an important role in regulation of the temperate state.
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20
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Pang JJ, Shin JS, Li SY. The Catalytic Role of RuBisCO for in situ CO 2 Recycling in Escherichia coli. Front Bioeng Biotechnol 2020; 8:543807. [PMID: 33330409 PMCID: PMC7734965 DOI: 10.3389/fbioe.2020.543807] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 10/13/2020] [Indexed: 01/22/2023] Open
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is a key enzyme responsible for biological CO2 assimilation. RuBisCO can be heterologously expressed in Escherichia coli so that glucose and CO2 are co-metabolized to achieve high mixotrophic metabolite production, where the theoretical yield of mixotrophic metabolite production is 2.4 mol(ethanol+acetate+pyruvate)/molglucose. However, RuBisCO is known for its low kcat and for forming inhibited complexes with its substrate ribulose-1,5-bisphosphate (RuBP) and other sugar phosphates, yet the inhibited form of RuBisCO can be reversed by RuBisCO activase (Rca). In this study, RuBisCO forms I and II were cloned and expressed in Escherichia coli for in situ CO2 recycling, where CO2 produced during glucose fermentation was recycled and co-metabolized with the glucose. In addition, forms I and II RuBisCO activases were co-expressed with RuBisCO in E. coli to determine their in vivo effects on in situ CO2 recycling. Form I RuBisCO activase (Rca1) was co-expressed with form I RuBisCO and form II RuBisCO activase (Rca2) was co-expressed with form II RuBisCO. The results showed that both form I and form II RuBisCO exhibit comparable activities in E. coli and generated similar levels of in situ CO2 recycling. A significant increase in the total metabolite yield from 1.5 ± 0.1 to 2.2 ± 0.1 mol(ethanol+acetate+pyruvate)/molglucose occurred when Rca2 was co-expressed with form II RuBisCO. Meanwhile, the total metabolite yield increased from 1.7 ± 0.1 to 2.0 ± 0.1 mol(ethanol+acetate+pyruvate)/molglucose when Rca1 was co-expressed with form I RuBisCO. This data suggests that both forms I and II RuBisCO are subject to in vivo RuBP inhibition yet can be relieved by the co-expression of Rca. Interestingly, it is suggested that the in vivo RuBP inhibition of form II RuBisCO can be more easily reversed compared to form I. When the catalytic power of RuBisCO is maintained by Rca, the high activity of phosphoribulokinase (Prk) plays an important role in directing glucose to the RuBisCO-based engineered pathway and fermentation yields of 2.1–2.3 mol(ethanol+acetate+pyruvate)/molglucose can be obtained. This study is the first to demonstrate that in vivo RuBP inhibition of RuBisCO can be a bottleneck for in situ CO2 recycling in E. coli.
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Affiliation(s)
- Ju-Jiun Pang
- Department of Chemical Engineering, National Chung Hsing University, Taichung City, Taiwan
| | - Jong-Shik Shin
- Department of Biotechnology, Yonsei University, Seoul, South Korea
| | - Si-Yu Li
- Department of Chemical Engineering, National Chung Hsing University, Taichung City, Taiwan.,Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung City, Taiwan
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21
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Ng J, Guo Z, Mueller-Cajar O. Rubisco activase requires residues in the large subunit N terminus to remodel inhibited plant Rubisco. J Biol Chem 2020; 295:16427-16435. [PMID: 32948656 PMCID: PMC7705312 DOI: 10.1074/jbc.ra120.015759] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/09/2020] [Indexed: 11/06/2022] Open
Abstract
The photosynthetic CO2 fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) forms dead-end inhibited complexes while binding multiple sugar phosphates, including its substrate ribulose 1,5-bisphosphate. Rubisco can be rescued from this inhibited form by molecular chaperones belonging to the ATPases associated with diverse cellular activities (AAA+ proteins) termed Rubisco activases (Rcas). The mechanism of green-type Rca found in higher plants has proved elusive, in part because until recently higher-plant Rubiscos could not be expressed recombinantly. Identifying the interaction sites between Rubisco and Rca is critical to formulate mechanistic hypotheses. Toward that end here we purify and characterize a suite of 33 Arabidopsis Rubisco mutants for their ability to be activated by Rca. Mutation of 17 surface-exposed large subunit residues did not yield variants that were perturbed in their interaction with Rca. In contrast, we find that Rca activity is highly sensitive to truncations and mutations in the conserved N terminus of the Rubisco large subunit. Large subunits lacking residues 1-4 are functional Rubiscos but cannot be activated. Both T5A and T7A substitutions result in functional carboxylases that are poorly activated by Rca, indicating the side chains of these residues form a critical interaction with the chaperone. Many other AAA+ proteins function by threading macromolecules through a central pore of a disc-shaped hexamer. Our results are consistent with a model in which Rca transiently threads the Rubisco large subunit N terminus through the axial pore of the AAA+ hexamer.
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Affiliation(s)
- Jediael Ng
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Zhijun Guo
- School of Biological Sciences, Nanyang Technological University, Singapore
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22
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Chaperone Machineries of Rubisco – The Most Abundant Enzyme. Trends Biochem Sci 2020; 45:748-763. [DOI: 10.1016/j.tibs.2020.05.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/19/2020] [Accepted: 05/04/2020] [Indexed: 12/14/2022]
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23
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Long-range intramolecular allostery and regulation in the dynein-like AAA protein Mdn1. Proc Natl Acad Sci U S A 2020; 117:18459-18469. [PMID: 32694211 DOI: 10.1073/pnas.2002792117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Mdn1 is an essential mechanoenzyme that uses the energy from ATP hydrolysis to physically reshape and remodel, and thus mature, the 60S subunit of the ribosome. This massive (>500 kDa) protein has an N-terminal AAA (ATPase associated with diverse cellular activities) ring, which, like dynein, has six ATPase sites. The AAA ring is followed by large (>2,000 aa) linking domains that include an ∼500-aa disordered (D/E-rich) region, and a C-terminal substrate-binding MIDAS domain. Recent models suggest that intramolecular docking of the MIDAS domain onto the AAA ring is required for Mdn1 to transmit force to its ribosomal substrates, but it is not currently understood what role the linking domains play, or why tethering the MIDAS domain to the AAA ring is required for protein function. Here, we use chemical probes, single-particle electron microscopy, and native mass spectrometry to study the AAA and MIDAS domains separately or in combination. We find that Mdn1 lacking the D/E-rich and MIDAS domains retains ATP and chemical probe binding activities. Free MIDAS domain can bind to the AAA ring of this construct in a stereo-specific bimolecular interaction, and, interestingly, this binding reduces ATPase activity. Whereas intramolecular MIDAS docking appears to require a treatment with a chemical inhibitor or preribosome binding, bimolecular MIDAS docking does not. Hence, tethering the MIDAS domain to the AAA ring serves to prevent, rather than promote, MIDAS docking in the absence of inducing signals.
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