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Williams JPC, Mouilleron S, Trapero RH, Bertran MT, Marsh JA, Walport LJ. Structural insight into the function of human peptidyl arginine deiminase 6. Comput Struct Biotechnol J 2024; 23:3258-3269. [PMID: 39286527 PMCID: PMC11402830 DOI: 10.1016/j.csbj.2024.08.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 08/15/2024] [Accepted: 08/15/2024] [Indexed: 09/19/2024] Open
Abstract
Peptidyl arginine deiminase 6 (PADI6 or PAD6) is vital for early embryonic development in mice and humans, yet its function remains elusive. PADI6 is less conserved than other PADIs and it is currently unknown whether it has a catalytic function. Here we show that human PADI6 dimerises like hPADIs 2-4, however, does not bind Ca2+ and is inactive in in vitro assays against standard PADI substrates. By determining the crystal structure of hPADI6, we show that hPADI6 is structured in the absence of Ca2+ where hPADI2 and hPADI4 are not, and the Ca-binding sites are not conserved. Moreover, we show that whilst the key catalytic aspartic acid and histidine residues are structurally conserved, the cysteine is displaced far from the active site centre and the hPADI6 active site pocket appears closed through a unique evolved mechanism in hPADI6, not present in the other PADIs. Taken together, these findings provide insight into how the function of hPADI6 may differ from the other PADIs based on its structure and provides a resource for characterising the damaging effect of clinically significant PADI6 variants.
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Affiliation(s)
- Jack P C Williams
- Department of Chemistry, Imperial College London, London, United Kingdom
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Stephane Mouilleron
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Rolando Hernandez Trapero
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - M Teresa Bertran
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Louise J Walport
- Department of Chemistry, Imperial College London, London, United Kingdom
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, United Kingdom
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2
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Aparecida Dos Santos France F, Maeda DK, Rodrigues AB, Ono M, Lopes Nogueira Marchetti F, Marchetti MM, Faustino Martins AC, Gomes RDS, Rainho CA. Exploring fatty acids from royal jelly as a source of histone deacetylase inhibitors: from the hive to applications in human well-being and health. Epigenetics 2024; 19:2400423. [PMID: 39255363 PMCID: PMC11404605 DOI: 10.1080/15592294.2024.2400423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 08/17/2024] [Accepted: 08/30/2024] [Indexed: 09/12/2024] Open
Abstract
A differential diet with royal jelly (RJ) during early larval development in honeybees shapes the phenotype, which is probably mediated by epigenetic regulation of gene expression. Evidence indicates that small molecules in RJ can modulate gene expression in mammalian cells, such as the fatty acid 10-hydroxy-2-decenoic acid (10-HDA), previously associated with the inhibition of histone deacetylase enzymes (HDACs). Therefore, we combined computational (molecular docking simulations) and experimental approaches for the screening of potential HDAC inhibitors (HDACi) among 32 RJ-derived fatty acids. Biochemical assays and gene expression analyses (Reverse Transcriptase - quantitative Polymerase Chain Reaction) were performed to evaluate the functional effects of the major RJ fatty acids, 10-HDA and 10-HDAA (10-hydroxy-decanoic acid), in two human cancer cell lines (HCT116 and MDA-MB-231). The molecular docking simulations indicate that these fatty acids might interact with class I HDACs, specifically with the catalytic domain of human HDAC2, likewise well-known HDAC inhibitors (HDACi) such as SAHA (suberoylanilide hydroxamic acid) and TSA (Trichostatin A). In addition, the combined treatment with 10-HDA and 10-HDAA inhibits the activity of human nuclear HDACs and leads to a slight increase in the expression of HDAC-coding genes in cancer cells. Our findings indicate that royal jelly fatty acids collectively contribute to HDAC inhibition and that 10-HDA and 10-HDAA are weak HDACi that facilitate the acetylation of lysine residues of chromatin, triggering an increase in gene expression levels in cancer cells.
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Affiliation(s)
| | - Debora Kazumi Maeda
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Ana Beatriz Rodrigues
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Mai Ono
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Franciele Lopes Nogueira Marchetti
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Marcos Martins Marchetti
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | | | | | - Cláudia Aparecida Rainho
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil
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3
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Aplakidou E, Vergoulidis N, Chasapi M, Venetsianou NK, Kokoli M, Panagiotopoulou E, Iliopoulos I, Karatzas E, Pafilis E, Georgakopoulos-Soares I, Kyrpides NC, Pavlopoulos GA, Baltoumas FA. Visualizing metagenomic and metatranscriptomic data: A comprehensive review. Comput Struct Biotechnol J 2024; 23:2011-2033. [PMID: 38765606 PMCID: PMC11101950 DOI: 10.1016/j.csbj.2024.04.060] [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: 01/27/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024] Open
Abstract
The fields of Metagenomics and Metatranscriptomics involve the examination of complete nucleotide sequences, gene identification, and analysis of potential biological functions within diverse organisms or environmental samples. Despite the vast opportunities for discovery in metagenomics, the sheer volume and complexity of sequence data often present challenges in processing analysis and visualization. This article highlights the critical role of advanced visualization tools in enabling effective exploration, querying, and analysis of these complex datasets. Emphasizing the importance of accessibility, the article categorizes various visualizers based on their intended applications and highlights their utility in empowering bioinformaticians and non-bioinformaticians to interpret and derive insights from meta-omics data effectively.
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Affiliation(s)
- Eleni Aplakidou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Nikolaos Vergoulidis
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Maria Chasapi
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Nefeli K. Venetsianou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Maria Kokoli
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Eleni Panagiotopoulou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Ioannis Iliopoulos
- Department of Basic Sciences, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Evangelos Karatzas
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Evangelos Pafilis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Nikos C. Kyrpides
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Georgios A. Pavlopoulos
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Center of New Biotechnologies & Precision Medicine, Department of Medicine, School of Health Sciences, National and Kapodistrian University of Athens, Greece
- Hellenic Army Academy, 16673 Vari, Greece
| | - Fotis A. Baltoumas
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
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Carpanta V, Clement H, Arenas I, Corzo G. A consensus recombinant elapid long-chain α-neurotoxin and how protein folding matters for antibody recognition and neutralization of elapid venoms. Biochem Biophys Res Commun 2024; 732:150420. [PMID: 39047403 DOI: 10.1016/j.bbrc.2024.150420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/10/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
Antivenoms are essential in the treatment of the neurotoxicity caused by elapid snakebites. However, there are elapid neurotoxins, e.g., long-chain α-neurotoxins (also known as long-chain three-finger toxins) that are barely neutralized by commercial elapid antivenoms; so, recombinant elapid neurotoxins could be an alternative or complements for improving antibody production against the lethal long-chain α-neurotoxins from elapid venoms. This work communicates the expression of a recombinant long-chain α-neurotoxin, named HisrLcNTx or rLcNTx, which based on the most lethal long-chain α-neurotoxins reported, was constructed de novo. The gene of rLcNTx was synthesized and introduced into the expression vector pQE30, which contains a proteolytic cleavage region for exscinding the mature protein, and His residues in tandem for affinity purification. The cloned pQE30/rLcNTx was transfected into Escherichia coli Origami cells to express rLcNTx. After expression, it was found in inclusion bodies, and folded in multiple Cys-Cys structural isoforms. To observe the capability of those isoforms to generate antibodies against native long-chain α-neurotoxins, groups of rabbits were immunized with different cocktails of Cys-Cys rLcNTx isoforms. In vitro, and in vivo analyses revealed that rabbit antibodies raised against different rLcNTx Cys-Cys isoforms were able to recognize pure native long-chain α-neurotoxins and their elapid venoms, but they were unable to neutralize bungarotoxin, a classical long-chain α-neurotoxin, and other elapid venoms. The rLcNTx Cys-Cys isoform 2 was the immunogen that produced the best neutralizing antibodies in rabbits. Yet to neutralize the elapid venoms from the black mamba Dendroaspis polylepis, and the coral shield cobra Aspidelaps lubricus, it was required to use two types of antibodies, the ones produced using rLcNTx Cys-Cys isoform 2 and antibodies produced using short-chain α-neurotoxins. Expression of recombinant elapid neurotoxins as immunogens could be an alternative to improve elapid antivenoms; nevertheless, recombinant elapid neurotoxins must be well-folded to be used as immunogens for obtaining neutralizing antibodies.
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Affiliation(s)
- Víctor Carpanta
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, UNAM, Apartado Postal 510-3, Cuernavaca, Morelos, 61500, Mexico
| | - Herlinda Clement
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, UNAM, Apartado Postal 510-3, Cuernavaca, Morelos, 61500, Mexico
| | - Iván Arenas
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, UNAM, Apartado Postal 510-3, Cuernavaca, Morelos, 61500, Mexico
| | - Gerardo Corzo
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, UNAM, Apartado Postal 510-3, Cuernavaca, Morelos, 61500, Mexico.
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Douradinha B. Computational strategies in Klebsiella pneumoniae vaccine design: navigating the landscape of in silico insights. Biotechnol Adv 2024; 76:108437. [PMID: 39216613 DOI: 10.1016/j.biotechadv.2024.108437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/07/2024] [Accepted: 08/25/2024] [Indexed: 09/04/2024]
Abstract
The emergence of multidrug-resistant Klebsiella pneumoniae poses a grave threat to global public health, necessitating urgent strategies for vaccine development. In this context, computational tools have emerged as indispensable assets, offering unprecedented insights into klebsiellal biology and facilitating the design of effective vaccines. Here, a review of the application of computational methods in the development of K. pneumoniae vaccines is presented, elucidating the transformative impact of in silico approaches. Through a systematic exploration of bioinformatics, structural biology, and immunoinformatics techniques, the complex landscape of K. pneumoniae pathogenesis and antigenicity was unravelled. Key insights into virulence factors, antigen discovery, and immune response mechanisms are discussed, highlighting the pivotal role of computational tools in accelerating vaccine development efforts. Advancements in epitope prediction, antigen selection, and vaccine design optimisation are examined, highlighting the potential of in silico approaches to update vaccine development pipelines. Furthermore, challenges and future directions in leveraging computational tools to combat K. pneumoniae are discussed, emphasizing the importance of multidisciplinary collaboration and data integration. This review provides a comprehensive overview of the current state of computational contributions to K. pneumoniae vaccine development, offering insights into innovative strategies for addressing this urgent global health challenge.
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6
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Kusch S, Frantzeskakis L, Lassen BD, Kümmel F, Pesch L, Barsoum M, Walden KD, Panstruga R. A fungal plant pathogen overcomes mlo-mediated broad-spectrum disease resistance by rapid gene loss. THE NEW PHYTOLOGIST 2024; 244:962-979. [PMID: 39155769 DOI: 10.1111/nph.20063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 08/03/2024] [Indexed: 08/20/2024]
Abstract
Hosts and pathogens typically engage in a coevolutionary arms race. This also applies to phytopathogenic powdery mildew fungi, which can rapidly overcome plant resistance and perform host jumps. Using experimental evolution, we show that the powdery mildew pathogen Blumeria hordei is capable of breaking the agriculturally important broad-spectrum resistance conditioned by barley loss-of-function mlo mutants. Partial mlo virulence of evolved B. hordei isolates is correlated with a distinctive pattern of adaptive mutations, including small-sized (c. 8-40 kb) deletions, of which one is linked to the de novo insertion of a transposable element. Occurrence of the mutations is associated with a transcriptional induction of effector protein-encoding genes that is absent in mlo-avirulent isolates on mlo mutant plants. The detected mutational spectrum comprises the same loci in at least two independently isolated mlo-virulent isolates, indicating convergent multigenic evolution. The mutational events emerged in part early (within the first five asexual generations) during experimental evolution, likely generating a founder population in which incipient mlo virulence was later stabilized by additional events. This work highlights the rapid dynamic genome evolution of an obligate biotrophic plant pathogen with a transposon-enriched genome.
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Affiliation(s)
- Stefan Kusch
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Lamprinos Frantzeskakis
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Birthe D Lassen
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Florian Kümmel
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Lina Pesch
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Mirna Barsoum
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Kim D Walden
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056, Aachen, Germany
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7
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Li Z, Chen J, Liu C, He S, Wang M, Wang L, Bhadauria V, Wang S, Cheng W, Liu H, Yang X, Xu M, Peng YL, Zhu W. Natural variations of maize ZmLecRK1 determine its interaction with ZmBAK1 and resistance patterns to multiple pathogens. MOLECULAR PLANT 2024; 17:1606-1623. [PMID: 39305013 DOI: 10.1016/j.molp.2024.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 08/28/2024] [Accepted: 09/18/2024] [Indexed: 10/04/2024]
Abstract
Maize (Zea mays) is one of the most important crops in the world, but its yield and quality are seriously affected by diverse diseases. Identifying broad-spectrum resistance genes is crucial for developing effective strategies to control the disease in maize. In a genome-wide study in maize, we identified a G-type lectin receptor kinase ZmLecRK1, as a new resistance protein against Pythium aphanidermatum, one of the causal pathogens of stalk rot in maize. Genetic analysis showed that the specific ZmLecRK1 allele can confer resistance to multiple pathogens in maize. The cell death and disease resistance phenotype mediated by the resistant variant of ZmLecRK1 requires the co-receptor ZmBAK1. A naturally occurring A404S variant in the extracellular domain of ZmLecRK1 determines the ZmLecRK1-ZmBAK1 interaction and the formation of ZmLecRK1-related protein complexes. Interestingly, the ZmLecRK1 susceptible variant was found to possess the amino acid S404 that is present in the ancestral variants of ZmLecRK1 and conserved among the majority of grass species, while the resistance variant of ZmLecRK1 with A404 is only present in a few maize inbred lines. Substitution of S by A at position 404 in ZmLecRK1-like proteins of sorghum and rice greatly enhances their ability to induce cell death. Further transcriptomic analysis reveals that ZmLecRK1 likely regulates gene expression related to the pathways in cell wall organization or biogenesis in response to pathogen infection. Taken together, these results suggest that the ZmLecRK1 resistance variant enhances its binding affinity to the co-receptor ZmBAK1, thereby enhancing the formation of active complexes for defense in maize. Our work highlights the biotechnological potential for generating disease-resistant crops by precisely modulating the activity of ZmLecRK1 and its homologs through targeted base editing.
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Affiliation(s)
- Zhenju Li
- State Key Laboratory of Maize Bio-breeding/College of Plant Protection/Ministry of Agriculture and Rural Affairs Key Laboratory of Surveillance and Management for Plant Quarantine Pests, China Agricultural University, Beijing 100193, P.R. China
| | - Junbin Chen
- State Key Laboratory of Maize Bio-breeding/College of Plant Protection/Ministry of Agriculture and Rural Affairs Key Laboratory of Surveillance and Management for Plant Quarantine Pests, China Agricultural University, Beijing 100193, P.R. China
| | - Chuang Liu
- State Key Laboratory of Maize Bio-breeding/College of Plant Protection/Ministry of Agriculture and Rural Affairs Key Laboratory of Surveillance and Management for Plant Quarantine Pests, China Agricultural University, Beijing 100193, P.R. China
| | - Shengfeng He
- State Key Laboratory of Maize Bio-breeding/College of Plant Protection/Ministry of Agriculture and Rural Affairs Key Laboratory of Surveillance and Management for Plant Quarantine Pests, China Agricultural University, Beijing 100193, P.R. China
| | - Mingyu Wang
- State Key Laboratory of Maize Bio-breeding/College of Plant Protection/Ministry of Agriculture and Rural Affairs Key Laboratory of Surveillance and Management for Plant Quarantine Pests, China Agricultural University, Beijing 100193, P.R. China; Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Zhejiang 310021, P.R. China
| | - Lei Wang
- Yazhouwan National Laboratory, Sanya, Hainan 572024, P.R. China
| | - Vijai Bhadauria
- Ministry of Agriculture and Rural Affairs Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, Beijing 100193, P.R. China
| | - Shiwei Wang
- Ministry of Agriculture and Rural Affairs Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, Beijing 100193, P.R. China
| | - Wenyu Cheng
- State Key Laboratory of Maize Bio-breeding/College of Plant Protection/Ministry of Agriculture and Rural Affairs Key Laboratory of Surveillance and Management for Plant Quarantine Pests, China Agricultural University, Beijing 100193, P.R. China
| | - Hui Liu
- State Key Laboratory of Maize Bio-breeding/College of Plant Protection/Ministry of Agriculture and Rural Affairs Key Laboratory of Surveillance and Management for Plant Quarantine Pests, China Agricultural University, Beijing 100193, P.R. China
| | - Xiaohong Yang
- State Key Laboratory of Plant Environmental Resilience, College of Agronomy and Biotechnology, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, P.R. China
| | - Mingliang Xu
- State Key Laboratory of Plant Environmental Resilience, College of Agronomy and Biotechnology, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, P.R. China
| | - You-Liang Peng
- Ministry of Agriculture and Rural Affairs Key Laboratory for Crop Pest Monitoring and Green Control, College of Plant Protection, China Agricultural University, Beijing 100193, P.R. China
| | - Wangsheng Zhu
- State Key Laboratory of Maize Bio-breeding/College of Plant Protection/Ministry of Agriculture and Rural Affairs Key Laboratory of Surveillance and Management for Plant Quarantine Pests, China Agricultural University, Beijing 100193, P.R. China.
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Tang S, Conte V, Zhang DJ, Žedaveinytė R, Lampe GD, Wiegand T, Tang LC, Wang M, Walker MWG, George JT, Berchowitz LE, Jovanovic M, Sternberg SH. De novo gene synthesis by an antiviral reverse transcriptase. Science 2024; 386:eadq0876. [PMID: 39116258 DOI: 10.1126/science.adq0876] [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: 04/25/2024] [Accepted: 07/17/2024] [Indexed: 08/10/2024]
Abstract
Defense-associated reverse transcriptase (DRT) systems perform DNA synthesis to protect bacteria against viral infection, but the identities and functions of their DNA products remain largely unknown. We show that DRT2 systems encode an unprecedented immune pathway that involves de novo gene synthesis through rolling circle reverse transcription of a noncoding RNA (ncRNA). Programmed template jumping on the ncRNA generates a concatemeric cDNA, which becomes double-stranded upon viral infection. This DNA product constitutes a protein-coding, nearly endless open reading frame (neo) gene whose expression leads to potent cell growth arrest, restricting the viral infection. Our work highlights an elegant expansion of genome coding potential through RNA-templated gene creation and challenges conventional paradigms of genetic information encoded along the one-dimensional axis of genomic DNA.
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Affiliation(s)
- Stephen Tang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Valentin Conte
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Dennis J Zhang
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Rimantė Žedaveinytė
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - George D Lampe
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Tanner Wiegand
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Lauren C Tang
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Megan Wang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Matt W G Walker
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Jerrin Thomas George
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Luke E Berchowitz
- Department of Genetics and Development, Columbia University, New York, NY, USA
- Taub Institute for Research on Alzheimer's and the Aging Brain, New York, NY, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Samuel H Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
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9
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Ramírez-Arenas PJ, Latisnere-Barragán H, García-Maldonado JQ, López-Cortés A. Highly diverse-Low abundance methanogenic communities in hypersaline microbial mats of Guerrero Negro B.C.S., assessed through microcosm experiments. PLoS One 2024; 19:e0303004. [PMID: 39365803 PMCID: PMC11451985 DOI: 10.1371/journal.pone.0303004] [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: 04/17/2024] [Accepted: 07/26/2024] [Indexed: 10/06/2024] Open
Abstract
Methanogenic communities of hypersaline microbial mats of Guerrero Negro, Baja California Sur, Mexico, have been recognized to be dominated by methylotrophic methanogens. However, recent studies of environmental samples have evidenced the presence of hydrogenotrophic and methyl-reducing methanogenic members, although at low relative abundances. Physical and geochemical conditions that stimulate the development of these groups in hypersaline environments, remains elusive. Thus, in this study the taxonomic diversity of methanogenic archaea of two sites of Exportadora de Sal S.A was assessed by mcrA gene high throughput sequencing from microcosm experiments with different substrates (both competitive and non-competitive). Results confirmed the dominance of the order Methanosarcinales in all treatments, but an increase in the abundance of Methanomassiliiccocales was also observed, mainly in the treatment without substrate addition. Moreover, incubations supplemented with hydrogen and carbon dioxide, as well as the mixture of hydrogen, carbon dioxide and trimethylamine, managed to stimulate the richness and abundance of other than Methanosarcinales methanogenic archaea. Several OTUs that were not assigned to known methanogens resulted phylogenetically distributed into at least nine orders. Environmental samples revealed a wide diversity of methanogenic archaea of low relative abundance that had not been previously reported for this environment, suggesting that the importance and diversity of methanogens in hypersaline ecosystems may have been overlooked. This work also provided insights into how different taxonomic groups responded to the evaluated incubation conditions.
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Affiliation(s)
| | | | - José Q. García-Maldonado
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Mérida, Yucatán, México
| | - Alejandro López-Cortés
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, México
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10
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Chu X, Wang L, Zhu Y, Feng Z, Guan Q, Song L, Luo Z. A unique cell division protein critical for the assembly of the bacterial divisome. eLife 2024; 12:RP87922. [PMID: 39361022 PMCID: PMC11449484 DOI: 10.7554/elife.87922] [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: 10/05/2024] Open
Abstract
Identification of unique essential bacterial genes is important for not only the understanding of their cell biology but also the development of new antimicrobials. Here, we report a previously unrecognized core component of the Acinetobacter baumannii divisome. Our results reveal that the protein, termed Aeg1 interacts with multiple cell division proteins, including FtsN, which is required for components of the divisome to localize to the midcell. We demonstrate that the FtsAE202K and FtsBE65A mutants effectively bypassed the need of Aeg1 by A. baumannii, as did the activation variants FtsWM254I and FtsWS274G. Our results suggest that Aeg1 is a cell division protein that arrives at the division site to initiate cell division by recruiting FtsN, which activates FtsQLB and FtsA to induce the septal peptidoglycan synthase FtsWI. The discovery of the new essential cell division protein has provided a new target for the development of antibacterial agents.
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Affiliation(s)
- Xiao Chu
- Department of Respiratory Medicine, Infectious Diseases and Pathogen Biology Center State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Lidong Wang
- Department of Respiratory Medicine, Infectious Diseases and Pathogen Biology Center State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Yiheng Zhu
- Department of Respiratory Medicine, Infectious Diseases and Pathogen Biology Center State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Zhengshan Feng
- Department of Respiratory Medicine, Infectious Diseases and Pathogen Biology Center State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Qingtian Guan
- Bioinformatics Laboratory, The First Hospital of Jilin University, Changchun, China
| | - Lei Song
- Department of Respiratory Medicine, Infectious Diseases and Pathogen Biology Center State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Zhaoqing Luo
- Department of Respiratory Medicine, Infectious Diseases and Pathogen Biology Center State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
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11
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Watanabe R, Zyla D, Parekh D, Hong C, Jones Y, Schendel SL, Wan W, Castillon G, Saphire EO. Intracellular Ebola virus nucleocapsid assembly revealed by in situ cryo-electron tomography. Cell 2024; 187:5587-5603.e19. [PMID: 39293445 PMCID: PMC11455616 DOI: 10.1016/j.cell.2024.08.044] [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: 04/09/2024] [Revised: 06/04/2024] [Accepted: 08/21/2024] [Indexed: 09/20/2024]
Abstract
Filoviruses, including the Ebola and Marburg viruses, cause hemorrhagic fevers with up to 90% lethality. The viral nucleocapsid is assembled by polymerization of the nucleoprotein (NP) along the viral genome, together with the viral proteins VP24 and VP35. We employed cryo-electron tomography of cells transfected with viral proteins and infected with model Ebola virus to illuminate assembly intermediates, as well as a 9 Å map of the complete intracellular assembly. This structure reveals a previously unresolved third and outer layer of NP complexed with VP35. The intrinsically disordered region, together with the C-terminal domain of this outer layer of NP, provides the constant width between intracellular nucleocapsid bundles and likely functions as a flexible tether to the viral matrix protein in the virion. A comparison of intracellular nucleocapsids with prior in-virion nucleocapsid structures reveals that the nucleocapsid further condenses vertically in the virion. The interfaces responsible for nucleocapsid assembly are highly conserved and offer targets for broadly effective antivirals.
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Affiliation(s)
- Reika Watanabe
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Dawid Zyla
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Diptiben Parekh
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Connor Hong
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Ying Jones
- Electron Microscopy Core, University of California, San Diego, La Jolla, CA 92037, USA
| | - Sharon L Schendel
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - William Wan
- Vanderbilt University Center for Structural Biology, Nashville, TN 37235, USA
| | - Guillaume Castillon
- Electron Microscopy Core, University of California, San Diego, La Jolla, CA 92037, USA
| | - Erica Ollmann Saphire
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
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12
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Rolo D, Sandoval-Ibáñez O, Thiele W, Schöttler MA, Gerlach I, Zoschke R, Schwartzmann J, Meyer EH, Bock R. CO-EXPRESSED WITH PSI ASSEMBLY1 (CEPA1) is a photosystem I assembly factor in Arabidopsis. THE PLANT CELL 2024; 36:4179-4211. [PMID: 38382089 PMCID: PMC11449006 DOI: 10.1093/plcell/koae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/12/2024] [Accepted: 01/24/2024] [Indexed: 02/23/2024]
Abstract
Photosystem I (PSI) forms a large macromolecular complex of ∼580 kDa that resides in the thylakoid membrane and mediates photosynthetic electron transfer. PSI is composed of 18 protein subunits and nearly 200 co-factors. The assembly of the complex in thylakoid membranes requires high spatial and temporal coordination, and is critically dependent on a sophisticated assembly machinery. Here, we report and characterize CO-EXPRESSED WITH PSI ASSEMBLY1 (CEPA1), a PSI assembly factor in Arabidopsis (Arabidopsis thaliana). The CEPA1 gene was identified bioinformatically as being co-expressed with known PSI assembly factors. Disruption of the CEPA1 gene leads to a pale phenotype and retarded plant development but does not entirely abolish photoautotrophy. Biophysical and biochemical analyses revealed that the phenotype is caused by a specific defect in PSI accumulation. We further show that CEPA1 acts at the post-translational level and co-localizes with PSI in nonappressed thylakoid membranes. In native gels, CEPA1 co-migrates with thylakoid protein complexes, including putative PSI assembly intermediates. Finally, protein-protein interaction assays suggest cooperation of CEPA1 with the PSI assembly factor PHOTOSYSTEM I ASSEMBLY3 (PSA3). Together, our data support an important but nonessential role of CEPA1 in PSI assembly.
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Affiliation(s)
- David Rolo
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Omar Sandoval-Ibáñez
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Wolfram Thiele
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Mark A Schöttler
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Ines Gerlach
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Reimo Zoschke
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Joram Schwartzmann
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Etienne H Meyer
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
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13
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Hamilton GE, Wadkovsky KN, Gladfelter AS. A single septin from a polyextremotolerant yeast recapitulates many canonical functions of septin hetero-oligomers. Mol Biol Cell 2024; 35:ar132. [PMID: 39196657 DOI: 10.1091/mbc.e24-05-0227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2024] Open
Abstract
Morphological complexity and plasticity are hallmarks of polyextremotolerant fungi. Septins are conserved cytoskeletal proteins and key contributors to cell polarity and morphogenesis. They sense membrane curvature, coordinate cell division, and influence diffusion at the plasma membrane. Four septin homologues are conserved from yeasts to humans, the systems in which septins have been most studied. But there is also a fifth family of opisthokont septins that remain biochemically mysterious. Members of this family, Group 5 septins, appear in the genomes of filamentous fungi, but are understudied due to their absence from ascomycete yeasts. Knufia petricola is an emerging model polyextremotolerant black fungus that can also serve as a model system for Group 5 septins. We have recombinantly expressed and biochemically characterized KpAspE, a Group 5 septin from K. petricola. This septin--by itself in vitro--recapitulates many functions of canonical septin hetero-octamers. KpAspE is an active GTPase that forms diverse homo-oligomers, binds shallow membrane curvatures, and interacts with the terminal subunit of canonical septin hetero-octamers. These findings raise the possibility that Group 5 septins govern the higher-order structures formed by canonical septins, which in K. petricola cells form extended filaments, and provide insight into how septin hetero-oligomers evolved from ancient homomers.
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Affiliation(s)
- Grace E Hamilton
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | | | - Amy S Gladfelter
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27708
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14
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Sun S, Wu P, Gao F, Yu X, Liu Y, Zheng C. Genome-wide identification and expression analysis of phytochrome-interacting factor genes during abiotic stress responses and secondary metabolism in the tea plant. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:108988. [PMID: 39094480 DOI: 10.1016/j.plaphy.2024.108988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 07/07/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024]
Abstract
Phytochrome-interacting factors (PIFs) are pivotal transcriptional regulators controlling photomorphogenesis, environmental responses, and development in plants. However, their specific roles in coordinating adaptation towards abiotic stress and metabolism remain underexplored in tea plants. Here, we identified seven PIF members from four distinct clades (PIF1, PIF3, PIF7, and PIF8). Promoter analysis implicated CsPIFs in integrating light, stress, hormone, and circadian signals. Most CsPIFs exhibited rapid increase in expression under shading, especially CsPIF7b/8a, which displayed significant changes in long-term shading condition. Under drought/salt stress, CsPIF3b emerged as a potential positive regulator. CsPIF3a was induced by low temperature and co-expressed with CsCBF1/3 and CsDREB2A cold response factors. Dual-luciferase assays confirmed that act as negative regulator of the CBF pathway. Expression profiling across 11 tea cultivars associated specific CsPIFs with chlorophyll biosynthesis and accumulation of anthocyanins, flavonols, and other metabolites. In summary, this study highlights the significance of CsPIFs as central coordinators in managing intricate transcriptional reactions to simultaneous abiotic stresses and metabolic adjustments in tea plants. This insight informs future strategies for enhancing this economically crucial crop through crop improvement initiatives.
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Affiliation(s)
- Shuai Sun
- College of Horticulture and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China; Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Peichen Wu
- Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Fuquan Gao
- Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Xiaomin Yu
- Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Ying Liu
- Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
| | - Chao Zheng
- Horticultural Plant Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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15
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Telizhenko V, Kosiol C, McGowen MR, Gol'din P. Relaxed selection in evolution of genes regulating limb development gives clue to variation in forelimb morphology of cetaceans and other mammals. Proc Biol Sci 2024; 291:20241106. [PMID: 39378996 DOI: 10.1098/rspb.2024.1106] [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: 05/13/2024] [Revised: 07/29/2024] [Accepted: 09/02/2024] [Indexed: 10/10/2024] Open
Abstract
Cetaceans have evolved unique limb structures, such as flippers, due to genetic changes during their transition to aquatic life. However, the full understanding of the genetic and evolutionary mechanisms behind these changes is still developing. By examining 25 limb-related protein-coding genes across various mammalian species, we compared genetic changes between aquatic mammals, like whales, and other mammals with unique limb structures such as bats, rodents and elephants. Our findings revealed significant modifications in limb-related genes, including variations in the Hox, GDF5 and Evx genes. Notably, a relaxed selection in several key genes was observed, suggesting a lifting of developmental constraints, which might have facilitated the emergence of morphological innovations in cetacean limb morphology. We also uncovered non-synonymous changes, insertions and deletions in these genes, particularly in the polyalanine tract of HOXD13, which are distinctive to cetaceans or convergent with other aquatic mammals. These genetic variations correlated with the diverse and specialized limb structures observed in cetaceans, indicating a complex interplay of relaxed selection and specific mutations in mammalian limb evolution.
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Affiliation(s)
| | - Carolin Kosiol
- University of St Andrews , St Andrews, Fife KY16 9TF, UK
| | - Michael R McGowen
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History , Washington, DC 20560, USA
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16
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Deep A, Liang Q, Enustun E, Pogliano J, Corbett KD. Architecture and activation mechanism of the bacterial PARIS defence system. Nature 2024; 634:432-439. [PMID: 39112702 DOI: 10.1038/s41586-024-07772-8] [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: 12/04/2023] [Accepted: 07/02/2024] [Indexed: 08/17/2024]
Abstract
Bacteria and their viruses (bacteriophages or phages) are engaged in an intense evolutionary arms race1-5. While the mechanisms of many bacterial antiphage defence systems are known1, how these systems avoid toxicity outside infection yet activate quickly after infection is less well understood. Here we show that the bacterial phage anti-restriction-induced system (PARIS) operates as a toxin-antitoxin system, in which the antitoxin AriA sequesters and inactivates the toxin AriB until triggered by the T7 phage counterdefence protein Ocr. Using cryo-electron microscopy, we show that AriA is related to SMC-family ATPases but assembles into a distinctive homohexameric complex through two oligomerization interfaces. In uninfected cells, the AriA hexamer binds to up to three monomers of AriB, maintaining them in an inactive state. After Ocr binding, the AriA hexamer undergoes a structural rearrangement, releasing AriB and allowing it to dimerize and activate. AriB is a toprim/OLD-family nuclease, the activation of which arrests cell growth and inhibits phage propagation by globally inhibiting protein translation through specific cleavage of a lysine tRNA. Collectively, our findings reveal the intricate molecular mechanisms of a bacterial defence system triggered by a phage counterdefence protein, and highlight how an SMC-family ATPase has been adapted as a bacterial infection sensor.
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Affiliation(s)
- Amar Deep
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Qishan Liang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Eray Enustun
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA
| | - Joe Pogliano
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA
| | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, USA.
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17
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Rahim F, Tao L, Khan K, Ali I, Zeb A, Khan I, Dil S, Abbas T, Hussain A, Zubair M, Zhang H, Hui M, Khan MA, Shah W, Shi Q. A homozygous ARMC3 splicing variant causes asthenozoospermia and flagellar disorganization in a consanguineous family. Clin Genet 2024; 106:437-447. [PMID: 39221575 DOI: 10.1111/cge.14575] [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: 03/07/2024] [Revised: 05/25/2024] [Accepted: 06/05/2024] [Indexed: 09/04/2024]
Abstract
Male infertility due to asthenozoospermia is quite frequent, but its etiology is poorly understood. We recruited two infertile brothers, born to first-cousin parents from Pakistan, displaying idiopathic asthenozoospermia with mild stuttering disorder but no ciliary-related symptoms. Whole-exome sequencing identified a splicing variant (c.916+1G>A) in ARMC3, recessively co-segregating with asthenozoospermia in the family. The ARMC3 protein is evolutionarily highly conserved and is mostly expressed in the brain and testicular tissue of human. The ARMC3 splicing mutation leads to the exclusion of exon 8, resulting in a predicted truncated protein (p.Glu245_Asp305delfs*16). Quantitative real-time PCR revealed a significant decrease at mRNA level for ARMC3 and Western blot analysis did not detect ARMC3 protein in the patient's sperm. Individuals homozygous for the ARMC3 splicing variant displayed reduced sperm motility with frequent morphological abnormalities of sperm flagella. Transmission electron microscopy of the affected individual IV: 2 revealed vacuolation in sperm mitochondria at the midpiece and disrupted flagellar ultrastructure in the principal and end piece. Altogether, our results indicate that this novel homozygous ARMC3 splicing mutation destabilizes sperm flagella and leads to asthenozoospermia in our patients, providing a novel marker for genetic counseling and diagnosis of male infertility.
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Affiliation(s)
- Fazal Rahim
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, China
| | - Liu Tao
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, China
| | - Khalid Khan
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, China
| | - Imtiaz Ali
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, China
| | - Aurang Zeb
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, China
| | - Ihsan Khan
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, China
| | - Sobia Dil
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, China
| | - Tanveer Abbas
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, China
| | - Ansar Hussain
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, China
| | - Muhammad Zubair
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, China
| | - Huan Zhang
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, China
| | - Ma Hui
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, China
| | - Muzammil Ahmad Khan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Wasim Shah
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, China
| | - Qinghua Shi
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, Institute of Health and Medicine, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, China
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18
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Feng R, Yang S, Zhao X, Sun B, Zhang S, Shen Q, Wan Q. Characterization of the Three DHFRs and K65P Variant: Enhanced Substrate Affinity and Molecular Dynamics Analysis. Protein J 2024; 43:935-948. [PMID: 39179691 DOI: 10.1007/s10930-024-10228-7] [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] [Accepted: 08/01/2024] [Indexed: 08/26/2024]
Abstract
Dihydrofolate reductase (DHFR) is ubiquitously present in all living organisms and plays a crucial role in the growth of the fungal pathogen R.solani. Sequence alignment confirmed the evolutionary conservation of the essential lid domain, with the amino acid 'P' within the PEKN lid domain appearing with a frequency of 89.5% in higher organisms and 11.8% in lower organisms. Consequently, a K65P variant was introduced into R.solani DHFR (rDHFR). Subsequent enzymatic kinetics assays were conducted for human DHFR (hDHFR), rDHFR, E. coli DHFR (eDHFR), and the K65P variant. hDHFR exhibited the highest kcat of 0.95 s-1, followed by rDHFR with 0.14 s-1, while eDHFR displayed the lowest kcat of 0.09 s-1. Remarkably, the K65P variant induced a significant reduction in Km, resulting in a 1.8-fold enhancement in catalytic efficiency (kcat/Km) relative to the wild type. Differential scanning fluorimetry and binding free energy calculations confirmed the enhanced substrate affinity for both folate and NADPH in the K65P variant. These results suggest that the K65P mutation enhances substrate affinity and catalytic efficiency in DHFR, highlighting the evolutionary and functional importance of the K65 residue.
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Affiliation(s)
- Ruirui Feng
- College of Science, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Shuanghao Yang
- College of Science, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Xingchu Zhao
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Bo Sun
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Shengkai Zhang
- Institute of Advanced Science Facilities, Shenzhen, 518107, People's Republic of China
| | - Qirong Shen
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Qun Wan
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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19
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Hoshino M, Cossard G, Haas FB, Kane EI, Kogame K, Jomori T, Wakimoto T, Glemin S, Coelho SM. Parallel loss of sexual reproduction in field populations of a brown alga sheds light on the mechanisms underlying the emergence of asexuality. Nat Ecol Evol 2024; 8:1916-1932. [PMID: 39152327 DOI: 10.1038/s41559-024-02490-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: 02/01/2024] [Accepted: 06/18/2024] [Indexed: 08/19/2024]
Abstract
Sexual reproduction is widespread, but asexual lineages have repeatedly arisen from sexual ancestors across a wide range of eukaryotic taxa. The molecular changes underpinning the switch to asexuality remain elusive, particularly in organisms with haploid sexual systems. Here we explore independent events of loss of sex in the brown alga Scytosiphon, examine the proximate and evolutionary mechanisms involved, and test the importance of sexual conflict on gene expression changes following loss of sex. We find that asexual females ('Amazons') lose ability to produce sex pheromone and, consequently, are incapable of attracting males, whereas they gain rapid parthenogenic development from large, unfertilized eggs. These phenotypic changes are accompanied by convergent changes in gene expression. Decay of female functions, rather than relaxation of sexual antagonism, may be a dominant force at play during the emergence of asexuality in haploid sexual systems. Moreover, we show that haploid purifying selection plays a key role in limiting the accumulation of deleterious alleles in Amazons, and we identify an autosomal locus associated with the Amazon phenotype. The sex chromosome, together with this autosomal locus, may underlie the switch to obligate asexuality in the Amazon populations.
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Affiliation(s)
- Masakazu Hoshino
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Research Center for Inland Seas, Kobe University, Rokkodai 1-1, Nadaku, Kobe, Japan
| | - Guillaume Cossard
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Fabian B Haas
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Emma I Kane
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Kazuhiro Kogame
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Takahiro Jomori
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | | | - Sylvain Glemin
- Laboratoire ECOBIO (Ecosystèmes, biodiversité, évolution), UMR 6553, CNRS, Université de Rennes, Rennes, France
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Susana M Coelho
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany.
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20
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Saha D, Pramanik A, Freville A, Siddiqui AA, Pal U, Banerjee C, Nag S, Debsharma S, Pramanik S, Mazumder S, Maiti NC, Datta S, van Ooij C, Bandyopadhyay U. Structure-function analysis of nucleotide housekeeping protein HAM1 from human malaria parasite Plasmodium falciparum. FEBS J 2024; 291:4349-4371. [PMID: 39003571 DOI: 10.1111/febs.17216] [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: 01/20/2024] [Revised: 03/29/2024] [Accepted: 06/20/2024] [Indexed: 07/15/2024]
Abstract
Non-canonical nucleotides, generated as oxidative metabolic by-products, significantly threaten the genome integrity of Plasmodium falciparum and thereby, their survival, owing to their mutagenic effects. PfHAM1, an evolutionarily conserved inosine/xanthosine triphosphate pyrophosphohydrolase, maintains nucleotide homeostasis in the malaria parasite by removing non-canonical nucleotides, although structure-function intricacies are hitherto poorly reported. Here, we report the X-ray crystal structure of PfHAM1, which revealed a homodimeric structure, additionally validated by size-exclusion chromatography-multi-angle light scattering analysis. The two monomeric units in the dimer were aligned in a parallel fashion, and critical residues associated with substrate and metal binding were identified, wherein a notable structural difference was observed in the β-sheet main frame compared to human inosine triphosphate pyrophosphatase. PfHAM1 exhibited Mg++-dependent pyrophosphohydrolase activity and the highest binding affinity to dITP compared to other non-canonical nucleotides as measured by isothermal titration calorimetry. Modifying the pfham1 genomic locus followed by live-cell imaging of expressed mNeonGreen-tagged PfHAM1 demonstrated its ubiquitous presence in the cytoplasm across erythrocytic stages with greater expression in trophozoites and schizonts. Interestingly, CRISPR-Cas9/DiCre recombinase-guided pfham1-null P. falciparum survived in culture under standard growth conditions, indicating its assistive role in non-canonical nucleotide clearance during intra-erythrocytic stages. This is the first comprehensive structural and functional report of PfHAM1, an atypical nucleotide-cleansing enzyme in P. falciparum.
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Affiliation(s)
- Debanjan Saha
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Atanu Pramanik
- Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Aline Freville
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, UK
| | - Asim Azhar Siddiqui
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Uttam Pal
- Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Chinmoy Banerjee
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Shiladitya Nag
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Subhashis Debsharma
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Saikat Pramanik
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Somnath Mazumder
- Department of Zoology, Raja Peary Mohan College, Uttarpara, India
| | - Nakul C Maiti
- Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Saumen Datta
- Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Christiaan van Ooij
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, UK
| | - Uday Bandyopadhyay
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Department of Biological Sciences, Bose Institute, Kolkata, India
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21
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Ceppi I, Dello Stritto MR, Mütze M, Braunshier S, Mengoli V, Reginato G, Võ HMP, Jimeno S, Acharya A, Roy M, Sanchez A, Halder S, Howard SM, Guérois R, Huertas P, Noordermeer SM, Seidel R, Cejka P. Mechanism of BRCA1-BARD1 function in DNA end resection and DNA protection. Nature 2024; 634:492-500. [PMID: 39261728 DOI: 10.1038/s41586-024-07909-9] [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: 11/20/2023] [Accepted: 08/05/2024] [Indexed: 09/13/2024]
Abstract
DNA double-strand break (DSB) repair by homologous recombination is initiated by DNA end resection, a process involving the controlled degradation of the 5'-terminated strands at DSB sites1,2. The breast cancer suppressor BRCA1-BARD1 not only promotes resection and homologous recombination, but it also protects DNA upon replication stress1,3-9. BRCA1-BARD1 counteracts the anti-resection and pro-non-homologous end-joining factor 53BP1, but whether it functions in resection directly has been unclear10-16. Using purified recombinant proteins, we show here that BRCA1-BARD1 directly promotes long-range DNA end resection pathways catalysed by the EXO1 or DNA2 nucleases. In the DNA2-dependent pathway, BRCA1-BARD1 stimulates DNA unwinding by the Werner or Bloom helicase. Together with MRE11-RAD50-NBS1 and phosphorylated CtIP, BRCA1-BARD1 forms the BRCA1-C complex17,18, which stimulates resection synergistically to an even greater extent. A mutation in phosphorylated CtIP (S327A), which disrupts its binding to the BRCT repeats of BRCA1 and hence the integrity of the BRCA1-C complex19-21, inhibits resection, showing that BRCA1-C is a functionally integrated ensemble. Whereas BRCA1-BARD1 stimulates resection in DSB repair, it paradoxically also protects replication forks from unscheduled degradation upon stress, which involves a homologous recombination-independent function of the recombinase RAD51 (refs. 4-6,8). We show that in the presence of RAD51, BRCA1-BARD1 instead inhibits DNA degradation. On the basis of our data, the presence and local concentration of RAD51 might determine the balance between the pronuclease and the DNA protection functions of BRCA1-BARD1 in various physiological contexts.
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Affiliation(s)
- Ilaria Ceppi
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Maria Rosaria Dello Stritto
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Martin Mütze
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | - Stefan Braunshier
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Valentina Mengoli
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Giordano Reginato
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Hồ Mỹ Phúc Võ
- Leiden University Medical Center, Leiden, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Sonia Jimeno
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
| | - Ananya Acharya
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Megha Roy
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Aurore Sanchez
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland
- Institut Curie, Paris Sciences and Lettres University, Sorbonne Université, CNRS UMR 3244, Dynamics of Genetic Information, Paris, France
| | - Swagata Halder
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland
- Biological Systems Engineering, Plaksha University, Mohali, India
| | - Sean Michael Howard
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland
- Department of Mechanical and Biomedical Engineering, Boise State University, Boise, ID, USA
| | - Raphaël Guérois
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Pablo Huertas
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
| | - Sylvie M Noordermeer
- Leiden University Medical Center, Leiden, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, Switzerland.
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22
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Adıgüzel AO, Şen F, Könen-Adıgüzel S, Kıdeyş AE, Karahan A, Doruk T, Tunçer M. Identification of Cutinolytic Esterase from Microplastic-Associated Microbiota Using Functional Metagenomics and Its Plastic Degrading Potential. Mol Biotechnol 2024; 66:2995-3012. [PMID: 37815749 DOI: 10.1007/s12033-023-00916-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 09/19/2023] [Indexed: 10/11/2023]
Abstract
Plastic pollution has threatened biodiversity and human health by shrinking habitats, reducing food quality, and limiting the activities of organisms. Therefore, global interest in discovering novel enzymes capable of degrading plastics has increased considerably. Within this context, the functional metagenomic approach, which allows for unlocking the functional potential of uncultivable microbial biodiversity, was used to discover a plastic-degrading enzyme. First, metagenomic libraries derived from microplastic-associated microbiota were screened for esterases capable of degrading both tributyrin and polycaprolactone. Clone KAD01 produced esterase highly active against p-nitrophenyl esters (C2-C16). The gene corresponding to the enzyme activity showed moderate identity (≤ 55.94%) to any known esterases/cutinases. The gene was extracellularly expressed with a 6× histidine tag in E. coli BL21(DE3), extracellularly. Titer of the enzyme (CEstKAD01) was raised from 21.32 to 35.17 U/mL by the statistical optimization of expression conditions and media components. CEstKAD01 was most active at pH 7.0 and 30 °C. It was noteworthy stable over a wide pH (6.0-10.0) and temperature (20-50 °C). The enzyme was active and stable in elevated NaCl concentrations up to 12% (w/v). Pre-incubation of CEstKAD01 with Mg2+, Mn2+, and Ca2+ increased the enzyme activity. CEstKAD01 displayed an excellent tolerance against various chemicals and solvents. It was determined that 1 mg of the enzyme caused the release of 5.39 ± 0.18 mM fatty acids from 1 g apple cutin in 120 min. Km and Vmax values of CEstKAD01 against p-nitrophenyl butyrate were calculated to be 1.48 mM and 20.37 µmol/min, respectively. The enzyme caused 6.94 ± 0.55, 8.71 ± 0.56, 7.47 ± 0.47, and 9.22 ± 0.18% of weight loss in polystyrene, high-density polyethylene, low-density polyethylene, and polyvinyl chloride after 30-day incubation. The scanning electron microscopy (SEM) analysis indicated the formation of holes and pits on the plastic surfaces supporting the degradation. In addition, the change in chemical structure in plastics treated with the enzyme was determined by Fourier Transform Infrared Spectroscopy (FTIR) analysis. Finally, the degradation products were found to have no genotoxic potential. To our knowledge, no cutinolytic esterase with the potential to degrade polystyrene (PS), high-density polyethylene (HDPE), low-density polyethylene (LDPE), and polyvinyl chloride (PVC) has been identified from metagenomes derived from microplastic-associated microbiota.
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Affiliation(s)
- Ali Osman Adıgüzel
- Department of Molecular Biology and Genetics, Faculty of Science, Ondokuz Mayıs University, Samsun, 55000, Turkey.
| | - Fatma Şen
- Department of Molecular Biology and Genetics, Faculty of Science, Ondokuz Mayıs University, Samsun, 55000, Turkey
| | | | - Ahmet Erkan Kıdeyş
- Department of Marine Biology and Fisheries, Institute of Marine Sciences, Middle East Technical University, Mersin, Turkey
| | - Arzu Karahan
- Department of Marine Biology and Fisheries, Institute of Marine Sciences, Middle East Technical University, Mersin, Turkey
| | - Tuğrul Doruk
- Department of Molecular Biology and Genetics, Faculty of Science, Ondokuz Mayıs University, Samsun, 55000, Turkey
| | - Münir Tunçer
- Department of Molecular Biology and Genetics, Faculty of Science, Ondokuz Mayıs University, Samsun, 55000, Turkey
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23
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Fabri LM, Moraes CM, Garçon DP, McNamara JC, Faria SC, Leone FA. Primary amino acid sequences of decapod (Na +, K +)-ATPase provide evolutionary insights into osmoregulatory mechanisms. Comp Biochem Physiol A Mol Integr Physiol 2024; 296:111696. [PMID: 39004301 DOI: 10.1016/j.cbpa.2024.111696] [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: 04/29/2024] [Revised: 07/08/2024] [Accepted: 07/08/2024] [Indexed: 07/16/2024]
Abstract
Decapod Crustacea exhibit a marine origin, but many taxa have occupied environments ranging from brackish to fresh water and terrestrial habitats, overcoming their inherent osmotic challenges. Osmotic and ionic regulation is achieved by the gill epithelia, driven by two active ATP-hydrolyzing ion transporters, the basal (Na+, K+)-ATPase and the apical V(H+)-ATPase. The kinetic characteristic of gill (Na+, K+)-ATPase and the mRNA expression of its α subunit have been widely studied in various decapod species under different salinity challenges. However, the evolution of the primary structure has not been explored, especially considering the functional modifications associated with decapod phylogeny. Here, we proposed a model for the topology of the decapod α subunit, identifying the sites and motifs involved in its function and regulation, as well as the patterns of its evolution assuming a decapod phylogeny. We also examined both the amino acid substitutions and their functional implications within the context of biochemical and physiological adaptation. The α-subunit of decapod crustaceans shows greater conservation (∼94% identity) compared to the β-subunit (∼40%). While the binding sites for ATP and modulators are conserved in the decapod enzyme, the residues involved in the α-β interaction are only partially conserved. In the phylogenetic context of the complete sequence of (Na+, K+)-ATPase α-subunit, most substitutions appear to be characteristic of the entire group, with specific changes for different subgroups, especially among brachyuran crabs. Interestingly, there was no consistent separation of α-subunit partial sequences related to habitat, suggesting that the convergent evolution for freshwater or terrestrial modes of life is not correlated with similar changes in the enzyme's primary amino acid sequence.
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Affiliation(s)
- Leonardo M Fabri
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Cintya M Moraes
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | - John C McNamara
- Departamento de Biologia Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil; Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil
| | - Samuel C Faria
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil
| | - Francisco A Leone
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil.
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24
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Feng W, Wang Z, Wang X, Chen S, Chen X, Chen C, Deng J, Zhuo X, Wang J. Phenotypic and genotypic characteristics of children with PCDH19 clustering epilepsy in China. Seizure 2024; 121:95-104. [PMID: 39146709 DOI: 10.1016/j.seizure.2024.07.023] [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: 04/07/2024] [Revised: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 08/17/2024] Open
Abstract
PURPOSE PCDH19 gene variants, termed PCDH19 clustering epilepsy, represent a distinct etiology of epilepsy. This study aimed to elucidate the clinical manifestations and explore the genotypes and phenotypes of children affected by PCDH19 clustering epilepsy. METHODS This retrospective study included medical history, magnetic resonance imaging, video-electroencephalography, and genetic analysis of patients diagnosed with PCDH19 Clustering Epilepsy at the Neurology Department of Beijing Children's Hospital from 2015 to 2023. Chi-square tests and logistic regression analyses were conducted to study the factors associated with developmental delay in patients. RESULTS The age at seizure onset ranged from 5 to 61 months among all 30 patients (median 14 months; IQR 9.25-22.5 months). Among the 30 patients, 29 were female and 1 was male. Clusters of seizures and fever-triggered seizures were observed, with the most prevalent seizure types being focal to bilateral tonic-clonic seizures (FBTCS). Seizures were successfully controlled in 15 patients. Unfortunately, one patient experienced a sudden unexpected death in epilepsy (SUDEP). Additionally, 14 patients had hereditary mutations, 14 had de novo mutations, 1 had both hereditary and de novo mutations, and 1 male patient had a mosaic component mutation of 0.64 due to a somatic mutation. Developmental delays were identified in 17 patients (56.7 %), and 6 patients (20 %) were diagnosed with autism spectrum disorder (ASD). Among the 17 patients, 9 experienced developmental delays before the onset of epilepsy, while 8 were initially normal but later developed developmental delays during disease progression. Statistical analysis revealed that the presence of drug-resistant epilepsy was an independent risk factor for the occurrence of developmental delays (P = 0.020, OR = 9.758, 95 % CI (1.440-66.111)). CONCLUSION In this study, 13 new potential rare pathogenic variations in PCDH19 clustering epilepsy were identified. The clinical features observed in patients are consistent with known phenotypic features, and we found that patients with drug-resistant epilepsy are more likely to have developmental delays. The severity of the phenotype in patients with PCDH19 variants ranged from drug-responsive seizures to refractory epilepsy.
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Affiliation(s)
- Weixing Feng
- Neurology Department, National Center for Children's Health China, Beijing Children Hospital affiliated to Capital Medical University, Beijing, 100045, China.
| | - Zihan Wang
- Department of Medical Genetics and Developmental Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 10069, China
| | - Xiaohui Wang
- Neurology Department, National Center for Children's Health China, Beijing Children Hospital affiliated to Capital Medical University, Beijing, 100045, China
| | - Shuhua Chen
- Neurology Department, National Center for Children's Health China, Beijing Children Hospital affiliated to Capital Medical University, Beijing, 100045, China
| | - Xiaoyi Chen
- Department of Neurology, Zhengzhou University Affiliated Children's Hospital (Zhengzhou Children's Hospital), Zhengzhou, 450018, China
| | - Chunhong Chen
- Neurology Department, National Center for Children's Health China, Beijing Children Hospital affiliated to Capital Medical University, Beijing, 100045, China
| | - Jie Deng
- Neurology Department, National Center for Children's Health China, Beijing Children Hospital affiliated to Capital Medical University, Beijing, 100045, China
| | - Xiuwei Zhuo
- Neurology Department, National Center for Children's Health China, Beijing Children Hospital affiliated to Capital Medical University, Beijing, 100045, China
| | - Jing Wang
- Department of Medical Genetics and Developmental Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 10069, China.
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25
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Williams FN, Travis KL, Haver HN, Umano AD, Guerra-Hernandez Y, Scaglione KM. Acute stress and multicellular development alter the solubility of the Dictyostelium Sup35 ortholog ERF3. Microbiol Spectr 2024:e0160724. [PMID: 39345220 DOI: 10.1128/spectrum.01607-24] [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: 08/05/2024] [Accepted: 08/26/2024] [Indexed: 10/01/2024] Open
Abstract
Among sequenced organisms, the genome of Dictyostelium discoideum is unique in that it encodes for a massive amount of repeat-rich sequences in the coding region of genes. This results in the Dictyostelium proteome encoding for thousands of repeat-rich proteins, with nearly 24% of the Dictyostelium proteome encoding Q/N-rich regions that are predicted to be prion like in nature. To begin investigating the role of prion-like proteins in Dictyostelium, we decided to investigate ERF3, the Dictyostelium ortholog of the well-characterized yeast prion protein Sup35. ERF3 lacks the Q/N-rich region required for prion formation in yeast, raising the question of whether this protein aggregates and has prion-like properties in Dictyostelium. Here, we found that ERF3 formed aggregates in response to acute cellular stress. However, unlike bona fide prions, we were unable to detect transmission of aggregates to progeny. We further found that aggregation of this protein is driven by the ordered C-terminal domain independently of the disordered N-terminal domain. Finally, we also observed aggregation of ERF3 under conditions that induce multicellular development, suggesting that this phenomenon may play a role in Dictyostelium development. Together, these findings suggest a role for regulated protein aggregation in Dictyostelium cells under stress and during development.IMPORTANCEPrion-like proteins have both beneficial and deleterious effects on cellular health, and many organisms have evolved distinct mechanisms to regulate the behaviors of these proteins. The social amoeba Dictyostelium discoideum contains the highest proportion of proteins predicted to be prion like and has mechanisms to suppress their aggregation. However, the potential roles and regulation of these proteins remain largely unknown. Here, we demonstrate that aggregation of the Dictyostelium translation termination factor ERF3 is induced by both acute cellular stress and by multicellular development. These findings imply that protein aggregation may have a regulated and functional role in the Dictyostelium stress response and during multicellular development.
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Affiliation(s)
- Felicia N Williams
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Kanesha L Travis
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Holly N Haver
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Anna D Umano
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Yaneli Guerra-Hernandez
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - K Matthew Scaglione
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
- Center for Neurodegeneration and Neurotherapeutics, Duke University, Durham, North Carolina, USA
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26
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Gent V, Lu YJ, Lukhele S, Dhar N, Dangor Z, Hosken N, Malley R, Madhi SA, Kwatra G. Surface protein distribution in Group B Streptococcus isolates from South Africa and identifying vaccine targets through in silico analysis. Sci Rep 2024; 14:22665. [PMID: 39349584 PMCID: PMC11442663 DOI: 10.1038/s41598-024-73175-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 09/16/2024] [Indexed: 10/04/2024] Open
Abstract
Group B Streptococcus (GBS) is a major cause of pneumonia, sepsis, and meningitis in infants younger than 3 months of age. Furthermore, GBS infection in pregnant women is associated with stillbirths and pre-term delivery. It also causes disease in immunocompromised adults and the elderly, but the highest incidence of the disease occurs in neonates and young infants. At this time, there are no licensed vaccines against GBS. Complete GBS genome sequencing has helped identify genetically conserved and immunogenic proteins, which could serve as vaccine immunogens. In this study, in silico reverse vaccinology method were used to evaluate the prevalence and conservation of GBS proteins in invasive and colonizing isolates from South African infants and women, respectively. Furthermore, this study aimed to predict potential GBS vaccine targets by evaluating metrics such as antigenicity, physico-chemical properties, subcellular localization, secondary and tertiary structures, and epitope prediction and conservation. A total of 648 invasive and 603 colonizing GBS isolate sequences were screened against a panel of 89 candidate GBS proteins. Ten of the 89 proteins were highly genetically conserved in invasive and colonizing GBS isolates, nine of which were computationally inferred proteins (gbs2106, SAN_1577, SAN_0356, SAN_1808, SAN_1685, SAN_0413, SAN_0990, SAN_1040, SAN_0226) and one was the surface Immunogenic Protein (SIP). Additionally, the nine proteins were predicted to be more antigenic than the SIP protein (antigenicity score of > 0.6498), highlighting their potential as GBS vaccine antigen targets.
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Affiliation(s)
- Vicky Gent
- South African Medical Research Council: Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ying-Jie Lu
- Division of Infectious Diseases, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sindiswa Lukhele
- South African Medical Research Council: Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nisha Dhar
- South African Medical Research Council: Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ziyaad Dangor
- South African Medical Research Council: Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nancy Hosken
- Center for Vaccine Innovation and Access, PATH, Seattle, WA, USA
| | - Richard Malley
- Division of Infectious Diseases, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Shabir A Madhi
- South African Medical Research Council: Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Wits Infectious Diseases and Oncology Research Institute, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gaurav Kwatra
- South African Medical Research Council: Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Department of Clinical Microbiology, Christian Medical College, Vellore, India.
- Division of Infectious Diseases, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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Dunce JM, Davies OR. BRCA2 stabilises RAD51 and DMC1 nucleoprotein filaments through a conserved interaction mode. Nat Commun 2024; 15:8292. [PMID: 39333100 PMCID: PMC11436757 DOI: 10.1038/s41467-024-52699-3] [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: 11/20/2023] [Accepted: 09/18/2024] [Indexed: 09/29/2024] Open
Abstract
BRCA2 is essential for DNA repair by homologous recombination in mitosis and meiosis. It interacts with recombinases RAD51 and DMC1 to facilitate the formation of nucleoprotein filaments on resected DNA ends that catalyse recombination-mediated repair. BRCA2's BRC repeats bind and disrupt RAD51 and DMC1 filaments, whereas its PhePP motifs bind recombinases and stabilise their nucleoprotein filaments. However, the mechanism of filament stabilisation has hitherto remained unknown. Here, we report the crystal structure of a BRCA2-DMC1 complex, revealing how core interaction sites of PhePP motifs bind to recombinases. The interaction mode is conserved for RAD51 and DMC1, which selectively bind to BRCA2's two distinct PhePP motifs via subtly divergent binding pockets. PhePP motif sequences surrounding their core interaction sites protect nucleoprotein filaments from BRC-mediated disruption. Hence, we report the structural basis of how BRCA2's PhePP motifs stabilise RAD51 and DMC1 nucleoprotein filaments for their essential roles in mitotic and meiotic recombination.
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Affiliation(s)
- James M Dunce
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Owen R Davies
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK.
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28
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Novales NA, Feustel KJ, He KL, Chanfreau GF, Clarke CF. Nonfunctional coq10 mutants maintain the ERMES complex and reveal true phenotypes associated with the loss of the coenzyme Q chaperone protein Coq10. J Biol Chem 2024:107820. [PMID: 39343004 DOI: 10.1016/j.jbc.2024.107820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 09/11/2024] [Accepted: 09/24/2024] [Indexed: 10/01/2024] Open
Abstract
Coenzyme Q (CoQ) is a redox-active lipid molecule that acts as an electron carrier in the mitochondrial electron transport chain. In Saccharomyces cerevisiae, CoQ is synthesized in the mitochondrial matrix by a multi-subunit protein-lipid complex termed the CoQ synthome, the spatial positioning of which is coordinated by the Endoplasmic Reticulum-Mitochondria Encounter Structure (ERMES). The MDM12 gene encoding the cytosolic subunit of ERMES, is co-expressed with COQ10, which encodes the putative CoQ chaperone Coq10, via a shared bidirectional promoter. Deletion of COQ10 results in respiratory deficiency, impaired CoQ biosynthesis, and reduced spatial coordination between ERMES and the CoQ Synthome. While Coq10 protein content is maintained upon deletion of MDM12, we show that deletion of COQ10 by replacement with a HIS3 marker results in diminished Mdm12 protein content. Since deletion of individual ERMES subunits prevents ERMES formation, we asked whether some or all of the phenotypes associated with COQ10 deletion result from ERMES dysfunction. To identify the phenotypes resulting solely due to the loss of Coq10, we constructed strains expressing a functionally impaired (coq10-L96S) or truncated (coq10-R147*) Coq10 isoform using CRISPR-Cas9. We show that both coq10 mutants preserve Mdm12 protein content and exhibit impaired respiratory capacity like the coq10Δ mutant, indicating that Coq10's function is vital for respiration regardless of ERMES integrity. Moreover, the maintenance of CoQ synthome stability and efficient CoQ biosynthesis observed for the coq10-R147* mutant suggests these deleterious phenotypes in the coq10Δ mutant result from ERMES disruption. Overall, this study clarifies the role of Coq10 in modulating CoQ biosynthesis.
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Affiliation(s)
- Noelle Alexa Novales
- Department of Chemistry & Biochemistry, Molecular Biology Institute, UCLA, Los Angeles, California 90095-1569
| | - Kelsey J Feustel
- Department of Chemistry & Biochemistry, Molecular Biology Institute, UCLA, Los Angeles, California 90095-1569
| | - Kevin L He
- Department of Chemistry & Biochemistry, Molecular Biology Institute, UCLA, Los Angeles, California 90095-1569
| | - Guillaume F Chanfreau
- Department of Chemistry & Biochemistry, Molecular Biology Institute, UCLA, Los Angeles, California 90095-1569
| | - Catherine F Clarke
- Department of Chemistry & Biochemistry, Molecular Biology Institute, UCLA, Los Angeles, California 90095-1569.
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29
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Iacovelli R, He S, Sokolova N, Lokhorst I, Borg M, Fodran P, Haslinger K. Discovery and Heterologous Expression of Functional 4- O-Dimethylallyl-l-tyrosine Synthases from Lichen-Forming Fungi. JOURNAL OF NATURAL PRODUCTS 2024; 87:2243-2254. [PMID: 39255066 PMCID: PMC11443524 DOI: 10.1021/acs.jnatprod.4c00619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 08/26/2024] [Accepted: 08/29/2024] [Indexed: 09/12/2024]
Abstract
Fungal aromatic prenyltransferases are a family of biosynthetic enzymes that catalyze the prenylation of a range of aromatic substrates during the biosynthesis of bioactive indole alkaloids, diketopiperazines, and meroterpenoids. Their broad substrate scope and soluble nature make these enzymes particularly adept for applications in biocatalysis; for example, the enzymatic derivatization of aromatic drugs improves their bioactivity. Here, we investigated four putative aromatic prenyltransferases from lichen-forming fungi, an underexplored group of organisms that produce more than 1,000 unique metabolites. We successfully expressed two enzymes, annotated as dimethylallyltryptophan synthases, from two lichen species in the heterologous host A. oryzae. Based on their in vivo activity, we hypothesize that these enzymes are in fact 4-O-dimethylallyl-l-tyrosine synthases. Our extensive bioinformatic analysis further confirmed that these and related lichen aromatic prenyltransferases are likely not active on indoles but rather on aromatic polyketides and phenylpropanoids, major metabolites in lichens. Overall, our work provides new insights into fungal aromatic prenyltransferases at the family level and enables future efforts aimed at identifying new candidates for biocatalytic transformations of aromatic compounds.
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Affiliation(s)
| | | | | | - Iris Lokhorst
- Department of Chemical and
Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Maikel Borg
- Department of Chemical and
Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Peter Fodran
- Department of Chemical and
Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Kristina Haslinger
- Department of Chemical and
Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
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30
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Rack JGM, Voorneveld J, Longarini EJ, Wijngaarden S, Zhu K, Peters A, Jhing Sia J, Prokhorova E, Ahel D, Matić I, Filippov DV, Ahel I. Reversal of tyrosine-linked ADP-ribosylation by ARH3 and PARG. J Biol Chem 2024:107838. [PMID: 39342999 DOI: 10.1016/j.jbc.2024.107838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 09/16/2024] [Accepted: 09/19/2024] [Indexed: 10/01/2024] Open
Abstract
ADP-ribosylation is an ancient posttranslational modification with exceptional versatility in terms of breadth of modification targets including at least seven different amino acid side chains, various moieties on nucleic acids and a variety of small chemical compounds. The spatiotemporal signalling dynamic of the different modification variations is tightly regulated and depends on the writers, erases, and readers of each type. Amongst these, tyrosine ADP-ribosylation (Tyr-ADPr) has been consistently detected as a novel modification type, but systematic analysis of its potential physiological role, modification establishment and reversal are still lacking. Here we present a reanalysis of recent ADP-ribosylome data and show that Tyr-ADPr sites are conserved and enriched amongst ribosome biogenesis and mRNA processing proteins and that these sites are affected by the status of ARH3 ADP-ribose hydrolase. To facilitate the study of Tyr-ADPr, we establish methodologies for the synthesis of well-defined Tyr-ADPr peptides and with these could show that Tyr-ADPr is reversed both by ARH3 and PARG enzymes. Together, our work lays the foundation for the future exploration of the Tyr-ADPr.
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Affiliation(s)
| | - Jim Voorneveld
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Edoardo José Longarini
- Research Group of Proteomics and ADP-ribosylation Signalling, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Sven Wijngaarden
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Alessandra Peters
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Jia Jhing Sia
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Evgeniia Prokhorova
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Dragana Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Ivan Matić
- Research Group of Proteomics and ADP-ribosylation Signalling, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany; Cologne Excellence Cluster for Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Dmitri V Filippov
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
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31
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Green AL, De Bellis D, Cowell E, Lenchine RV, Penn T, Kris LP, McEvoy-May J, Bihari S, Dixon DL, Carr JM. The Y498T499-SARS-CoV-2 spike (S) protein interacts poorly with rat ACE2 and does not affect the rat lung. Access Microbiol 2024; 6:000839.v3. [PMID: 39346684 PMCID: PMC11432600 DOI: 10.1099/acmi.0.000839.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 09/05/2024] [Indexed: 10/01/2024] Open
Abstract
The rat is a useful laboratory model for respiratory diseases. SARS-CoV-2 proteins, such as the spike (S) protein, can induce inflammation. This study has investigated the ability of the Q498Y, P499T (QP-YT) amino acid change, described in the S-protein of the mouse-adapted laboratory SARS-CoV-2 MA strain, to interact with rat angiotensin converting enzyme-2 (ACE2) and stimulate responses in rat lungs. A real-time S-ACE2 quantitative fusion assay shows that ancestral and L452R S-proteins fuse with human but not rat ACE2 expressed on HEK293 (human embryonic kidney-293) cells. The QP-YT S-protein retains the ability to fuse with human ACE2 and increases the binding to rat ACE2. Although lower lung of the rat contains both ACE2 and TMPRSS2 (transmembrane serine protease 2) target cells, intratracheal delivery of ancestral or QP-YT S-protein pseudotyped lentivirus did not induce measurable respiratory changes, inflammatory infiltration or innate mRNA responses. Isolation of primary cells from rat alveoli demonstrated the presence of cells expressing ACE2 and TMPRSS2. Infection of these cells, however, with ancestral or QP-YT S-protein pseudotyped lentivirus was not observed, and the QP-YT S-protein pseudotyped lentivirus poorly infected HEK293 cells expressing rat ACE2. Analysis of the amino acid changes across the S-ACE2 interface highlights not only the Y498 interaction with H353 as a likely facilitator of binding to rat ACE2 but also other amino acids that could improve this interaction. Thus, rat lungs contain cells expressing receptors for SARS-CoV-2, and the QP-YT S-protein variant can bind to rat ACE2, but this does not result in infection or stimulate responses in the lung. Further, amino acid changes in S-protein may enhance this interaction to improve the utility of the rat model for defining the role of the S-protein in driving lung inflammation.
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Affiliation(s)
- Amy L Green
- College of Medicine and Public Health, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
| | - Dylan De Bellis
- College of Medicine and Public Health, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Evangeline Cowell
- College of Medicine and Public Health, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
| | - Roman V Lenchine
- College of Medicine and Public Health, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
| | - Timothy Penn
- College of Medicine and Public Health, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
| | - Luke P Kris
- College of Medicine and Public Health, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
| | - James McEvoy-May
- College of Medicine and Public Health, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Shailesh Bihari
- College of Medicine and Public Health, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Dani-Louise Dixon
- College of Medicine and Public Health, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Jillian M Carr
- College of Medicine and Public Health, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
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32
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Bellutti L, Macaisne N, El Mossadeq L, Ganeswaran T, Canman JC, Dumont J. Regulation of outer kinetochore assembly during meiosis I and II by CENP-A and KNL-2/M18BP1 in C. elegans oocytes. Curr Biol 2024:S0960-9822(24)01215-6. [PMID: 39353426 DOI: 10.1016/j.cub.2024.09.004] [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: 03/05/2024] [Revised: 07/24/2024] [Accepted: 09/02/2024] [Indexed: 10/04/2024]
Abstract
During cell division, chromosomes build kinetochores that attach to spindle microtubules. Kinetochores usually form at the centromeres, which contain CENP-A nucleosomes. The outer kinetochore, which is the core attachment site for microtubules, is composed of the KMN network (Knl1c, Mis12c, and Ndc80c complexes) and is recruited downstream of CENP-A and its partner CENP-C. In C. elegans oocytes, kinetochores have been suggested to form independently of CENP-A nucleosomes. Yet kinetochore formation requires CENP-C, which acts in parallel to the nucleoporin MEL-28ELYS. Here, we used a combination of RNAi and Degron-based depletion of CENP-A (or downstream CENP-C) to demonstrate that both proteins are in fact responsible for a portion of outer kinetochore assembly during meiosis I and are essential for accurate chromosome segregation. The remaining part requires the coordinated action of KNL-2 (ortholog of human M18BP1) and of the nucleoporin MEL-28ELYS. Accordingly, co-depletion of CENP-A (or CENP-C) and KNL-2M18BP1 (or MEL-28ELYS) prevented outer kinetochore assembly in oocytes during meiosis I. We further found that KNL-2M18BP1 and MEL-28ELYS are interdependent for kinetochore localization. Using engineered mutants, we demonstrated that KNL-2M18BP1 recruits MEL-28ELYS at meiotic kinetochores through a specific N-terminal domain, independently of its canonical CENP-A loading factor activity. Finally, we found that meiosis II outer kinetochore assembly was solely dependent on the canonical CENP-A/CENP-C pathway. Thus, like in most cells, outer kinetochore assembly in C. elegans oocytes depends on centromeric chromatin. However, during meiosis I, an additional KNL-2M18BP1 and MEL-28ELYS pathway acts in a non-redundant manner and in parallel to canonical centromeric chromatin.
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Affiliation(s)
- Laura Bellutti
- Université Paris Cité, CNRS, Institut Jacques Monod, 75013 Paris, France
| | - Nicolas Macaisne
- Université Paris Cité, CNRS, Institut Jacques Monod, 75013 Paris, France
| | - Layla El Mossadeq
- Université Paris Cité, CNRS, Institut Jacques Monod, 75013 Paris, France
| | | | - Julie C Canman
- Columbia University, Irving Medical Center, Department of Pathology and Cell Biology, New York, NY 10032, USA
| | - Julien Dumont
- Université Paris Cité, CNRS, Institut Jacques Monod, 75013 Paris, France.
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Zhang C, He L, Ding B, Yang H. Identification and functional characterization of the chitinase and chitinase-like gene family in Myzus persicae (Sulzer) during molting. PEST MANAGEMENT SCIENCE 2024. [PMID: 39319496 DOI: 10.1002/ps.8436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 09/06/2024] [Accepted: 09/09/2024] [Indexed: 09/26/2024]
Abstract
BACKGROUND The crucial role of insect chitinase in molting, pupation, and emergence renders it a promising target for pest control strategies. Despite the extensive investigation of chitinase genes in various pests, there is still a lack of systematic identification and functional analysis related to aphid chitinase. RESULTS We systematically identified a total of nine chitinase/chitinase-like genes and one ENGase gene, which included eight Cht genes, one IDGF gene, and one ENGase gene. Through phylogenetic analysis, the chitinase proteins were classified into nine distinct groups (I, II, III, V, VI, VIII, X, other, and ENGase). The expression profile revealed that the epidermis exhibited relatively high expression levels for three chitinase genes: MpCht5, MpCht7, and MpCht10. Furthermore, transcriptional levels of nine chitinase genes were up-regulated following treatment with 20-hydroxyecdysone (20E) hormone. Silencing MpCht3, MpCht5, MpCht7, MpCht10, and MpCht11-2 via RNA interference (RNAi) during the molting stage resulted in nymph shrinking, hindering normal molting and leading to death. Additionally, it was observed that silencing of MpIDGF induced the body color of the aphids to change from reddish brown to colorless after molting, culminating in eventual mortality. CONCLUSION Our findings suggest that chitinase/chitinase-like genes play a crucial role in the molting process of Myzus persicae. Utilizing RNAi technology, we aimed to elucidate the precise function of MpCht genes in the molting mechanism of M. persicae, this discovery establishes a significant theoretical foundation for future research on aphid control, with chitinase as the target. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Chao Zhang
- Institute of Entomology, Guizhou University, Guiyang, P. R. China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang, P. R. China
- Scientific Observing and Experimental Station of Crop Pests in Guiyang, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang, P. R. China
| | - Li He
- Institute of Entomology, Guizhou University, Guiyang, P. R. China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang, P. R. China
- Scientific Observing and Experimental Station of Crop Pests in Guiyang, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang, P. R. China
- Forestry Development Centre, Zhenfeng County Forestry Bureau, Southwest Guizhou Buyi and Miao Autonomous Prefecture, Guizhou, P. R. China
| | - Bo Ding
- Institute of Entomology, Guizhou University, Guiyang, P. R. China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang, P. R. China
- Scientific Observing and Experimental Station of Crop Pests in Guiyang, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang, P. R. China
| | - Hong Yang
- Institute of Entomology, Guizhou University, Guiyang, P. R. China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang, P. R. China
- Scientific Observing and Experimental Station of Crop Pests in Guiyang, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Guiyang, P. R. China
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Hall I, Zablock K, Sobetski R, Weidmann CA, Keane SC. Functional Validation of SAM Riboswitch Element A from Listeria monocytogenes. Biochemistry 2024. [PMID: 39323220 DOI: 10.1021/acs.biochem.4c00247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
SreA is one of seven candidate S-adenosyl methionine (SAM) class I riboswitches identified in Listeria monocytogenes, a saprophyte and opportunistic foodborne pathogen. SreA precedes genes encoding a methionine ATP-binding cassette (ABC) transporter, which imports methionine and is presumed to regulate transcription of its downstream genes in a SAM-dependent manner. The proposed role of SreA in controlling the transcription of genes encoding an ABC transporter complex may have important implications for how the bacteria senses and responds to the availability of the metabolite SAM in the diverse environments in which L. monocytogenes persists. Here we validate SreA as a functional SAM-I riboswitch through ligand binding studies, structure characterization, and transcription termination assays. We determined that SreA has both a structure and SAM binding properties similar to those of other well-characterized SAM-I riboswitches. Despite the apparent structural similarities to previously described SAM-I riboswitches, SreA induces transcription termination in response to comparatively lower (nanomolar) ligand concentrations. Furthermore, SreA is a leaky riboswitch that permits some transcription of the downstream gene even in the presence of millimolar SAM, suggesting that L. monocytogenes may "dampen" the expression of genes for methionine import but likely does not turn them "OFF".
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Affiliation(s)
- Ian Hall
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kaitlyn Zablock
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Raeleen Sobetski
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Chase A Weidmann
- Department of Biological Chemistry, Center for RNA Biomedicine, Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Sarah C Keane
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
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35
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Demuysere M, Ducret A, Grangeasse C. Molecular dissection of the chromosome partitioning protein RocS and regulation by phosphorylation. J Bacteriol 2024:e0029124. [PMID: 39315781 DOI: 10.1128/jb.00291-24] [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: 07/25/2024] [Accepted: 09/10/2024] [Indexed: 09/25/2024] Open
Abstract
Chromosome segregation in bacteria is a critical process ensuring that each daughter cell receives an accurate copy of the genetic material during cell division. Active segregation factors, such as the ParABS system or SMC complexes, are usually essential for this process, but they are surprisingly dispensable in Streptococcus pneumoniae. Rather, chromosome segregation in S. pneumoniae relies on the protein Regulator of Chromosome Segregation (RocS), although the molecular mechanisms involved remain elusive. By combining genetics, in vivo imaging, and biochemical approaches, we dissected the molecular features of RocS involved in chromosome segregation. We investigated the respective functions of the three RocS domains, specifically the C-terminal amphipathic helix (AH), the N-terminal DNA-binding domain (DBD), and the coiled-coil domain (CCD) separating the AH and the DBD. Notably, we found that a single AH is not sufficient for membrane binding and that RocS requires prior oligomerization to interact with the membrane. We further demonstrated that this self-interaction was driven by the N-terminal part of the CCD. On the other hand, we revealed that the C-terminal part of the CCD corresponds to a domain of unknown function (DUF 536) and is defined by three conserved glutamines, which play a crucial role in RocS-mediated chromosome segregation. Finally, we showed that the DBD is phosphorylated by the unique serine-threonine kinase of S. pneumoniae StkP and that mimicking this phosphorylation abrogated RocS binding to DNA. Overall, this study offers new insights into chromosome segregation in Streptococci and paves the way for a deeper understanding of RocS-like proteins in other bacteria.IMPORTANCEBacteria have evolved a variety of mechanisms to properly segregate their genetic material during cell division. In this study, we performed a molecular dissection of the chromosome partitioning protein Regulator of Chromosome Segregation (RocS), a pillar element of chromosome segregation in S. pneumoniae that is also generally conserved in the Streptococcaceae family. Our systematic investigation sheds light on the molecular features required for successful pneumococcal chromosome segregation and the regulation of RocS by phosphorylation. In addition, our study also revealed that RocS shares functional domains with the Par protein, involved in an atypical plasmid segregation system. Therefore, we expect that our findings may serve to extend our understanding of RocS and RocS-like proteins while broadening the repertoire of partitioning systems used in bacteria.
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Affiliation(s)
- Margaux Demuysere
- Molecular Microbiology and Structural Biochemistry, Université de Lyon, CNRS, Lyon, France
| | - Adrien Ducret
- Molecular Microbiology and Structural Biochemistry, Université de Lyon, CNRS, Lyon, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, Université de Lyon, CNRS, Lyon, France
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36
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Rosignoli S, Pacelli M, Manganiello F, Paiardini A. An outlook on structural biology after AlphaFold: tools, limits and perspectives. FEBS Open Bio 2024. [PMID: 39313455 DOI: 10.1002/2211-5463.13902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 08/19/2024] [Accepted: 09/13/2024] [Indexed: 09/25/2024] Open
Abstract
AlphaFold and similar groundbreaking, AI-based tools, have revolutionized the field of structural bioinformatics, with their remarkable accuracy in ab-initio protein structure prediction. This success has catalyzed the development of new software and pipelines aimed at incorporating AlphaFold's predictions, often focusing on addressing the algorithm's remaining challenges. Here, we present the current landscape of structural bioinformatics shaped by AlphaFold, and discuss how the field is dynamically responding to this revolution, with new software, methods, and pipelines. While the excitement around AI-based tools led to their widespread application, it is essential to acknowledge that their practical success hinges on their integration into established protocols within structural bioinformatics, often neglected in the context of AI-driven advancements. Indeed, user-driven intervention is still as pivotal in the structure prediction process as in complementing state-of-the-art algorithms with functional and biological knowledge.
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Affiliation(s)
- Serena Rosignoli
- Department of Biochemical sciences "A. Rossi Fanelli", Sapienza Università di Roma, Italy
| | - Maddalena Pacelli
- Department of Biochemical sciences "A. Rossi Fanelli", Sapienza Università di Roma, Italy
| | - Francesca Manganiello
- Department of Biochemical sciences "A. Rossi Fanelli", Sapienza Università di Roma, Italy
| | - Alessandro Paiardini
- Department of Biochemical sciences "A. Rossi Fanelli", Sapienza Università di Roma, Italy
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37
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Belvin BR, Musayev FN, Escalante CR, Lewis JP. Full-length structure and heme binding in the transcriptional regulator HcpR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.06.611725. [PMID: 39282349 PMCID: PMC11398531 DOI: 10.1101/2024.09.06.611725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
Abstract
HcpR is a CRP-family transcriptional regulator found in many Gram-negative anaerobic bacteria. In the perio-pathogen Porphyromonas gingivalis, HcpR is crucial for the response to reactive nitrogen species such as nitric oxide (NO). Binding of NO to the heme group of HcpR leads to transcription of the redox enzyme Hcp. However, the molecular mechanisms of heme binding to HcpR remain unknown. In this study we present the 2.3 Å structure of the P. gingivalis HcpR. Interdomain interactions present in the structure help to form a hydrophobic pocket in the N-terminal sensing domain. A comparison analysis with other CRP-family members reveals that the molecular mechanisms of HcpR-mediated regulation may be distinct from other family members. Using docking studies, we identify a putative heme binding site in the sensing domain. In vitro complementation and mutagenesis studies verify Met68 as an important residue in activation of HcpR. Finally, heme binding studies with purified forms of recombinant HcpR support Met68 and His149 residues as important for proper heme coordination in HcpR.
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38
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Tang Y, Zhang J, Guan J, Liang W, Petassi M, Zhang Y, Jiang X, Wang M, Wu W, Ou HY, Peters J. Transposition with Tn3-family elements occurs through interaction with the host β-sliding clamp processivity factor. Nucleic Acids Res 2024; 52:10416-10430. [PMID: 39119921 PMCID: PMC11417375 DOI: 10.1093/nar/gkae674] [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: 03/01/2024] [Revised: 07/18/2024] [Accepted: 07/23/2024] [Indexed: 08/10/2024] Open
Abstract
Tn3 family transposons are a widespread group of replicative transposons, notorious for contributing to the dissemination of antibiotic resistance, particularly the global prevalence of carbapenem resistance. The transposase (TnpA) of these elements catalyzes DNA breakage and rejoining reactions required for transposition. However, the molecular mechanism for target site selection with these elements remains unclear. Here, we identify a QLxxLR motif in N-terminal of Tn3 TnpAs and demonstrate that this motif allows interaction between TnpA of Tn3 family transposon Tn1721 and the host β-sliding clamp (DnaN), the major processivity factor of the DNA replication machinery. The TnpA-DnaN interaction is essential for Tn1721 transposition. Our work unveils a mechanism whereby Tn3 family transposons can bias transposition into certain replisomes through an interaction with the host replication machinery. This study further expands the diversity of mobile elements that use interaction with the host replication machinery to bias integration.
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Affiliation(s)
- Yu Tang
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200123, China
| | - Jianfeng Zhang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai 200040, China
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiahao Guan
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei Liang
- Department of Laboratory Medicine, The First Affiliated Hospital of Ningbo University, Ningbo 315010, China
| | - Michael T Petassi
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Yumeng Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaofei Jiang
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
| | - Minggui Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Wenjuan Wu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200123, China
| | - Hong-Yu Ou
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Joseph E Peters
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
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Shin J, Meinke G, Bohm AA, Bullock PA. A model for polyomavirus helicase activity derived in part from the AlphaFold2 structure of SV40 T-antigen. J Virol 2024:e0111924. [PMID: 39311578 DOI: 10.1128/jvi.01119-24] [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: 08/11/2024] [Indexed: 09/27/2024] Open
Abstract
The mechanism used by polyomavirus and other viral SF3 helicases to unwind DNA at replication forks remains unknown. Using AlphaFold2, we have determined the structure of a representative SF3 helicase, the SV40 T-antigen (T-ag). This model has been analyzed in terms of the features of T-ag required for helicase activity, particularly the proximity of the T-ag origin binding domain (OBD) to the replication fork and the distribution of basic residues on the surface of the OBD that are known to play roles in DNA unwinding. These and related studies provide additional evidence that the T-ag OBDs have a role in the unwinding of DNA at the replication fork. Nuclear magnetic resonance and modeling experiments also indicate that protonated histidines on the surface of the T-ag OBD play an important role in the unwinding process, and additional modeling studies indicate that protonated histidines are essential in other SF3 and SF6 helicases. Finally, a model for T-ag's helicase activity is presented, which is a variant of the "rope climber." According to this model, the hands are the N-terminal OBD domains that interact with the replication fork, while the C-terminal helicase domains contain the feet that bind to single-stranded DNA. IMPORTANCE Enzymes termed helicases are essential for the replication of DNA tumor viruses. Unfortunately, much remains to be determined about this class of enzymes, including their structures and the mechanism(s) they employ to unwind DNA. Herein, we present the full-length structure of a model helicase encoded by a DNA tumor virus. Moreover, this AI-based structure has been analyzed in terms of its basic functional properties, such as the orientation of the helicase at replication forks and the relative locations of the amino acid residues that are critical for helicase activity. Obtaining this information is important because it permits proposals regarding how DNA is routed through these model helicases. Also presented is structural evidence that the conclusions drawn from our detailed analyses of one model helicase, encoded by one class of tumor viruses, are likely to apply to other viral and eukaryotic helicases.
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Affiliation(s)
- Jong Shin
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Gretchen Meinke
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Alex A Bohm
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Peter A Bullock
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts, USA
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40
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Chieffi D, Bongiorno D, Licitra A, Campanile F, Fusco V. A Novel Approach Based on Real-Time PCR with High-Resolution Melting Analysis for the Simultaneous Identification of Staphylococcus aureus and Staphylococcus argenteus. Foods 2024; 13:3004. [PMID: 39335932 PMCID: PMC11431256 DOI: 10.3390/foods13183004] [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: 08/26/2024] [Revised: 09/14/2024] [Accepted: 09/19/2024] [Indexed: 09/30/2024] Open
Abstract
Staphylococcus (S.) aureus is a pathogenic bacterium able to cause several diseases in humans and animals as well as foodborne intoxications. S. argenteus, being phenotypically and genotypically related to S. aureus, is part of the so-called S. aureus complex and recently recognized as an emerging pathogen able to cause, like S. aureus, several diseases both in humans and animals, and foodborne poisoning outbreaks. However, it has been reported that the widely used conventional PCR of Brakstad et al. [Journal of Clinical Microbiology, 30(7), 1654-1660, (1992)] targeting the thermostable nuclease gene may provide false-positive S. aureus, as it is able to amplify also S. argenteus. Here, we developed a novel two-step approach that, following the PCR of Brakstad et al. (1992), discriminates S. aureus from S. argenteus by a real-time PCR with high-resolution melting analysis (rt-PCR-HRM). In particular, targeting a polymorphic 137 bp region of the sodA gene, our developed rt-PCR-HRM method clearly discriminated S. aureus from S. argenteus, showing a remarkable difference in their amplification product melting temperatures (approximately 1.3 °C) as well as distinct melting curve shapes. The good sensitivity, reproducibility, user friendliness, and cost effectiveness of the developed method are advantageous attributes that will allow not only its easy employment to correctly identify misidentified isolates present in various collections of S. aureus, but also expand the still lacking knowledge on the prevalence and distribution of S. argenteus.
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Affiliation(s)
- Daniele Chieffi
- Institute of Sciences of Food Production, National Research Council of Italy (CNR-ISPA), 70126 Bari, Italy
| | - Dafne Bongiorno
- Medical Molecular Microbiology and Antibiotic Resistance Laboratory (MMARLab), Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, 95123 Catania, Italy
| | - Anna Licitra
- Institute of Sciences of Food Production, National Research Council of Italy (CNR-ISPA), 70126 Bari, Italy
| | - Floriana Campanile
- Medical Molecular Microbiology and Antibiotic Resistance Laboratory (MMARLab), Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, 95123 Catania, Italy
| | - Vincenzina Fusco
- Institute of Sciences of Food Production, National Research Council of Italy (CNR-ISPA), 70126 Bari, Italy
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41
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Haidurov A, Budanov AV. Locked in Structure: Sestrin and GATOR-A Billion-Year Marriage. Cells 2024; 13:1587. [PMID: 39329768 PMCID: PMC11429811 DOI: 10.3390/cells13181587] [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: 07/11/2024] [Revised: 09/16/2024] [Accepted: 09/17/2024] [Indexed: 09/28/2024] Open
Abstract
Sestrins are a conserved family of stress-responsive proteins that play a crucial role in cellular metabolism, stress response, and ageing. Vertebrates have three Sestrin genes (SESN1, SESN2, and SESN3), while invertebrates encode only one. Initially identified as antioxidant proteins that regulate cell viability, Sestrins are now recognised as crucial inhibitors of the mechanistic target of rapamycin complex 1 kinase (mTORC1), a central regulator of anabolism, cell growth, and autophagy. Sestrins suppress mTORC1 through an inhibitory interaction with the GATOR2 protein complex, which, in concert with GATOR1, signals to inhibit the lysosomal docking of mTORC1. A leucine-binding pocket (LBP) is found in most vertebrate Sestrins, and when bound with leucine, Sestrins do not bind GATOR2, prompting mTORC1 activation. This review examines the evolutionary conservation of Sestrins and their functional motifs, focusing on their origins and development. We highlight that the most conserved regions of Sestrins are those involved in GATOR2 binding, and while analogues of Sestrins exist in prokaryotes, the unique feature of eukaryotic Sestrins is their structural presentation of GATOR2-binding motifs.
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Affiliation(s)
- Alexander Haidurov
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Pearse Street, D02 R590 Dublin, Ireland
| | - Andrei V. Budanov
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Pearse Street, D02 R590 Dublin, Ireland
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42
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Liu Q, Xu Y, Li X, Qi T, Li B, Wang H, Zhu Y. Genome-Wide Identification and Characterization of MYB Transcription Factors in Sudan Grass under Drought Stress. PLANTS (BASEL, SWITZERLAND) 2024; 13:2645. [PMID: 39339621 PMCID: PMC11435211 DOI: 10.3390/plants13182645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 09/17/2024] [Accepted: 09/20/2024] [Indexed: 09/30/2024]
Abstract
Sudan grass (Sorghum sudanense S.) is a warm-season annual grass with high yield, rich nutritional value, good regeneration, and tolerance to biotic and abiotic stresses. However, prolonged drought affects the yield and quality of Sudan grass. As one of the largest families of multifunctional transcription factors in plants, MYB is widely involved in regulating plant growth and development, hormonal signaling, and stress responses at the gene transcription level. However, the regulatory role of MYB genes has not been well characterized in Sudan grass under abiotic stress. In this study, 113 MYB genes were identified in the Sudan grass genome and categorized into three groups by phylogenetic analysis. The promoter regions of SsMYB genes contain different cis-regulatory elements, which are involved in developmental, hormonal, and stress responses, and may be closely related to their diverse regulatory functions. In addition, collinearity analysis showed that the expansion of the SsMYB gene family occurred mainly through segmental duplications. Under drought conditions, SsMYB genes showed diverse expression patterns, which varied at different time points. Interaction networks of 74 SsMYB genes were predicted based on motif binding sites, expression correlations, and protein interactions. Heterologous expression showed that SsMYB8, SsMYB15, and SsMYB64 all significantly enhanced the drought tolerance of yeast cells. Meanwhile, the subcellular localization of all three genes is in the nucleus. Overall, this study provides new insights into the evolution and function of MYB genes and provides valuable candidate genes for breeding efforts in Sudan grass.
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Affiliation(s)
| | | | | | | | | | | | - Yongqun Zhu
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Q.L.); (Y.X.); (X.L.); (T.Q.); (B.L.); (H.W.)
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43
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Wang C, Liu Y, Li Y, Guo L, Li C. Analysis of bZIP transcription factors in Rhododendron simsii and functional study of RsbZIP6 in regulating anthocyanin biosynthesis. Int J Biol Macromol 2024; 280:135889. [PMID: 39307497 DOI: 10.1016/j.ijbiomac.2024.135889] [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: 08/05/2024] [Revised: 09/19/2024] [Accepted: 09/19/2024] [Indexed: 09/26/2024]
Abstract
The basic leucine zipper (bZIP) transcription factors play a critical role in various plant biological processes, including anthocyanin biosynthesis. This study focuses on Rhododendron simsii, a notable ornamental species with insufficiently explored bZIP transcription factors. We identified 66 bZIP transcription factors in the R. simsii genome and conducted comprehensive bioinformatics analyses to determine their gene localization, phylogenetic relationships, grouping, gene/protein structure, duplication events, synteny, and expression profiles. Our analysis identified RsbZIP6, a homolog of HY5 known to influence anthocyanin biosynthesis in many plants, as a potential regulator of this pathway. We cloned the complete coding sequence of RsbZIP6, which encodes a 170-amino acid protein spanning 510 bp. Subcellular localization analysis verified the nuclear presence of the RsbZIP6 protein. RT-qPCR analysis revealed the highest expression of RsbZIP6 in petals, which correlated with anthocyanin accumulation. Transgenic experiments indicated that overexpressing RsbZIP6 in Arabidopsis enhanced anthocyanin accumulation by upregulating genes involved in anthocyanin biosynthesis (4CL, CHS, CHI, DFR, F3H, F3'H, ANS and UF3GT). Our findings enhance understanding of the bZIP transcription factor family in R. simsii and underscore the vital role of RsbZIP6 in anthocyanin biosynthesis, providing insights for future genetic enhancement strategies.
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Affiliation(s)
- Cheng Wang
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China; Hubei Province Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Xiaogan 432000, China
| | - Yilin Liu
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Yan Li
- Department of Biology and Chemical Engineering, Weihai Vocational College, Weihai 264200, China
| | - Lifan Guo
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Changchun Li
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China; Hubei Province Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, Xiaogan 432000, China.
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44
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Listian SA, Mazur AC, Kol M, Ufelmann E, Eising S, Fröhlich F, Walter S, Holthuis JCM, Barisch C. Complex sphingolipid profiling and identification of an inositol-phosphorylceramide synthase in Dictyostelium discoideum. iScience 2024; 27:110609. [PMID: 39286488 PMCID: PMC11402645 DOI: 10.1016/j.isci.2024.110609] [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: 01/09/2024] [Revised: 06/12/2024] [Accepted: 07/26/2024] [Indexed: 09/19/2024] Open
Abstract
Dictyostelium discoideum is a professional phagocyte frequently used to study cellular processes underlying the recognition, engulfment, and infection course of microbial pathogens. Sphingolipids are abundant components of the plasma membrane that bind cholesterol, control membrane properties, participate in signal transmission, and serve as adhesion molecules in recognition processes relevant to immunity and infection. By combining lipidomics with a bioinformatics-based cloning strategy, we show here that D. discoideum produces phosphoinositol-containing sphingolipids with predominantly phytoceramide backbones. Cell-free expression of candidate inositol-phosphorylceramide (IPC) synthases from D. discoideum enabled identification of an enzyme that selectively catalyzes the transfer of phosphoinositol from phosphatidylinositol onto ceramide. The IPC synthase, DdIPCS1, shares multiple sequence motifs with yeast IPC and human sphingomyelin synthases and localizes to the Golgi apparatus as well as the contractile vacuole of D. discoideum. These findings open up important opportunities for exploring a role of sphingolipids in phagocytosis and infection across major evolutionary boundaries.
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Affiliation(s)
- Stevanus A Listian
- Division of Molecular Infection Biology, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Anna-Carina Mazur
- Division of Molecular Infection Biology, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- Division of Host-Microbe Interactome, Research Center Borstel (FZB) - Leibniz Lung Center, Borstel, Germany
- Department of Biology, University of Hamburg, Hamburg, Germany
| | - Matthijs Kol
- Division of Molecular Cell Biology, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
- Center of Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Edwin Ufelmann
- Division of Molecular Infection Biology, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Sebastian Eising
- Division of Molecular Membrane Biology, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Florian Fröhlich
- Division of Molecular Membrane Biology, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
- Center of Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Stefan Walter
- Center of Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Joost C M Holthuis
- Division of Molecular Cell Biology, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
- Center of Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Caroline Barisch
- Division of Molecular Infection Biology, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
- Center of Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- Division of Host-Microbe Interactome, Research Center Borstel (FZB) - Leibniz Lung Center, Borstel, Germany
- Department of Biology, University of Hamburg, Hamburg, Germany
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45
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Akbari Ahangar A, Elhanafy E, Blanton H, Li J. Mapping structural distribution and gating-property impacts of disease-associated mutations in voltage-gated sodium channels. iScience 2024; 27:110678. [PMID: 39286500 PMCID: PMC11404175 DOI: 10.1016/j.isci.2024.110678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 06/18/2024] [Accepted: 08/02/2024] [Indexed: 09/19/2024] Open
Abstract
Thousands of voltage-gated sodium (Nav) channel variants contribute to a variety of disorders, including epilepsy, cardiac arrhythmia, and pain disorders. Yet, the effects of more variants remain unclear. The conventional gain-of-function (GoF) or loss-of-function (LoF) classifications are frequently employed to interpret mutations' effects and guide therapy for sodium channelopathies. Our study challenges this binary classification by analyzing 525 mutations associated with 34 diseases across 366 electrophysiology studies, revealing that diseases with similar GoF/LoF effects can stem from unique molecular mechanisms. Utilizing UniProt data, we mapped over 2,400 disease-associated missense mutations across Nav channels. This analysis pinpoints key mutation hotspots and maps patterns of gating-property impacts for the mutations, respectively, located around the selectivity filter, activation gate, fast inactivation region, and voltage-sensing domains. This study shows great potential to enhance prediction accuracy for mutational effects based on the structural context, paving the way for targeted drug design in precision medicine.
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Affiliation(s)
- Amin Akbari Ahangar
- Department of Biomolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA
| | - Eslam Elhanafy
- Department of Biomolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA
| | - Hayden Blanton
- Department of Biomolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA
| | - Jing Li
- Department of Biomolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA
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46
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Qin Z, Yuan B, Qu G, Sun Z. Rational enzyme design by reducing the number of hotspots and library size. Chem Commun (Camb) 2024; 60:10451-10463. [PMID: 39210728 DOI: 10.1039/d4cc01394h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Biocatalysts that are eco-friendly, sustainable, and highly specific have great potential for applications in the production of fine chemicals, food, detergents, biofuels, pharmaceuticals, and more. However, due to factors such as low activity, narrow substrate scope, poor thermostability, or incorrect selectivity, most natural enzymes cannot be directly used for large-scale production of the desired products. To overcome these obstacles, protein engineering methods have been developed over decades and have become powerful and versatile tools for adapting enzymes with improved catalytic properties or new functions. The vastness of the protein sequence space makes screening a bottleneck in obtaining advantageous mutated enzymes in traditional directed evolution. In the realm of mathematics, there are two major constraints in the protein sequence space: (1) the number of residue substitutions (M); and (2) the number of codons encoding amino acids as building blocks (N). This feature review highlights protein engineering strategies to reduce screening efforts from two dimensions by reducing the numbers M and N, and also discusses representative seminal studies of rationally engineered natural enzymes to deliver new catalytic functions.
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Affiliation(s)
- Zongmin Qin
- University of Chinese Academy of Sciences, Beijing 100049, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Bo Yuan
- University of Chinese Academy of Sciences, Beijing 100049, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin 300308, China
| | - Ge Qu
- University of Chinese Academy of Sciences, Beijing 100049, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin 300308, China
| | - Zhoutong Sun
- University of Chinese Academy of Sciences, Beijing 100049, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin 300308, China
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47
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Sahu AK, Shah RA, Nashier D, Sharma P, Varada R, Lahry K, Singh S, Shetty S, Hussain T, Varshney U. Physiological significance of the two isoforms of initiator tRNAs in Escherichia coli. J Bacteriol 2024; 206:e0025124. [PMID: 39171914 PMCID: PMC11411947 DOI: 10.1128/jb.00251-24] [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: 06/20/2024] [Accepted: 07/31/2024] [Indexed: 08/23/2024] Open
Abstract
Escherichia coli possesses four initiator tRNA (i-tRNA) genes, three of which are present together as metZWV and the fourth one as metY. In E. coli B, all four genes (metZWV and metY) encode i-tRNAfMet1, in which the G at position 46 is modified to m7G46 by TrmB (m7G methyltransferase). However, in E. coli K, because of a single-nucleotide polymorphism, metY encodes a variant, i-tRNAfMet2, having an A in place of m7G46. We generated E. coli strains to explore the importance of this polymorphism in i-tRNAs. The strains were sustained either on metYA46 (metY of E. coli K origin encoding i-tRNAfMet2) or its derivative metYG46 (encoding i-tRNAfMet1) in single (chromosomal) or plasmid-borne copies. We show that the strains sustained on i-tRNAfMet1 have a growth fitness advantage over those sustained on i-tRNAfMet2. The growth fitness advantages are more pronounced for the strains sustained on i-tRNAfMet1 in nutrient-rich media than in nutrient-poor media. The growth fitness of the strains correlates well with the relative stabilities of the i-tRNAs in vivo. Furthermore, the atomistic molecular dynamics simulations support the higher stability of i-tRNAfMet1 than that of i-tRNAfMet2. The stability of i-tRNAfMet1 remains unaffected upon the deletion of TrmB. These studies highlight how metYG46 and metYA46 alleles might influence the growth fitness of E. coli under certain nutrient-limiting conditions. IMPORTANCE Escherichia coli harbors four initiator tRNA (i-tRNA) genes: three of these at metZWV and the fourth one at metY loci. In E. coli B, all four genes encode i-tRNAfMet1. In E. coli K, because of a single-nucleotide polymorphism, metY encodes a variant, i-tRNAfMet2, having an A in place of G at position 46 of i-tRNA sequence in metY. We show that G46 confers stability to i-tRNAfMet1. The strains sustained on i-tRNAfMet1 have a growth fitness advantage over those sustained on i-tRNAfMet2. Strains harboring metYG46 (B mimic) or metYA46 (K mimic) show that while in the nutrient-rich media, the K mimic is outcompeted rapidly; in the nutrient-poor medium, the K mimic is outcompeted less rapidly.
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Affiliation(s)
- Amit Kumar Sahu
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Riyaz Ahmad Shah
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Divya Nashier
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Prafful Sharma
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
| | - Rajagopal Varada
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Kuldeep Lahry
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Sudhir Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Sunil Shetty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Tanweer Hussain
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
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Yang F, Sun X, Lu J, Zhang L, Du G, Li J, Xu R, Kang Z. Immobilized high-performance heparin lyase III for efficient preparation of low molecular weight heparin. Int J Biol Macromol 2024; 280:135833. [PMID: 39306163 DOI: 10.1016/j.ijbiomac.2024.135833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 09/09/2024] [Accepted: 09/18/2024] [Indexed: 09/30/2024]
Abstract
Heparin lyase III has garnered widespread attention due to its high specificity and minimal loss of anticoagulant activity during the preparation of low molecular weight heparin (LMWH), a crucial anticoagulant drug in clinical practice. However, low expression levels and complex preparation processes limit its practical application. To address these challenges, high-performance Bacteroides thetaiotaomicron heparin lyase III (Bhep III) variants were engineered and immobilized for LMWH preparation. First, we enhanced enzyme expression by adding a solubility-enhancing tag and optimizing the N-terminal coding sequence, which resulted in a Bhep III activity level of 2.9 × 103 U/L with 8-fold increase. After evolution guided the design of rational mutations, the variant Bhep III K85A/Q95F/S471T generated higher activity (5.4 × 104 U/L in 5-L fermenter), which is, to our knowledge, the highest reported to date in the literature, being 1.7-fold that of the wild type and demonstrating 2-fold increase of the thermal stability. By screening and optimizing the C-terminal self-assembling tag, we successfully immobilized Bhep III, further increasing its thermal stability by 12-fold, and allowing for the multi-batch preparation of LMWH with simple centrifugation. The immobilized heparin lyase III demonstrated sufficient reusability in enzymatic reactions, facilitating efficient industrial-scale production of LMWH.
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Affiliation(s)
- Fengling Yang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China; The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China; The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China; Jiaxing Institute of Future Food, Jiaxing 314050, China
| | - Xiaoyuan Sun
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China; The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Jie Lu
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China; The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Linpei Zhang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Guocheng Du
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China; The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China; The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Ruirui Xu
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China; The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China.
| | - Zhen Kang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China; The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China; The Science Center for Future Foods, Jiangnan University, Wuxi 214122, China.
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49
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Pham S, Zhao B, Neetu N, Sankaran B, Patil K, Ramani S, Song Y, Estes MK, Palzkill T, Prasad BV. CONFORMATIONAL FLEXIBILITY IS A CRITICAL FACTOR IN DESIGNING BROAD-SPECTRUM HUMAN NOROVIRUS PROTEASE INHIBITORS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.16.613336. [PMID: 39345439 PMCID: PMC11430002 DOI: 10.1101/2024.09.16.613336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Human norovirus (HuNoV) infection is a global health and economic burden. Currently, there are no licensed HuNoV vaccines or antiviral drugs available. The protease encoded by the HuNoV genome plays a critical role in virus replication by cleaving the polyprotein and is, therefore, an excellent target for developing small molecule inhibitors. While rupintrivir, a potent small-molecule inhibitor of several picornavirus proteases, effectively inhibits GI.1 protease, it is an order of magnitude less effective against GII protease. Other GI.1 protease inhibitors also tend to be less effective against GII proteases. To understand the structural basis for the potency difference, we determined the crystal structures of proteases of GI.1, pandemic GII.4 (Houston and Sydney), and GII.3 in complex with rupintrivir. These structures show that the open substrate pocket in GI protease binds rupintrivir without requiring significant conformational changes, whereas, in GII proteases, the closed pocket flexibly extends, reorienting arginine-112 in the BII-CII loop to accommodate rupintrivir. Structures of R112A protease mutants with rupintrivir, coupled with enzymatic and inhibition studies, suggest R112 is involved in displacing both substrate and ligands from the active site, implying a role in the release of cleaved products during polyprotein processing. Thus, the primary determinant for differential inhibitor potency between the GI and GII proteases is the increased flexibility in the BII-CII loop of the GII proteases caused by H-G mutation in this loop. Therefore, the inherent flexibility of the BII-CII loop in GII proteases is a critical factor to consider when developing broad-spectrum inhibitors for HuNoV proteases.
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Affiliation(s)
- Son Pham
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Boyang Zhao
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Neetu Neetu
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Molecular Biophysics, and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, CA, USA
| | - Ketki Patil
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Yongcheng Song
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Mary K. Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Timothy Palzkill
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - B.V. Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
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50
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Roberts CG, Kaur S, Ogden AJ, Divine ME, Warren GD, Kang D, Kirienko NV, Geurink PP, Mulder MP, Nakayasu ES, McDermott JE, Adkins JN, Aballay A, Pruneda JN. A functional screen for ubiquitin regulation identifies an E3 ligase secreted by Pseudomonas aeruginosa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.18.613774. [PMID: 39345563 PMCID: PMC11430079 DOI: 10.1101/2024.09.18.613774] [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
Ubiquitin signaling controls many aspects of eukaryotic biology, including targeted protein degradation and immune defense. Remarkably, invading bacterial pathogens have adapted secreted effector proteins that hijack host ubiquitination to gain control over host responses. These ubiquitin-targeted effectors can exhibit, for example, E3 ligase or deubiquitinase activities, often without any sequence or structural homology to eukaryotic ubiquitin regulators. Such convergence in function poses a challenge to the discovery of additional bacterial virulence factors that target ubiquitin. To overcome this, we have developed a workflow to harvest natively secreted bacterial effectors and functionally screen them for ubiquitin regulatory activities. After benchmarking this approach on diverse ligase and deubiquitinase activities from Salmonella Typhimurium, Enteropathogenic Escherichia coli, and Shigella flexneri, we applied it to the identification of a cryptic E3 ligase activity secreted by Pseudomonas aeruginosa. We identified an unreported P. aeruginosa E3 ligase, which we have termed Pseudomonas Ub ligase 1 (PUL-1), that resembles none of the other E3 ligases previously established in or outside of the eukaryotic system. Importantly, in an animal model of P. aeruginosa infection, PUL-1 ligase activity plays an important role in regulating virulence. Thus, our workflow for the functional identification of ubiquitin-targeted effector proteins carries promise for expanding our appreciation of how host ubiquitin regulation contributes to bacterial pathogenesis.
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Affiliation(s)
- Cameron G. Roberts
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Supender Kaur
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Aaron J. Ogden
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Michael E. Divine
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Gus D. Warren
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Donghoon Kang
- Department of Biosciences, Rice University, Houston, TX 77005, USA
| | | | - Paul P. Geurink
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Monique P.C. Mulder
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ernesto S. Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Jason E. McDermott
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Joshua N. Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Alejandro Aballay
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jonathan N. Pruneda
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
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