1
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Oehlmann NN, Rebelein JG. Generating Site Saturation Mutagenesis Libraries and Transferring Them to Broad Host-Range Plasmids Using Golden Gate Cloning. Methods Mol Biol 2025; 2850:251-264. [PMID: 39363076 DOI: 10.1007/978-1-0716-4220-7_14] [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: 10/05/2024]
Abstract
Protein engineering is an established method for tailoring enzymatic reactivity. A commonly used method is directed evolution, where the mutagenesis and natural selection process is mimicked and accelerated in the laboratory. Here, we describe a reliable method for generating saturation mutagenesis libraries by Golden Gate cloning in a broad host range plasmid containing the pBBR1 replicon. The applicability is demonstrated by generating a mutant library of the iron nitrogenase gene cluster (anfHDGK) of Rhodobacter capsulatus, which is subsequently screened for the improved formation of molecular hydrogen.
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Affiliation(s)
- Niels N Oehlmann
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Johannes G Rebelein
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.
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2
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Ingelman H, Heffernan JK, Harris A, Brown SD, Shaikh KM, Saqib AY, Pinheiro MJ, de Lima LA, Martinez KR, Gonzalez-Garcia RA, Hawkins G, Daleiden J, Tran L, Zeleznik H, Jensen RO, Reynoso V, Schindel H, Jänes J, Simpson SD, Köpke M, Marcellin E, Valgepea K. Autotrophic adaptive laboratory evolution of the acetogen Clostridium autoethanogenum delivers the gas-fermenting strain LAbrini with superior growth, products, and robustness. N Biotechnol 2024; 83:1-15. [PMID: 38871051 DOI: 10.1016/j.nbt.2024.06.002] [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] [Received: 04/12/2024] [Revised: 06/05/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024]
Abstract
Microbes able to convert gaseous one-carbon (C1) waste feedstocks are increasingly important to transition to the sustainable production of renewable chemicals and fuels. Acetogens are interesting biocatalysts since gas fermentation using Clostridium autoethanogenum has been commercialised. However, most acetogen strains need complex nutrients, display slow growth, and are not robust for bioreactor fermentations. In this work, we used three different and independent adaptive laboratory evolution (ALE) strategies to evolve the wild-type C. autoethanogenum to grow faster, without yeast extract and to be robust in operating continuous bioreactor cultures. Multiple evolved strains with improved phenotypes were isolated on minimal media with one strain, named "LAbrini", exhibiting superior performance regarding the maximum specific growth rate, product profile, and robustness in continuous cultures. Whole-genome sequencing of the evolved strains identified 25 mutations. Of particular interest are two genes that acquired seven different mutations across the three ALE strategies, potentially as a result of convergent evolution. Reverse genetic engineering of mutations in potentially sporulation-related genes CLAU_3129 (spo0A) and CLAU_1957 recovered all three superior features of our ALE strains through triggering significant proteomic rearrangements. This work provides a robust C. autoethanogenum strain "LAbrini" to accelerate phenotyping and genetic engineering and to better understand acetogen metabolism.
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Affiliation(s)
- Henri Ingelman
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia
| | - James K Heffernan
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia
| | | | | | | | - Asfand Yar Saqib
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia
| | - Marina J Pinheiro
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia
| | - Lorena Azevedo de Lima
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia
| | - Karen Rodriguez Martinez
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia
| | - Ricardo A Gonzalez-Garcia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia
| | | | | | | | | | | | | | | | - Jürgen Jänes
- Institute of Molecular Systems Biology, ETH Zürich, 8049 Zürich, Switzerland
| | | | | | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia.
| | - Kaspar Valgepea
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia.
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3
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Li Y, Pinones M, Breeland A, Jiang P. Single-round QuikChange PCR for engineering multiple site-directed mutations in plasmid DNA. Anal Biochem 2024; 694:115621. [PMID: 39019205 DOI: 10.1016/j.ab.2024.115621] [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: 04/16/2024] [Revised: 06/08/2024] [Accepted: 07/14/2024] [Indexed: 07/19/2024]
Abstract
Mutational study is a cornerstone methodology in biochemistry and genetics, and many mutagenesis strategies have been invented to promote the efficiency of gene engineering. In this study, we developed a simple and timesaving approach to integrate simultaneous mutagenesis at discrete sites. By using plasmid as a template and compatible oligonucleotide primers per the QuikChange strategy, our method was able to introduce multiple nucleotide insertions, deletions and replacements in one round of polymerase chain reaction. The longest insertion and deletion were achieved with 28 bp and 16 bp mismatch respectively. For minor nucleotide replacements (mismatch no more than 4 bp), mutations were achieved at up to 4 discrete locations. Usually, a successful clone with all desired mutations was found by screening 5 colonies. Clones with a subset of mutations may be stocked into the library of mutants or used as templates in the next rounds of mutagenic PCR to accomplish the entire construction project. This method can be applied to build up a combinatory library of mutants through saturation mutagenesis at multiple sites. It is promising to facilitate the research of protein biochemistry, forward genetics and synthetic biology.
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Affiliation(s)
- Yunxiang Li
- Division of Chemistry and Biochemistry, Texas Woman's University, Denton, TX, 76204, USA.
| | - Mileina Pinones
- Division of Chemistry and Biochemistry, Texas Woman's University, Denton, TX, 76204, USA
| | - Alexis Breeland
- Division of Biology, Texas Woman's University, Denton, TX, 76204, USA
| | - Peilin Jiang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA
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4
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Lowe TL, Valencia DA, Velasquez VE, Quinlan ME, Clarke SG. Methylation and phosphorylation of formin homology domain proteins (Fhod1 and Fhod3) by protein arginine methyltransferase 7 (PRMT7) and Rho Kinase (ROCK1). J Biol Chem 2024:107857. [PMID: 39368550 DOI: 10.1016/j.jbc.2024.107857] [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: 04/08/2024] [Revised: 09/13/2024] [Accepted: 09/26/2024] [Indexed: 10/07/2024] Open
Abstract
Protein post translational modifications (PTMs) can regulate biological processes by altering an amino acid's bulkiness, charge, and hydrogen bonding interactions. Common modifications include phosphorylation, methylation, acetylation and ubiquitylation. Although a primary focus of studying PTMs is understanding the effects of a single amino acid modification, the possibility of additional modifications increases the complexity. For example, substrate recognition motifs for arginine methyltransferases and some serine/threonine kinases overlap, leading to potential enzymatic crosstalk. In this study we have shown that the human family of formin homology domain containing proteins (Fhods) contain a substrate recognition motif specific for human protein arginine methyltransferase 7 (PRMT7). In particular, PRMT7 methylates two arginine residues in the diaphanous autoinhibitory domain (DAD) of the family of Fhod proteins: R1588 and/or R1590 of Fhod3 isoform 4. Additionally, we confirmed that S1589 and S1595 in the DAD domain of Fhod3 can be phosphorylated by Rho/ROCK1 kinase. Significantly, we have determined that if S1589 is phosphorylated then PRMT7 cannot subsequently methylate R1588 or R1590. In contrast, if R1588 or R1590 of Fhod3 is methylated then ROCK1 phosphorylation activity is only slightly affected. Finally, we show that the interaction of the N-terminal DID domain can also inhibit the methylation of the DAD domain. Taken together these results suggest that the family of Fhod proteins, potential in vivo substrates for PRMT7, might be regulated by a combination of methylation and phosphorylation.
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Affiliation(s)
- Troy L Lowe
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA; Molecular Biology Institute, University of California - Los Angeles, Los Angeles, CA, USA
| | - Dylan A Valencia
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA; Molecular Biology Institute, University of California - Los Angeles, Los Angeles, CA, USA
| | - Vicente E Velasquez
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Margot E Quinlan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA; Molecular Biology Institute, University of California - Los Angeles, Los Angeles, CA, USA
| | - Steven G Clarke
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA; Molecular Biology Institute, University of California - Los Angeles, Los Angeles, CA, USA.
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5
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Betts PC, Blakely SJ, Rutkowski BN, Bender B, Klingler C, Froese JT. Engineering of Rieske dioxygenase variants with improved cis-dihydroxylation activity for benzoates. Biotechnol Bioeng 2024; 121:3144-3154. [PMID: 38951963 DOI: 10.1002/bit.28786] [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: 04/04/2024] [Revised: 06/13/2024] [Accepted: 06/16/2024] [Indexed: 07/03/2024]
Abstract
Rieske dioxygenases have a long history of being utilized as green chemical tools in the organic synthesis of high-value compounds, due to their capacity to perform the cis-dihydroxylation of a wide variety of aromatic substrates. The practical utility of these enzymes has been hampered however by steric and electronic constraints on their substrate scopes, resulting in limited reactivity with certain substrate classes. Herein, we report the engineering of a widely used member of the Rieske dioxygenase class of enzymes, toluene dioxygenase (TDO), to produce improved variants with greatly increased activity for the cis-dihydroxylation of benzoates. Through rational mutagenesis and screening, TDO variants with substantially improved activity over the wild-type enzyme were identified. Homology modeling, docking studies, molecular dynamics simulations, and substrate tunnel analysis were applied in an effort to elucidate how the identified mutations resulted in improved activity for this polar substrate class. These analyses revealed modification of the substrate tunnel as the likely cause of the improved activity observed with the best-performing enzyme variants.
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Affiliation(s)
- Phillip C Betts
- Department of Chemistry, Ball State University, Muncie, Indiana, USA
| | - Spencer J Blakely
- Department of Chemistry, Ball State University, Muncie, Indiana, USA
| | | | - Brandon Bender
- Department of Chemistry, Ball State University, Muncie, Indiana, USA
| | - Cole Klingler
- Department of Chemistry, Ball State University, Muncie, Indiana, USA
| | - Jordan T Froese
- Department of Chemistry, Ball State University, Muncie, Indiana, USA
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6
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Ranzau BL, Robinson TD, Scully JM, Kapelczack ED, Dean TS, TeSlaa T, Schmitt DL. A Genetically Encoded Fluorescent Biosensor for Intracellular Measurement of Malonyl-CoA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.27.615526. [PMID: 39386450 PMCID: PMC11463626 DOI: 10.1101/2024.09.27.615526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Malonyl-CoA is the essential building block of fatty acids and regulates cell function through protein malonylation and allosteric regulation of signaling networks. Accordingly, the production and use of malonyl-CoA is finely tuned by the cellular energy status. Most studies of malonyl-CoA dynamics rely on bulk approaches that take only a snapshot of the average metabolic state of a population of cells, missing out on dynamic changes in malonyl-CoA and fatty acid biosynthesis that could be occurring within a single cell. To overcome this limitation, we have developed a genetically encoded fluorescent protein-based biosensor for malonyl-CoA that can be used to capture malonyl-CoA dynamics in single cells. This biosensor, termed Malibu (malonyl-CoA i ntracellular biosensor to understand dynamics), exhibits an excitation-ratiometric change in response to malonyl-CoA binding. We first used Malibu to monitor malonyl-CoA dynamics during inhibition of fatty acid biosynthesis using cerulenin in E. coli , observing an increase in Malibu response in a time- and dose-dependent manner. In HeLa cells, we used Malibu to monitor the impact of fatty acid biosynthesis inhibition on malonyl-CoA dynamics in single cells, finding that two inhibitors of fatty acid biosynthesis, cerulenin and orlistat, which inhibit different steps of fatty acid biosynthesis, increase malonyl-CoA levels. Altogether, we have developed a new genetically encoded biosensor for malonyl-CoA, which can be used to sensitively study malonyl-CoA dynamics in single cells, providing an unparalleled view into fatty acid biosynthesis.
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7
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Górniak I, Stephens Z, Erramilli SK, Gawda T, Kossiakoff AA, Zimmer J. Structural insights into translocation and tailored synthesis of hyaluronan. Nat Struct Mol Biol 2024:10.1038/s41594-024-01389-1. [PMID: 39322765 DOI: 10.1038/s41594-024-01389-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 08/14/2024] [Indexed: 09/27/2024]
Abstract
Hyaluronan (HA) is an essential component of the vertebrate extracellular matrix. It is a heteropolysaccharide of N-acetylglucosamine (GlcNAc) and glucuronic acid (GlcA) reaching several megadaltons in healthy tissues. HA is synthesized and translocated in a coupled reaction by HA synthase (HAS). Here, structural snapshots of HAS provide insights into HA biosynthesis, from substrate recognition to HA elongation and translocation. We monitor the extension of a GlcNAc primer with GlcA, reveal the coordination of the uridine diphosphate product by a conserved gating loop and capture the opening of a translocation channel to coordinate a translocating HA polymer. Furthermore, we identify channel-lining residues that modulate HA product lengths. Integrating structural and biochemical analyses suggests an avenue for polysaccharide engineering based on finely tuned enzymatic activity and HA coordination.
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Affiliation(s)
- Ireneusz Górniak
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Zachery Stephens
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Satchal K Erramilli
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Tomasz Gawda
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Jochen Zimmer
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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8
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Lopatto EDB, Pinkner JS, Sanick DA, Potter RF, Liu LX, Bazán Villicaña J, Tamadonfar KO, Ye Y, Zimmerman MI, Gualberto NC, Dodson KW, Janetka JW, Hunstad DA, Hultgren SJ. Conformational ensembles in Klebsiella pneumoniae FimH impact uropathogenesis. Proc Natl Acad Sci U S A 2024; 121:e2409655121. [PMID: 39288182 PMCID: PMC11441496 DOI: 10.1073/pnas.2409655121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 08/01/2024] [Indexed: 09/19/2024] Open
Abstract
Klebsiella pneumoniae is an important pathogen causing difficult-to-treat urinary tract infections (UTIs). Over 1.5 million women per year suffer from recurrent UTI, reducing quality of life and causing substantial morbidity and mortality, especially in the hospital setting. Uropathogenic E. coli (UPEC) is the most prevalent cause of UTI. Like UPEC, K. pneumoniae relies on type 1 pili, tipped with the mannose-binding adhesin FimH, to cause cystitis. However, K. pneumoniae FimH is a poor binder of mannose, despite a mannose-binding pocket identical to UPEC FimH. FimH is composed of two domains that are in an equilibrium between tense (low-affinity) and relaxed (high-affinity) conformations. Substantial interdomain interactions in the tense conformation yield a low-affinity, deformed mannose-binding pocket, while domain-domain interactions are broken in the relaxed state, resulting in a high-affinity binding pocket. Using crystallography, we identified the structural basis by which domain-domain interactions direct the conformational equilibrium of K. pneumoniae FimH, which is strongly shifted toward the low-affinity tense state. Removal of the pilin domain restores mannose binding to the lectin domain, thus showing that poor mannose binding by K. pneumoniae FimH is not an inherent feature of the mannose-binding pocket. Phylogenetic analyses of K. pneumoniae genomes found that FimH sequences are highly conserved. However, we surveyed a collection of K. pneumoniae isolates from patients with long-term indwelling catheters and identified isolates that possessed relaxed higher-binding FimH variants, which increased K. pneumoniae fitness in bladder infection models, suggesting that long-term residence within the urinary tract may select for higher-binding FimH variants.
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Affiliation(s)
- Edward D B Lopatto
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110
| | - Jerome S Pinkner
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110
| | - Denise A Sanick
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110
| | - Robert F Potter
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
| | - Lily X Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110
| | - Jesús Bazán Villicaña
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110
| | - Kevin O Tamadonfar
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110
| | - Yijun Ye
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110
| | - Maxwell I Zimmerman
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110
| | - Nathaniel C Gualberto
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110
| | - Karen W Dodson
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110
| | - James W Janetka
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110
| | - David A Hunstad
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110
| | - Scott J Hultgren
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110
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9
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Anderson AC, Schultz BJ, Snow ED, Brott AS, Stangherlin S, Malloch T, London JR, Walker S, Clarke AJ. The mechanism of peptidoglycan O-acetylation in Gram-negative bacteria typifies bacterial MBOAT-SGNH acyltransferases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.17.613324. [PMID: 39345430 PMCID: PMC11429678 DOI: 10.1101/2024.09.17.613324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Bacterial cell envelope polymers are commonly modified with acyl groups that provide fitness advantages. Many polymer acylation pathways involve pairs of membrane-bound O-acyltransferase (MBOAT) and SGNH family proteins. As an example, the MBOAT protein PatA and the SGNH protein PatB are required in Gram-negative bacteria for peptidoglycan O-acetylation. The mechanism for how MBOAT-SGNH transferases move acyl groups from acyl-CoA donors made in the cytoplasm to extracellular polymers is unclear. Using the peptidoglycan O-acetyltransferase proteins PatAB, we explore the mechanism of MBOAT-SGNH pairs. We find that the MBOAT protein PatA catalyzes auto-acetylation of an invariant Tyr residue in its conserved C-terminal hexapeptide motif. We also show that PatB can use a synthetic hexapeptide containing an acetylated tyrosine to donate an acetyl group to a peptidoglycan mimetic. Finally, we report the structure of PatB, finding that it has structural features that shape its activity as an O-acetyltransferase and distinguish it from other SGNH esterases and hydrolases. Taken together, our results support a model for peptidoglycan acylation in which a tyrosine-containing peptide at the MBOAT's C-terminus shuttles an acyl group from the MBOAT active site to the SGNH active site, where it is transferred to peptidoglycan. This model likely applies to other systems containing MBOAT-SGNH pairs, such as those that O-acetylate alginate, cellulose, and secondary cell wall polysaccharides. The use of an acyl-tyrosine intermediate for MBOAT-SGNH acyl transfer is also shared with AT3-SGNH proteins, a second major group of acyltransferases that modify cell envelope polymers.
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Affiliation(s)
- Alexander C. Anderson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario Canada N1G 2W1
| | - Bailey J. Schultz
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Eric D. Snow
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Ashley S. Brott
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario Canada N1G 2W1
| | - Stefen Stangherlin
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario Canada N1G 2W1
| | - Tyler Malloch
- Department of Chemistry & Biochemistry, Wilfrid Laurier University, Waterloo, Ontario Canada N2L 3C5
| | - Jalen R. London
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Suzanne Walker
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Anthony J. Clarke
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario Canada N1G 2W1
- Department of Chemistry & Biochemistry, Wilfrid Laurier University, Waterloo, Ontario Canada N2L 3C5
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10
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Li F, Scheller S, Lienemann M. A growth-based screening strategy for engineering the catalytic activity of an oxygen-sensitive formate dehydrogenase. Appl Environ Microbiol 2024; 90:e0147224. [PMID: 39194220 PMCID: PMC11409667 DOI: 10.1128/aem.01472-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Accepted: 07/27/2024] [Indexed: 08/29/2024] Open
Abstract
Enzyme engineering is a powerful tool for improving or altering the properties of biocatalysts for industrial, research, and therapeutic applications. Fast and accurate screening of variant libraries is often the bottleneck of enzyme engineering and may be overcome by growth-based screening strategies with simple processes to enable high throughput. The currently available growth-based screening strategies have been widely employed for enzymes but not yet for catalytically potent and oxygen-sensitive metalloenzymes. Here, we present a screening system that couples the activity of an oxygen-sensitive formate dehydrogenase to the growth of Escherichia coli. This system relies on the complementation of the E. coli formate hydrogenlyase (FHL) complex by Mo-dependent formate dehydrogenase H (EcFDH-H). Using an EcFDH-H-deficient strain, we demonstrate that growth inhibition by acidic glucose fermentation products can be alleviated by FHL complementation. This allows the identification of catalytically active EcFDH-H variants at a readily measurable cell density readout, reduced handling efforts, and a low risk of oxygen contamination. Furthermore, a good correlation between cell density and formate oxidation activity was established using EcFDH-H variants with variable catalytic activities. As proof of concept, the growth assay was employed to screen a library of 1,032 EcFDH-H variants and reduced the library size to 96 clones. During the subsequent colorimetric screening of these clones, the variant A12G exhibiting an 82.4% enhanced formate oxidation rate was identified. Since many metal-dependent formate dehydrogenases and hydrogenases form functional complexes resembling E. coli FHL, the demonstrated growth-based screening strategy may be adapted to components of such electron-transferring complexes.IMPORTANCEOxygen-sensitive metalloenzymes are highly potent catalysts that allow the reduction of chemically inert substrates such as CO2 and N2 at ambient pressure and temperature and have, therefore, been considered for the sustainable production of biofuels and commodity chemicals such as ammonia, formic acid, and glycine. A proven method to optimize natural enzymes for such applications is enzyme engineering using high-throughput variant library screening. However, most screening methods are incompatible with the oxygen sensitivity of these metalloenzymes and thereby limit their relevance for the development of biosynthetic production processes. A microtiter plate-based assay was developed for the screening of metal-dependent formate dehydrogenase that links the activity of the tested enzyme variant to the growth of the anaerobically grown host cell. The presented work extends the application range of growth-based screening to metalloenzymes and is thereby expected to advance their adoption to biosynthesis applications.
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Affiliation(s)
- Feilong Li
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | - Silvan Scheller
- Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
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11
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Cha JH, Lee SH, Yun Y, Choi WH, Koo H, Jung SH, Chae HB, Lee DH, Lee SJ, Jo DH, Kim JH, Song JJ, Chae JH, Lee JH, Park J, Kang JY, Bae S, Lee SY. Discovery of novel disease-causing mutation in SSBP1 and its correction using adenine base editor to improve mitochondrial function. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102257. [PMID: 39104869 PMCID: PMC11299580 DOI: 10.1016/j.omtn.2024.102257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/14/2024] [Indexed: 08/07/2024]
Abstract
Mutations in nuclear genes regulating mitochondrial DNA (mtDNA) replication are associated with mtDNA depletion syndromes. Using whole-genome sequencing, we identified a heterozygous mutation (c.272G>A:p.Arg91Gln) in single-stranded DNA-binding protein 1 (SSBP1), a crucial protein involved in mtDNA replisome. The proband manifested symptoms including sensorineural deafness, congenital cataract, optic atrophy, macular dystrophy, and myopathy. This mutation impeded multimer formation and DNA-binding affinity, leading to reduced efficiency of mtDNA replication, altered mitochondria dynamics, and compromised mitochondrial function. To correct this mutation, we tested two adenine base editor (ABE) variants on patient-derived fibroblasts. One variant, NG-Cas9-based ABE8e (NG-ABE8e), showed higher editing efficacy (≤30%) and enhanced mitochondrial replication and function, despite off-target editing frequencies; however, risks from bystander editing were limited due to silent mutations and off-target sites in non-translated regions. The other variant, NG-Cas9-based ABE8eWQ (NG-ABE8eWQ), had a safer therapeutic profile with very few off-target effects, but this came at the cost of lower editing efficacy (≤10% editing). Despite this, NG-ABE8eWQ-edited cells still restored replication and improved mtDNA copy number, which in turn recovery of compromised mitochondrial function. Taken together, base editing-based gene therapies may be a promising treatment for mitochondrial diseases, including those associated with SSBP1 mutations.
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Affiliation(s)
- Ju Hyuen Cha
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seok-Hoon Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yejin Yun
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Won Hoon Choi
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hansol Koo
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung Ho Jung
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Ho Byung Chae
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | | | - Seok Jae Lee
- Fight Against Angiogenesis-Related Blindness (FARB) Laboratory, Clinical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dong Hyun Jo
- Department of Anatomy and Cell Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jeong Hun Kim
- Fight Against Angiogenesis-Related Blindness (FARB) Laboratory, Clinical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jae-Jin Song
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Jong-Hee Chae
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jun Ho Lee
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jiho Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Jin Young Kang
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Sangsu Bae
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Medical Research Center of Genomic Medicine Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sang-Yeon Lee
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, Republic of Korea
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12
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Verma AK, Sharma P, Islam Z, Biswal AK, Tak Y, Sahi C. Arabidopsis Dph4 is an Hsp70 Cochaperone with Iron-Binding Properties. ACS OMEGA 2024; 9:37650-37661. [PMID: 39281955 PMCID: PMC11391554 DOI: 10.1021/acsomega.4c01776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 07/06/2024] [Accepted: 07/30/2024] [Indexed: 09/18/2024]
Abstract
J-domain proteins (JDPs) are obligate cochaperones of Hsp70s with a wide range of functions in protein homeostasis. Although the J-domain is required for the stimulation of Hsp70s ATPase activity, the functional specificity of JDPs is governed by domains or regions other than the J-domain. Jjj3/Dph4, a class III JDP, is required for diphthamide (DPH) biosynthesis in eukaryotes, including yeast and mammals. Dph4 has a conserved N-terminal J-domain and an uncharacterized C-terminal domain containing a signature CSL zinc finger motif. Previously, we showed that the Dph4 ortholog in Arabidopsis thaliana (atDjC13/AtJjj3/AtDph4) could restore DPH biosynthesis in yeast jjj3Δ mutant in a J-domain-dependent manner. Here, we characterize the C-terminal CSL motif of AtDph4 using yeast genetic and biochemical approaches. The CSL motif of AtDph4 is essential for DPH biosynthesis, and like human Dph4, AtDph4 showed distinct iron-binding activity, which is not present in its yeast counterpart. ScDph4 and AtDph4 proteins exhibit distinct iron-binding capabilities, as evidenced by UV-vis spectrophotometry, SEM-EDS (energy-dispersive spectroscopy function on the scanning electron microscope) and electron paramagnetic resonance (EPR) spectra analyses. Collectively, our data suggests that beyond their role as an Hsp70 cochaperone, Dph4 homologues in complex eukaryotes may have iron-binding abilities, indicating a potential role in iron-sulfur cluster assembly and iron homeostasis.
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Affiliation(s)
- Amit Kumar Verma
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066, India
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, Texas 75390-9096, United States
| | - Priya Sharma
- Department of Botany, Faculty of Science, University of Delhi, Delhi 110007, India
| | - Zeyaul Islam
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066, India
- Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, PO Box 34110 Doha, Qatar
| | - Anup Kumar Biswal
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066, India
| | - Yogesh Tak
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brian Institute, UT Southwestern Medical Center, Dallas, Texas 75390-9096, United States
| | - Chandan Sahi
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066, India
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13
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Watanabe N, Savchenko A. Molecular insights into the initiation step of the Rcs signaling pathway. Structure 2024; 32:1381-1393.e4. [PMID: 38964336 DOI: 10.1016/j.str.2024.06.003] [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: 12/07/2023] [Revised: 04/05/2024] [Accepted: 06/07/2024] [Indexed: 07/06/2024]
Abstract
The Rcs pathway is repressed by the inner membrane protein IgaA under non-stressed conditions. This repression is hypothesized to be relieved by the binding of the outer membrane-anchored RcsF to IgaA. However, the precise mechanism by which RcsF binding triggers the signaling remains unclear. Here, we present the 1.8 Å resolution crystal structure capturing the interaction between IgaA and RcsF. Our comparative structural analysis, examining both the bound and unbound states of the periplasmic domain of IgaA (IgaAp), highlights rotational flexibility within IgaAp. Conversely, the conformation of RcsF remains unchanged upon binding. Our in vivo and in vitro studies do not support the model of a stable complex involving RcsF, IgaAp, and RcsDp. Instead, we demonstrate that the elements beyond IgaAp play a role in the interaction between IgaA and RcsD. These findings collectively allow us to propose a potential mechanism for the signaling across the inner membrane through IgaA.
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Affiliation(s)
- Nobuhiko Watanabe
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada; Center for Structural Biology for Infectious Diseases (CSBID) Chicago, IL, USA
| | - Alexei Savchenko
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada; Center for Structural Biology for Infectious Diseases (CSBID) Chicago, IL, USA.
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14
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Díaz-Basilio F, Vergara-Mendoza M, Romero-Rodríguez J, Hernández-Rizo S, Escobedo-Calvario A, Fuentes-Romero LL, Pérez-Patrigeon S, Murakami-Ogasawara A, Gomez-Palacio M, Reyes-Terán G, Jiang W, Vázquez-Pérez JA, Marín-Hernández Á, Romero-Rodríguez DP, Gutiérrez-Ruiz MC, Viveros-Rogel M, Espinosa E. The ecto-enzyme CD38 modulates CD4T cell immunometabolic responses and participates in HIV pathogenesis. J Leukoc Biol 2024; 116:440-455. [PMID: 38466822 DOI: 10.1093/jleuko/qiae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/31/2024] [Accepted: 02/23/2024] [Indexed: 03/13/2024] Open
Abstract
Despite abundant evidence correlating T cell CD38 expression and HIV infection pathogenesis, its role as a CD4T cell immunometabolic regulator remains unclear. We find that CD38's extracellular glycohydrolase activity restricts metabolic reprogramming after T cell receptor (TCR)-engaging stimulation in Jurkat T CD4 cells, together with functional responses, while reducing intracellular nicotinamide adenine dinucleotide and nicotinamide mononucleotide concentrations. Selective elimination of CD38's ectoenzyme function licenses them to decrease the oxygen consumption rate/extracellular acidification rate ratio upon TCR signaling and to increase cycling, proliferation, survival, and CD40L induction. Pharmacological inhibition of ecto-CD38 catalytic activity in TM cells from chronic HIV-infected patients rescued TCR-triggered responses, including differentiation and effector functions, while reverting abnormally increased basal glycolysis, cycling, and spontaneous proinflammatory cytokine production. Additionally, ecto-CD38 blockage normalized basal and TCR-induced mitochondrial morphofunctionality, while increasing respiratory capacity in cells from HIV+ patients and healthy individuals. Ectoenzyme CD38's immunometabolic restriction of TCR-involving stimulation is relevant to CD4T cell biology and to the deleterious effects of CD38 overexpression in HIV disease.
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Affiliation(s)
- Fernando Díaz-Basilio
- Laboratory of Integrative Immunology, National Institute of Respiratory Diseases Ismael Cosío Villegas, Calzada de Tlalpan 4502, Tlalpan, 14080 Mexico City, Mexico
- PECEM Graduate Program, Faculty of Medicine, National Autonomous University of Mexico, Circuito Escolar, Ciudad Universitaria, Coyoacán, 04510 Mexico City, Mexico
| | - Moisés Vergara-Mendoza
- Department of Infectious Diseases, National Institute of Medical Sciences and Nutrition Salvador Zubirán, Vasco de Quiroga 15, Tlalpan, 14080 Mexico City, Mexico
| | - Jessica Romero-Rodríguez
- Flow Cytometry Core Facility, National Institute of Respiratory Diseases Ismael Cosío Villegas, Calzada de Tlalpan 4502, Tlalpan, 14080 Mexico City, Mexico
| | - Sharik Hernández-Rizo
- Laboratory for Cellular Physiology and Translational Medicine, Department of Health Sciences, Autonomous Metropolitan University, Instituto Nacional de Cardiología Ignacio Chávez, Juan Badiano 1, Tlalpan, 14080 Mexico City, Mexico
| | - Alejandro Escobedo-Calvario
- Laboratory for Cellular Physiology and Translational Medicine, Department of Health Sciences, Autonomous Metropolitan University, Instituto Nacional de Cardiología Ignacio Chávez, Juan Badiano 1, Tlalpan, 14080 Mexico City, Mexico
| | - Luis-León Fuentes-Romero
- Department of Infectious Diseases, National Institute of Medical Sciences and Nutrition Salvador Zubirán, Vasco de Quiroga 15, Tlalpan, 14080 Mexico City, Mexico
| | - Santiago Pérez-Patrigeon
- Department of Infectious Diseases, National Institute of Medical Sciences and Nutrition Salvador Zubirán, Vasco de Quiroga 15, Tlalpan, 14080 Mexico City, Mexico
| | - Akio Murakami-Ogasawara
- Center for Research in Infectious Diseases (CIENI), National Institute of Respiratory Diseases Ismael Cosío Villegas, Calzada de Tlalpan 4502, Tlalpan, 14080 Mexico City, Mexico
| | - María Gomez-Palacio
- Center for Research in Infectious Diseases (CIENI), National Institute of Respiratory Diseases Ismael Cosío Villegas, Calzada de Tlalpan 4502, Tlalpan, 14080 Mexico City, Mexico
| | - Gustavo Reyes-Terán
- Center for Research in Infectious Diseases (CIENI), National Institute of Respiratory Diseases Ismael Cosío Villegas, Calzada de Tlalpan 4502, Tlalpan, 14080 Mexico City, Mexico
| | - Wei Jiang
- Department of Microbiology and Immunology, Medical University of South Carolina, Ashley Ave. BSB- 214C, Charleston, SC 29425, United States
| | - Joel-Armando Vázquez-Pérez
- Laboratory for Emergent Diseases and COPD, National Institute of Respiratory Diseases Ismael Cosío Villegas, Calzada de Tlalpan 4502, Tlalpan, 14080 Mexico City, Mexico
| | - Álvaro Marín-Hernández
- Department of Biochemistry, National Institute of Cardiology Ignacio Chávez, Juan Badiano 1, Tlalpan, 14080 Mexico City, Mexico
| | - Dámaris-Priscila Romero-Rodríguez
- Flow Cytometry Core Facility, National Institute of Respiratory Diseases Ismael Cosío Villegas, Calzada de Tlalpan 4502, Tlalpan, 14080 Mexico City, Mexico
| | - María-Concepción Gutiérrez-Ruiz
- Laboratory for Cellular Physiology and Translational Medicine, Department of Health Sciences, Autonomous Metropolitan University, Instituto Nacional de Cardiología Ignacio Chávez, Juan Badiano 1, Tlalpan, 14080 Mexico City, Mexico
| | - Mónica Viveros-Rogel
- Department of Infectious Diseases, National Institute of Medical Sciences and Nutrition Salvador Zubirán, Vasco de Quiroga 15, Tlalpan, 14080 Mexico City, Mexico
| | - Enrique Espinosa
- Laboratory of Integrative Immunology, National Institute of Respiratory Diseases Ismael Cosío Villegas, Calzada de Tlalpan 4502, Tlalpan, 14080 Mexico City, Mexico
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15
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Du Y, Ma C, Moore SA, Xiao W. Zinc finger 4 negatively controls the transcriptional activator Fzf1 in Saccharomyces cerevisiae. MLIFE 2024; 3:391-402. [PMID: 39359679 PMCID: PMC11442136 DOI: 10.1002/mlf2.12141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/22/2024] [Accepted: 05/08/2024] [Indexed: 10/04/2024]
Abstract
Fzf1 is a Saccharomyces cerevisiae transcription factor containing five zinc fingers (ZFs). It regulates the expression of at least five downstream genes, including SSU1, YHB1, DDI2/3, and YNR064c, by recognizing a consensus sequence, CS2, found in these gene promoters. These gene products are involved in cellular responses to various chemical stresses. For example, SSU1 encodes a sodium sulfite efflux protein that confers sulfite resistance. However, the underlying molecular mechanism through which Fzf1 responds to chemical stress and coordinates target gene activation remains elusive. Interestingly, several mutations in the fourth ZF (ZF4) of Fzf1 have previously been reported to confer either sulfite resistance or elevated basal-level expression of YHB1, indicating that ZF4 negatively impacts Fzf1 activity. Since ZF4 is dispensable for CS2 binding in vitro, we hypothesized that ZF4 is a negative regulator of Fzf1 and that chemically induced Fzf1-regulated gene expression occurs via de-repression. All five genes examined were cross-induced by corresponding chemicals in an Fzf1-dependent manner, and all three ZF4 mutations and a ZF4 deletion conferred increased basal-level expression and SSU1-dependent sulfite resistance. A ZF4 deletion did not alter the target DNA binding, consistent with the observed codominant phenotype. These observations collectively reveal that Fzf1 remains inactive by default at the target promoters and that its activation is at least partially achieved by self-derepression through chemical modification and/or a conformational change.
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Affiliation(s)
- Ying Du
- Department of Biochemistry, Microbiology and Immunology University of Saskatchewan Saskatoon Saskatchewan Canada
| | - Chaoqun Ma
- Department of Biochemistry, Microbiology and Immunology University of Saskatchewan Saskatoon Saskatchewan Canada
| | - Stanley A Moore
- Department of Biochemistry, Microbiology and Immunology University of Saskatchewan Saskatoon Saskatchewan Canada
| | - Wei Xiao
- Department of Biochemistry, Microbiology and Immunology University of Saskatchewan Saskatoon Saskatchewan Canada
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16
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Le Meur RA, Pecen TJ, Le Meur KV, Nagel ZD, Chazin WJ. Molecular basis and functional consequences of the interaction between the base excision repair DNA glycosylase NEIL1 and RPA. J Biol Chem 2024; 300:107579. [PMID: 39025455 PMCID: PMC11387677 DOI: 10.1016/j.jbc.2024.107579] [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: 12/29/2023] [Revised: 06/22/2024] [Accepted: 06/25/2024] [Indexed: 07/20/2024] Open
Abstract
NEIL1 is a DNA glycosylase that recognizes and initiates base excision repair of oxidized bases. The ubiquitous ssDNA binding scaffolding protein, replication protein A (RPA), modulates NEIL1 activity in a manner that depends on DNA structure. Interaction between NEIL1 and RPA has been reported, but the molecular basis of this interaction has yet to be investigated. Using a combination of NMR spectroscopy and isothermal titration calorimetry (ITC), we show that NEIL1 interacts with RPA through two contact points. An interaction with the RPA32C protein recruitment domain was mapped to a motif in the common interaction domain (CID) of NEIL1 and a dissociation constant (Kd) of 200 nM was measured. A substantially weaker secondary interaction with the tandem RPA70AB ssDNA binding domains was also mapped to the CID. Together these two contact points reveal NEIL1 has a high overall affinity (Kd ∼ 20 nM) for RPA. A homology model of the complex of RPA32C with the NEIL1 RPA binding motif in the CID was generated and used to design a set of mutations in NEIL1 to disrupt the interaction, which was confirmed by ITC. The mutant NEIL1 remains catalytically active against a thymine glycol lesion in duplex DNA in vitro. Testing the functional effect of disrupting the NEIL1-RPA interaction in vivo using a Fluorescence Multiplex-Host Cell Reactivation (FM-HCR) reporter assay revealed an unexpected role for NEIL1 in nucleotide excision repair. These findings are discussed in the context of the role of NEIL1 in replication-associated repair.
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Affiliation(s)
- Rémy A Le Meur
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Turner J Pecen
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Kateryna V Le Meur
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Zachary D Nagel
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.
| | - Walter J Chazin
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA.
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17
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Jiang Z, Meyer AN, Yang W, Donoghue DJ. The oncogenic fusion protein EML4-NTRK3 requires three salt bridges for stability and biological activity. Heliyon 2024; 10:e36278. [PMID: 39253179 PMCID: PMC11381775 DOI: 10.1016/j.heliyon.2024.e36278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 08/07/2024] [Accepted: 08/13/2024] [Indexed: 09/11/2024] Open
Abstract
Aim of study Chromosomal translocations involving neurotrophic receptor tyrosine kinases (NTRKs) have been identified in 20 % of soft tissue sarcomas. This work focuses on the EML4-NTRK3 translocation identified in cases of Infantile Fibrosarcoma, which contains the coiled-coil multimerization domain of Echinoderm Microtubule-like protein 4 (EML4) fused with the tyrosine kinase domain of Neurotrophic Receptor Tyrosine Kinase 3 (NTRK3). The aim of the study was to test the importance of tyrosine kinase activity and multimerization for the oncogenic activity of EML4-NTRK3. Methods These studies examined EML4-NTRK3 proteins containing a kinase-dead or WT kinase domain, together with mutations in specific salt bridge residues within the coiled-coil domain. Biological activity was assayed using focus assays in NIH3T3 cells. The MAPK/ERK, JAK/STAT3 and PI3K/AKT pathways were analyzed for downstream activation of signaling pathways. Localization of EML4-NTRK3 proteins was examined by immunofluorescence microscopy, and the ability of the EML4 coiled-coil domain to drive protein multimerization was examined by biochemical assays. Results Activation of EML4-NTRK3 relies on both the tyrosine kinase activity of NTRK3 and salt-bridge stabilization within the coiled-coil domain of EML4. The tyrosine kinase activity of NTRK3 is essential for the biological activation of EML4-NTRK3. Furthermore, EML4-NTRK3 activates downstream signaling pathways MAPK/ERK, JAK/STAT3 and PKC/PLCγ. The disruption of three specific salt bridge interactions within the EML4 coiled-coil domain of EML4-NTRK3 blocks downstream activation, biological activity, and the ability to hetero-multimerize with EML4. We also demonstrate that EML4-NTRK3 is localized in the cytoplasm and fails to associate with microtubules. Concluding statement These data suggest potential therapeutic strategies for Infantile Fibrosarcoma cases bearing EML4-NTRK3 fusion through inhibition of salt bridge interactions and disruption of multimerization.
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Affiliation(s)
- Zian Jiang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093-0367 USA
| | - April N Meyer
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093-0367 USA
| | - Wei Yang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093-0367 USA
| | - Daniel J Donoghue
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093-0367 USA
- UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093-0367, USA
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18
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Das PK, Kielian M. Rubella virus assembly requirements and evolutionary relationships with novel rubiviruses. mBio 2024:e0196524. [PMID: 39207105 DOI: 10.1128/mbio.01965-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 08/01/2024] [Indexed: 09/04/2024] Open
Abstract
Rubella virus (RuV) is an enveloped virus that usually causes mild disease in children, but can produce miscarriage or severe congenital birth defects. While in nature RuV only infects humans, the discovery of the related Ruhugu (RuhV) and Rustrela (RusV) viruses highlights the spillover potential of mammalian rubiviruses to humans. RuV buds into the Golgi, but its assembly and exit are not well understood. We identified a potential late domain motif 278PPAY281 at the C-terminus of the RuV E2 envelope protein. Such late domain motifs can promote virus budding by recruiting the cellular ESCRT machinery. An E2 Y281A mutation reduced infectious virus production by >3 logs and inhibited virus particle production. However, RuV was insensitive to inhibition by dominant-negative VPS4, and thus appeared ESCRT-independent. The E2 Y281A mutation did not significantly inhibit the production of the viral structural proteins capsid (Cp), E2, and E1, or dimerization, glycosylation, Golgi transport, and colocalization of E2 and E1. However, E2 Y281A significantly reduced glycoprotein-Cp colocalization and interaction, and inhibited Cp localization to the Golgi. Revertants of the E2 Y281A mutant contained an E2 281V substitution or the second site mutations [E2 N277I + Cp D215A]. These mutations promoted virus growth, particle production, E2/Cp colocalization and Cp-Golgi localization. Both the E2 substitutions 281V and 277I were found at the corresponding positions in the RuhV E2 protein. Taken together, our data identify a key interaction of the RuV E2 endodomain with the Cp during RuV biogenesis, and support the close evolutionary relationship between human and animal rubiviruses. IMPORTANCE Rubella virus (RuV) is an enveloped virus that only infects humans, where transplacental infection can cause miscarriage or congenital birth defects. We identified a potential late domain, 278PPAY281, at the C terminus of the E2 envelope protein. However, rather than this domain recruiting the cellular ESCRT machinery as predicted, our data indicate that E2 Y281 promotes a critical interaction of the E2 endodomain with the capsid protein, leading to capsid's localization to the Golgi where virus budding occurs. Revertant analysis demonstrated that two substitutions on the E2 protein could partially rescue virus growth and Cp-Golgi localization. Both residues were found at the corresponding positions in Ruhugu virus E2, supporting the close evolutionary relationship between RuV and Ruhugu virus, a recently discovered rubivirus from bats.
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Affiliation(s)
- Pratyush Kumar Das
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Margaret Kielian
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA
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19
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Rosenkranz RRE, Vraggalas S, Keller M, Sankaranarayanan S, McNicoll F, Löchli K, Bublak D, Benhamed M, Crespi M, Berberich T, Bazakos C, Feldbrügge M, Schleiff E, Müller-McNicoll M, Zarnack K, Fragkostefanakis S. A plant-specific clade of serine/arginine-rich proteins regulates RNA splicing homeostasis and thermotolerance in tomato. Nucleic Acids Res 2024:gkae730. [PMID: 39180404 DOI: 10.1093/nar/gkae730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/31/2024] [Accepted: 08/09/2024] [Indexed: 08/26/2024] Open
Abstract
Global warming poses a threat for crops, therefore, the identification of thermotolerance mechanisms is a priority. In plants, the core factors that regulate transcription under heat stress (HS) are well described and include several HS transcription factors (HSFs). Despite the relevance of alternative splicing in HS response and thermotolerance, the core regulators of HS-sensitive alternative splicing have not been identified. In tomato, alternative splicing of HSFA2 is important for acclimation to HS. Here, we show that several members of the serine/arginine-rich family of splicing factors (SRSFs) suppress HSFA2 intron splicing. Individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP) combined with RNA-Seq revealed that RS2Z35 and RS2Z36, which make up a plant-specific clade of SR proteins, not only regulate HSFA2 but approximately 50% of RNAs that undergo HS-sensitive alternative splicing, with preferential binding to purine-rich RNA motifs. Single and double CRISPR rs2z mutant lines show a dysregulation of splicing and exhibit lower basal and acquired thermotolerance compared to wild type plants. Our results suggest that RS2Z35 and RS2Z36 have a central role in mitigation of the negative effects of HS on RNA splicing homeostasis, and their emergence might have contributed to the increased capacity of plants to acclimate to high temperatures.
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Affiliation(s)
- Remus R E Rosenkranz
- Institute of Molecular Biosciences, Molecular and Cell Biology of Plants, Goethe University Frankfurt, Frankfurt, Germany
| | - Stavros Vraggalas
- Institute of Molecular Biosciences, Molecular and Cell Biology of Plants, Goethe University Frankfurt, Frankfurt, Germany
| | - Mario Keller
- Buchmann Institute of Molecular Life Sciences & Institute of Molecular Biosciences, Computational RNA Biology, Goethe University Frankfurt, Frankfurt, Germany
| | | | - François McNicoll
- Institute of Molecular Biosciences, RNA Regulation in Higher Eukaryotes, Goethe University Frankfurt, Frankfurt, Germany
| | - Karin Löchli
- Institute of Molecular Biosciences, Molecular and Cell Biology of Plants, Goethe University Frankfurt, Frankfurt, Germany
| | - Daniela Bublak
- Institute of Molecular Biosciences, Molecular and Cell Biology of Plants, Goethe University Frankfurt, Frankfurt, Germany
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay, Université Paris-Saclay-CNRS, Orsay, France
| | - Martin Crespi
- Institute of Plant Sciences Paris-Saclay, Université Paris-Saclay-CNRS, Orsay, France
| | - Thomas Berberich
- Senckenberg Biodiversity and Climate Research Center, Frankfurt, Germany
| | - Christos Bazakos
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Köln, Germany
- Institute of Plant Breeding and Genetic Resources, ELGO DEMETER, Thessaloniki, Greece
| | - Michael Feldbrügge
- Institute of Microbiology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Enrico Schleiff
- Institute of Molecular Biosciences, Molecular and Cell Biology of Plants, Goethe University Frankfurt, Frankfurt, Germany
| | - Michaela Müller-McNicoll
- Institute of Molecular Biosciences, RNA Regulation in Higher Eukaryotes, Goethe University Frankfurt, Frankfurt, Germany
- Max-Planck Institute for Biophysics, Frankfurt, Germany
| | - Kathi Zarnack
- Buchmann Institute of Molecular Life Sciences & Institute of Molecular Biosciences, Computational RNA Biology, Goethe University Frankfurt, Frankfurt, Germany
| | - Sotirios Fragkostefanakis
- Institute of Molecular Biosciences, Molecular and Cell Biology of Plants, Goethe University Frankfurt, Frankfurt, Germany
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20
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Cui L, Wang J, Orlando F, Giacconi R, Malavolta M, Bartozzi B, Galeazzi R, Giorgini G, Pesce L, Cardarelli F, Quagliarini E, Renzi S, Xiao S, Pozzi D, Provinciali M, Caracciolo G, Marchini C, Amici A. Enhancing Immune Responses against SARS-CoV-2 Variants in Aged Mice with INDUK: A Chimeric DNA Vaccine Encoding the Spike S1-TM Subunits. ACS OMEGA 2024; 9:34624-34635. [PMID: 39157118 PMCID: PMC11325517 DOI: 10.1021/acsomega.4c03285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 08/20/2024]
Abstract
Currently available vaccines against COVID-19 showed high efficacy against the original strain of SARS-CoV-2 but progressively lower efficacy against new variants. In response to emerging SARS-CoV-2 strains, we propose chimeric DNA vaccines encoding the spike antigen, including a combination of selected key mutations from different variants of concern. We developed two DNA vaccines, pVAX-S1-TM-D614G and pVAX-S1-TM-INDUK (INDUK), encoding the SARS-CoV-2 S1 spike subunit in fusion with the transmembrane region that allows protein trimerization as predicted by in silico analysis. pVAX-S1-TM-D614G included the dominant D614G substitution, while the chimeric vaccine INDUK contained additional selected mutations from the Delta (E484Q and L452R) and Alpha (N501Y and A570D) variants. Considering that aging is a risk factor for severe disease and that suboptimal vaccine responses were observed in older individuals, the immunogenicity of pVAX-S1-TM-D614G and INDUK was tested in both young and aged C57BL/6 mice. Two vaccine doses were able to trigger significant anti-SARS-CoV-2 antibody production, showing neutralizing activity. ELISA tests confirmed that antibodies induced by pVAX-S1-TM-D614G and INDUK were able to recognize both Wuhan Spike and Delta variant Spike as trimers, while neutralizing antibodies were detected by an ACE2:SARS-CoV-2 Spike S1 inhibitor screening assay, designed to assess the capacity of antibodies to block the interaction between the viral spike S1 protein and the ACE2 receptor. Although antibody titer declined within six months, a third booster dose significantly increased the magnitude of humoral response, even in aged individuals, suggesting that immune recall can improve antibody response durability. The analysis of cellular responses demonstrated that vaccination with INDUK elicited an increase in the percentage of SARS-CoV-2-specific IFN-γ producing T lymphocytes in immunized young mice and TNF-α-producing T lymphocytes in both young and aged mice. These findings not only hold immediate promise for addressing evolving challenges in SARS-CoV-2 vaccination but also open avenues to refine strategies and elevate the effectiveness of next-generation vaccines.
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Affiliation(s)
- Lishan Cui
- School
of Biosciences and Veterinary Medicine, University of Camerino, via Gentile III da Varano, 62032 Camerino, Italy
| | - Junbiao Wang
- School
of Biosciences and Veterinary Medicine, University of Camerino, via Gentile III da Varano, 62032 Camerino, Italy
| | - Fiorenza Orlando
- Experimental
Animal Models for Aging Unit, Scientific Technological Area, IRRCS INRCA, 60100 Ancona, Italy
| | - Robertina Giacconi
- Advanced
Technology Center for Aging Research, IRCCS
INRCA, 60100Ancona, Italy
| | - Marco Malavolta
- Advanced
Technology Center for Aging Research, IRCCS
INRCA, 60100Ancona, Italy
| | - Beatrice Bartozzi
- Advanced
Technology Center for Aging Research, IRCCS
INRCA, 60100Ancona, Italy
| | - Roberta Galeazzi
- Department
of Life and Environmental Sciences, Marche
Polytechnic University, 60131 Ancona, Italy
| | - Giorgia Giorgini
- Department
of Life and Environmental Sciences, Marche
Polytechnic University, 60131 Ancona, Italy
| | - Luca Pesce
- NEST
Laboratory, Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Francesco Cardarelli
- NEST
Laboratory, Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Erica Quagliarini
- NanoDelivery
Lab, Department of Molecular Medicine, Sapienza
University of Rome, viale
Regina Elena 291, 00161 Rome, Italy
| | - Serena Renzi
- NanoDelivery
Lab, Department of Molecular Medicine, Sapienza
University of Rome, viale
Regina Elena 291, 00161 Rome, Italy
| | - Siyao Xiao
- NanoDelivery
Lab, Department of Molecular Medicine, Sapienza
University of Rome, viale
Regina Elena 291, 00161 Rome, Italy
| | - Daniela Pozzi
- NanoDelivery
Lab, Department of Molecular Medicine, Sapienza
University of Rome, viale
Regina Elena 291, 00161 Rome, Italy
| | - Mauro Provinciali
- Experimental
Animal Models for Aging Unit, Scientific Technological Area, IRRCS INRCA, 60100 Ancona, Italy
| | - Giulio Caracciolo
- NanoDelivery
Lab, Department of Molecular Medicine, Sapienza
University of Rome, viale
Regina Elena 291, 00161 Rome, Italy
| | - Cristina Marchini
- School
of Biosciences and Veterinary Medicine, University of Camerino, via Gentile III da Varano, 62032 Camerino, Italy
| | - Augusto Amici
- School
of Biosciences and Veterinary Medicine, University of Camerino, via Gentile III da Varano, 62032 Camerino, Italy
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21
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Kang H, Park D, Kim J. Logical regulation of endogenous gene expression using programmable, multi-input processing CRISPR guide RNAs. Nucleic Acids Res 2024; 52:8595-8608. [PMID: 38943344 DOI: 10.1093/nar/gkae549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 06/07/2024] [Accepted: 06/13/2024] [Indexed: 07/01/2024] Open
Abstract
The CRISPR-Cas system provides a versatile RNA-guided approach for a broad range of applications. Thanks to advances in RNA synthetic biology, the engineering of guide RNAs (gRNAs) has enabled the conditional control of the CRISPR-Cas system. However, achieving precise regulation of the CRISPR-Cas system for efficient modulation of internal metabolic processes remains challenging. In this work, we developed a robust dCas9 regulator with engineered conditional gRNAs to enable tight control of endogenous genes. Our conditional gRNAs in Escherichia coli can control gene expression upon specific interaction with trigger RNAs with a dynamic range as high as 130-fold, evaluating up to a three-input logic A OR (B AND C). The conditional gRNA-mediated targeting of endogenous metabolic genes, lacZ, malT and poxB, caused differential regulation of growth in Escherichia coli via metabolic flux control. Further, conditional gRNAs could regulate essential cytoskeleton genes, ftsZ and mreB, to control cell filamentation and division. Finally, three types of two-input logic gates could be applied for the conditional control of ftsZ regulation, resulting in morphological changes. The successful operation and application of conditional gRNAs based on programmable RNA interactions suggests that our system could be compatible with other Cas-effectors and implemented in other host organisms.
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Affiliation(s)
- Hansol Kang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Dongwon Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Jongmin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
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22
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Lameront P, Shabanian M, Currie LMJ, Fust C, Li C, Clews A, Meng B. Elucidating the Subcellular Localization of GLRaV-3 Proteins Encoded by the Unique Gene Block in N. benthamiana Suggests Implications on Plant Host Suppression. Biomolecules 2024; 14:977. [PMID: 39199365 PMCID: PMC11352578 DOI: 10.3390/biom14080977] [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: 07/02/2024] [Revised: 07/26/2024] [Accepted: 07/30/2024] [Indexed: 09/01/2024] Open
Abstract
Grapevine leafroll-associated virus 3 (GLRaV-3) is a formidable threat to the stability of the global grape and wine industries. It is the primary etiological agent of grapevine leafroll disease (GLD) and significantly impairs vine health, fruit quality, and yield. GLRaV-3 is a member of the genus Ampelovirus, Closteroviridae family. Viral genes within the 3' proximal unique gene blocks (UGB) remain highly variable and poorly understood. The UGBs of Closteroviridae viruses include diverse open reading frames (ORFs) that have been shown to contribute to viral functions such as the suppression of the host RNA silencing defense response and systemic viral spread. This study investigates the role of GLRaV-3 ORF8, ORF9, and ORF10, which encode the proteins p21, p20A, and p20B, respectively. These genes represent largely unexplored facets of the GLRaV-3 genome. Here, we visualize the subcellular localization of wildtype and mutagenized GLRaV-3 ORFs 8, 9, and 10, transiently expressed in Nicotiana benthamiana. Our results indicate that p21 localizes to the cytosol, p20A associates with microtubules, and p20B is trafficked into the nucleus to carry out the suppression of host RNA silencing. The findings presented herein provide a foundation for future research aimed at the characterization of the functions of these ORFs. In the long run, it would also facilitate the development of innovative strategies to understand GLRaV-3, mitigate its spread, and impacts on grapevines and the global wine industry.
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Affiliation(s)
- Patrick Lameront
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada; (M.S.); (L.M.J.C.); (C.F.); (C.L.); (A.C.); (B.M.)
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23
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Sabath K, Qiu C, Jonas S. Assembly mechanism of Integrator's RNA cleavage module. Mol Cell 2024; 84:2882-2899.e10. [PMID: 39032489 DOI: 10.1016/j.molcel.2024.06.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 05/17/2024] [Accepted: 06/26/2024] [Indexed: 07/23/2024]
Abstract
The modular Integrator complex is a transcription regulator that is essential for embryonic development. It attenuates coding gene expression via premature transcription termination and performs 3'-processing of non-coding RNAs. For both activities, Integrator requires endonuclease activity that is harbored by an RNA cleavage module consisting of INTS4-9-11. How correct assembly of Integrator modules is achieved remains unknown. Here, we show that BRAT1 and WDR73 are critical biogenesis factors for the human cleavage module. They maintain INTS9-11 inactive during maturation by physically blocking the endonuclease active site and prevent premature INTS4 association. Furthermore, BRAT1 facilitates import of INTS9-11 into the nucleus, where it is joined by INTS4. Final BRAT1 release requires locking of the mature cleavage module conformation by inositol hexaphosphate (IP6). Our data explain several neurodevelopmental disorders caused by BRAT1, WDR73, and INTS11 mutations as Integrator assembly defects and reveal that IP6 is an essential co-factor for cleavage module maturation.
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Affiliation(s)
- Kevin Sabath
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Chunhong Qiu
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Stefanie Jonas
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
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24
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Szymanik KH, Hancks DC, Sullivan CS. Viral piracy of host RNA phosphatase DUSP11 by avipoxviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.06.606876. [PMID: 39211142 PMCID: PMC11361023 DOI: 10.1101/2024.08.06.606876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Proper recognition of viral pathogens is an essential part of the innate immune response. A common viral replicative intermediate and chemical signal that cells use to identify pathogens is the presence of a triphosphorylated 5' end (5'ppp) RNA, which activates the cytosolic RNA sensor RIG-I and initiates downstream antiviral signaling. While 5'pppRNA generated by viral RNA-dependent RNA polymerases (RdRps) can be a potent activator of the immune response, endogenous RNA polymerase III (RNAPIII) transcripts can retain the 5'pppRNA generated during transcription and induce a RIG-I-mediated immune response. We have previously shown that host RNA triphosphatase dual-specificity phosphatase 11 (DUSP11) can act on both host and viral RNAs, altering their levels and reducing their ability to induce RIG-I activation. Our previous work explored how artificially altered DUSP11 can impact immune activation, prompting further exploration into natural contexts of altered DUSP11. Here, we have identified viral DUSP11 homologs (vDUSP11s) present in some avipoxviruses. Consistent with the known functions of endogenous DUSP11, we have shown that expression of vDUSP11s: 1) reduces levels of endogenous RNAPIII transcripts, 2) reduces a cell's sensitivity to 5'pppRNA-mediated immune activation, and 3) restores virus infection defects seen in the absence of DUSP11. Our results identify a virus-relevant context where DUSP11 activity has been co-opted to alter RNA metabolism and influence the outcome of infection.
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25
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Cleere MM, Gardner KH. Optogenetic control of phosphate-responsive genes using single component fusion proteins in Saccharomyces cerevisiae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.02.605841. [PMID: 39131330 PMCID: PMC11312615 DOI: 10.1101/2024.08.02.605841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Blue light illumination can be detected by Light-Oxygen-Voltage (LOV) photosensing proteins and translated into a range of biochemical responses, facilitating the generation of novel optogenetic tools to control cellular function. Here we develop new variants of our previously described VP-EL222 light-dependent transcription factor and apply them to study the phosphate-responsive signaling (PHO) pathway in the budding yeast Saccharomyces cerevisiae, exemplifying the utilities of these new tools. Focusing first on the VP-EL222 protein itself, we quantified the tunability of gene expression as a function of light intensity and duration, and demonstrated that this system can tolerate the addition of substantially larger effector domains without impacting function. We further demonstrated the utility of several EL222-driven transcriptional controllers in both plasmid and genomic settings, using the PHO5 and PHO84 promoters in their native chromosomal contexts as examples. These studies highlight the utility of light-controlled gene activation using EL222 tethered to either artificial transcription domains or yeast activator proteins (Pho4). Similarly, we demonstrate the ability to optogenetically repress gene expression with EL222 fused to the yeast Ume6 protein. We finally investigated the effects of moving EL222 recruitment sites to different locations within the PHO5 and PHO84 promoters, as well as determining how this artificial light-controlled regulation could be integrated with the native controls dependent on inorganic phosphate (Pi) availability. Taken together, our work expands the applicability of these versatile optogenetic tools in the types of functionality they can deliver and biological questions that can be probed.
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Affiliation(s)
- Matthew M Cleere
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY 10016
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- Biochemistry, Chemistry, and Biology Ph.D. Programs, Graduate Center, City University of New York, New York, NY 10016
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031
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26
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Schroeter KL, Rolfe N, Forrester TJB, Kimber MS, Seah SYK. Shy is a proteobacterial steroid hydratase which catalyzes steroid side chain degradation without requiring a catalytically inert partner domain. J Biol Chem 2024; 300:107509. [PMID: 38944126 PMCID: PMC11321319 DOI: 10.1016/j.jbc.2024.107509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/01/2024] Open
Abstract
Shy (side chain hydratase) and Sal (side chain aldolase), are involved in successive reactions in the pathway of bile acid side chain catabolism in Proteobacteria. Untagged Shy copurified with His-tagged Sal indicating that the two enzymes form a complex. Shy contains a MaoC and a DUF35 domain. When coexpressed with Sal, the DUF35 domain but not the MaoC domain of Shy was observed to copurify with Sal, indicating Sal interacts with Shy through its DUF35 domain. The MaoC domain of Shy (ShyMaoC) remained catalytically viable and could hydrate cholyl-enoyl-CoA with similar catalytic efficiency as in the Shy-Sal complex. Sal expressed with the DUF35 domain of Shy (Sal-ShyDUF35) was similarly competent for the retro-aldol cleavage of cholyl-3-OH-CoA. ShyMaoC showed a preference for C5 side chain bile acid substrates, exhibiting low activity toward C3 side chain substrates. The ShyMaoC structure was determined by X-ray crystallography, showing a hot dog fold with a short central helix surrounded by a twisted antiparallel β-sheet. Modeling and mutagenesis studies suggest that the bile acid substrate occupies the large open cleft formed by the truncated central helix and repositioning of the active site housing. ShyMaoC therefore contains two substrate binding sites per homodimer, making it distinct from previously characterized MaoC steroid hydratases that are (pseudo) heterodimers with one substrate binding site per dimer. The characterization of Shy provides insight into how MaoC family hydratases have adapted to accommodate large polycyclic substrates that can facilitate future engineering of these enzymes to produce novel steroid pharmaceuticals.
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Affiliation(s)
- Kurt L Schroeter
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Nicolas Rolfe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Taylor J B Forrester
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Matthew S Kimber
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Stephen Y K Seah
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
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27
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Godek J, Sivinski J, Watson ER, Lebario F, Xu W, Stevens M, Zerio CJ, Ambrose AJ, Zhu X, Trindl CA, Zhang DD, Johnson SM, Lander GC, Chapman E. Bis-sulfonamido-2-phenylbenzoxazoles Validate the GroES/EL Chaperone System as a Viable Antibiotic Target. J Am Chem Soc 2024; 146:20845-20856. [PMID: 39041457 DOI: 10.1021/jacs.4c05057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
We recently reported on small-molecule inhibitors of the GroES/GroEL chaperone system as potential antibiotics against Escherichia coli and the ESKAPE pathogens but were unable to establish GroES/GroEL as the cellular target, leading to cell death. In this study, using two of our most potent bis-sulfonamido-2-phenylbenzoxazoles (PBZs), we established the binding site of the PBZ molecules using cryo-EM and found that GroEL was the cellular target responsible for the mode of action. Cryo-EM revealed that PBZ1587 binds at the GroEL ring-ring interface (RRI). A cellular reporter assay confirmed that PBZ1587 engaged GroEL in cells, but cellular rescue experiments showed potential off-target effects. This prompted us to explore a closely related analogue, PBZ1038, which is also bound to the RRI. Biochemical characterization showed potent inhibition of Gram-negative chaperonins but much lower potency of chaperonin from a Gram-positive organism, Enterococcus faecium. A cellular reporter assay showed that PBZ1038 also engaged GroEL in cells and that the cytotoxic phenotype could be rescued by a chromosomal copy of E. faecium GroEL/GroES or by expressing a recalcitrant RRI mutant. These data argue that PBZ1038's antimicrobial action is exerted through inhibition of GroES/GroEL, validating this chaperone system as an antibiotic target.
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Affiliation(s)
- Jack Godek
- College of Medicine, Department of Pharmacology and Therapeutics, Center for Inflammation Science and Systems Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, University of Florida, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jared Sivinski
- College of Pharmacy, Department of Pharmacology and Toxicology, The University of Arizona, 1703 E. Mabel Street, P.O. Box 210207, Tucson, Arizona 85721, United States
| | - Edmond R Watson
- Department of Integrative Structural and Computational Biology, Scripps Research, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Felicidad Lebario
- College of Medicine, Department of Pharmacology and Therapeutics, Center for Inflammation Science and Systems Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, University of Florida, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Wenli Xu
- College of Pharmacy, Department of Pharmacology and Toxicology, The University of Arizona, 1703 E. Mabel Street, P.O. Box 210207, Tucson, Arizona 85721, United States
| | - Mckayla Stevens
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Dr., Indianapolis, Indiana 46202, United States
| | - Christopher J Zerio
- College of Pharmacy, Department of Pharmacology and Toxicology, The University of Arizona, 1703 E. Mabel Street, P.O. Box 210207, Tucson, Arizona 85721, United States
| | - Andrew J Ambrose
- College of Pharmacy, Department of Pharmacology and Toxicology, The University of Arizona, 1703 E. Mabel Street, P.O. Box 210207, Tucson, Arizona 85721, United States
| | - Xiaoyi Zhu
- College of Medicine, Department of Pharmacology and Therapeutics, Center for Inflammation Science and Systems Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, University of Florida, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Carlee A Trindl
- College of Medicine, Department of Pharmacology and Therapeutics, Center for Inflammation Science and Systems Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, University of Florida, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Donna D Zhang
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Center for Inflammation Science and Systems Medicine, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Steven M Johnson
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Dr., Indianapolis, Indiana 46202, United States
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, Scripps Research, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Eli Chapman
- College of Medicine, Department of Pharmacology and Therapeutics, Center for Inflammation Science and Systems Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, University of Florida, 130 Scripps Way, Jupiter, Florida 33458, United States
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28
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Harold RL, Tulsian NK, Narasimamurthy R, Yaitanes N, Hernandez MGA, Lee HW, Crosby P, Tripathi SM, Virshup DM, Partch CL. Isoform-specific C-terminal phosphorylation drives autoinhibition of Casein Kinase 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.24.538174. [PMID: 39131317 PMCID: PMC11312495 DOI: 10.1101/2023.04.24.538174] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Casein kinase 1 δ (CK1δ) controls essential biological processes including circadian rhythms and Wnt signaling, but how its activity is regulated is not well understood. CK1δ is inhibited by autophosphorylation of its intrinsically disordered C-terminal tail. Two CK1 splice variants, δ 1 and δ 2 , are known to have very different effects on circadian rhythms. These variants differ only in the last 16 residues of the tail, referred to as the extreme C-termini (XCT), but with marked changes in potential phosphorylation sites. Here we test if the XCT of these variants have different effects in autoinhibition of the kinase. Using NMR and HDX-MS, we show that the δ 1 XCT is preferentially phosphorylated by the kinase and the δ 1 tail makes more extensive interactions across the kinase domain. Mutation of δ1 -specific XCT phosphorylation sites increases kinase activity both in vitro and in cells and leads to changes in circadian period, similar to what is reported in vivo. Mechanistically, loss of the phosphorylation sites in XCT disrupts tail interaction with the kinase domain. δ1 autoinhibition relies on conserved anion binding sites around the CK1 active site, demonstrating a common mode of product inhibition of CK1δ . These findings demonstrate how a phosphorylation cycle controls the activity of this essential kinase.
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Affiliation(s)
- Rachel L. Harold
- Department of Chemistry & Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064
| | - Nikhil K. Tulsian
- Department of Biological Sciences, National University of Singapore, Singapore 117543
- MSD International GmBH (Singapore), Neuros, 8 Biomedical Grove, Singapore, 138665
| | | | - Noelle Yaitanes
- Department of Chemistry & Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064
| | - Maria G. Ayala Hernandez
- Department of Chemistry & Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064
| | - Hsiau-Wei Lee
- Department of Chemistry & Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064
| | - Priya Crosby
- Department of Chemistry & Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064
| | - Sarvind M. Tripathi
- Department of Chemistry & Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064
| | - David M. Virshup
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857
- Department of Pediatrics, Duke University Medical Center, Durham, NC 27710
| | - Carrie L. Partch
- Department of Chemistry & Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064
- Center for Circadian Biology, University of California San Diego, La Jolla, CA 92093
- Lead contact
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29
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Rouchidane Eyitayo A, Daury L, Priault M, Manon S. The membrane insertion of the pro-apoptotic protein Bax is a Tom22-dependent multi-step process: a study in nanodiscs. Cell Death Discov 2024; 10:335. [PMID: 39043635 PMCID: PMC11266675 DOI: 10.1038/s41420-024-02108-x] [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: 03/18/2024] [Revised: 07/11/2024] [Accepted: 07/17/2024] [Indexed: 07/25/2024] Open
Abstract
Membrane insertion of the pro-apoptotic protein Bax was investigated by setting up cell-free synthesis of full-length Bax in the presence of pre-formed nanodiscs. While Bax was spontaneously poorly inserted in nanodiscs, co-synthesis with the mitochondrial receptor Tom22 stimulated Bax membrane insertion. The initial interaction of Bax with the lipid bilayer exposed the hydrophobic GALLL motif in Hα1 leading to Bax precipitation through hydrophobic interactions. The same motif was recognized by Tom22, triggering conformational changes leading to the extrusion and the ensuing membrane insertion of the C-terminal hydrophobic Hα9. Tom22 was also required for Bax-membrane insertion after Bax was activated either by BH3-activators or by its release from Bcl-xL by WEHI-539. The effect of Tom22 was impaired by D154Y substitution in Bax-Hα7 and T174P substitution in Bax-Hα9, which are found in several tumors. Conversely, a R9E substitution promoted a spontaneous insertion of Bax in nanodiscs, in the absence of Tom22. Both Tom22-activated Bax and BaxR9E alone permeabilized liposomes to dextran-10kDa and formed ~5-nm-diameter pores in nanodiscs. The concerted regulation of Bax membrane insertion by Tom22 and BH3-activators is discussed.
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Affiliation(s)
| | - Laetitia Daury
- CNRS, Université de Bordeaux, UMR 5248, CBMN, Pessac, France
| | - Muriel Priault
- CNRS, Université de Bordeaux, UMR 5095, IBGC, Bordeaux, France
| | - Stéphen Manon
- CNRS, Université de Bordeaux, UMR 5095, IBGC, Bordeaux, France.
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30
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Liu Y, Gu Y, Chen Y, Wang X, Zhou G, Li J, Wang M, Fang S, Yang Y. Translocational attenuation mediated by the PERK-SRP14 axis is a protective mechanism of unfolded protein response. Cell Rep 2024; 43:114402. [PMID: 38943644 DOI: 10.1016/j.celrep.2024.114402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 05/06/2024] [Accepted: 06/11/2024] [Indexed: 07/01/2024] Open
Abstract
The unfolded protein response (UPR) relieves endoplasmic reticulum (ER) stress through multiple strategies, including reducing protein synthesis, increasing protein folding capabilities, and enhancing misfolded protein degradation. After a multi-omics analysis, we find that signal recognition particle 14 (SRP14), an essential component of the SRP, is markedly reduced in cells undergoing ER stress. Further experiments indicate that SRP14 reduction requires PRKR-like ER kinase (PERK)-mediated eukaryotic translation initiation factor 2α (eIF2α) phosphorylation but is independent of ATF4 or ATF3 transcription factors. The decrease of SRP14 correlates with reduced translocation of fusion proteins and endogenous cathepsin D. Enforced expression of an SRP14 variant with elongation arrest capability prevents the reduced translocation of cathepsin D in stressed cells, whereas an SRP14 mutant without the activity does not. Finally, overexpression of SRP14 augments the UPR and aggravates ER-stress-induced cell death. These data suggest that translocational attenuation mediated by the PERK-SRP14 axis is a protective measure for the UPR to mitigate ER stress.
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Affiliation(s)
- Yaofu Liu
- China Regional Research Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), Taizhou, Jiangsu 225316, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China; Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuexi Gu
- China Regional Research Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), Taizhou, Jiangsu 225316, China
| | - Ying Chen
- Academy of Pharmacy, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | - Xuan Wang
- China Regional Research Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), Taizhou, Jiangsu 225316, China
| | - Guangfeng Zhou
- China Regional Research Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), Taizhou, Jiangsu 225316, China
| | - Jing Li
- Academy of Pharmacy, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | - Mu Wang
- Academy of Pharmacy, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China.
| | - Shengyun Fang
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Yili Yang
- China Regional Research Centre, International Centre for Genetic Engineering and Biotechnology (ICGEB), Taizhou, Jiangsu 225316, China.
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31
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Mühlenbeck H, Tsutsui Y, Lemmon MA, Bender KW, Zipfel C. Allosteric activation of the co-receptor BAK1 by the EFR receptor kinase initiates immune signaling. eLife 2024; 12:RP92110. [PMID: 39028038 PMCID: PMC11259431 DOI: 10.7554/elife.92110] [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: 07/20/2024] Open
Abstract
Transmembrane signaling by plant receptor kinases (RKs) has long been thought to involve reciprocal trans-phosphorylation of their intracellular kinase domains. The fact that many of these are pseudokinase domains, however, suggests that additional mechanisms must govern RK signaling activation. Non-catalytic signaling mechanisms of protein kinase domains have been described in metazoans, but information is scarce for plants. Recently, a non-catalytic function was reported for the leucine-rich repeat (LRR)-RK subfamily XIIa member EFR (elongation factor Tu receptor) and phosphorylation-dependent conformational changes were proposed to regulate signaling of RKs with non-RD kinase domains. Here, using EFR as a model, we describe a non-catalytic activation mechanism for LRR-RKs with non-RD kinase domains. EFR is an active kinase, but a kinase-dead variant retains the ability to enhance catalytic activity of its co-receptor kinase BAK1/SERK3 (brassinosteroid insensitive 1-associated kinase 1/somatic embryogenesis receptor kinase 3). Applying hydrogen-deuterium exchange mass spectrometry (HDX-MS) analysis and designing homology-based intragenic suppressor mutations, we provide evidence that the EFR kinase domain must adopt its active conformation in order to activate BAK1 allosterically, likely by supporting αC-helix positioning in BAK1. Our results suggest a conformational toggle model for signaling, in which BAK1 first phosphorylates EFR in the activation loop to stabilize its active conformation, allowing EFR in turn to allosterically activate BAK1.
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Affiliation(s)
- Henning Mühlenbeck
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of ZürichZürichSwitzerland
| | - Yuko Tsutsui
- Department of Pharmacology, Yale University School of MedicineNew HavenUnited States
- Yale Cancer Biology Institute, Yale University West CampusWest HavenUnited States
| | - Mark A Lemmon
- Department of Pharmacology, Yale University School of MedicineNew HavenUnited States
- Yale Cancer Biology Institute, Yale University West CampusWest HavenUnited States
| | - Kyle W Bender
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of ZürichZürichSwitzerland
| | - Cyril Zipfel
- Institute of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of ZürichZürichSwitzerland
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
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Malard F, Dias K, Baudy M, Thore S, Vialet B, Barthélémy P, Fribourg S, Karginov FV, Campagne S. Molecular Basis for the Calcium-Dependent Activation of the Ribonuclease EndoU. RESEARCH SQUARE 2024:rs.3.rs-4654759. [PMID: 39070628 PMCID: PMC11275989 DOI: 10.21203/rs.3.rs-4654759/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Ribonucleases (RNases) are ubiquitous enzymes that process or degrade RNA, essential for cellular functions and immune responses. The EndoU-like superfamily includes endoribonucleases conserved across bacteria, eukaryotes, and certain viruses, with an ancient evolutionary link to the ribonuclease A-like superfamily. Both bacterial EndoU and animal RNase A share a similar fold and function independently of cofactors. In contrast, the eukaryotic EndoU catalytic domain requires divalent metal ions for catalysis, possibly due to an N-terminal extension near the catalytic core. In this study, we used biophysical and computational techniques along with in vitro assays to investigate the calcium-dependent activation of human EndoU. We determined the crystal structure of EndoU bound to calcium and found that calcium binding remote from the catalytic triad triggers water-mediated intramolecular signaling and structural changes, activating the enzyme through allostery. Calcium-binding involves residues from both the catalytic core and the N-terminal extension, indicating that the N-terminal extension interacts with the catalytic core to modulate activity in response to calcium. Our findings suggest that similar mechanisms may be present across all eukaryotic EndoUs, highlighting a unique evolutionary adaptation that connects endoribonuclease activity to cellular signaling in eukaryotes.
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Affiliation(s)
- Florian Malard
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
- Univ. Bordeaux, CNRS, INSERM, IECB, US1, UAR 3033, F-33600 Pessac, France
| | - Kristen Dias
- Department of Molecular, Cell and Systems Biology, Institute for Integrative Genome Biology, University of California at Riverside, Riverside, CA, 92521, USA
| | - Margaux Baudy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
- Univ. Bordeaux, CNRS, INSERM, IECB, US1, UAR 3033, F-33600 Pessac, France
| | - Stéphane Thore
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Brune Vialet
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Philippe Barthélémy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Sébastien Fribourg
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Fedor V Karginov
- Department of Molecular, Cell and Systems Biology, Institute for Integrative Genome Biology, University of California at Riverside, Riverside, CA, 92521, USA
| | - Sébastien Campagne
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
- Univ. Bordeaux, CNRS, INSERM, IECB, US1, UAR 3033, F-33600 Pessac, France
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33
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Sabath K, Nabih A, Arnold C, Moussa R, Domjan D, Zaugg JB, Jonas S. Basis of gene-specific transcription regulation by the Integrator complex. Mol Cell 2024; 84:2525-2541.e12. [PMID: 38906142 DOI: 10.1016/j.molcel.2024.05.027] [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: 07/05/2023] [Revised: 03/04/2024] [Accepted: 05/29/2024] [Indexed: 06/23/2024]
Abstract
The Integrator complex attenuates gene expression via the premature termination of RNA polymerase II (RNAP2) at promoter-proximal pausing sites. It is required for stimulus response, cell differentiation, and neurodevelopment, but how gene-specific and adaptive regulation by Integrator is achieved remains unclear. Here, we identify two sites on human Integrator subunits 13/14 that serve as binding hubs for sequence-specific transcription factors (TFs) and other transcription effector complexes. When Integrator is attached to paused RNAP2, these hubs are positioned upstream of the transcription bubble, consistent with simultaneous TF-promoter tethering. The TFs co-localize with Integrator genome-wide, increase Integrator abundance on target genes, and co-regulate responsive transcriptional programs. For instance, sensory cilia formation induced by glucose starvation depends on Integrator-TF contacts. Our data suggest TF-mediated promoter recruitment of Integrator as a widespread mechanism for targeted transcription regulation.
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Affiliation(s)
- Kevin Sabath
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.
| | - Amena Nabih
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Christian Arnold
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Rim Moussa
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - David Domjan
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Judith B Zaugg
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Stefanie Jonas
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland.
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34
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Guicherd M, Ben Khaled M, Guéroult M, Nomme J, Dalibey M, Grimaud F, Alvarez P, Kamionka E, Gavalda S, Noël M, Vuillemin M, Amillastre E, Labourdette D, Cioci G, Tournier V, Kitpreechavanich V, Dubois P, André I, Duquesne S, Marty A. An engineered enzyme embedded into PLA to make self-biodegradable plastic. Nature 2024; 631:884-890. [PMID: 39020178 DOI: 10.1038/s41586-024-07709-1] [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: 05/04/2023] [Accepted: 06/12/2024] [Indexed: 07/19/2024]
Abstract
Plastic production reached 400 million tons in 2022 (ref. 1), with packaging and single-use plastics accounting for a substantial amount of this2. The resulting waste ends up in landfills, incineration or the environment, contributing to environmental pollution3. Shifting to biodegradable and compostable plastics is increasingly being considered as an efficient waste-management alternative4. Although polylactide (PLA) is the most widely used biosourced polymer5, its biodegradation rate under home-compost and soil conditions remains low6-8. Here we present a PLA-based plastic in which an optimized enzyme is embedded to ensure rapid biodegradation and compostability at room temperature, using a scalable industrial process. First, an 80-fold activity enhancement was achieved through structure-based rational engineering of a new hyperthermostable PLA hydrolase. Second, the enzyme was uniformly dispersed within the PLA matrix by means of a masterbatch-based melt extrusion process. The liquid enzyme formulation was incorporated in polycaprolactone, a low-melting-temperature polymer, through melt extrusion at 70 °C, forming an 'enzymated' polycaprolactone masterbatch. Masterbatch pellets were integrated into PLA by melt extrusion at 160 °C, producing an enzymated PLA film (0.02% w/w enzyme) that fully disintegrated under home-compost conditions within 20-24 weeks, meeting home-composting standards. The mechanical and degradation properties of the enzymated film were compatible with industrial packaging applications, and they remained intact during long-term storage. This innovative material not only opens new avenues for composters and biomethane production but also provides a feasible industrial solution for PLA degradation.
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Affiliation(s)
- M Guicherd
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- Carbios, Clermont-Ferrand, France
| | - M Ben Khaled
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - M Guéroult
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- Carbios, Clermont-Ferrand, France
| | - J Nomme
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | | | - P Alvarez
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - E Kamionka
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - S Gavalda
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- Carbios, Clermont-Ferrand, France
| | - M Noël
- Carbiolice, Clermont-Ferrand, France
| | - M Vuillemin
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - E Amillastre
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - D Labourdette
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - G Cioci
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | - V Kitpreechavanich
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - P Dubois
- Center of Innovation and Research in Materials & Polymers, University of Mons, Mons, Belgium
| | - I André
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
| | - S Duquesne
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - A Marty
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
- Carbios, Clermont-Ferrand, France.
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Litschko C, Di Domenico V, Schulze J, Li S, Ovchinnikova OG, Voskuilen T, Bethe A, Cifuente JO, Marina A, Budde I, Mast TA, Sulewska M, Berger M, Buettner FFR, Lowary TL, Whitfield C, Codée JDC, Schubert M, Guerin ME, Fiebig T. Transition transferases prime bacterial capsule polymerization. Nat Chem Biol 2024:10.1038/s41589-024-01664-8. [PMID: 38951648 DOI: 10.1038/s41589-024-01664-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 06/04/2024] [Indexed: 07/03/2024]
Abstract
Capsules are long-chain carbohydrate polymers that envelop the surfaces of many bacteria, protecting them from host immune responses. Capsule biosynthesis enzymes are potential drug targets and valuable biotechnological tools for generating vaccine antigens. Despite their importance, it remains unknown how structurally variable capsule polymers of Gram-negative pathogens are linked to the conserved glycolipid anchoring these virulence factors to the bacterial membrane. Using Actinobacillus pleuropneumoniae as an example, we demonstrate that CpsA and CpsC generate a poly(glycerol-3-phosphate) linker to connect the glycolipid with capsules containing poly(galactosylglycerol-phosphate) backbones. We reconstruct the entire capsule biosynthesis pathway in A. pleuropneumoniae serotypes 3 and 7, solve the X-ray crystal structure of the capsule polymerase CpsD, identify its tetratricopeptide repeat domain as essential for elongating poly(glycerol-3-phosphate) and show that CpsA and CpsC stimulate CpsD to produce longer polymers. We identify the CpsA and CpsC product as a wall teichoic acid homolog, demonstrating similarity between the biosynthesis of Gram-positive wall teichoic acid and Gram-negative capsules.
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Affiliation(s)
- Christa Litschko
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
- German Center for Infection Research, Partner Site Hannover-Braunschweig, Hannover, Germany
| | - Valerio Di Domenico
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Spain
- Structural Glycobiology Laboratory, Department of Structural and Molecular Biology; Molecular Biology Institute of Barcelona, Spanish National Research Council, Barcelona Science Park, Tower R, Barcelona, Spain
| | - Julia Schulze
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Sizhe Li
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Olga G Ovchinnikova
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Thijs Voskuilen
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Andrea Bethe
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Javier O Cifuente
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Spain
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences, Basque Research and Technology Alliance, Bizkaia Technology Park, Derio, Spain
| | - Alberto Marina
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences, Basque Research and Technology Alliance, Bizkaia Technology Park, Derio, Spain
| | - Insa Budde
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Tim A Mast
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Małgorzata Sulewska
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Monika Berger
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Falk F R Buettner
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
- Proteomics, Institute of Theoretical Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany
| | - Todd L Lowary
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Mario Schubert
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
- Department of Biology, Chemistry and Pharmacy, Free University of Berlin, Berlin, Germany
| | - Marcelo E Guerin
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Spain.
- Structural Glycobiology Laboratory, Department of Structural and Molecular Biology; Molecular Biology Institute of Barcelona, Spanish National Research Council, Barcelona Science Park, Tower R, Barcelona, Spain.
- Structural Glycobiology Laboratory, Center for Cooperative Research in Biosciences, Basque Research and Technology Alliance, Bizkaia Technology Park, Derio, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
| | - Timm Fiebig
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany.
- German Center for Infection Research, Partner Site Hannover-Braunschweig, Hannover, Germany.
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36
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Yang W, Meyer AN, Jiang Z, Jiang X, Donoghue DJ. Critical domains for NACC2-NTRK2 fusion protein activation. PLoS One 2024; 19:e0301730. [PMID: 38935636 PMCID: PMC11210774 DOI: 10.1371/journal.pone.0301730] [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: 08/20/2023] [Accepted: 03/20/2024] [Indexed: 06/29/2024] Open
Abstract
Neurotrophic receptor tyrosine kinases (NTRKs) belong to the receptor tyrosine kinase (RTK) family. NTRKs are responsible for the activation of multiple downstream signaling pathways that regulate cell growth, proliferation, differentiation, and apoptosis. NTRK-associated mutations often result in oncogenesis and lead to aberrant activation of downstream signaling pathways including MAPK, JAK/STAT, and PLCγ1. This study characterizes the NACC2-NTRK2 oncogenic fusion protein that leads to pilocytic astrocytoma and pediatric glioblastoma. This fusion joins the BTB domain (Broad-complex, Tramtrack, and Bric-a-brac) domain of NACC2 (Nucleus Accumbens-associated protein 2) with the transmembrane helix and tyrosine kinase domain of NTRK2. We focus on identifying critical domains for the biological activity of the fusion protein. Mutations were introduced in the charged pocket of the BTB domain or in the monomer core, based on a structural comparison of the NACC2 BTB domain with that of PLZF, another BTB-containing protein. Mutations were also introduced into the NTRK2-derived portion to allow comparison of two different breakpoints that have been clinically reported. We show that activation of the NTRK2 kinase domain relies on multimerization of the BTB domain in NACC2-NTRK2. Mutations which disrupt BTB-mediated multimerization significantly reduce kinase activity and downstream signaling. The ability of these mutations to abrogate biological activity suggests that BTB domain inhibition could be a potential treatment for NACC2-NTRK2-induced cancers. Removal of the transmembrane helix leads to enhanced stability of the fusion protein and increased activity of the NACC2-NTRK2 fusion, suggesting a mechanism for the oncogenicity of a distinct NACC2-NTRK2 isoform observed in pediatric glioblastoma.
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Affiliation(s)
- Wei Yang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - April N. Meyer
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Zian Jiang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Xuan Jiang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Daniel J. Donoghue
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
- UCSD Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
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37
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Mindrebo JT, Lander GC. Structural and mechanistic studies on human LONP1 redefine the hand-over-hand translocation mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600538. [PMID: 38979310 PMCID: PMC11230189 DOI: 10.1101/2024.06.24.600538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
AAA+ enzymes use energy from ATP hydrolysis to remodel diverse cellular targets. Structures of substrate-bound AAA+ complexes suggest that these enzymes employ a conserved hand-over-hand mechanism to thread substrates through their central pore. However, the fundamental aspects of the mechanisms governing motor function and substrate processing within specific AAA+ families remain unresolved. We used cryo-electron microscopy to structurally interrogate reaction intermediates from in vitro biochemical assays to inform the underlying regulatory mechanisms of the human mitochondrial AAA+ protease, LONP1. Our results demonstrate that substrate binding allosterically regulates proteolytic activity, and that LONP1 can adopt a configuration conducive to substrate translocation even when the ATPases are bound to ADP. These results challenge the conventional understanding of the hand-over-hand translocation mechanism, giving rise to an alternative model that aligns more closely with biochemical and biophysical data on related enzymes like ClpX, ClpA, the 26S proteasome, and Lon protease.
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Affiliation(s)
- Jeffrey T. Mindrebo
- Department of Integrative Structural and Computational Biology, Scripps Research; La Jolla, CA, USA
| | - Gabriel C. Lander
- Department of Integrative Structural and Computational Biology, Scripps Research; La Jolla, CA, USA
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38
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Manthei KA, Munson LM, Nandakumar J, Simmons LA. Structural and biochemical characterization of the mitomycin C repair exonuclease MrfB. Nucleic Acids Res 2024; 52:6347-6359. [PMID: 38661211 PMCID: PMC11194089 DOI: 10.1093/nar/gkae308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 04/03/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024] Open
Abstract
Mitomycin C (MMC) repair factor A (mrfA) and factor B (mrfB), encode a conserved helicase and exonuclease that repair DNA damage in the soil-dwelling bacterium Bacillus subtilis. Here we have focused on the characterization of MrfB, a DEDDh exonuclease in the DnaQ superfamily. We solved the structure of the exonuclease core of MrfB to a resolution of 2.1 Å, in what appears to be an inactive state. In this conformation, a predicted α-helix containing the catalytic DEDDh residue Asp172 adopts a random coil, which moves Asp172 away from the active site and results in the occupancy of only one of the two catalytic Mg2+ ions. We propose that MrfB resides in this inactive state until it interacts with DNA to become activated. By comparing our structure to an AlphaFold prediction as well as other DnaQ-family structures, we located residues hypothesized to be important for exonuclease function. Using exonuclease assays we show that MrfB is a Mg2+-dependent 3'-5' DNA exonuclease. We show that Leu113 aids in coordinating the 3' end of the DNA substrate, and that a basic loop is important for substrate binding. This work provides insight into the function of a recently discovered bacterial exonuclease important for the repair of MMC-induced DNA adducts.
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Affiliation(s)
- Kelly A Manthei
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lia M Munson
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lyle A Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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Chen SK, Liu J, Van Nynatten A, Tudor-Price BM, Chang BSW. Sampling Strategies for Experimentally Mapping Molecular Fitness Landscapes Using High-Throughput Methods. J Mol Evol 2024:10.1007/s00239-024-10179-8. [PMID: 38886207 DOI: 10.1007/s00239-024-10179-8] [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: 02/28/2024] [Accepted: 05/20/2024] [Indexed: 06/20/2024]
Abstract
Empirical studies of genotype-phenotype-fitness maps of proteins are fundamental to understanding the evolutionary process, in elucidating the space of possible genotypes accessible through mutations in a landscape of phenotypes and fitness effects. Yet, comprehensively mapping molecular fitness landscapes remains challenging since all possible combinations of amino acid substitutions for even a few protein sites are encoded by an enormous genotype space. High-throughput mapping of genotype space can be achieved using large-scale screening experiments known as multiplexed assays of variant effect (MAVEs). However, to accommodate such multi-mutational studies, the size of MAVEs has grown to the point where a priori determination of sampling requirements is needed. To address this problem, we propose calculations and simulation methods to approximate minimum sampling requirements for multi-mutational MAVEs, which we combine with a new library construction protocol to experimentally validate our approximation approaches. Analysis of our simulated data reveals how sampling trajectories differ between simulations of nucleotide versus amino acid variants and among mutagenesis schemes. For this, we show quantitatively that marginal gains in sampling efficiency demand increasingly greater sampling effort when sampling for nucleotide sequences over their encoded amino acid equivalents. We present a new library construction protocol that efficiently maximizes sequence variation, and demonstrate using ultradeep sequencing that the library encodes virtually all possible combinations of mutations within the experimental design. Insights learned from our analyses together with the methodological advances reported herein are immediately applicable toward pooled experimental screens of arbitrary design, enabling further assay upscaling and expanded testing of genotype space.
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Affiliation(s)
- Steven K Chen
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Jing Liu
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Alexander Van Nynatten
- Department of Biological Science, University of Toronto Scarborough, Toronto, ON, Canada
| | | | - Belinda S W Chang
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada.
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, Canada.
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, Canada.
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40
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Sun Z, Wu YX, Liu LZ, Tian YP, Li XD, Geng C. P3N-PIPO but not P3 is the avirulence determinant in melon carrying the Wmr resistance against watermelon mosaic virus, although they contain a common genetic determinant. J Virol 2024; 98:e0050724. [PMID: 38775482 PMCID: PMC11237411 DOI: 10.1128/jvi.00507-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 04/21/2024] [Indexed: 06/14/2024] Open
Abstract
Viruses employ a series of diverse translational strategies to expand their coding capacity, which produces viral proteins with common domains and entangles virus-host interactions. P3N-PIPO, which is a transcriptional slippage product from the P3 cistron, is a potyviral protein dedicated to intercellular movement. Here, we show that P3N-PIPO from watermelon mosaic virus (WMV) triggers cell death when transiently expressed in Cucumis melo accession PI 414723 carrying the Wmr resistance gene. Surprisingly, expression of the P3N domain, shared by both P3N-PIPO and P3, can alone induce cell death, whereas expression of P3 fails to activate cell death in PI 414723. Confocal microscopy analysis revealed that P3N-PIPO targets plasmodesmata (PD) and P3N associates with PD, while P3 localizes in endoplasmic reticulum in melon cells. We also found that mutations in residues L35, L38, P41, and I43 of the P3N domain individually disrupt the cell death induced by P3N-PIPO, but do not affect the PD localization of P3N-PIPO. Furthermore, WMV mutants with L35A or I43A can systemically infect PI 414723 plants. These key residues guide us to discover some WMV isolates potentially breaking the Wmr resistance. Through searching the NCBI database, we discovered some WMV isolates with variations in these key sites, and one naturally occurring I43V variation enables WMV to systemically infect PI 414723 plants. Taken together, these results demonstrate that P3N-PIPO, but not P3, is the avirulence determinant recognized by Wmr, although the shared N terminal P3N domain can alone trigger cell death.IMPORTANCEThis work reveals a novel viral avirulence (Avr) gene recognized by a resistance (R) gene. This novel viral Avr gene is special because it is a transcriptional slippage product from another virus gene, which means that their encoding proteins share the common N-terminal domain but have distinct C-terminal domains. Amazingly, we found that it is the common N-terminal domain that determines the Avr-R recognition, but only one of the viral proteins can be recognized by the R protein to induce cell death. Next, we found that these two viral proteins target different subcellular compartments. In addition, we discovered some virus isolates with variations in the common N-terminal domain and one naturally occurring variation that enables the virus to overcome the resistance. These results show how viral proteins with common domains interact with a host resistance protein and provide new evidence for the arms race between plants and viruses.
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Affiliation(s)
- Zhen Sun
- Department of Plant Pathology, Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong, China
| | - Yu-Xuan Wu
- Department of Plant Pathology, Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong, China
| | - Ling-Zhi Liu
- Department of Plant Pathology, Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong, China
| | - Yan-Ping Tian
- Department of Plant Pathology, Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong, China
| | - Xiang-Dong Li
- Department of Plant Pathology, Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong, China
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong, China
| | - Chao Geng
- Department of Plant Pathology, Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong, China
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41
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Parnell EJ, Jenson EE, Miller MP. A conserved site on Ndc80 complex facilitates dynamic recruitment of Mps1 to yeast kinetochores to promote accurate chromosome segregation. Curr Biol 2024; 34:2294-2307.e4. [PMID: 38776906 PMCID: PMC11178286 DOI: 10.1016/j.cub.2024.04.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/27/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
Accurate chromosome segregation relies on kinetochores carrying out multiple functions, including establishing and maintaining microtubule attachments, forming precise bi-oriented attachments between sister chromatids, and activating the spindle assembly checkpoint. Central to these processes is the highly conserved Ndc80 complex. This kinetochore subcomplex interacts directly with microtubules but also serves as a critical platform for recruiting kinetochore-associated factors and as a key substrate for error correction kinases. The precise manner in which these kinetochore factors interact and regulate each other's function remains unknown, considerably hindering our understanding of how Ndc80 complex-dependent processes function together to orchestrate accurate chromosome segregation. Here, we aimed to uncover the role of Nuf2's CH domain, a component of the Ndc80 complex, in ensuring these processes. Through extensive mutational analysis, we identified a conserved interaction domain composed of two segments in Nuf2's CH domain that form the binding site for Mps1 within the yeast Ndc80 complex. Interestingly, this site also associates with the Dam1 complex, suggesting Mps1 recruitment may be subject to regulation by competitive binding with other factors. Mutants disrupting this "interaction hub" exhibit defects in spindle assembly checkpoint function and severe chromosome segregation errors. Significantly, specifically restoring Mps1-Ndc80 complex association rescues these defects. Our findings shed light on the intricate regulation of Ndc80 complex-dependent functions and highlight the essential role of Mps1 in kinetochore bi-orientation and accurate chromosome segregation.
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Affiliation(s)
- Emily J Parnell
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Erin E Jenson
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Matthew P Miller
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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Xu XJ, Sun XJ, Liu CJ, Chen XZ, Zhu Q, Tian YP, Li XD. Development of an attenuated potato virus Y mutant carrying multiple mutations in helper-component protease for cross-protection. Virus Res 2024; 344:199369. [PMID: 38608732 PMCID: PMC11035042 DOI: 10.1016/j.virusres.2024.199369] [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: 03/03/2024] [Revised: 04/06/2024] [Accepted: 04/10/2024] [Indexed: 04/14/2024]
Abstract
Tobacco (Nicotiana tabacum) is one of the major cash crops in China. Potato virus Y (PVY), a representative member of the genus Potyvirus, greatly reduces the quality and yield of tobacco leaves by inducing veinal necrosis. Mild strain-mediated cross-protection is an attractive method of controlling diseases caused by PVY. Currently, there is a lack of effective and stable attenuated PVY mutants. Potyviral helper component-protease (HC-Pro) is a likely target for the development of mild strains. Our previous studies showed that the residues lysine at positions 124 and 182 (K124 and K182) in HC-Pro were involved in PVY virulence, and the conserved KITC motif in HC-Pro was involved in aphid transmission. In this study, to improve the stability of PVY mild strains, K at position 50 (K50) in KITC motif, K124, and K182 were separately substituted with glutamic acid (E), leucine (L), and arginine (R), resulting in a triple-mutant PVY-HCELR. The mutant PVY-HCELR had attenuated virulence and did not induce leaf veinal necrosis symptoms in tobacco plants and could not be transmitted by Myzus persicae. Furthermore, PVY-HCELR mutant was genetically stable after six serial passages, and only caused mild mosaic symptoms in tobacco plants even at 90 days post inoculation. The tobacco plants cross-protected by PVY-HCELR mutant showed high resistance to the wild-type PVY. This study showed that PVY-HCELR mutant was a promising mild mutant for cross-protection to control PVY.
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Affiliation(s)
- Xiao-Jie Xu
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, Yantai, Shandong 264025, China; Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Xu-Jie Sun
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Chun-Ju Liu
- Weifang Tobacco Corporation, Weifang, Shandong 261031, China
| | - Xiu-Zhai Chen
- Linyi Tobacco Corporation, Linyi, Shandong 276000, China
| | - Qing Zhu
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Yan-Ping Tian
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, China.
| | - Xiang-Dong Li
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, China.
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43
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Ernst L, Lyu H, Liu P, Paetz C, Sayed HMB, Meents T, Ma H, Beerhues L, El-Awaad I, Liu B. Regiodivergent biosynthesis of bridged bicyclononanes. Nat Commun 2024; 15:4525. [PMID: 38806518 PMCID: PMC11133429 DOI: 10.1038/s41467-024-48879-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 05/15/2024] [Indexed: 05/30/2024] Open
Abstract
Medicinal compounds from plants include bicyclo[3.3.1]nonane derivatives, the majority of which are polycyclic polyprenylated acylphloroglucinols (PPAPs). Prototype molecules are hyperforin, the antidepressant constituent of St. John's wort, and garcinol, a potential anticancer compound. Their complex structures have inspired innovative chemical syntheses, however, their biosynthesis in plants is still enigmatic. PPAPs are divided into two subclasses, named type A and B. Here we identify both types in Hypericum sampsonii plants and isolate two enzymes that regiodivergently convert a common precursor to pivotal type A and B products. Molecular modelling and substrate docking studies reveal inverted substrate binding modes in the two active site cavities. We identify amino acids that stabilize these alternative binding scenarios and use reciprocal mutagenesis to interconvert the enzymatic activities. Our studies elucidate the unique biochemistry that yields type A and B bicyclo[3.3.1]nonane cores in plants, thereby providing key building blocks for biotechnological efforts to sustainably produce these complex compounds for preclinical development.
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Affiliation(s)
- Lukas Ernst
- Technische Universität Braunschweig, Institute of Pharmaceutical Biology, Braunschweig, Germany.
| | - Hui Lyu
- Max Planck Institute for Chemical Ecology, NMR/Biosynthesis Group, Jena, Germany
| | - Pi Liu
- Chinese Academy of Sciences, Tianjin Institute of Industrial Biotechnology, Biodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin, China
| | - Christian Paetz
- Max Planck Institute for Chemical Ecology, NMR/Biosynthesis Group, Jena, Germany
| | - Hesham M B Sayed
- Technische Universität Braunschweig, Institute of Pharmaceutical Biology, Braunschweig, Germany
- Assiut University, Faculty of Pharmacy, Department of Pharmacognosy, Assiut, Egypt
| | - Tomke Meents
- Technische Universität Braunschweig, Institute of Pharmaceutical Biology, Braunschweig, Germany
| | - Hongwu Ma
- Chinese Academy of Sciences, Tianjin Institute of Industrial Biotechnology, Biodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin, China
| | - Ludger Beerhues
- Technische Universität Braunschweig, Institute of Pharmaceutical Biology, Braunschweig, Germany
- Technische Universität Braunschweig, Center of Pharmaceutical Engineering, Braunschweig, Germany
| | - Islam El-Awaad
- Technische Universität Braunschweig, Institute of Pharmaceutical Biology, Braunschweig, Germany.
- Assiut University, Faculty of Pharmacy, Department of Pharmacognosy, Assiut, Egypt.
- Technische Universität Braunschweig, Center of Pharmaceutical Engineering, Braunschweig, Germany.
| | - Benye Liu
- Technische Universität Braunschweig, Institute of Pharmaceutical Biology, Braunschweig, Germany.
- Technische Universität Braunschweig, Center of Pharmaceutical Engineering, Braunschweig, Germany.
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44
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Huang WRH, Braam C, Kretschmer C, Villanueva SL, Liu H, Ferik F, van der Burgh AM, Boeren S, Wu J, Zhang L, Nürnberger T, Wang Y, Seidl MF, Evangelisti E, Stuttmann J, Joosten MHAJ. Receptor-like cytoplasmic kinases of different subfamilies differentially regulate SOBIR1/BAK1-mediated immune responses in Nicotiana benthamiana. Nat Commun 2024; 15:4339. [PMID: 38773116 PMCID: PMC11109355 DOI: 10.1038/s41467-024-48313-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/26/2024] [Indexed: 05/23/2024] Open
Abstract
Cell-surface receptors form the front line of plant immunity. The leucine-rich repeat (LRR)-receptor-like kinases SOBIR1 and BAK1 are required for the functionality of the tomato LRR-receptor-like protein Cf-4, which detects the secreted effector Avr4 of the pathogenic fungus Fulvia fulva. Here, we show that the kinase domains of SOBIR1 and BAK1 directly phosphorylate each other and that residues Thr522 and Tyr469 of the kinase domain of Nicotiana benthamiana SOBIR1 are required for its kinase activity and for interacting with signalling partners, respectively. By knocking out multiple genes belonging to different receptor-like cytoplasmic kinase (RLCK)-VII subfamilies in N. benthamiana:Cf-4, we show that members of RLCK-VII-6, -7, and -8 differentially regulate the Avr4/Cf-4-triggered biphasic burst of reactive oxygen species. In addition, members of RLCK-VII-7 play an essential role in resistance against the oomycete pathogen Phytophthora palmivora. Our study provides molecular evidence for the specific roles of RLCKs downstream of SOBIR1/BAK1-containing immune complexes.
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Affiliation(s)
- Wen R H Huang
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
- The Sainsbury Laboratory, University of East Anglia, Norwich, United Kingdom.
| | - Ciska Braam
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Carola Kretschmer
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, 06120, Halle, Germany
| | - Sergio Landeo Villanueva
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Huan Liu
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Filiz Ferik
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, 06120, Halle, Germany
| | - Aranka M van der Burgh
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Teaching and Learning Centre, Wageningen University & Research, Droevendaalsesteeg 4, 6708 PB, Wageningen, The Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University and Research, Wageningen, the Netherlands
| | - Jinbin Wu
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lisha Zhang
- Department of Plant Biochemistry, Centre for Plant Molecular Biology (ZMBP), Eberhard Karls University Tübingen, Auf der Morgenstelle 32, D-72076, Tübingen, Germany
| | - Thorsten Nürnberger
- Department of Plant Biochemistry, Centre for Plant Molecular Biology (ZMBP), Eberhard Karls University Tübingen, Auf der Morgenstelle 32, D-72076, Tübingen, Germany
| | - Yulu Wang
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Michael F Seidl
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Edouard Evangelisti
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Université Côte d'Azur, INRAE UMR 1355, CNRS UMR 7254, Institut Sophia Agrobiotech (ISA), 06903, Sophia Antipolis, France
| | - Johannes Stuttmann
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle-Wittenberg, 06120, Halle, Germany
- Aix Marseille University, CEA, CNRS, BIAM, UMR7265, LEMiRE (Microbial Ecology of the Rhizosphere), 13115, Saint‑Paul lez Durance, France
| | - Matthieu H A J Joosten
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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Hong T, Luo Q, Ma H, Wang X, Li X, Shen C, Pang J, Wang Y, Chen Y, Zhang C, Su Z, Dong H, Tang X. Structural basis of negative regulation of CRISPR-Cas7-11 by TPR-CHAT. Signal Transduct Target Ther 2024; 9:111. [PMID: 38735995 PMCID: PMC11089037 DOI: 10.1038/s41392-024-01821-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 04/06/2024] [Accepted: 04/08/2024] [Indexed: 05/14/2024] Open
Abstract
CRISPR‒Cas7-11 is a Type III-E CRISPR-associated nuclease that functions as a potent RNA editing tool. Tetratrico-peptide repeat fused with Cas/HEF1-associated signal transducer (TPR-CHAT) acts as a regulatory protein that interacts with CRISPR RNA (crRNA)-bound Cas7-11 to form a CRISPR-guided caspase complex (Craspase). However, the precise modulation of Cas7-11's nuclease activity by TPR-CHAT to enhance its utility requires further study. Here, we report cryo-electron microscopy (cryo-EM) structures of Desulfonema ishimotonii (Di) Cas7-11-crRNA, complexed with or without the full length or the N-terminus of TPR-CHAT. These structures unveil the molecular features of the Craspase complex. Structural analysis, combined with in vitro nuclease assay and electrophoretic mobility shift assay, reveals that DiTPR-CHAT negatively regulates the activity of DiCas7-11 by preventing target RNA from binding through the N-terminal 65 amino acids of DiTPR-CHAT (DiTPR-CHATNTD). Our work demonstrates that DiTPR-CHATNTD can function as a small unit of DiCas7-11 regulator, potentially enabling safe applications to prevent overcutting and off-target effects of the CRISPR‒Cas7-11 system.
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Affiliation(s)
- Tian Hong
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Qinghua Luo
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- Frontiers Medical Center, Tianfu Jincheng Laboratory, West China Hospital, Sichuan University, Chengdu, China
| | - Haiyun Ma
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Xin Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Xinqiong Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Chongrong Shen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Jie Pang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Yan Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Yuejia Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Changbin Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Zhaoming Su
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.
| | - Haohao Dong
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.
- Frontiers Medical Center, Tianfu Jincheng Laboratory, West China Hospital, Sichuan University, Chengdu, China.
| | - Xiaodi Tang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.
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46
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Rajappa S, Krishnamurthy P, Huang H, Yu D, Friml J, Xu J, Kumar PP. The translocation of a chloride channel from the Golgi to the plasma membrane helps plants adapt to salt stress. Nat Commun 2024; 15:3978. [PMID: 38729926 PMCID: PMC11087495 DOI: 10.1038/s41467-024-48234-z] [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: 09/19/2022] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
A key mechanism employed by plants to adapt to salinity stress involves maintaining ion homeostasis via the actions of ion transporters. While the function of cation transporters in maintaining ion homeostasis in plants has been extensively studied, little is known about the roles of their anion counterparts in this process. Here, we describe a mechanism of salt adaptation in plants. We characterized the chloride channel (CLC) gene AtCLCf, whose expression is regulated by WRKY transcription factor under salt stress in Arabidopsis thaliana. Loss-of-function atclcf seedlings show increased sensitivity to salt, whereas AtCLCf overexpression confers enhanced resistance to salt stress. Salt stress induces the translocation of GFP-AtCLCf fusion protein to the plasma membrane (PM). Blocking AtCLCf translocation using the exocytosis inhibitor brefeldin-A or mutating the small GTPase gene AtRABA1b/BEX5 (RAS GENES FROM RAT BRAINA1b homolog) increases salt sensitivity in plants. Electrophysiology and liposome-based assays confirm the Cl-/H+ antiport function of AtCLCf. Therefore, we have uncovered a mechanism of plant adaptation to salt stress involving the NaCl-induced translocation of AtCLCf to the PM, thus facilitating Cl- removal at the roots, and increasing the plant's salinity tolerance.
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Affiliation(s)
- Sivamathini Rajappa
- Department of Biological Sciences and Research Centre on Sustainable Urban Farming, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - Pannaga Krishnamurthy
- Department of Biological Sciences and Research Centre on Sustainable Urban Farming, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
- NUS Environmental Research Institute, National University of Singapore, #02-01, T-Lab Building, 5A Engineering Drive 1, Singapore, 117411, Singapore
| | - Hua Huang
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Electrophysiology Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore
- Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore: Level 5, Centre for Life Sciences, 28 Medical Drive, Singapore, 117456, Singapore
- Cardiovascular Diseases Program, National University of Singapore, 14 Medical Drive, MD6, #08-01, Singapore, 117599, Singapore
| | - Dejie Yu
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Electrophysiology Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore
- Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore: Level 5, Centre for Life Sciences, 28 Medical Drive, Singapore, 117456, Singapore
- Cardiovascular Diseases Program, National University of Singapore, 14 Medical Drive, MD6, #08-01, Singapore, 117599, Singapore
| | - Jiří Friml
- Institute of Science and Technology Austria (IST Austria) Am Campus 1, 3400, Klosterneuburg, Austria
| | - Jian Xu
- Department of Plant Systems Physiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Huygens Building, Heyendaalseweg 135, 6500 AJ, Nijmegen, The Netherlands
| | - Prakash P Kumar
- Department of Biological Sciences and Research Centre on Sustainable Urban Farming, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.
- NUS Environmental Research Institute, National University of Singapore, #02-01, T-Lab Building, 5A Engineering Drive 1, Singapore, 117411, Singapore.
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47
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Mühlenbeck H, Tsutsui Y, Lemmon MA, Bender KW, Zipfel C. Allosteric activation of the co-receptor BAK1 by the EFR receptor kinase initiates immune signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.23.554490. [PMID: 37662281 PMCID: PMC10473708 DOI: 10.1101/2023.08.23.554490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Transmembrane signaling by plant receptor kinases (RKs) has long been thought to involve reciprocal trans-phosphorylation of their intracellular kinase domains. The fact that many of these are pseudokinase domains, however, suggests that additional mechanisms must govern RK signaling activation. Non-catalytic (pseudo)kinase signaling mechanisms have been described in metazoans, but information is scarce for plants. Recently, a non-catalytic function was reported for the leucine-rich repeat (LRR)-RK subfamily XIIa member EFR (ELONGATION FACTOR TU RECEPTOR) and phosphorylation-dependent conformational changes were proposed to regulate signaling of RKs with non-RD kinase domains. Here, using EFR as a model, we describe a non-catalytic activation mechanism for LRR-RKs with non-RD kinase domains. EFR is an active kinase, but a kinase-dead variant retains the ability to enhance catalytic activity of its co-receptor kinase BAK1/SERK3 (BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1/SOMATIC EMBRYOGENESIS RECEPTOR KINASE 3). Applying hydrogen-deuterium exchange mass spectrometry (HDX-MS) analysis and designing homology-based intragenic suppressor mutations, we provide evidence that the EFR kinase domain must adopt its active conformation in order to activate BAK1 allosterically, likely by supporting αC-helix positioning in BAK1. Our results suggest a conformational toggle model for signaling, in which BAK1 first phosphorylates EFR in the activation loop to stabilize its active conformation, allowing EFR in turn to allosterically activate BAK1.
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48
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Khudayberdiev S, Weiss K, Heinze A, Colombaretti D, Trausch N, Linne U, Rust MB. The actin-binding protein CAP1 represses MRTF-SRF-dependent gene expression in mouse cerebral cortex. Sci Signal 2024; 17:eadj0032. [PMID: 38713765 DOI: 10.1126/scisignal.adj0032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 04/15/2024] [Indexed: 05/09/2024]
Abstract
Serum response factor (SRF) is an essential transcription factor for brain development and function. Here, we explored how an SRF cofactor, the actin monomer-sensing myocardin-related transcription factor MRTF, is regulated in mouse cortical neurons. We found that MRTF-dependent SRF activity in vitro and in vivo was repressed by cyclase-associated protein CAP1. Inactivation of the actin-binding protein CAP1 reduced the amount of actin monomers in the cytoplasm, which promoted nuclear MRTF translocation and MRTF-SRF activation. This function was independent of cofilin1 and actin-depolymerizing factor, and CAP1 loss of function in cortical neurons was not compensated by endogenous CAP2. Transcriptomic and proteomic analyses of cerebral cortex lysates from wild-type and Cap1 knockout mice supported the role of CAP1 in repressing MRTF-SRF-dependent signaling in vivo. Bioinformatic analysis identified likely MRTF-SRF target genes, which aligned with the transcriptomic and proteomic results. Together with our previous studies that implicated CAP1 in axonal growth cone function as well as the morphology and plasticity of excitatory synapses, our findings establish CAP1 as a crucial actin regulator in the brain relevant for formation of neuronal networks.
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Affiliation(s)
- Sharof Khudayberdiev
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032 Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), University of Marburg and Justus-Liebig-University Giessen, Hans-Meerwein-Strasse 6, 35032 Marburg, Germany
| | - Kerstin Weiss
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032 Marburg, Germany
| | - Anika Heinze
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032 Marburg, Germany
| | - Dalila Colombaretti
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032 Marburg, Germany
| | - Nathan Trausch
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032 Marburg, Germany
| | - Uwe Linne
- Department of Chemistry, Philipps-University Marburg, 35032 Marburg, Germany
| | - Marco B Rust
- Molecular Neurobiology Group, Institute of Physiological Chemistry, Philipps-University of Marburg, 35032 Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), University of Marburg and Justus-Liebig-University Giessen, Hans-Meerwein-Strasse 6, 35032 Marburg, Germany
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49
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Pappas CT, Mayfield RM, Dickerson AE, Mi-Mi L, Gregorio CC. Human disease-causing mutations result in loss of leiomodin 2 through nonsense-mediated mRNA decay. PLoS Genet 2024; 20:e1011279. [PMID: 38748723 PMCID: PMC11132695 DOI: 10.1371/journal.pgen.1011279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 05/28/2024] [Accepted: 04/30/2024] [Indexed: 05/30/2024] Open
Abstract
The leiomodin (Lmod) family of actin-binding proteins play a critical role in muscle function, highlighted by the fact that mutations in all three family members (LMOD1-3) result in human myopathies. Mutations in the cardiac predominant isoform, LMOD2 lead to severe neonatal dilated cardiomyopathy. Most of the disease-causing mutations in the LMOD gene family are nonsense, or frameshift, mutations predicted to result in expression of truncated proteins. However, in nearly all cases of disease, little to no LMOD protein is expressed. We show here that nonsense-mediated mRNA decay, a cellular mechanism which eliminates mRNAs with premature termination codons, underlies loss of mutant protein from two independent LMOD2 disease-causing mutations. Furthermore, we generated steric-blocking oligonucleotides that obstruct deposition of the exon junction complex, preventing nonsense-mediated mRNA decay of mutant LMOD2 transcripts, thereby restoring mutant protein expression. Our investigation lays the initial groundwork for potential therapeutic intervention in LMOD-linked myopathies.
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Affiliation(s)
- Christopher T. Pappas
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, Arizona, United States of America
| | - Rachel M. Mayfield
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, Arizona, United States of America
| | - Ava E. Dickerson
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, Arizona, United States of America
| | - Lei Mi-Mi
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, Arizona, United States of America
| | - Carol C. Gregorio
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, Arizona, United States of America
- Department of Medicine and Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
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50
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Zhao J, Elgeti M, O'Brien ES, Sár CP, Ei Daibani A, Heng J, Sun X, White E, Che T, Hubbell WL, Kobilka BK, Chen C. Ligand efficacy modulates conformational dynamics of the µ-opioid receptor. Nature 2024; 629:474-480. [PMID: 38600384 PMCID: PMC11078757 DOI: 10.1038/s41586-024-07295-2] [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: 11/30/2022] [Accepted: 03/11/2024] [Indexed: 04/12/2024]
Abstract
The µ-opioid receptor (µOR) is an important target for pain management1 and molecular understanding of drug action on µOR will facilitate the development of better therapeutics. Here we show, using double electron-electron resonance and single-molecule fluorescence resonance energy transfer, how ligand-specific conformational changes of µOR translate into a broad range of intrinsic efficacies at the transducer level. We identify several conformations of the cytoplasmic face of the receptor that interconvert on different timescales, including a pre-activated conformation that is capable of G-protein binding, and a fully activated conformation that markedly reduces GDP affinity within the ternary complex. Interaction of β-arrestin-1 with the μOR core binding site appears less specific and occurs with much lower affinity than binding of Gi.
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Affiliation(s)
- Jiawei Zhao
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Matthias Elgeti
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
- Institute for Drug Discovery, University of Leipzig Medical Center, Leipzig, Germany.
| | - Evan S O'Brien
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Cecília P Sár
- Institute of Organic and Medicinal Chemistry, School of Pharmaceutical Sciences, University of Pécs, Pécs, Hungary
| | - Amal Ei Daibani
- Department of Anesthesiology, Washington University School of Medicine, St Louis, MO, USA
| | - Jie Heng
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Xiaoou Sun
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Elizabeth White
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Tao Che
- Department of Anesthesiology, Washington University School of Medicine, St Louis, MO, USA
| | - Wayne L Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Chunlai Chen
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China.
- School of Life Sciences, Tsinghua University, Beijing, China.
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