1
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Wagner J, Carvajal AI, Bracher A, Beck F, Wan W, Bohn S, Körner R, Baumeister W, Fernandez-Busnadiego R, Hartl FU. Visualizing chaperonin function in situ by cryo-electron tomography. Nature 2024:10.1038/s41586-024-07843-w. [PMID: 39169181 DOI: 10.1038/s41586-024-07843-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 07/18/2024] [Indexed: 08/23/2024]
Abstract
Chaperonins are large barrel-shaped complexes that mediate ATP-dependent protein folding1-3. The bacterial chaperonin GroEL forms juxtaposed rings that bind unfolded protein and the lid-shaped cofactor GroES at their apertures. In vitro analyses of the chaperonin reaction have shown that substrate protein folds, unimpaired by aggregation, while transiently encapsulated in the GroEL central cavity by GroES4-6. To determine the functional stoichiometry of GroEL, GroES and client protein in situ, here we visualized chaperonin complexes in their natural cellular environment using cryo-electron tomography. We find that, under various growth conditions, around 55-70% of GroEL binds GroES asymmetrically on one ring, with the remainder populating symmetrical complexes. Bound substrate protein is detected on the free ring of the asymmetrical complex, defining the substrate acceptor state. In situ analysis of GroEL-GroES chambers, validated by high-resolution structures obtained in vitro, showed the presence of encapsulated substrate protein in a folded state before release into the cytosol. Based on a comprehensive quantification and conformational analysis of chaperonin complexes, we propose a GroEL-GroES reaction cycle that consists of linked asymmetrical and symmetrical subreactions mediating protein folding. Our findings illuminate the native conformational and functional chaperonin cycle directly within cells.
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Affiliation(s)
- Jonathan Wagner
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
- Research Group Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
- Institute of Neuropathology, University Medical Center Göttingen, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Alonso I Carvajal
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Andreas Bracher
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Beck
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - William Wan
- Vanderbilt University Center for Structural Biology, Nashville, TN, USA
| | - Stefan Bohn
- Research Group CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany
- Institute of Structural Biology, Helmholtz Center Munich, Oberschleissheim, Germany
| | - Roman Körner
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Wolfgang Baumeister
- Research Group Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany.
| | - Ruben Fernandez-Busnadiego
- Institute of Neuropathology, University Medical Center Göttingen, Göttingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
- Faculty of Physics, University of Göttingen, Göttingen, Germany.
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany.
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2
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Mao J, Yang X, Yan C, Wang F, Zheng R. Proteomic analysis of carbapenem-resistant Klebsiella pneumoniae outer membrane vesicles under the action of phages combined with tigecycline. Ann Clin Microbiol Antimicrob 2024; 23:73. [PMID: 39164718 PMCID: PMC11337635 DOI: 10.1186/s12941-024-00734-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 08/06/2024] [Indexed: 08/22/2024] Open
Abstract
BACKGROUND Klebsiella pneumoniae is the most commonly encountered pathogen in clinical practice. Widespread use of broad-spectrum antibiotics has led to the current global dissemination of carbapenem-resistant K. pneumoniae, which poses a significant threat to antibacterial treatment efficacy and public health. Outer membrane vesicles (OMVs) have been identified as carriers capable of facilitating the transfer of virulence and resistance genes. However, the role of OMVs in carbapenem-resistant K. pneumoniae under external pressures such as antibiotic and phage treatments remains unclear. METHODS To isolate and purify OMVs under the pressure of phages and tigecycline, we subjected K. pneumoniae 0692 harboring plasmid-mediated blaNDM-1 and blaKPC-2 genes to density gradient separation. The double-layer plate method was used to isolate MJ1, which efficiently lysed K. pneumoniae 0692 cells. Transmission electron microscopy (TEM) was used to characterize the isolated phages and extract OMV groups for relevant morphological identification. Determination of protein content of each OMV group was conducted through bicinchoninic acid assay (BCA) and proteomic analysis. RESULTS K. pneumoniae 0692 released OMVs in response to different environmental stimuli, which were characterized through TEM as having the typical structure and particle size of OMVs. Phage or tigecycline treatment alone resulted in a slight increase in the mean protein concentration of OMVs secreted by K. pneumoniae 0692 compared to that in the untreated group. However, when phage treatment was combined with tigecycline, there was a significant reduction in the average protein concentration of OMVs compared to tigecycline treatment alone. Proteomics showed that OMVs encapsulated numerous functional proteins and that under different external stresses of phages and tigecycline, the proteins carried by K. pneumoniae 0692-derived OMVs were significantly upregulated or downregulated compared with those in the untreated group. CONCLUSIONS This study confirmed the ability of OMVs to carry abundant proteins and highlighted the important role of OMV-associated proteins in bacterial responses to phages and tigecycline, representing an important advancement in microbial resistance research.
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Affiliation(s)
- Jing Mao
- Department of Clinical Laboratory, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
- The Affiliated Hospital of College of Medical, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Xiaoyu Yang
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
- Regenerative Medicine Research Center, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Cheng Yan
- Department of Clinical Laboratory, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
- The Affiliated Hospital of College of Medical, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Fan Wang
- Department of Clinical Laboratory, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China.
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China.
| | - Rui Zheng
- Department of Clinical Laboratory, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China.
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China.
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3
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Mallik S, Poch D, Burick S, Schlieker C. Protein folding and quality control during nuclear transport. Curr Opin Cell Biol 2024; 90:102407. [PMID: 39142062 DOI: 10.1016/j.ceb.2024.102407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 07/06/2024] [Accepted: 07/16/2024] [Indexed: 08/16/2024]
Abstract
The spatial separation of protein synthesis from the compartmental destiny of proteins led to the evolution of transport systems that are efficient and yet highly specific. Co-translational transport has emerged as a strategy to avoid cytosolic aggregation of folding intermediates and the need for energy-consuming unfolding strategies to enable transport through narrow conduits connecting compartments. While translation and compartmental translocation are at times tightly coordinated, we know very little about the temporal coordination of translation, protein folding, and nuclear import. Here, we consider the implications of co-translational engagement of nuclear import machinery. We propose that the dynamic interplay of karyopherins and intrinsically disordered nucleoporins create a favorable protein folding environment for cargo en route to the nuclear compartment while maintaining a barrier function of the nuclear pore complex. Our model is discussed in the context of neurological disorders that are tied to defects in nuclear transport and protein quality control.
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Affiliation(s)
- Sunanda Mallik
- Yale University, Department of Molecular Biophysics and Biochemistry, New Haven, CT, USA
| | - Dylan Poch
- Yale University, Department of Molecular Biophysics and Biochemistry, New Haven, CT, USA
| | - Sophia Burick
- Yale University, Department of Molecular Biophysics and Biochemistry, New Haven, CT, USA
| | - Christian Schlieker
- Yale University, Department of Molecular Biophysics and Biochemistry, New Haven, CT, USA; Yale School of Medicine, Department of Cell Biology, New Haven, CT, USA.
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4
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Nishijima M, Kobayashi K, Masuda-Endo M, Yoda H, Koike-Takeshita A. Regioselective photocyclodimerization of 2-anthracenecarboxylic acid through ATP hydrolysis-driven conformational change using simulation prediction-designed GroEL mutant. J Biosci Bioeng 2024:S1389-1723(24)00191-9. [PMID: 39097441 DOI: 10.1016/j.jbiosc.2024.07.002] [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: 07/03/2023] [Revised: 06/25/2024] [Accepted: 07/01/2024] [Indexed: 08/05/2024]
Abstract
GroEL, a chaperone protein responsible for peptide and denatured protein folding, undergoes substantial conformational changes driven by ATP binding and hydrolysis during folding. Utilizing these conformational changes, we demonstrated the GroEL-mediated regioselective photocyclodimerization of 2-anthracenecarboxylic acid (AC) using ATP hydrolysis as an external stimulus. We designed and prepared an optimal GroEL mutant to employ in a docking simulation that has been actively used in recent years. Based on the large difference in the motif of hydrogen bonds between AC and GroEL mutant compared with the wild-type, we predicted that GroELMEL, in which the 307‒309th amino acid residues were mutated to Ala, could alter the orientation of bound AC in GroEL. The GroELMEL-mediated photocyclodimerization of AC can be used for regioselective inversion upon ATP addition to a moderate extent.
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Affiliation(s)
- Masaki Nishijima
- National Institute of Technology (KOSEN), Wakayama College, 77 Noshima, Gobo, Wakayama 644-0023, Japan.
| | - Kota Kobayashi
- Department of Applied Chemistry and Bioscience, Graduate School of Engineering, Kanagawa Institute of Technology, 1030 Shimo-ogino, Atsugi, Kanagawa 243-0292, Japan
| | - Megumi Masuda-Endo
- Biomedical Research Center, Kanagawa Institute of Technology, 1030 Shimo-ogino, Atsugi, Kanagawa 243-0292, Japan
| | - Hiromi Yoda
- Department of Applied Chemistry and Bioscience, Graduate School of Engineering, Kanagawa Institute of Technology, 1030 Shimo-ogino, Atsugi, Kanagawa 243-0292, Japan; Biomedical Research Center, Kanagawa Institute of Technology, 1030 Shimo-ogino, Atsugi, Kanagawa 243-0292, Japan
| | - Ayumi Koike-Takeshita
- Department of Applied Chemistry and Bioscience, Graduate School of Engineering, Kanagawa Institute of Technology, 1030 Shimo-ogino, Atsugi, Kanagawa 243-0292, Japan; Biomedical Research Center, Kanagawa Institute of Technology, 1030 Shimo-ogino, Atsugi, Kanagawa 243-0292, Japan
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5
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Reingewertz TH, Ben-Maimon M, Zafrir Z, Tuller T, Horovitz A. Synonymous and non-synonymous codon substitutions can alleviate dependence on GroEL for folding. Protein Sci 2024; 33:e5087. [PMID: 39074255 DOI: 10.1002/pro.5087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/03/2024] [Accepted: 06/05/2024] [Indexed: 07/31/2024]
Abstract
The Escherichia coli GroEL/ES chaperonin system facilitates protein folding in an ATP-driven manner. There are <100 obligate clients of this system in E. coli although GroEL can interact and assist the folding of a multitude of proteins in vitro. It has remained unclear, however, which features distinguish obligate clients from all the other proteins in an E. coli cell. To address this question, we established a system for selecting mutations in mouse dihydrofolate reductase (mDHFR), a GroEL interactor, that diminish its dependence on GroEL for folding. Strikingly, both synonymous and non-synonymous codon substitutions were found to reduce mDHFR's dependence on GroEL. The non-synonymous substitutions increase the rate of spontaneous folding whereas computational analysis indicates that the synonymous substitutions appear to affect translation rates at specific sites.
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Affiliation(s)
- Tali Haviv Reingewertz
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Miki Ben-Maimon
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Zohar Zafrir
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
- The Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel
| | - Amnon Horovitz
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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6
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Braxton JR, Shao H, Tse E, Gestwicki JE, Southworth DR. Asymmetric apical domain states of mitochondrial Hsp60 coordinate substrate engagement and chaperonin assembly. Nat Struct Mol Biol 2024:10.1038/s41594-024-01352-0. [PMID: 38951622 DOI: 10.1038/s41594-024-01352-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/07/2024] [Indexed: 07/03/2024]
Abstract
The mitochondrial chaperonin, mitochondrial heat shock protein 60 (mtHsp60), promotes the folding of newly imported and transiently misfolded proteins in the mitochondrial matrix, assisted by its co-chaperone mtHsp10. Despite its essential role in mitochondrial proteostasis, structural insights into how this chaperonin progresses through its ATP-dependent client folding cycle are not clear. Here, we determined cryo-EM structures of a hyperstable disease-associated human mtHsp60 mutant, V72I. Client density is identified in three distinct states, revealing interactions with the mtHsp60 apical domains and C termini that coordinate client positioning in the folding chamber. We further identify an asymmetric arrangement of the apical domains in the ATP state, in which an alternating up/down configuration positions interaction surfaces for simultaneous recruitment of mtHsp10 and client retention. Client is then fully encapsulated in mtHsp60-10, revealing prominent contacts at two discrete sites that potentially support maturation. These results identify distinct roles for the apical domains in coordinating client capture and progression through the chaperone cycle, supporting a conserved mechanism of group I chaperonin function.
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Affiliation(s)
- Julian R Braxton
- Graduate Program in Chemistry and Chemical Biology, University of California San Francisco, San Francisco, CA, USA
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Hao Shao
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Eric Tse
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Jason E Gestwicki
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA.
| | - Daniel R Southworth
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA, USA.
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7
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Wickramaratne AC, Wickner S, Kravats AN. Hsp90, a team player in protein quality control and the stress response in bacteria. Microbiol Mol Biol Rev 2024; 88:e0017622. [PMID: 38534118 PMCID: PMC11332350 DOI: 10.1128/mmbr.00176-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024] Open
Abstract
SUMMARYHeat shock protein 90 (Hsp90) participates in proteostasis by facilitating protein folding, activation, disaggregation, prevention of aggregation, degradation, and protection against degradation of various cellular proteins. It is highly conserved from bacteria to humans. In bacteria, protein remodeling by Hsp90 involves collaboration with the Hsp70 molecular chaperone and Hsp70 cochaperones. In eukaryotes, protein folding by Hsp90 is more complex and involves collaboration with many Hsp90 cochaperones as well as Hsp70 and Hsp70 cochaperones. This review focuses primarily on bacterial Hsp90 and highlights similarities and differences between bacterial and eukaryotic Hsp90. Seminal research findings that elucidate the structure and the mechanisms of protein folding, disaggregation, and reactivation promoted by Hsp90 are discussed. Understanding the mechanisms of bacterial Hsp90 will provide fundamental insight into the more complex eukaryotic chaperone systems.
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Affiliation(s)
- Anushka C. Wickramaratne
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Sue Wickner
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrea N. Kravats
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
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8
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Mahto FK, Bhattacharya A, Bhattacharya S. Molecular dynamics simulations shows real-time lid opening in Hsp70 chaperone. J Mol Graph Model 2024; 129:108726. [PMID: 38377794 DOI: 10.1016/j.jmgm.2024.108726] [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: 10/07/2023] [Revised: 12/12/2023] [Accepted: 02/08/2024] [Indexed: 02/22/2024]
Abstract
The stress-inducible mammalian heat shock protein Hsp70 and its bacterial orthologue DnaK are highly conserved molecular chaperones and a crucial part of the machinery responsible for protein folding and homeostasis. Hsp70 is a three-domain, 70 kDa protein that cycles between an ATP-bound state in which all three domains are securely coupled into one unit and an ADP-bound state in which they are loosely attached via a flexible interdomain linker. The Hsp70 presents an alluring novel therapeutic target since it is crucial for maintaining cellular proteostasis and is particularly crucial to cancer cells. We have performed molecular dynamics simulations of the SBD (substrate binding domain) along with the Lid domain in response to experimental efforts to identify small molecule inhibitors that impair the functioning of Hsp70. Our intent has been to characterize the motion of the SBD/Lid allosteric machinery and in, addition, to identify the effect of the PET16 molecule on this motion. Interestingly, we noticed the opening of the entire Lid domain in the apo-form of the dimer. The configuration of the open structure was very different from previously published structures (PDB 4JN4) of the open and docked conformation of the ATP bound form. MD simulations revealed the Lid to be capable of far greater dynamical excursions than has been anticipated by experimental structural biology. This is of value in future drug discovery efforts targeted to modulating Hsp70 activity. The PET16 molecule appears to be weakly bound and its effect on the dynamics of the complex is yet to be elucidated.
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Affiliation(s)
- Farindra Kumar Mahto
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
| | | | - Swati Bhattacharya
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
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9
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Dupuy E, Collet JF. Entering deeper into the mysteries of the GroEL-GroES nanomachine. Curr Opin Microbiol 2024; 79:102480. [PMID: 38714141 DOI: 10.1016/j.mib.2024.102480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 05/09/2024]
Abstract
In the densely populated intracellular milieu, polypeptides are at constant risk of nonspecific interactions and aggregation, posing a threat to essential cellular functions. Cells rely on a network of protein folding factors to deal with this challenge. The Hsp60 family of molecular chaperones, which depend on ATP for function, stands out in the proteostasis network by a characteristic structure comprising two multimeric rings arranged back to back. This review provides an updated overview of GroEL, the bacterial Hsp60, and its GroES (Hsp10) cofactor. Specifically, we highlight recent breakthroughs in understanding the intricate folding mechanisms of the GroEL-GroES nanomachine and explore the newly discovered interaction between GroEL and the chaperedoxin CnoX. Despite considerable research on the GroEL-GroES system, numerous questions remain to be explored.
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Affiliation(s)
- Emile Dupuy
- WELBIO department, WEL Research Institute, Avenue Pasteur 6, 1300 Wavre, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Jean-François Collet
- WELBIO department, WEL Research Institute, Avenue Pasteur 6, 1300 Wavre, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium.
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10
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Nair ZJ, Gao IH, Firras A, Chong KKL, Hill ED, Choo PY, Colomer-Winter C, Chen Q, Manzano C, Pethe K, Kline KA. An essential protease, FtsH, influences daptomycin resistance acquisition in Enterococcus faecalis. Mol Microbiol 2024; 121:1021-1038. [PMID: 38527904 DOI: 10.1111/mmi.15253] [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: 07/31/2023] [Revised: 03/11/2024] [Accepted: 03/11/2024] [Indexed: 03/27/2024]
Abstract
Daptomycin is a last-line antibiotic commonly used to treat vancomycin-resistant Enterococci, but resistance evolves rapidly and further restricts already limited treatment options. While genetic determinants associated with clinical daptomycin resistance (DAPR) have been described, information on factors affecting the speed of DAPR acquisition is limited. The multiple peptide resistance factor (MprF), a phosphatidylglycerol-modifying enzyme involved in cationic antimicrobial resistance, is linked to DAPR in pathogens such as methicillin-resistant Staphylococcus aureus. Since Enterococcus faecalis encodes two paralogs of mprF and clinical DAPR mutations do not map to mprF, we hypothesized that functional redundancy between the paralogs prevents mprF-mediated resistance and masks other evolutionary pathways to DAPR. Here, we performed in vitro evolution to DAPR in mprF mutant background. We discovered that the absence of mprF results in slowed DAPR evolution and is associated with inactivating mutations in ftsH, resulting in the depletion of the chaperone repressor HrcA. We also report that ftsH is essential in the parental, but not in the ΔmprF, strain where FtsH depletion results in growth impairment in the parental strain, a phenotype associated with reduced extracellular acidification and reduced ability for metabolic reduction. This presents FtsH and HrcA as enticing targets for developing anti-resistance strategies.
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Affiliation(s)
- Zeus Jaren Nair
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Interdisciplinary Graduate Programme, Graduate College, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Iris Hanxing Gao
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Aslam Firras
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Kelvin Kian Long Chong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Interdisciplinary Graduate Programme, Graduate College, Nanyang Technological University, Singapore, Singapore
| | - Eric D Hill
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Pei Yi Choo
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Cristina Colomer-Winter
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Qingyan Chen
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Caroline Manzano
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Kevin Pethe
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
| | - Kimberly A Kline
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
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11
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Zhang Y, Ma F, Chen J, Chen Y, Xu L, Li A, Liu Y, Ma R, Shi L. Controlled Refolding of Denatured IL-12 Using In Situ Antigen-Capturing Nanochaperone Remarkably Reduces the Systemic Toxicity and Enhances Cancer Immunotherapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2309927. [PMID: 38387609 DOI: 10.1002/adma.202309927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 01/27/2024] [Indexed: 02/24/2024]
Abstract
Cytokines are powerful in cancer immunotherapy, however, their therapeutic potential is limited by the severe systemic toxicity. Here a potent strategy to reduce the toxicity of systemic cytokine therapy by delivering its denatured form using a finely designed nanochaperone, is described. It is demonstrated that even if the denatured protein cargos are occasionally released under normal physiological conditions they are still misfolded, while can effectively refold into native states and release to function in tumor microenvironment. Consequently, the systemic toxicity of cytokines is nearly completely overcome. Moreover, an immunogenic cell death (ICD)-inducing chemotherapeutic is further loaded and delivered to tumor using this nanochaperone to trigger the release of tumor-associated antigens (TAAs) that are subsequently captured in situ by nanochaperone and then reflows into lymph nodes (LNs) to promote antigen cross-presentation. This optimized personalized nanochaperone-vaccine demonstrates unprecedented suppressive effects against large, advanced tumors, and in combination with immune checkpoint blockade (ICB) therapy results in a significant abscopal effect and inhibition of postoperative tumor recurrence and metastasis. Hence, this approach provides a simple and universal delivery strategy to reduce the systemic toxicities of cytokines, as well as provides a robust personalized cancer vaccination platform, which may find wide applications in cancer immunotherapy.
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Affiliation(s)
- Yongxin Zhang
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Feihe Ma
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Jiajing Chen
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Yujie Chen
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Linlin Xu
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Ang Li
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Yang Liu
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Rujiang Ma
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Linqi Shi
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin, 300192, P. R. China
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12
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Kinger S, Jagtap YA, Kumar P, Choudhary A, Prasad A, Prajapati VK, Kumar A, Mehta G, Mishra A. Proteostasis in neurodegenerative diseases. Adv Clin Chem 2024; 121:270-333. [PMID: 38797543 DOI: 10.1016/bs.acc.2024.04.002] [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: 05/29/2024]
Abstract
Proteostasis is essential for normal function of proteins and vital for cellular health and survival. Proteostasis encompasses all stages in the "life" of a protein, that is, from translation to functional performance and, ultimately, to degradation. Proteins need native conformations for function and in the presence of multiple types of stress, their misfolding and aggregation can occur. A coordinated network of proteins is at the core of proteostasis in cells. Among these, chaperones are required for maintaining the integrity of protein conformations by preventing misfolding and aggregation and guide those with abnormal conformation to degradation. The ubiquitin-proteasome system (UPS) and autophagy are major cellular pathways for degrading proteins. Although failure or decreased functioning of components of this network can lead to proteotoxicity and disease, like neuron degenerative diseases, underlying factors are not completely understood. Accumulating misfolded and aggregated proteins are considered major pathomechanisms of neurodegeneration. In this chapter, we have described the components of three major branches required for proteostasis-chaperones, UPS and autophagy, the mechanistic basis of their function, and their potential for protection against various neurodegenerative conditions, like Alzheimer's, Parkinson's, and Huntington's disease. The modulation of various proteostasis network proteins, like chaperones, E3 ubiquitin ligases, proteasome, and autophagy-associated proteins as therapeutic targets by small molecules as well as new and unconventional approaches, shows promise.
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Affiliation(s)
- Sumit Kinger
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, India
| | - Yuvraj Anandrao Jagtap
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, India
| | - Prashant Kumar
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, India
| | - Akash Choudhary
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, India
| | - Amit Prasad
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, University of Delhi South Campus, Dhaula Kuan, New Delhi, India
| | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, Madhya Pradesh, India
| | - Gunjan Mehta
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, India.
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13
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Roterman I, Stapor K, Dułak D, Konieczny L. External Force Field for Protein Folding in Chaperonins-Potential Application in In Silico Protein Folding. ACS OMEGA 2024; 9:18412-18428. [PMID: 38680295 PMCID: PMC11044213 DOI: 10.1021/acsomega.4c00409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/26/2024] [Accepted: 03/29/2024] [Indexed: 05/01/2024]
Abstract
The present study discusses the influence of the TRiC chaperonin involved in the folding of the component of reovirus mu1/σ3. The TRiC chaperone is treated as a provider of a specific external force field in the fuzzy oil drop model during the structural formation of a target folded protein. The model also determines the status of the final product, which represents the structure directed by an external force field in the form of a chaperonin. This can be used for in silico folding as the process is environment-dependent. The application of the model enables the quantitative assessment of the folding dependence of an external force field, which appears to have universal application.
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Affiliation(s)
- Irena Roterman
- Department
of Bioinformatics and Telemedicine, Jagiellonian
University—Medical College, Medyczna 7, Kraków 30-688, Poland
| | - Katarzyna Stapor
- Faculty
of Automatic, Electronics and Computer Science, Department of Applied
Informatics, Silesian University of Technology, Akademicka 16, Gliwice 44-100, Poland
| | - Dawid Dułak
- ABB
Business Services Sp. z o.o, ul Żegańska 1, Warszawa 04-713, Poland
| | - Leszek Konieczny
- Chair
of Medical Biochemistry—Jagiellonian University—Medical
College, Kopernika 7, Kraków 31-034, Poland
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14
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Khorsand FR, Aziziyan F, Khajeh K. Factors influencing amyloid fibril formation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:55-83. [PMID: 38811089 DOI: 10.1016/bs.pmbts.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Protein aggregation is a complex process with several stages that lead to the formation of complex structures and shapes with a broad variability in stability and toxicity. The aggregation process is affected by various factors and environmental conditions that disrupt the protein's original state, including internal factors like mutations, expression levels, and polypeptide chain truncation, as well as external factors, such as dense molecular surroundings, post-translation modifications, and interactions with other proteins, nucleic acids, small molecules, metal ions, chaperones, and lipid membranes. During the aggregation process, the biological activity of an aggregating protein may be reduced or eliminated, whereas the resulting aggregates may have the potential to be immunogenic, or they may have other undesirable properties. Finding the cause(s) of protein aggregation and controlling it to an acceptable level is among the most crucial topics of research in academia and biopharmaceutical companies. This chapter aims to review intrinsic pathways of protein aggregation and potential extrinsic variables that influence this process.
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Affiliation(s)
| | - Fatemeh Aziziyan
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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15
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Goh KJ, Stubenrauch CJ, Lithgow T. The TAM, a Translocation and Assembly Module for protein assembly and potential conduit for phospholipid transfer. EMBO Rep 2024; 25:1711-1720. [PMID: 38467907 PMCID: PMC11014939 DOI: 10.1038/s44319-024-00111-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 02/08/2024] [Accepted: 02/20/2024] [Indexed: 03/13/2024] Open
Abstract
The assembly of β-barrel proteins into the bacterial outer membrane is an essential process enabling the colonization of new environmental niches. The TAM was discovered as a module of the β-barrel protein assembly machinery; it is a heterodimeric complex composed of an outer membrane protein (TamA) bound to an inner membrane protein (TamB). The TAM spans the periplasm, providing a scaffold through the peptidoglycan layer and catalyzing the translocation and assembly of β-barrel proteins into the outer membrane. Recently, studies on another membrane protein (YhdP) have suggested that TamB might play a role in phospholipid transport to the outer membrane. Here we review and re-evaluate the literature covering the experimental studies on the TAM over the past decade, to reconcile what appear to be conflicting claims on the function of the TAM.
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Affiliation(s)
- Kwok Jian Goh
- Centre to Impact AMR, Monash University, Melbourne, VIC, 3800, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Christopher J Stubenrauch
- Centre to Impact AMR, Monash University, Melbourne, VIC, 3800, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia
| | - Trevor Lithgow
- Centre to Impact AMR, Monash University, Melbourne, VIC, 3800, Australia.
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, VIC, 3800, Australia.
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16
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Alfaro-Sifuentes R, Lares-Jiménez LF, Rojas-Hernández S, Carrasco-Yépez MM, Rojas-Ortega DA, Rodriguez-Anaya LZ, Gonzalez-Galaviz JR, Lares-Villa F. Immunogens in Balamuthia mandrillaris: a proteomic exploration. Parasitol Res 2024; 123:173. [PMID: 38536506 DOI: 10.1007/s00436-024-08193-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 03/20/2024] [Indexed: 04/04/2024]
Abstract
Balamuthia mandrillaris is the causative agent of granulomatous amoebic encephalitis, a rare and often fatal infection affecting the central nervous system. The amoeba is isolated from diverse environmental sources and can cause severe infections in both immunocompromised and immunocompetent individuals. Given the limited understanding of B. mandrillaris, our research aimed to explore its protein profile, identifying potential immunogens crucial for early granulomatous amoebic encephalitis diagnosis. Cultures of B. mandrillaris and other amoebas were grown under axenic conditions, and total amoebic extracts were obtained. Proteomic analyses, including two-dimensional electrophoresis and mass spectrometry, were performed. A 50-kDa band showed a robust recognition of antibodies from immunized BALB/c mice; peptides contained in this band were matched with elongation factor-1 alpha, which emerged as a putative key immunogen. Besides, lectin blotting revealed the presence of glycoproteins in B. mandrillaris, and confocal microscopy demonstrated the focal distribution of the 50-kDa band throughout trophozoites. Cumulatively, these observations suggest the participation of the 50-kDa band in adhesion and recognition mechanisms. Thus, these collective findings demonstrate some protein characteristics of B. mandrillaris, opening avenues for understanding its pathogenicity and developing diagnostic and therapeutic strategies.
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Affiliation(s)
- Rosalía Alfaro-Sifuentes
- Programa de Doctorado en Ciencias Especialidad en Biotecnología, Departamento de Biotecnología y Ciencias Alimentarias, Instituto Tecnológico de Sonora, 85000, Ciudad Obregón, Sonora, México.
| | - Luis Fernando Lares-Jiménez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, 85000, Ciudad Obregón, Sonora, México
| | - Saul Rojas-Hernández
- Laboratorio de Inmunología Molecular, Instituto Politécnico Nacional, Escuela Superior de Medicina, Salvador Díaz Mirón Esq. Plan de San Luis S/N, Miguel Hidalgo, Casco de Santo Tomas, Ciudad de México, México
| | | | - Diego Alexander Rojas-Ortega
- Centro de Investigación en Ciencias de La Salud (CICSA), FCS, Universidad Anáhuac México, 52786, Huixquilucan, Estado de México, México
| | | | | | - Fernando Lares-Villa
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, 85000, Ciudad Obregón, Sonora, México.
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17
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Dupuy É, Collet JF. [A molecular assistant for redox quality control of GroEL/ES substrates]. Med Sci (Paris) 2024; 40:229-231. [PMID: 38520093 DOI: 10.1051/medsci/2024005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024] Open
Affiliation(s)
- Émile Dupuy
- Département WELBIO, WEL research institute, Wavre, Belgique - Institut de Duve, Université catholique de Louvain, Bruxelles, Belgique
| | - Jean-François Collet
- Département WELBIO, WEL research institute, Wavre, Belgique - Institut de Duve, Université catholique de Louvain, Bruxelles, Belgique
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18
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Marie A, Georgescauld F, Johnson KR, Ray S, Engen JR, Ivanov AR. Native Capillary Electrophoresis-Mass Spectrometry of Near 1 MDa Non-Covalent GroEL/GroES/Substrate Protein Complexes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306824. [PMID: 38191978 PMCID: PMC10953559 DOI: 10.1002/advs.202306824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/21/2023] [Indexed: 01/10/2024]
Abstract
Protein complexes are essential for proteins' folding and biological function. Currently, native analysis of large multimeric protein complexes remains challenging. Structural biology techniques are time-consuming and often cannot monitor the proteins' dynamics in solution. Here, a capillary electrophoresis-mass spectrometry (CE-MS) method is reported to characterize, under near-physiological conditions, the conformational rearrangements of ∽1 MDa GroEL upon complexation with binding partners involved in a protein folding cycle. The developed CE-MS method is fast (30 min per run), highly sensitive (low-amol level), and requires ∽10 000-fold fewer samples compared to biochemical/biophysical techniques. The method successfully separates GroEL14 (∽800 kDa), GroEL7 (∽400 kDa), GroES7 (∽73 kDa), and NanA4 (∽130 kDa) oligomers. The non-covalent binding of natural substrate proteins with GroEL14 can be detected and quantified. The technique allows monitoring of GroEL14 conformational changes upon complexation with (ATPγS)4-14 and GroES7 (∽876 kDa). Native CE-pseudo-MS3 analyses of wild-type (WT) GroEL and two GroEL mutants result in up to 60% sequence coverage and highlight subtle structural differences between WT and mutated GroEL. The presented results demonstrate the superior CE-MS performance for multimeric complexes' characterization versus direct infusion ESI-MS. This study shows the CE-MS potential to provide information on binding stoichiometry and kinetics for various protein complexes.
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Affiliation(s)
- Anne‐Lise Marie
- Barnett Institute of Chemical and Biological AnalysisDepartment of Chemistry and Chemical BiologyNortheastern University360 Huntington AvenueBostonMA02115USA
| | - Florian Georgescauld
- Barnett Institute of Chemical and Biological AnalysisDepartment of Chemistry and Chemical BiologyNortheastern University360 Huntington AvenueBostonMA02115USA
| | - Kendall R. Johnson
- Barnett Institute of Chemical and Biological AnalysisDepartment of Chemistry and Chemical BiologyNortheastern University360 Huntington AvenueBostonMA02115USA
| | - Somak Ray
- Barnett Institute of Chemical and Biological AnalysisDepartment of Chemistry and Chemical BiologyNortheastern University360 Huntington AvenueBostonMA02115USA
| | - John R. Engen
- Barnett Institute of Chemical and Biological AnalysisDepartment of Chemistry and Chemical BiologyNortheastern University360 Huntington AvenueBostonMA02115USA
| | - Alexander R. Ivanov
- Barnett Institute of Chemical and Biological AnalysisDepartment of Chemistry and Chemical BiologyNortheastern University360 Huntington AvenueBostonMA02115USA
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19
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Zhao L, Cai Z, Li Y, Zhang Y. Engineering Rubisco to enhance CO 2 utilization. Synth Syst Biotechnol 2024; 9:55-68. [PMID: 38273863 PMCID: PMC10809010 DOI: 10.1016/j.synbio.2023.12.006] [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: 08/28/2023] [Revised: 12/15/2023] [Accepted: 12/25/2023] [Indexed: 01/27/2024] Open
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is a pivotal enzyme that mediates the fixation of CO2. As the most abundant protein on earth, Rubisco has a significant impact on global carbon, water, and nitrogen cycles. However, the significantly low carboxylation activity and competing oxygenase activity of Rubisco greatly impede high carbon fixation efficiency. This review first summarizes the current efforts in directly or indirectly modifying plant Rubisco, which has been challenging due to its high conservation and limitations in chloroplast transformation techniques. However, recent advancements in understanding Rubisco biogenesis with the assistance of chaperones have enabled successful heterologous expression of all Rubisco forms, including plant Rubisco, in microorganisms. This breakthrough facilitates the acquisition and evaluation of modified proteins, streamlining the measurement of their activity. Moreover, the establishment of a screening system in E. coli opens up possibilities for obtaining high-performance mutant enzymes through directed evolution. Finally, this review emphasizes the utilization of Rubisco in microorganisms, not only expanding their carbon-fixing capabilities but also holding significant potential for enhancing biotransformation processes.
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Affiliation(s)
- Lei Zhao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhen Cai
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yin Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanping Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
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20
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Ekeberg T, Assalauova D, Bielecki J, Boll R, Daurer BJ, Eichacker LA, Franken LE, Galli DE, Gelisio L, Gumprecht L, Gunn LH, Hajdu J, Hartmann R, Hasse D, Ignatenko A, Koliyadu J, Kulyk O, Kurta R, Kuster M, Lugmayr W, Lübke J, Mancuso AP, Mazza T, Nettelblad C, Ovcharenko Y, Rivas DE, Rose M, Samanta AK, Schmidt P, Sobolev E, Timneanu N, Usenko S, Westphal D, Wollweber T, Worbs L, Xavier PL, Yousef H, Ayyer K, Chapman HN, Sellberg JA, Seuring C, Vartanyants IA, Küpper J, Meyer M, Maia FRNC. Observation of a single protein by ultrafast X-ray diffraction. LIGHT, SCIENCE & APPLICATIONS 2024; 13:15. [PMID: 38216563 PMCID: PMC10786860 DOI: 10.1038/s41377-023-01352-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 01/14/2024]
Abstract
The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many. It was one of the arguments for building X-ray free-electron lasers. According to theory, the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier, and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes. This was first demonstrated on biological samples a decade ago on the giant mimivirus. Since then, a large collaboration has been pushing the limit of the smallest sample that can be imaged. The ability to capture snapshots on the timescale of atomic vibrations, while keeping the sample at room temperature, may allow probing the entire conformational phase space of macromolecules. Here we show the first observation of an X-ray diffraction pattern from a single protein, that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays, and demonstrate that the concept of diffraction before destruction extends to single proteins. From the pattern, it is possible to determine the approximate orientation of the protein. Our experiment demonstrates the feasibility of ultrafast imaging of single proteins, opening the way to single-molecule time-resolved studies on the femtosecond timescale.
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Affiliation(s)
- Tomas Ekeberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
| | - Dameli Assalauova
- Deutsches Electronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | | | - Rebecca Boll
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Benedikt J Daurer
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, OX11 0DE, UK
| | - Lutz A Eichacker
- University of Stavanger, Centre Organelle Research, Richard-Johnsensgate 4, 4021, Stavanger, Norway
| | - Linda E Franken
- Leibniz Institute for Experimental Virology (HPI), Centre for Structural Systems Biology, Notkestraße 85, 22607, Hamburg, Germany
| | - Davide E Galli
- Dipartimento di Fisica "Aldo Pontremoli", Università degli Studi di Milano, via Celoria 16, 20133, Milano, Italy
| | - Luca Gelisio
- Deutsches Electronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Lars Gumprecht
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
| | - Laura H Gunn
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
| | | | - Dirk Hasse
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
| | - Alexandr Ignatenko
- Deutsches Electronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Jayanath Koliyadu
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- Biomedical and X-Ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, SE-10691, Stockholm, Sweden
| | - Olena Kulyk
- ELI Beamlines/IoP Institute of Physics AS CR, v.v.i., Na Slovance 2, 182 21, Prague 8, Czech Republic
| | - Ruslan Kurta
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Markus Kuster
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Wolfgang Lugmayr
- Multi-User CryoEM Facility, Centre for Structural Systems Biology, Notkestr.85, 22607, Hamburg, Germany
- University Medical Center Hamburg-Eppendorf (UKE), Martinistrasse 52, 20246, Hamburg, Germany
| | - Jannik Lübke
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Adrian P Mancuso
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Tommaso Mazza
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Carl Nettelblad
- Division of Scientific Computing, Science for Life Laboratory, Department of Information Technology, Uppsala University, Box 337, SE-75105, Uppsala, Sweden
| | | | | | - Max Rose
- Deutsches Electronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Amit K Samanta
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
| | | | - Egor Sobolev
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Nicusor Timneanu
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120, Uppsala, Sweden
| | - Sergey Usenko
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Daniel Westphal
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
| | - Tamme Wollweber
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Lena Worbs
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Paul Lourdu Xavier
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Hazem Yousef
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Kartik Ayyer
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761, Hamburg, Germany
- Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Jonas A Sellberg
- Biomedical and X-Ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, SE-10691, Stockholm, Sweden
| | - Carolin Seuring
- Multi-User CryoEM Facility, Centre for Structural Systems Biology, Notkestr.85, 22607, Hamburg, Germany
- Department of Chemistry, Universität Hamburg, 20146, Hamburg, Germany
| | - Ivan A Vartanyants
- Deutsches Electronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Jochen Küpper
- Center for Free-Electron Laser Science, DESY, 22607, Hamburg, Germany
- The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Michael Meyer
- European XFEL, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden.
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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21
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Sun C, Slade L, Mbonu P, Ordner H, Mitchell C, Mitchell M, Liang FC. Membrane protein chaperone and sodium chloride modulate the kinetics and morphology of amyloid beta aggregation. FEBS J 2024; 291:158-176. [PMID: 37786925 DOI: 10.1111/febs.16967] [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: 12/13/2022] [Revised: 07/04/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
Abstract
Protein aggregation is a biological phenomenon caused by the accumulation of misfolded proteins. Amyloid beta (Aβ) peptides are derived from the cleavage of a larger membrane protein molecule and accumulate to form plaques extracellularly. According to the amyloid hypothesis, accumulation of Aβ aggregates in the brain is primarily responsible for the pathogenesis of Alzheimer's disease (AD). Therefore, the disassembly of Aβ aggregates may provide opportunities for alleviating or treating AD. Here, we show that the novel protein targeting machinery from chloroplast, chloroplast signal recognition particle 43 (cpSRP43), is an ATP-independent membrane protein chaperone that can both prevent and reverse Aβ aggregation effectively. Using of thioflavin T dye, we obtained the aggregation kinetics of Aβ aggregation and determined that the chaperone prevents Aβ aggregation in a concentration-dependent manner. Size exclusion chromatography and sedimentation assays showed that 10-fold excess of cpSRP43 can keep Aβ in the soluble monomeric form. Electron microscopy showed that the fibril structure was disrupted in the presence of this chaperone. Importantly, cpSRP43 utilizes the binding energy to actively remodel the preformed Aβ aggregates without assistance by a co-chaperone and ATP, emphasizing its unique function among protein chaperones. Moreover, when sodium chloride concentration is higher than 25 mm, the Aβ aggregation rate increases drastically to form tightly associated aggregates and generate more oligomers. Our results demonstrate that the presence of cpSRP43 and low NaCl levels inhibit or retard Aβ peptide aggregation, potentially opening new avenues to strategically develop an effective treatment for AD.
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Affiliation(s)
- Christopher Sun
- Department of Biology, Midwestern State University, Wichita Falls, TX, USA
| | - Leah Slade
- Department of Chemistry, Midwestern State University, Wichita Falls, TX, USA
| | - Prisca Mbonu
- Department of Biology, Midwestern State University, Wichita Falls, TX, USA
| | - Hunter Ordner
- Department of Chemistry, Midwestern State University, Wichita Falls, TX, USA
| | - Connor Mitchell
- Department of Chemistry, Midwestern State University, Wichita Falls, TX, USA
| | - Matthew Mitchell
- Department of Chemistry, Midwestern State University, Wichita Falls, TX, USA
| | - Fu-Cheng Liang
- Department of Chemistry, Midwestern State University, Wichita Falls, TX, USA
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22
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Mistry AC, Chowdhury D, Chakraborty S, Haldar S. Elucidating the novel mechanisms of molecular chaperones by single-molecule technologies. Trends Biochem Sci 2024; 49:38-51. [PMID: 37980187 DOI: 10.1016/j.tibs.2023.10.009] [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: 05/23/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/20/2023]
Abstract
Molecular chaperones play central roles in sustaining protein homeostasis and preventing protein aggregation. Most studies of these systems have been performed in bulk, providing averaged measurements, though recent single-molecule approaches have provided an in-depth understanding of the molecular mechanisms of their activities and structural rearrangements during substrate recognition. Chaperone activities have been observed to be substrate specific, with some associated with ATP-dependent structural dynamics and others via interactions with co-chaperones. This Review aims to describe the novel mechanisms of molecular chaperones as revealed by single-molecule approaches, and to provide insights into their functioning and its implications for protein homeostasis and human diseases.
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Affiliation(s)
- Ayush Chandrakant Mistry
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Debojyoti Chowdhury
- Department of Chemical and Biological Sciences, S.N. Bose National Center for Basic Sciences, Kolkata, West Bengal 700106, India
| | - Soham Chakraborty
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Shubhasis Haldar
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana 131029, India; Department of Chemical and Biological Sciences, S.N. Bose National Center for Basic Sciences, Kolkata, West Bengal 700106, India; Department of Chemistry, Ashoka University, Sonepat, Haryana 131029, India.
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23
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Takemura S, Shimada N, Maruyama A. Malachite green-derivatized cationic comb-type copolymer acts as a photoresponsive artificial chaperone. JOURNAL OF BIOMATERIALS SCIENCE. POLYMER EDITION 2023; 34:2463-2482. [PMID: 37787160 DOI: 10.1080/09205063.2023.2265127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 09/01/2023] [Indexed: 10/04/2023]
Abstract
Molecular chaperones play vital roles in various physiological reactions by regulating the folding and assembly of biomacromolecules. We have demonstrated that cationic comb-type copolymers exhibit chaperone activity for anionic biomolecules including DNA and ionic peptide via the formation of soluble interpolyelectrolyte complexes. The development of smart artificial chaperones that can be spatiotemporally controlled by a remotely guided signal would expand the functions of artificial chaperones. Herein, to enable photocontrol of chaperone activity, a cationic comb-type copolymer bearing malachite green as a photoresponsive unit was designed. We first prepared a series of carboxylic acid derivatives of malachite green identified a derivative that could be quickly and quantitatively converted to the cationic form from the nonionic form by photoirradiation. This derivative was conjugated to the cationic comb-type copolymer, poly(allylamine)-graft-poly(ethylene glycol) through a condensation reaction. Upon photoirradiation, the copolymer bearing 9 mol% malachite green enhanced the membrane disruptive activity of acidic peptide E5 and induced morphological changes in liposomes. This demonstration of photoresponsive activation of chaperoning activity of a copolymer suggests that the installation of carboxyl derivatives of malachite green will impart photoresponsiveness to various materials including biopolymers.
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Affiliation(s)
- Seiya Takemura
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Naohiko Shimada
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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24
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Yang M, Zhang Y, Deng F, Wu X, Chen Y, Ma F, Shi L. Development of self-cooperative nanochaperones with enhanced activity to facilitate protein refolding. MATERIALS HORIZONS 2023; 10:5547-5554. [PMID: 37843027 DOI: 10.1039/d3mh00619k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Regulating protein folding including assisting de novo folding, preventing misfolding and aggregation, and facilitating refolding of proteins are of significant importance for retaining protein's biological activities. Here, we report a mixed shell polymeric micelle (MSPM)-based self-cooperative nanochaperone (self-CO-nChap) with enhanced activity to facilitate protein refolding. This self-CO-nChap was fabricated by introducing Hsp40-mimetic artificial carriers into the traditional nanochaperone to cooperate with the Hsp70-mimetic confined hydrophobic microdomains. The artificial carrier facilitates transfer and immobilization of client proteins into confined hydrophobic microdomains, by which significantly improving self-CO-nChap's capability to inhibit unfolding and aggregation of client proteins, and finally facilitating refolding. Compared to traditional nanochaperones, the self-CO-nChap significantly enhances the thermal stability of horseradish peroxidase (HRP) epicyclically under harsher conditions. Moreover, the self-CO-nChap efficiently protects misfolding-prone proteins, such as immunoglobulin G (IgG) antibody from thermal denaturation, which is hardly achieved using traditional nanochaperones. In addition, a kinetic partitioning mechanism was devised to explain how self-CO-nChap facilitates refolding by regulating the cooperative effect of kinetics between the nanochaperone and client proteins. This work provides a novel strategy for the design of protein folding regulatory materials, including nanochaperones.
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Affiliation(s)
- Menglin Yang
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry and College of Chemistry, Nankai University, Tianjin, 300071, P.R. China.
| | - Yanli Zhang
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry and College of Chemistry, Nankai University, Tianjin, 300071, P.R. China.
| | - Fei Deng
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry and College of Chemistry, Nankai University, Tianjin, 300071, P.R. China.
| | - Xiaohui Wu
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry and College of Chemistry, Nankai University, Tianjin, 300071, P.R. China.
| | - Yujie Chen
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry and College of Chemistry, Nankai University, Tianjin, 300071, P.R. China.
| | - Feihe Ma
- State Key Laboratory of Separation Membranes and Membrane Processes and School of Materials Science and Engineering, Tiangong University, Tianjin, 300387, P.R. China.
| | - Linqi Shi
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry and College of Chemistry, Nankai University, Tianjin, 300071, P.R. China.
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25
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Jo SH, Jeon HJ, Song WS, Lee JS, Kwon JE, Park JH, Kim YR, Kim MG, Baek JH, Kwon SY, Kim JS, Yang YH, Kim YG. Unveiling the inhibition mechanism of Clostridioides difficile by Bifidobacterium longum via multiomics approach. Front Microbiol 2023; 14:1293149. [PMID: 38029200 PMCID: PMC10663266 DOI: 10.3389/fmicb.2023.1293149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Antibiotic-induced gut microbiota disruption constitutes a major risk factor for Clostridioides difficile infection (CDI). Further, antibiotic therapy, which is the standard treatment option for CDI, exacerbates gut microbiota imbalance, thereby causing high recurrent CDI incidence. Consequently, probiotic-based CDI treatment has emerged as a long-term management and preventive option. However, the mechanisms underlying the therapeutic effects of probiotics for CDI remain uninvestigated, thereby creating a knowledge gap that needs to be addressed. To fill this gap, we used a multiomics approach to holistically investigate the mechanisms underlying the therapeutic effects of probiotics for CDI at a molecular level. We first screened Bifidobacterium longum owing to its inhibitory effect on C. difficile growth, then observed the physiological changes associated with the inhibition of C. difficile growth and toxin production via a multiomics approach. Regarding the mechanism underlying C. difficile growth inhibition, we detected a decrease in intracellular adenosine triphosphate (ATP) synthesis due to B. longum-produced lactate and a subsequent decrease in (deoxy)ribonucleoside triphosphate synthesis. Via the differential regulation of proteins involved in translation and protein quality control, we identified B. longum-induced proteinaceous stress. Finally, we found that B. longum suppressed the toxin production of C. difficile by replenishing proline consumed by it. Overall, the findings of the present study expand our understanding of the mechanisms by which probiotics inhibit C. difficile growth and contribute to the development of live biotherapeutic products based on molecular mechanisms for treating CDI.
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Affiliation(s)
- Sung-Hyun Jo
- Department of Chemical Engineering, Soongsil University, Seoul, Republic of Korea
| | - Hyo-Jin Jeon
- Department of Chemical Engineering, Soongsil University, Seoul, Republic of Korea
| | - Won-Suk Song
- Department of Chemical Engineering, Soongsil University, Seoul, Republic of Korea
| | - Jae-Seung Lee
- Department of Chemical Engineering, Soongsil University, Seoul, Republic of Korea
| | - Ji-Eun Kwon
- Department of Chemical Engineering, Soongsil University, Seoul, Republic of Korea
| | - Ji-Hyeon Park
- Department of Chemical Engineering, Soongsil University, Seoul, Republic of Korea
| | - Ye-Rim Kim
- Department of Chemical Engineering, Soongsil University, Seoul, Republic of Korea
| | - Min-Gyu Kim
- Department of Chemical Engineering, Soongsil University, Seoul, Republic of Korea
| | - Ji-Hyun Baek
- Department of Chemical Engineering, Soongsil University, Seoul, Republic of Korea
| | - Seo-Young Kwon
- Department of Chemical Engineering, Soongsil University, Seoul, Republic of Korea
| | - Jae-Seok Kim
- Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Republic of Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Yun-Gon Kim
- Department of Chemical Engineering, Soongsil University, Seoul, Republic of Korea
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26
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Ries F, Weil HL, Herkt C, Mühlhaus T, Sommer F, Schroda M, Willmund F. Competition co-immunoprecipitation reveals the interactors of the chloroplast CPN60 chaperonin machinery. PLANT, CELL & ENVIRONMENT 2023; 46:3371-3391. [PMID: 37606545 DOI: 10.1111/pce.14697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/28/2023] [Accepted: 08/11/2023] [Indexed: 08/23/2023]
Abstract
The functionality of all metabolic processes in chloroplasts depends on a balanced integration of nuclear- and chloroplast-encoded polypeptides into the plastid's proteome. The chloroplast chaperonin machinery is an essential player in chloroplast protein folding under ambient and stressful conditions, with a more intricate structure and subunit composition compared to the orthologous GroEL/ES chaperonin of Escherichia coli. However, its exact role in chloroplasts remains obscure, mainly because of very limited knowledge about the interactors. We employed the competition immunoprecipitation method for the identification of the chaperonin's interactors in Chlamydomonas reinhardtii. Co-immunoprecipitation of the target complex in the presence of increasing amounts of isotope-labelled competitor epitope and subsequent mass spectrometry analysis specifically allowed to distinguish true interactors from unspecifically co-precipitated proteins. Besides known substrates such as RbcL and the expected complex partners, we revealed numerous new interactors with high confidence. Proteins that qualify as putative substrate proteins differ from bulk chloroplast proteins by a higher content of beta-sheets, lower alpha-helical conformation and increased aggregation propensity. Immunoprecipitations targeted against a subunit of the co-chaperonin lid revealed the ClpP protease as a specific partner complex, pointing to a close collaboration of these machineries to maintain protein homeostasis in the chloroplast.
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Affiliation(s)
- Fabian Ries
- Molecular Genetics of Eukaryotes, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Heinrich Lukas Weil
- Computational Systems Biology, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Claudia Herkt
- Molecular Genetics of Eukaryotes, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Timo Mühlhaus
- Computational Systems Biology, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Frederik Sommer
- Molecular Biotechnology and Systems Biology, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Michael Schroda
- Molecular Biotechnology and Systems Biology, University of Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, University of Kaiserslautern-Landau, Kaiserslautern, Germany
- Plant Physiology/Synmikro, University of Marburg, Marburg, Germany
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27
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Rivera-Ramírez A, Salgado-Morales R, Onofre-Lemus J, García-Gómez BI, Lanz-Mendoza H, Dantán-González E. Evaluation and Characterization of the Insecticidal Activity and Synergistic Effects of Different GroEL Proteins from Bacteria Associated with Entomopathogenic Nematodes on Galleria mellonella. Toxins (Basel) 2023; 15:623. [PMID: 37999486 PMCID: PMC10674725 DOI: 10.3390/toxins15110623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/15/2023] [Accepted: 10/17/2023] [Indexed: 11/25/2023] Open
Abstract
GroEL is a chaperonin that helps other proteins fold correctly. However, alternative activities, such as acting as an insect toxin, have also been discovered. This work evaluates the chaperonin and insecticidal activity of different GroEL proteins from entomopathogenic nematodes on G. mellonella. The ability to synergize with the ExoA toxin of Pseudomonas aeruginosa was also investigated. The GroELXn protein showed the highest insecticidal activity among the different GroELs. In addition, it was able to significantly activate the phenoloxidase system of the target insects. This could tell us about the mechanism by which it exerts its toxicity on insects. GroEL proteins can enhance the toxic activity of the ExoA toxin, which could be related to its chaperonin activity. However, there is a significant difference in the synergistic effect that is more related to its alternative activity as an insecticidal toxin.
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Affiliation(s)
- Abraham Rivera-Ramírez
- Center for Population Health Research, National Institute of Public Health, Cuernavaca 62100, Mexico;
| | - Rosalba Salgado-Morales
- Biotechnology Research Center, Autonomous University of the State of Morelos, Av. Universidad 1001, Chamilpa, Cuernavaca 62209, Mexico; (R.S.-M.); (J.O.-L.)
| | - Janette Onofre-Lemus
- Biotechnology Research Center, Autonomous University of the State of Morelos, Av. Universidad 1001, Chamilpa, Cuernavaca 62209, Mexico; (R.S.-M.); (J.O.-L.)
| | - Blanca I. García-Gómez
- Biotechnology Institute, National Autonomous University of Mexico, A.P. 510-3, Cuernavaca 62250, Mexico;
| | - Humberto Lanz-Mendoza
- Center for Research on Infectious Diseases, National Institute of Public Health, Cuernavaca 62100, Mexico;
| | - Edgar Dantán-González
- Biotechnology Research Center, Autonomous University of the State of Morelos, Av. Universidad 1001, Chamilpa, Cuernavaca 62209, Mexico; (R.S.-M.); (J.O.-L.)
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28
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Delerue T, Chareyre S, Anantharaman V, Gilmore MC, Popham DL, Cava F, Aravind L, Ramamurthi KS. Bacterial cell surface nanoenvironment requires a specialized chaperone to activate a peptidoglycan biosynthetic enzyme. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.06.561273. [PMID: 37986874 PMCID: PMC10659427 DOI: 10.1101/2023.10.06.561273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Bacillus subtilis spores are produced inside the cytosol of a mother cell. Spore surface assembly requires the SpoVK protein in the mother cell, but its function is unknown. Here, we report that SpoVK is a dedicated chaperone from a distinct higher-order clade of AAA+ ATPases that activates the peptidoglycan glycosyltransferase MurG during sporulation, even though MurG does not normally require activation by a chaperone during vegetative growth. MurG redeploys to the spore surface during sporulation, where we show that the local pH is reduced and propose that this change in cytosolic nanoenvironment necessitates a specific chaperone for proper MurG function. Further, we show that SpoVK participates in a developmental checkpoint in which improper spore surface assembly inactivates SpoVK, which leads to sporulation arrest. The AAA+ ATPase clade containing SpoVK includes other dedicated chaperones involved in secretion, cell-envelope biosynthesis, and carbohydrate metabolism, suggesting that such fine-tuning might be a widespread feature of different subcellular nanoenvironments.
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Affiliation(s)
- Thomas Delerue
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Sylvia Chareyre
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael C. Gilmore
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - David L. Popham
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Felipe Cava
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - L. Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Kumaran S. Ramamurthi
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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29
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Piedmont ER, Christensen EE, Krauss TD, Partridge BE. Amphiphilic dendrons as supramolecular holdase chaperones. RSC Chem Biol 2023; 4:754-759. [PMID: 37799582 PMCID: PMC10549246 DOI: 10.1039/d3cb00086a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/05/2023] [Indexed: 10/07/2023] Open
Abstract
The aggregation of incompletely or incorrectly folded proteins is implicated in diseases including Alzheimer's, cataracts, and other maladies. Natural systems express protein chaperones to prevent or even reverse harmful protein aggregation. Synthetic chaperone-like systems have sought to mimic the action of their biological counterparts but typically require substantial optimization and high concentrations to be functional, or lack programmability that would enable the targeting of specific protein substrates. Here we report a series of amphiphilic dendrons that undergo assembly and inhibit the aggregation of fragment 16-22 amyloid β protein (Aβ16-22). We show that monodisperse dendrons with hydrophilic tetraethylene glycol chains and a hydrophobic core based on naphthyl and benzyl ethers undergo supramolecular assembly in aqueous solutions to form sphere-like particles. The solubility of these dendrons and their assemblies is tuned by varying the relative sizes of their hydrophilic and hydrophobic regions. Two water-soluble dendrons are discovered and shown, via fluorescence experiments with rhodamine 6G, to generate a hydrophobic environment. Furthermore, we demonstrate that sub-stoichiometric concentrations of these amphiphilic dendrons stabilize Aβ16-22 peptide with respect to aggregation, mimicking the activity of holdase chaperones. Our results highlight the potential of these amphiphilic molecules as the basis for a novel approach to artificial chaperones that may address many of the challenges associated with existing synthetic chaperone mimics.
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Affiliation(s)
| | - Erin E Christensen
- Department of Chemistry, University of Rochester Rochester NY 14627-0216 USA
| | - Todd D Krauss
- Department of Chemistry, University of Rochester Rochester NY 14627-0216 USA
- Institute of Optics, University of Rochester Rochester NY 14627-0186 USA
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30
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Diogo-Jr R, de Resende Von Pinho EV, Pinto RT, Zhang L, Condori-Apfata JA, Pereira PA, Vilela DR. Maize heat shock proteins-prospection, validation, categorization and in silico analysis of the different ZmHSP families. STRESS BIOLOGY 2023; 3:37. [PMID: 37981586 PMCID: PMC10482818 DOI: 10.1007/s44154-023-00104-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 07/05/2023] [Indexed: 11/21/2023]
Abstract
Among the plant molecular mechanisms capable of effectively mitigating the effects of adverse weather conditions, the heat shock proteins (HSPs), a group of chaperones with multiple functions, stand out. At a time of full progress on the omic sciences, they look very promising in the genetic engineering field, especially in order to conceive superior genotypes, potentially tolerant to abiotic stresses (AbSts). Recently, some works concerning certain families of maize HSPs (ZmHSPs) were published. However, there was still a lack of a study that, with a high degree of criteria, would fully conglomerate them. Using distinct but complementary strategies, we have prospected as many ZmHSPs candidates as possible, gathering more than a thousand accessions. After detailed data mining, we accounted for 182 validated ones, belonging to seven families, which were subcategorized into classes with potential for functional parity. In them, we identified dozens of motifs with some degree of similarity with proteins from different kingdoms, which may help explain some of their still poorly understood means of action. Through in silico and in vitro approaches, we compared their expression levels after controlled exposure to several AbSts' sources, applied at diverse tissues, on varied phenological stages. Based on gene ontology concepts, we still analyzed them from different perspectives of term enrichment. We have also searched, in model plants and close species, for potentially orthologous genes. With all these new insights, which culminated in a plentiful supplementary material, rich in tables, we aim to constitute a fertile consultation source for those maize researchers attracted by these interesting stress proteins.
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Affiliation(s)
- Rubens Diogo-Jr
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, (47907), USA.
- Department of Agriculture, Federal University of Lavras (UFLA), Lavras, MG, (37200-900), Brazil.
| | | | - Renan Terassi Pinto
- Faculty of Philosophy and Sciences at Ribeirao Preto, University of Sao Paulo (USP), Ribeirao Preto, SP, (14040-901), Brazil
| | - Lingrui Zhang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, (47907), USA
| | - Jorge Alberto Condori-Apfata
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, (47907), USA
- Faculty of Engineering and Agricultural Sciences, Universidad Nacional Toribio Rodriguez de Mendoza de Amazonas (UNTRM), Chachapoyas, AM, (01001), Peru
| | - Paula Andrade Pereira
- Department of Agriculture, Federal University of Lavras (UFLA), Lavras, MG, (37200-900), Brazil
| | - Danielle Rezende Vilela
- Department of Agriculture, Federal University of Lavras (UFLA), Lavras, MG, (37200-900), Brazil
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31
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Piplani B, Kumar CMS, Lund PA, Chaudhuri TK. Mycobacterial chaperonins in cellular proteostasis: Evidence for chaperone function of Cpn60.1 and Cpn60.2-mediated protein folding. Mol Microbiol 2023; 120:210-223. [PMID: 37350285 PMCID: PMC10952152 DOI: 10.1111/mmi.15109] [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: 12/14/2022] [Revised: 06/04/2023] [Accepted: 06/06/2023] [Indexed: 06/24/2023]
Abstract
Mycobacterium tuberculosis encodes two chaperonin proteins, MtbCpn60.1 and MtbCpn60.2, that share substantial sequence similarity with the Escherichia coli chaperonin, GroEL. However, unlike GroEL, MtbCpn60.1 and MtbCpn60.2 purify as lower-order oligomers. Previous studies have shown that MtbCpn60.2 can functionally replace GroEL in E. coli, while the function of MtbCpn60.1 remained an enigma. Here, we demonstrate the molecular chaperone function of MtbCpn60.1 and MtbCpn60.2, by probing their ability to assist the folding of obligate chaperonin clients, DapA, FtsE and MetK, in an E. coli strain depleted of endogenous GroEL. We show that both MtbCpn60.1 and MtbCpn60.2 support cell survival and cell division by assisting the folding of DapA and FtsE, but only MtbCpn60.2 completely rescues GroEL-depleted E. coli cells. We also show that, unlike MtbCpn60.2, MtbCpn60.1 has limited ability to support cell growth and proliferation and assist the folding of MetK. Our findings suggest that the client pools of GroEL and MtbCpn60.2 overlap substantially, while MtbCpn60.1 folds only a small subset of GroEL clients. We conclude that the differences between MtbCpn60.1 and MtbCpn60.2 may be a consequence of their intrinsic sequence features, which affect their thermostability, efficiency, clientomes and modes of action.
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Affiliation(s)
- Bakul Piplani
- Kusuma School of Biological SciencesIndian Institute of Technology DelhiIndia
| | - C. M. Santosh Kumar
- School of BiosciencesUniversity of BirminghamBirmingham
- Institute of Microbiology and InfectionUniversity of BirminghamBirminghamUK
| | - Peter A. Lund
- School of BiosciencesUniversity of BirminghamBirmingham
- Institute of Microbiology and InfectionUniversity of BirminghamBirminghamUK
| | - Tapan K. Chaudhuri
- Kusuma School of Biological SciencesIndian Institute of Technology DelhiIndia
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Liebermann DG, Jungwirth J, Riven I, Barak Y, Levy D, Horovitz A, Haran G. From Microstates to Macrostates in the Conformational Dynamics of GroEL: A Single-Molecule Förster Resonance Energy Transfer Study. J Phys Chem Lett 2023:6513-6521. [PMID: 37440608 PMCID: PMC10388350 DOI: 10.1021/acs.jpclett.3c01281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
The chaperonin GroEL is a multisubunit molecular machine that assists in protein folding in the Escherichia coli cytosol. Past studies have shown that GroEL undergoes large allosteric conformational changes during its reaction cycle. Here, we report single-molecule Förster resonance energy transfer measurements that directly probe the conformational transitions of one subunit within GroEL and its single-ring variant under equilibrium conditions. We find that four microstates span the conformational manifold of the protein and interconvert on the submillisecond time scale. A unique set of relative populations of these microstates, termed a macrostate, is obtained by varying solution conditions, e.g., adding different nucleotides or the cochaperone GroES. Strikingly, ATP titration studies demonstrate that the partition between the apo and ATP-ligated conformational macrostates traces a sigmoidal response with a Hill coefficient similar to that obtained in bulk experiments of ATP hydrolysis. These coinciding results from bulk measurements for an entire ring and single-molecule measurements for a single subunit provide new evidence for the concerted allosteric transition of all seven subunits.
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Chen JP, Gong JS, Su C, Li H, Xu ZH, Shi JS. Improving the soluble expression of difficult-to-express proteins in prokaryotic expression system via protein engineering and synthetic biology strategies. Metab Eng 2023; 78:99-114. [PMID: 37244368 DOI: 10.1016/j.ymben.2023.05.007] [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: 04/09/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023]
Abstract
Solubility and folding stability are key concerns for difficult-to-express proteins (DEPs) restricted by amino acid sequences and superarchitecture, resolved by the precise distribution of amino acids and molecular interactions as well as the assistance of the expression system. Therefore, an increasing number of tools are available to achieve efficient expression of DEPs, including directed evolution, solubilization partners, chaperones, and affluent expression hosts, among others. Furthermore, genome editing tools, such as transposons and CRISPR Cas9/dCas9, have been developed and expanded to construct engineered expression hosts capable of efficient expression ability of soluble proteins. Accounting for the accumulated knowledge of the pivotal factors in the solubility and folding stability of proteins, this review focuses on advanced technologies and tools of protein engineering, protein quality control systems, and the redesign of expression platforms in prokaryotic expression systems, as well as advances of the cell-free expression technologies for membrane proteins production.
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Affiliation(s)
- Jin-Ping Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Jin-Song Gong
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China.
| | - Chang Su
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China
| | - Heng Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China
| | - Zheng-Hong Xu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, School of Biotechnology, Jiangnan University, Wuxi, 214122, PR China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Jin-Song Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
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Diankristanti PA, Effendi SSW, Hsiang CC, Ng IS. High-level itaconic acid (IA) production using engineered Escherichia coli Lemo21(DE3) toward sustainable biorefinery. Enzyme Microb Technol 2023; 167:110231. [PMID: 37003250 DOI: 10.1016/j.enzmictec.2023.110231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/17/2023] [Accepted: 03/19/2023] [Indexed: 03/31/2023]
Abstract
Itaconic acid (IA) serves as a prominent building block for polyamides as sustainable material. In vivo IA production is facing the competing side reactions, byproducts accumulation, and long cultivation time. Therefore, the utilization of whole-cell biocatalysts to carry out production from citrate is an alternative approach to sidestep the current limitations. In this study, in vitro reaction of IA was obtained 72.44 g/L by using engineered E. coli Lemo21(DE3) harboring the aconitase (Acn, EC 4.2.1.3) and cis-aconitate decarboxylase (CadA, EC 4.1.1.6) which was cultured in glycerol-based minimal medium. IA productivity enhancement was observed after cold-treating the biocatalysts in - 80 °C for 24 h prior to the reaction, reaching 81.6 g/L. On the other hand, a new seeding strategy in Terrific Broth (TB) as a nutritionally rich medium was employed to maintain the biocatalysts stability up to 30 days. Finally, the highest IA titer of 98.17 g/L was attained using L21::7G chassis, that has a pLemo plasmid and integration of GroELS to the chromosome. The high-level of IA production along with the biocatalyst reutilization enables the economic viability toward a sustainable biorefinery.
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Peng S, Chu Z, Lu J, Li D, Wang Y, Yang S, Zhang Y. Overexpression of chaperones GroEL/ES from Escherichia coli enhances indigo biotransformation production of cytochrome P450 BM3 mutant. Biotechnol Lett 2023:10.1007/s10529-023-03397-5. [PMID: 37243776 DOI: 10.1007/s10529-023-03397-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 04/08/2023] [Accepted: 05/11/2023] [Indexed: 05/29/2023]
Abstract
The self-sufficient cytochrome P450 BM3 mutant (A74G/F87V/D168H/L188Q) can serve as a biocatalyst for whole-cell catalysis process of indigo. Nevertheless, the bioconversion yield of indigo is generally low under normal cultivation conditions (37 °C, 250 rpm). In this study, a recombinant E. coli BL21(DE3) strain was constructed to co-express the P450 BM3 mutant gene and GroEL/ES genes to investigate whether GroEL/ES can promote the indigo bioconversion yield in E. coli. The results revealed that the GroEL/ES system could significantly increase the indigo bioconversion yield, and the indigo bioconversion yield of the strain co-expressing P450 BM3 mutant and GroEL/ES was about 21-fold that of the strain only expressing the P450 BM3 mutant. In addition, the P450 BM3 enzyme content and in vitro indigo bioconversion yield were determined to explore the underlying mechanism for the improvement of indigo bioconversion yield. The results revealed that GroEL/ES did not increase indigo bioconversion yield by increasing the content of P450 BM3 enzyme and its enzymatic transformation efficiency. Moreover, GroEL/ES could improve the intracellular nicotinamide adenine dinucleotide phosphate (NADPH)/NADP+ ratio. Given that NADPH is an important coenzyme in the catalytic process of indigo, the underlying mechanism for the improvement of indigo bioconversion yield is probably related to an increase in the intracellular NADPH/NADP+ ratio.
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Affiliation(s)
- Shuaiying Peng
- Department of Biological Sciences and Biotechnology, Jiangxi Agricultural University, NO.1101 Fangzhimin Avenue, Nanchang, 330045, China.
| | - Zhongmei Chu
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, NO.500 Caobao Road, Shanghai, 200233, China
| | - Jianfeng Lu
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, NO.500 Caobao Road, Shanghai, 200233, China
| | - Dongxiao Li
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, NO.500 Caobao Road, Shanghai, 200233, China
| | - Yonghong Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Shengli Yang
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, NO.500 Caobao Road, Shanghai, 200233, China
| | - Yi Zhang
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, NO.500 Caobao Road, Shanghai, 200233, China.
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Liu C, Jin M, Wang S, Han W, Zhao Q, Wang Y, Xu C, Diao L, Yin Y, Peng C, Bao L, Wang Y, Cong Y. Pathway and mechanism of tubulin folding mediated by TRiC/CCT along its ATPase cycle revealed using cryo-EM. Commun Biol 2023; 6:531. [PMID: 37193829 DOI: 10.1038/s42003-023-04915-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/04/2023] [Indexed: 05/18/2023] Open
Abstract
The eukaryotic chaperonin TRiC/CCT assists the folding of about 10% of cytosolic proteins through an ATP-driven conformational cycle, and the essential cytoskeleton protein tubulin is the obligate substrate of TRiC. Here, we present an ensemble of cryo-EM structures of endogenous human TRiC throughout its ATPase cycle, with three of them revealing endogenously engaged tubulin in different folding stages. The open-state TRiC-tubulin-S1 and -S2 maps show extra density corresponding to tubulin in the cis-ring chamber of TRiC. Our structural and XL-MS analyses suggest a gradual upward translocation and stabilization of tubulin within the TRiC chamber accompanying TRiC ring closure. In the closed TRiC-tubulin-S3 map, we capture a near-natively folded tubulin-with the tubulin engaging through its N and C domains mainly with the A and I domains of the CCT3/6/8 subunits through electrostatic and hydrophilic interactions. Moreover, we also show the potential role of TRiC C-terminal tails in substrate stabilization and folding. Our study delineates the pathway and molecular mechanism of TRiC-mediated folding of tubulin along the ATPase cycle of TRiC, and may also inform the design of therapeutic agents targeting TRiC-tubulin interactions.
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Affiliation(s)
- Caixuan Liu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Mingliang Jin
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Shutian Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Wenyu Han
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Qiaoyu Zhao
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yifan Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Cong Xu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Lei Diao
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yue Yin
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, CAS, 201210, Shanghai, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, CAS, 201210, Shanghai, China
| | - Lan Bao
- University of Chinese Academy of Sciences, 100049, Beijing, China
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yanxing Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yao Cong
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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37
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Braxton JR, Shao H, Tse E, Gestwicki JE, Southworth DR. Asymmetric apical domain states of mitochondrial Hsp60 coordinate substrate engagement and chaperonin assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.15.540872. [PMID: 37293102 PMCID: PMC10245740 DOI: 10.1101/2023.05.15.540872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The mitochondrial chaperonin, mtHsp60, promotes the folding of newly imported and transiently misfolded proteins in the mitochondrial matrix, assisted by its co-chaperone mtHsp10. Despite its essential role in mitochondrial proteostasis, structural insights into how this chaperonin binds to clients and progresses through its ATP-dependent reaction cycle are not clear. Here, we determined cryo-electron microscopy (cryo-EM) structures of a hyperstable disease-associated mtHsp60 mutant, V72I, at three stages in this cycle. Unexpectedly, client density is identified in all states, revealing interactions with mtHsp60's apical domains and C-termini that coordinate client positioning in the folding chamber. We further identify a striking asymmetric arrangement of the apical domains in the ATP state, in which an alternating up/down configuration positions interaction surfaces for simultaneous recruitment of mtHsp10 and client retention. Client is then fully encapsulated in mtHsp60/mtHsp10, revealing prominent contacts at two discrete sites that potentially support maturation. These results identify a new role for the apical domains in coordinating client capture and progression through the cycle, and suggest a conserved mechanism of group I chaperonin function.
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Affiliation(s)
- Julian R. Braxton
- Graduate Program in Chemistry and Chemical Biology; University of California, San Francisco; San Francisco, CA 94158, USA
- Institute for Neurodegenerative Diseases; University of California, San Francisco; San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry; University of California, San Francisco; San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics; University of California, San Francisco; San Francisco, CA 94158, USA
| | - Hao Shao
- Institute for Neurodegenerative Diseases; University of California, San Francisco; San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry; University of California, San Francisco; San Francisco, CA 94158, USA
| | - Eric Tse
- Institute for Neurodegenerative Diseases; University of California, San Francisco; San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics; University of California, San Francisco; San Francisco, CA 94158, USA
| | - Jason E. Gestwicki
- Institute for Neurodegenerative Diseases; University of California, San Francisco; San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry; University of California, San Francisco; San Francisco, CA 94158, USA
| | - Daniel R. Southworth
- Institute for Neurodegenerative Diseases; University of California, San Francisco; San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics; University of California, San Francisco; San Francisco, CA 94158, USA
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38
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Gupta A, Lentzsch AM, Siegel A, Yu Z, Chio US, Cheng Y, Shan SO. Dodecamer assembly of a metazoan AAA + chaperone couples substrate extraction to refolding. SCIENCE ADVANCES 2023; 9:eadf5336. [PMID: 37163603 PMCID: PMC10171807 DOI: 10.1126/sciadv.adf5336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 04/04/2023] [Indexed: 05/12/2023]
Abstract
Ring-forming AAA+ chaperones solubilize protein aggregates and protect organisms from proteostatic stress. In metazoans, the AAA+ chaperone Skd3 in the mitochondrial intermembrane space (IMS) is critical for human health and efficiently refolds aggregated proteins, but its underlying mechanism is poorly understood. Here, we show that Skd3 harbors both disaggregase and protein refolding activities enabled by distinct assembly states. High-resolution structures of Skd3 hexamers in distinct conformations capture ratchet-like motions that mediate substrate extraction. Unlike previously described disaggregases, Skd3 hexamers further assemble into dodecameric cages in which solubilized substrate proteins can attain near-native states. Skd3 mutants defective in dodecamer assembly retain disaggregase activity but are impaired in client refolding, linking the disaggregase and refolding activities to the hexameric and dodecameric states of Skd3, respectively. We suggest that Skd3 is a combined disaggregase and foldase, and this property is particularly suited to meet the complex proteostatic demands in the mitochondrial IMS.
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Affiliation(s)
- Arpit Gupta
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alfred M. Lentzsch
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alex Siegel
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Zanlin Yu
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Un Seng Chio
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Shu-ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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39
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Liu R, Pan Y, Wang N, Tang D, Urlacher VB, Li S. Comparative biochemical characterization of mammalian-derived CYP11A1s with cholesterol side-chain cleavage activities. J Steroid Biochem Mol Biol 2023; 229:106268. [PMID: 36764495 DOI: 10.1016/j.jsbmb.2023.106268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
Steroid drugs, the second largest class of pharmaceuticals after antibiotics, have shown significant anti-inflammatory, anti-allergic, and endocrine-regulating effects. A group of cytochrome P450 enzymes, namely, CYP11A1 isoenzymes from different organisms are capable of converting cholesterol into pregnenolone, which is a pivotal reaction in both steroid metabolism and (bio)synthetic network of steroid products. However, the low activity of CYP11A1s greatly restricts the industrial application of these cholesterol side-chain cleavage enzymes. Herein, we investigate ten CYP11A1 enzymes of different origins and in vitro characterize two CYP11A1s with a relatively higher expression level from Capra hircus and Sus scrofa, together with the CYP11A1s from Homo sapiens and Bos taurus as references. Towards five selected sterol substrates with different side chain structures, S. scrofa CYP11A1 displays relatively higher activities. Through redox partners combination screening, we reveal the optimal redox partner pair of S. scrofa adrenodoxin and C. hircus adrenodoxin reductase. Moreover, the semi-rational mutagenesis for the active sites and substrate entrance channels of human and bovine CYP11A1s is performed based on comparative analysis of their crystal structures. The mutant mBtCYP11A1-Q377A derived from mature B. taurus CYP11A1 shows a 1.46 times higher activity than the wild type enzyme. These results not only demonstrate the tunability of the highly conserved CYP11A1 isoenzymes, but also lay a foundation for the following engineering efforts on these industrially relevant P450 enzymes.
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Affiliation(s)
- Ruxin Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Yunjun Pan
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Ning Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China; College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, China
| | - Dandan Tang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Vlada B Urlacher
- Institute of Biochemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China.
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40
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Nguyen ND, Pulsford SB, Hee WY, Rae BD, Rourke LM, Price GD, Long BM. Towards engineering a hybrid carboxysome. PHOTOSYNTHESIS RESEARCH 2023; 156:265-277. [PMID: 36892800 PMCID: PMC10154267 DOI: 10.1007/s11120-023-01009-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/17/2023] [Indexed: 05/03/2023]
Abstract
Carboxysomes are bacterial microcompartments, whose structural features enable the encapsulated Rubisco holoenzyme to operate in a high-CO2 environment. Consequently, Rubiscos housed within these compartments possess higher catalytic turnover rates relative to their plant counterparts. This particular enzymatic property has made the carboxysome, along with associated transporters, an attractive prospect to incorporate into plant chloroplasts to increase future crop yields. To date, two carboxysome types have been characterized, the α-type that has fewer shell components and the β-type that houses a faster Rubisco. While research is underway to construct a native carboxysome in planta, work investigating the internal arrangement of carboxysomes has identified conserved Rubisco amino acid residues between the two carboxysome types which could be engineered to produce a new, hybrid carboxysome. In theory, this hybrid carboxysome would benefit from the simpler α-carboxysome shell architecture while simultaneously exploiting the higher Rubisco turnover rates in β-carboxysomes. Here, we demonstrate in an Escherichia coli expression system, that the Thermosynechococcus elongatus Form IB Rubisco can be imperfectly incorporated into simplified Cyanobium α-carboxysome-like structures. While encapsulation of non-native cargo can be achieved, T. elongatus Form IB Rubisco does not interact with the Cyanobium carbonic anhydrase, a core requirement for proper carboxysome functionality. Together, these results suggest a way forward to hybrid carboxysome formation.
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Affiliation(s)
- Nghiem Dinh Nguyen
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Acton, ACT, 2601, Australia
| | - Sacha B Pulsford
- Australian Research Council Centre of Excellence in Synthetic Biology, Research School of Chemistry, The Australian National University, Building 46, Sullivan's Creek Road, Acton, ACT, 2601, Australia
| | - Wei Yi Hee
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
| | - Benjamin D Rae
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Acton, ACT, 2601, Australia
| | - Loraine M Rourke
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Acton, ACT, 2601, Australia
| | - G Dean Price
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Acton, ACT, 2601, Australia.
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia.
- Division of Plant Sciences, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Canberra, ACT, 2601, Australia.
| | - Benedict M Long
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Acton, ACT, 2601, Australia
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
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41
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Caruso Bavisotto C, Provenzano A, Passantino R, Marino Gammazza A, Cappello F, San Biagio PL, Bulone D. Oligomeric State and Holding Activity of Hsp60. Int J Mol Sci 2023; 24:ijms24097847. [PMID: 37175554 PMCID: PMC10177986 DOI: 10.3390/ijms24097847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/22/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
Similar to its bacterial homolog GroEL, Hsp60 in oligomeric conformation is known to work as a folding machine, with the assistance of co-chaperonin Hsp10 and ATP. However, recent results have evidenced that Hsp60 can stabilize aggregation-prone molecules in the absence of Hsp10 and ATP by a different, "holding-like" mechanism. Here, we investigated the relationship between the oligomeric conformation of Hsp60 and its ability to inhibit fibrillization of the Ab40 peptide. The monomeric or tetradecameric form of the protein was isolated, and its effect on beta-amyloid aggregation was separately tested. The structural stability of the two forms of Hsp60 was also investigated using differential scanning calorimetry (DSC), light scattering, and circular dichroism. The results showed that the protein in monomeric form is less stable, but more effective against amyloid fibrillization. This greater functionality is attributed to the disordered nature of the domains involved in subunit contacts.
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Affiliation(s)
- Celeste Caruso Bavisotto
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), Institute of Anatomy and Histology, University of Palermo, 90127 Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
| | - Alessia Provenzano
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, 90146 Palermo, Italy
| | - Rosa Passantino
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, 90146 Palermo, Italy
| | - Antonella Marino Gammazza
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), Institute of Anatomy and Histology, University of Palermo, 90127 Palermo, Italy
| | - Francesco Cappello
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), Institute of Anatomy and Histology, University of Palermo, 90127 Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139 Palermo, Italy
| | | | - Donatella Bulone
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, 90146 Palermo, Italy
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42
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Wang Y, Liu X, Li Y, Yang Y, Liu C, Linhardt RJ, Zhang F, Bai Z. Enhanced production of recombinant proteins in Corynebacterium glutamicum using a molecular chaperone. J GEN APPL MICROBIOL 2023. [PMID: 36878578 DOI: 10.2323/jgam.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Protein synthesis in Corynebacterium glutamicum is critical for applications in biotechnology and medicine. However, the use of C. glutamicum for protein production is limited by its low expression and aggregation. To overcome these limitations, a molecular chaperone plasmid system was developed in this study to improve the efficiency of recombinant protein synthesis in C. glutamicum. The effect of molecular chaperones on target protein synthesis (Single-chain variable fragment, Scfv) under three different promoter strengths was tested. In addition, the plasmid containing the molecular chaperone and target protein was verified for growth stability and plasmid stability. This expression model was further validated using two recombinant proteins, human interferon-beta (Hifn) and hirudin variant III (Rhv3). Finally, the Rhv3 protein was purified, and analysis of Rhv3 activity confirmed that the use of a molecular chaperone led to an improvement in test protein synthesis. Thus, the use of molecular chaperones is believed to will improve recombinant proteins synthesis in C. glutamicum.
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Affiliation(s)
- Yali Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University.,National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University
| | - Xiuxia Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University.,National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University
| | - Ye Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University.,National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University
| | - Yankun Yang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University.,National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University
| | - Chunli Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University.,National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University
| | - Robert J Linhardt
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute
| | - Fuming Zhang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute
| | - Zhonghu Bai
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University.,National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University
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43
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Minami S, Niwa T, Uemura E, Koike R, Taguchi H, Ota M. Prediction of chaperonin GroE substrates using small structural patterns of proteins. FEBS Open Bio 2023; 13:779-794. [PMID: 36869604 PMCID: PMC10068320 DOI: 10.1002/2211-5463.13590] [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: 10/18/2022] [Revised: 02/22/2023] [Accepted: 03/03/2023] [Indexed: 03/05/2023] Open
Abstract
Molecular chaperones are indispensable proteins that assist the folding of aggregation-prone proteins into their functional native states, thereby maintaining organized cellular systems. Two of the best-characterized chaperones are the Escherichia coli chaperonins GroEL and GroES (GroE), for which in vivo obligate substrates have been identified by proteome-wide experiments. These substrates comprise various proteins but exhibit remarkable structural features. They include a number of α/β proteins, particularly those adopting the TIM β/α barrel fold. This observation led us to speculate that GroE obligate substrates share a structural motif. Based on this hypothesis, we exhaustively compared substrate structures with the MICAN alignment tool, which detects common structural patterns while ignoring the connectivity or orientation of secondary structural elements. We selected four (or five) substructures with hydrophobic indices that were mostly included in substrates and excluded in others, and developed a GroE obligate substrate discriminator. The substructures are structurally similar and superimposable on the 2-layer 2α4β sandwich, the most popular protein substructure, implying that targeting this structural pattern is a useful strategy for GroE to assist numerous proteins. Seventeen false positives predicted by our methods were experimentally examined using GroE-depleted cells, and 9 proteins were confirmed to be novel GroE obligate substrates. Together, these results demonstrate the utility of our common substructure hypothesis and prediction method.
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Affiliation(s)
| | - Tatsuya Niwa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Eri Uemura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Ryotaro Koike
- Graduate School of Informatics, Nagoya University, Japan
| | - Hideki Taguchi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Motonori Ota
- Graduate School of Informatics, Nagoya University, Japan.,Institute for Glyco-core Research, Nagoya University, Japan
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44
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Dupuy E, Van der Verren SE, Lin J, Wilson MA, Dachsbeck AV, Viela F, Latour E, Gennaris A, Vertommen D, Dufrêne YF, Iorga BI, Goemans CV, Remaut H, Collet JF. A molecular device for the redox quality control of GroEL/ES substrates. Cell 2023; 186:1039-1049.e17. [PMID: 36764293 PMCID: PMC10044410 DOI: 10.1016/j.cell.2023.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 10/27/2022] [Accepted: 01/10/2023] [Indexed: 02/11/2023]
Abstract
Hsp60 chaperonins and their Hsp10 cofactors assist protein folding in all living cells, constituting the paradigmatic example of molecular chaperones. Despite extensive investigations of their structure and mechanism, crucial questions regarding how these chaperonins promote folding remain unsolved. Here, we report that the bacterial Hsp60 chaperonin GroEL forms a stable, functionally relevant complex with the chaperedoxin CnoX, a protein combining a chaperone and a redox function. Binding of GroES (Hsp10 cofactor) to GroEL induces CnoX release. Cryoelectron microscopy provided crucial structural information on the GroEL-CnoX complex, showing that CnoX binds GroEL outside the substrate-binding site via a highly conserved C-terminal α-helix. Furthermore, we identified complexes in which CnoX, bound to GroEL, forms mixed disulfides with GroEL substrates, indicating that CnoX likely functions as a redox quality-control plugin for GroEL. Proteins sharing structural features with CnoX exist in eukaryotes, suggesting that Hsp60 molecular plugins have been conserved through evolution.
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Affiliation(s)
- Emile Dupuy
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Sander Egbert Van der Verren
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, VIB, 1050 Brussels, Belgium
| | - Jiusheng Lin
- Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA
| | - Mark Alan Wilson
- Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA
| | - Alix Vincent Dachsbeck
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Felipe Viela
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Croix du Sud 4-5, 1348 Louvain-la-neuve, Belgium
| | - Emmanuelle Latour
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Alexandra Gennaris
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Didier Vertommen
- de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Yves Frédéric Dufrêne
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Croix du Sud 4-5, 1348 Louvain-la-neuve, Belgium
| | - Bogdan Iuliu Iorga
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium; Université Paris-Saclay, CNRS UPR 2301, Institut de Chimie des Substances Naturelles, 91198 Gif-sur-Yvette, France
| | - Camille Véronique Goemans
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium; European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Han Remaut
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, VIB, 1050 Brussels, Belgium.
| | - Jean-François Collet
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium.
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45
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Rong Y, Jensen SI, Lindorff-Larsen K, Nielsen AT. Folding of heterologous proteins in bacterial cell factories: Cellular mechanisms and engineering strategies. Biotechnol Adv 2023; 63:108079. [PMID: 36528238 DOI: 10.1016/j.biotechadv.2022.108079] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/20/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
The expression of correctly folded and functional heterologous proteins is important in many biotechnological production processes, whether it is enzymes, biopharmaceuticals or biosynthetic pathways for production of sustainable chemicals. For industrial applications, bacterial platform organisms, such as E. coli, are still broadly used due to the availability of tools and proven suitability at industrial scale. However, expression of heterologous proteins in these organisms can result in protein aggregation and low amounts of functional protein. This review provides an overview of the cellular mechanisms that can influence protein folding and expression, such as co-translational folding and assembly, chaperone binding, as well as protein quality control, across different model organisms. The knowledge of these mechanisms is then linked to different experimental methods that have been applied in order to improve functional heterologous protein folding, such as codon optimization, fusion tagging, chaperone co-production, as well as strain and protein engineering strategies.
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Affiliation(s)
- Yixin Rong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Sheila Ingemann Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark.
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46
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Zimmerman AE, Podowski JC, Gallagher GE, Coleman ML, Waldbauer JR. Tracking nitrogen allocation to proteome biosynthesis in a marine microbial community. Nat Microbiol 2023; 8:498-509. [PMID: 36635571 DOI: 10.1038/s41564-022-01303-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 12/12/2022] [Indexed: 01/14/2023]
Abstract
Microbial growth in many environments is limited by nitrogen availability, yet there is limited understanding of how complex communities compete for and allocate this resource. Here we develop a broadly applicable approach to track biosynthetic incorporation of 15N-labelled nitrogen substrates into microbial community proteomes, enabling quantification of protein turnover and N allocation to specific cellular functions in individual taxa. Application to oligotrophic ocean surface water identifies taxa-specific substrate preferences and a distinct subset of protein functions undergoing active biosynthesis. The cyanobacterium Prochlorococcus is the most effective competitor for acquisition of ammonium and urea and shifts its proteomic allocation of N over the day/night cycle. Our approach reveals that infrastructure and protein-turnover functions comprise substantial biosynthetic demand for N in Prochlorococcus and a range of other microbial taxa. The direct interrogation of the proteomic underpinnings of N limitation with 15N-tracking proteomics illuminates how nutrient stress differentially influences metabolism in co-existing microbes.
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Affiliation(s)
- Amy E Zimmerman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA.,Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Justin C Podowski
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA.,Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL, USA
| | - Gwendolyn E Gallagher
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA.,New York Sea Grant, Stony Brook University, Stony Brook, NY, USA
| | - Maureen L Coleman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Jacob R Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, USA.
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47
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Yeung N, Murata D, Iijima M, Sesaki H. Role of human HSPE1 for OPA1 processing independent of HSPD1. iScience 2023; 26:106067. [PMID: 36818283 PMCID: PMC9929679 DOI: 10.1016/j.isci.2023.106067] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/27/2022] [Accepted: 01/23/2023] [Indexed: 01/27/2023] Open
Abstract
The human mtHSP60/HSPD1-mtHSP10/HSPE1 system prevents protein misfolding and maintains proteostasis in the mitochondrial matrix. Altered activities of this chaperonin system have been implicated in human diseases, such as cancer and neurodegeneration. However, how defects in HSPD1 and HSPE1 affect mitochondrial structure and dynamics remains elusive. In the current study, we address this fundamental question in a human cell line, HEK293T. We found that the depletion of HSPD1 or HSPE1 results in fragmentation of mitochondria, suggesting a decrease in mitochondrial fusion. Supporting this notion, HSPE1 depletion led to proteolytic inactivation of OPA1, a dynamin-related GTPase that fuses the mitochondrial membrane. This OPA1 inactivation was mediated by a stress-activated metalloprotease, OMA1. In contrast, HSPD1 depletion did not induce OMA1 activation or OPA1 cleavage. These data suggest that HSPE1 controls mitochondrial morphology through a mechanism separate from its chaperonin activity.
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Affiliation(s)
- Nelson Yeung
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daisuke Murata
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Miho Iijima
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hiromi Sesaki
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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48
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Taguchi H, Koike-Takeshita A. In vivo client proteins of the chaperonin GroEL-GroES provide insight into the role of chaperones in protein evolution. Front Mol Biosci 2023; 10:1091677. [PMID: 36845542 PMCID: PMC9950496 DOI: 10.3389/fmolb.2023.1091677] [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: 11/07/2022] [Accepted: 01/30/2023] [Indexed: 02/12/2023] Open
Abstract
Protein folding is often hampered by intermolecular protein aggregation, which can be prevented by a variety of chaperones in the cell. Bacterial chaperonin GroEL is a ring-shaped chaperone that forms complexes with its cochaperonin GroES, creating central cavities to accommodate client proteins (also referred as substrate proteins) for folding. GroEL and GroES (GroE) are the only indispensable chaperones for bacterial viability, except for some species of Mollicutes such as Ureaplasma. To understand the role of chaperonins in the cell, one important goal of GroEL research is to identify a group of obligate GroEL/GroES clients. Recent advances revealed hundreds of in vivo GroE interactors and obligate chaperonin-dependent clients. This review summarizes the progress on the in vivo GroE client repertoire and its features, mainly for Escherichia coli GroE. Finally, we discuss the implications of the GroE clients for the chaperone-mediated buffering of protein folding and their influences on protein evolution.
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Affiliation(s)
- Hideki Taguchi
- Cell Biology Center, Tokyo Institute of Technology, Yokohama, Japan,*Correspondence: Hideki Taguchi,
| | - Ayumi Koike-Takeshita
- Department of Applied Bioscience, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
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49
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Larson J, Tokmina-Lukaszewska M, Fausset H, Spurzem S, Cox S, Cooper G, Copié V, Bothner B. Arsenic Exposure Causes Global Changes in the Metalloproteome of Escherichia coli. Microorganisms 2023; 11:382. [PMID: 36838347 PMCID: PMC9965246 DOI: 10.3390/microorganisms11020382] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/03/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Arsenic is a toxic metalloid with differential biological effects, depending on speciation and concentration. Trivalent arsenic (arsenite, AsIII) is more toxic at lower concentrations than the pentavalent form (arsenate, AsV). In E. coli, the proteins encoded by the arsRBC operon are the major arsenic detoxification mechanism. Our previous transcriptional analyses indicate broad changes in metal uptake and regulation upon arsenic exposure. Currently, it is not known how arsenic exposure impacts the cellular distribution of other metals. This study examines the metalloproteome of E. coli strains with and without the arsRBC operon in response to sublethal doses of AsIII and AsV. Size exclusion chromatography coupled with inductively coupled plasma mass spectrometry (SEC-ICPMS) was used to investigate the distribution of five metals (56Fe, 24Mg, 66Zn, 75As, and 63Cu) in proteins and protein complexes under native conditions. Parallel analysis by SEC-UV-Vis spectroscopy monitored the presence of protein cofactors. Together, these data reveal global changes in the metalloproteome, proteome, protein cofactors, and soluble intracellular metal pools in response to arsenic stress in E. coli. This work brings to light one outcome of metal exposure and suggests that metal toxicity on the cellular level arises from direct and indirect effects.
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Affiliation(s)
| | | | | | | | | | | | | | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59715, USA
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50
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Richter AS, Nägele T, Grimm B, Kaufmann K, Schroda M, Leister D, Kleine T. Retrograde signaling in plants: A critical review focusing on the GUN pathway and beyond. PLANT COMMUNICATIONS 2023; 4:100511. [PMID: 36575799 PMCID: PMC9860301 DOI: 10.1016/j.xplc.2022.100511] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/05/2022] [Accepted: 12/22/2022] [Indexed: 06/01/2023]
Abstract
Plastids communicate their developmental and physiological status to the nucleus via retrograde signaling, allowing nuclear gene expression to be adjusted appropriately. Signaling during plastid biogenesis and responses of mature chloroplasts to environmental changes are designated "biogenic" and "operational" controls, respectively. A prominent example of the investigation of biogenic signaling is the screen for gun (genomes uncoupled) mutants. Although the first five gun mutants were identified 30 years ago, the functions of GUN proteins in retrograde signaling remain controversial, and that of GUN1 is hotly disputed. Here, we provide background information and critically discuss recently proposed concepts that address GUN-related signaling and some novel gun mutants. Moreover, considering heme as a candidate in retrograde signaling, we revisit the spatial organization of heme biosynthesis and export from plastids. Although this review focuses on GUN pathways, we also highlight recent progress in the identification and elucidation of chloroplast-derived signals that regulate the acclimation response in green algae and plants. Here, stress-induced accumulation of unfolded/misassembled chloroplast proteins evokes a chloroplast-specific unfolded protein response, which leads to changes in the expression levels of nucleus-encoded chaperones and proteases to restore plastid protein homeostasis. We also address the importance of chloroplast-derived signals for activation of flavonoid biosynthesis leading to production of anthocyanins during stress acclimation through sucrose non-fermenting 1-related protein kinase 1. Finally, a framework for identification and quantification of intercompartmental signaling cascades at the proteomic and metabolomic levels is provided, and we discuss future directions of dissection of organelle-nucleus communication.
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Affiliation(s)
- Andreas S Richter
- Physiology of Plant Metabolism, Institute for Biosciences, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany
| | - Thomas Nägele
- Plant Evolutionary Cell Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Bernhard Grimm
- Institute of Biology/Plant Physiology, Humboldt-Universität zu Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - Kerstin Kaufmann
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - Michael Schroda
- Molecular Biotechnology and Systems Biology, TU Kaiserslautern, Kaiserslautern, Germany
| | - Dario Leister
- Plant Molecular Biology (Botany), Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Tatjana Kleine
- Plant Molecular Biology (Botany), Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.
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