1
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Lehotsky K, Neville N, Jia Z. Protocol for detecting histidine polyphosphate modification of human proteins via MBP-tagged expression in E. coli. STAR Protoc 2024; 5:102947. [PMID: 38470910 PMCID: PMC10943961 DOI: 10.1016/j.xpro.2024.102947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/27/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
Polyphosphate exhibits a unique post-translational modification-like function, known as histidine polyphosphate modification (HPM), marked by a robust non-covalent interaction with histidine repeat proteins. Here, we present a protocol for detecting HPM of human proteins via maltose-binding protein-tagged expression in E. coli. We describe steps for detecting HPM by observing electrophoretic mobility shifts on NuPAGE gels followed by western blot. We then detail procedures for analyzing the influence of ionic strength and pH on HPM. For complete details on the use and execution of this protocol, please refer to Neville et al.1.
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Affiliation(s)
- Kirsten Lehotsky
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston K7L 3N6, Canada
| | - Nolan Neville
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston K7L 3N6, Canada
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston K7L 3N6, Canada.
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2
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Cumming A, Khananisho D, Balka M, Liljestrand N, Daley DO. Biosensor that Detects Stress Caused by Periplasmic Proteins. ACS Synth Biol 2024; 13:1477-1491. [PMID: 38676700 PMCID: PMC11106774 DOI: 10.1021/acssynbio.3c00720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/19/2024] [Accepted: 04/11/2024] [Indexed: 04/29/2024]
Abstract
Escherichia coli is often used as a factory to produce recombinant proteins. In many cases, the recombinant protein needs disulfide bonds to fold and function correctly. These proteins are genetically fused to a signal peptide so that they are secreted to the oxidizing environment of the periplasm (where the enzymes required for disulfide bond formation exist). Currently, it is difficult to determine in vivo whether a recombinant protein is efficiently secreted from the cytoplasm and folded in the periplasm or if there is a bottleneck in one of these steps because cellular capacity has been exceeded. To address this problem, we have developed a biosensor that detects cellular stress caused by (1) inefficient secretion of proteins from the cytoplasm and (2) aggregation of proteins in the periplasm. We demonstrate how the fluorescence fingerprint obtained from the biosensor can be used to identify induction conditions that do not exceed the capacity of the cell and therefore do not cause cellular stress. These induction conditions result in more effective biomass and in some cases higher titers of soluble recombinant proteins.
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Affiliation(s)
- Alister
J. Cumming
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE-19468, Sweden
| | - Diana Khananisho
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE-19468, Sweden
| | - Mateusz Balka
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE-19468, Sweden
| | - Nicklas Liljestrand
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE-19468, Sweden
| | - Daniel O. Daley
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE-19468, Sweden
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3
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da Silva AR, Gunawan F, Boezio GLM, Faure E, Théron A, Avierinos JF, Lim S, Jha SG, Ramadass R, Guenther S, Looso M, Zaffran S, Juan T, Stainier DYR. egr3 is a mechanosensitive transcription factor gene required for cardiac valve morphogenesis. SCIENCE ADVANCES 2024; 10:eadl0633. [PMID: 38748804 PMCID: PMC11095463 DOI: 10.1126/sciadv.adl0633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 04/11/2024] [Indexed: 05/19/2024]
Abstract
Biomechanical forces, and their molecular transducers, including key mechanosensitive transcription factor genes, such as KLF2, are required for cardiac valve morphogenesis. However, klf2 mutants fail to completely recapitulate the valveless phenotype observed under no-flow conditions. Here, we identify the transcription factor EGR3 as a conserved biomechanical force transducer critical for cardiac valve formation. We first show that egr3 null zebrafish display a complete and highly penetrant loss of valve leaflets, leading to severe blood regurgitation. Using tissue-specific loss- and gain-of-function tools, we find that during cardiac valve formation, Egr3 functions cell-autonomously in endothelial cells, and identify one of its effectors, the nuclear receptor Nr4a2b. We further find that mechanical forces up-regulate egr3/EGR3 expression in the developing zebrafish heart and in porcine valvular endothelial cells, as well as during human aortic valve remodeling. Altogether, these findings reveal that EGR3 is necessary to transduce the biomechanical cues required for zebrafish cardiac valve morphogenesis, and potentially for pathological aortic valve remodeling in humans.
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Affiliation(s)
- Agatha Ribeiro da Silva
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
| | - Felix Gunawan
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
| | - Giulia L. M. Boezio
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
| | - Emilie Faure
- Aix Marseille Université, INSERM, MMG, U1251, 13005 Marseille, France
| | - Alexis Théron
- Aix Marseille Université, INSERM, MMG, U1251, 13005 Marseille, France
- Service de Chirurgie Cardiaque, AP-HM, Hôpital de la Timone, 13005 Marseille, France
| | - Jean-François Avierinos
- Aix Marseille Université, INSERM, MMG, U1251, 13005 Marseille, France
- Service de Cardiologie, AP-HM, Hôpital de la Timone, 13005 Marseille, France
| | - SoEun Lim
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany
| | - Shivam Govind Jha
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany
| | - Radhan Ramadass
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany
| | - Stefan Guenther
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Bioinformatics and Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mario Looso
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stéphane Zaffran
- Aix Marseille Université, INSERM, MMG, U1251, 13005 Marseille, France
| | - Thomas Juan
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
| | - Didier Y. R. Stainier
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
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4
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Neville N, Lehotsky K, Klupt KA, Downey M, Jia Z. Polyphosphate attachment to lysine repeats is a non-covalent protein modification. Mol Cell 2024; 84:1802-1810.e4. [PMID: 38701741 DOI: 10.1016/j.molcel.2024.03.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 03/12/2024] [Accepted: 03/29/2024] [Indexed: 05/05/2024]
Abstract
Polyphosphate (polyP) is a chain of inorganic phosphate that is present in all domains of life and affects diverse cellular phenomena, ranging from blood clotting to cancer. A study by Azevedo et al. described a protein modification whereby polyP is attached to lysine residues within polyacidic serine and lysine (PASK) motifs via what the authors claimed to be covalent phosphoramidate bonding. This was based largely on the remarkable ability of the modification to survive extreme denaturing conditions. Our study demonstrates that lysine polyphosphorylation is non-covalent, based on its sensitivity to ionic strength and lysine protonation and absence of phosphoramidate bond formation, as analyzed via 31P NMR. Ionic interaction with lysine residues alone is sufficient for polyP modification, and we present a new list of non-PASK lysine repeat proteins that undergo polyP modification. This work clarifies the biochemistry of polyP-lysine modification, with important implications for both studying and modulating this phenomenon. This Matters Arising paper is in response to Azevedo et al. (2015), published in Molecular Cell. See also the Matters Arising Response by Azevedo et al. (2024), published in this issue.
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Affiliation(s)
- Nolan Neville
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Kirsten Lehotsky
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Kody A Klupt
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Michael Downey
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Ottawa Institute of Systems Biology, Ottawa, ON K1H 8M5, Canada
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
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5
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McLean ZL, Gao D, Correia K, Roy JCL, Shibata S, Farnum IN, Valdepenas-Mellor Z, Kovalenko M, Rapuru M, Morini E, Ruliera J, Gillis T, Lucente D, Kleinstiver BP, Lee JM, MacDonald ME, Wheeler VC, Mouro Pinto R, Gusella JF. Splice modulators target PMS1 to reduce somatic expansion of the Huntington's disease-associated CAG repeat. Nat Commun 2024; 15:3182. [PMID: 38609352 PMCID: PMC11015039 DOI: 10.1038/s41467-024-47485-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 03/30/2024] [Indexed: 04/14/2024] Open
Abstract
Huntington's disease (HD) is a dominant neurological disorder caused by an expanded HTT exon 1 CAG repeat that lengthens huntingtin's polyglutamine tract. Lowering mutant huntingtin has been proposed for treating HD, but genetic modifiers implicate somatic CAG repeat expansion as the driver of onset. We find that branaplam and risdiplam, small molecule splice modulators that lower huntingtin by promoting HTT pseudoexon inclusion, also decrease expansion of an unstable HTT exon 1 CAG repeat in an engineered cell model. Targeted CRISPR-Cas9 editing shows this effect is not due to huntingtin lowering, pointing instead to pseudoexon inclusion in PMS1. Homozygous but not heterozygous inactivation of PMS1 also reduces CAG repeat expansion, supporting PMS1 as a genetic modifier of HD and a potential target for therapeutic intervention. Although splice modulation provides one strategy, genome-wide transcriptomics also emphasize consideration of cell-type specific effects and polymorphic variation at both target and off-target sites.
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Affiliation(s)
- Zachariah L McLean
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Dadi Gao
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Kevin Correia
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Jennie C L Roy
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA
| | - Shota Shibata
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Iris N Farnum
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Zoe Valdepenas-Mellor
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Marina Kovalenko
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Manasa Rapuru
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Elisabetta Morini
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA
| | - Jayla Ruliera
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Tammy Gillis
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Diane Lucente
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Harvard Medical School, Boston, MA, 02115, USA
| | - Jong-Min Lee
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Marcy E MacDonald
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Vanessa C Wheeler
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - Ricardo Mouro Pinto
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA
| | - James F Gusella
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA.
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA.
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6
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Billman ZP, Kovacs SB, Wei B, Kang K, Cissé OH, Miao EA. Caspase-1 activates gasdermin A in non-mammals. eLife 2024; 12:RP92362. [PMID: 38497531 PMCID: PMC10948149 DOI: 10.7554/elife.92362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024] Open
Abstract
Gasdermins oligomerize to form pores in the cell membrane, causing regulated lytic cell death called pyroptosis. Mammals encode five gasdermins that can trigger pyroptosis: GSDMA, B, C, D, and E. Caspase and granzyme proteases cleave the linker regions of and activate GSDMB, C, D, and E, but no endogenous activation pathways are yet known for GSDMA. Here, we perform a comprehensive evolutionary analysis of the gasdermin family. A gene duplication of GSDMA in the common ancestor of caecilian amphibians, reptiles, and birds gave rise to GSDMA-D in mammals. Uniquely in our tree, amphibian, reptile, and bird GSDMA group in a separate clade than mammal GSDMA. Remarkably, GSDMA in numerous bird species contain caspase-1 cleavage sites like YVAD or FASD in the linker. We show that GSDMA from birds, amphibians, and reptiles are all cleaved by caspase-1. Thus, GSDMA was originally cleaved by the host-encoded protease caspase-1. In mammals the caspase-1 cleavage site in GSDMA is disrupted; instead, a new protein, GSDMD, is the target of caspase-1. Mammal caspase-1 uses exosite interactions with the GSDMD C-terminal domain to confer the specificity of this interaction, whereas we show that bird caspase-1 uses a stereotypical tetrapeptide sequence to confer specificity for bird GSDMA. Our results reveal an evolutionarily stable association between caspase-1 and the gasdermin family, albeit a shifting one. Caspase-1 repeatedly changes its target gasdermin over evolutionary time at speciation junctures, initially cleaving GSDME in fish, then GSDMA in amphibians/reptiles/birds, and finally GSDMD in mammals.
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Affiliation(s)
- Zachary Paul Billman
- Department of Integrative Immunobiology; Molecular Genetics and Microbiology; Pathology; and Cell Biology, Duke University School of MedicineDurhamUnited States
- Department of Microbiology and Immunology, University of North Carolina at Chapel HillChapel HillUnited States
| | - Stephen Bela Kovacs
- Department of Integrative Immunobiology; Molecular Genetics and Microbiology; Pathology; and Cell Biology, Duke University School of MedicineDurhamUnited States
- Department of Microbiology and Immunology, University of North Carolina at Chapel HillChapel HillUnited States
| | - Bo Wei
- Department of Integrative Immunobiology; Molecular Genetics and Microbiology; Pathology; and Cell Biology, Duke University School of MedicineDurhamUnited States
| | - Kidong Kang
- Department of Integrative Immunobiology; Molecular Genetics and Microbiology; Pathology; and Cell Biology, Duke University School of MedicineDurhamUnited States
| | - Ousmane H Cissé
- Critical Care Medicine Department, National Institutes of Health Clinical CenterBethesdaUnited States
| | - Edward A Miao
- Department of Integrative Immunobiology; Molecular Genetics and Microbiology; Pathology; and Cell Biology, Duke University School of MedicineDurhamUnited States
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7
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Nußbaum P, Kureisaite-Ciziene D, Bellini D, van der Does C, Kojic M, Taib N, Yeates A, Tourte M, Gribaldo S, Loose M, Löwe J, Albers SV. Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. Nat Microbiol 2024; 9:698-711. [PMID: 38443575 DOI: 10.1038/s41564-024-01600-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 01/08/2024] [Indexed: 03/07/2024]
Abstract
Cell division in all domains of life requires the orchestration of many proteins, but in Archaea most of the machinery remains poorly characterized. Here we investigate the FtsZ-based cell division mechanism in Haloferax volcanii and find proteins containing photosynthetic reaction centre (PRC) barrel domains that play an essential role in archaeal cell division. We rename these proteins cell division protein B 1 (CdpB1) and CdpB2. Depletions and deletions in their respective genes cause severe cell division defects, generating drastically enlarged cells. Fluorescence microscopy of tagged FtsZ1, FtsZ2 and SepF in CdpB1 and CdpB2 mutant strains revealed an unusually disordered divisome that is not organized into a distinct ring-like structure. Biochemical analysis shows that SepF forms a tripartite complex with CdpB1/2 and crystal structures suggest that these two proteins might form filaments, possibly aligning SepF and the FtsZ2 ring during cell division. Overall our results indicate that PRC-domain proteins play essential roles in FtsZ-based cell division in Archaea.
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Affiliation(s)
- Phillip Nußbaum
- Molecular Biology of Archaea, Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Dom Bellini
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Chris van der Does
- Molecular Biology of Archaea, Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Marko Kojic
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Najwa Taib
- Evolutionary Biology of the Microbial Cell Laboratory, Institut Pasteur, Université Paris Cité, Paris, France
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, Paris, France
| | - Anna Yeates
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Maxime Tourte
- Molecular Biology of Archaea, Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Simonetta Gribaldo
- Evolutionary Biology of the Microbial Cell Laboratory, Institut Pasteur, Université Paris Cité, Paris, France
| | - Martin Loose
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Microbiology, Faculty of Biology, University of Freiburg, Freiburg, Germany.
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.
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8
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Abell-King C, Pokhrel A, Rice SA, Duggin IG, Söderström B. Multispecies bacterial invasion of human host cells. Pathog Dis 2024; 82:ftae012. [PMID: 38794885 PMCID: PMC11180983 DOI: 10.1093/femspd/ftae012] [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: 03/18/2024] [Revised: 05/05/2024] [Accepted: 05/23/2024] [Indexed: 05/26/2024] Open
Abstract
Urinary tract infection (UTI), one of the most common bacterial infections worldwide, is a typical example of an infection that is often polymicrobial in nature. While the overall infection course is known on a macroscale, bacterial behavior is not fully understood at the cellular level and bacterial pathophysiology during multispecies infection is not well characterized. Here, using clinically relevant bacteria, human epithelial bladder cells and human urine, we establish co-infection models combined with high resolution imaging to compare single- and multi-species bladder cell invasion events in three common uropathogens: uropathogenic Escherichia coli (UPEC), Klebsiella pneumoniae and Enterococcus faecalis. While all three species invaded the bladder cells, under flow conditions the Gram-positive E. faecalis was significantly less invasive compared to the Gram-negative UPEC and K. pneumoniae. When introduced simultaneously during an infection experiment, all three bacterial species sometimes invaded the same bladder cell, at differing frequencies suggesting complex interactions between bacterial species and bladder cells. Inside host cells, we observed encasement of E. faecalis colonies specifically by UPEC. During subsequent dispersal from the host cells, only the Gram-negative bacteria underwent infection-related filamentation (IRF). Taken together, our data suggest that bacterial multispecies invasions of single bladder cells are frequent and support earlier studies showing intraspecies cooperation on a biochemical level during UTI.
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Affiliation(s)
- Charlotte Abell-King
- Australian Institute for Microbiology and Infection, University of Technology, Sydney, Ultimo, NSW, 2007, Australia
| | - Alaska Pokhrel
- Australian Institute for Microbiology and Infection, University of Technology, Sydney, Ultimo, NSW, 2007, Australia
| | - Scott A Rice
- Australian Institute for Microbiology and Infection, University of Technology, Sydney, Ultimo, NSW, 2007, Australia
- Microbiomes for One Systems Health and Agriculture and Food, CSIRO, Westmead NSW, 2145 Sydney, Australia
| | - Iain G Duggin
- Australian Institute for Microbiology and Infection, University of Technology, Sydney, Ultimo, NSW, 2007, Australia
| | - Bill Söderström
- Australian Institute for Microbiology and Infection, University of Technology, Sydney, Ultimo, NSW, 2007, Australia
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9
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Billman ZP, Kovacs SB, Wei B, Kang K, Cissé OH, Miao EA. Caspase-1 activates gasdermin A in non-mammals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.28.559989. [PMID: 37987010 PMCID: PMC10659411 DOI: 10.1101/2023.09.28.559989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Gasdermins oligomerize to form pores in the cell membrane, causing regulated lytic cell death called pyroptosis. Mammals encode five gasdermins that can trigger pyroptosis: GSDMA, B, C, D, and E. Caspase and granzyme proteases cleave the linker regions of and activate GSDMB, C, D, and E, but no endogenous activation pathways are yet known for GSDMA. Here, we perform a comprehensive evolutionary analysis of the gasdermin family. A gene duplication of GSDMA in the common ancestor of caecilian amphibians, reptiles and birds gave rise to GSDMA-D in mammals. Uniquely in our tree, amphibian, reptile and bird GSDMA group in a separate clade than mammal GSDMA. Remarkably, GSDMA in numerous bird species contain caspase-1 cleavage sites like YVAD or FASD in the linker. We show that GSDMA from birds, amphibians, and reptiles are all cleaved by caspase-1. Thus, GSDMA was originally cleaved by the host-encoded protease caspase-1. In mammals the caspase-1 cleavage site in GSDMA is disrupted; instead, a new protein, GSDMD, is the target of caspase-1. Mammal caspase-1 uses exosite interactions with the GSDMD C-terminal domain to confer the specificity of this interaction, whereas we show that bird caspase-1 uses a stereotypical tetrapeptide sequence to confer specificity for bird GSDMA. Our results reveal an evolutionarily stable association between caspase-1 and the gasdermin family, albeit a shifting one. Caspase-1 repeatedly changes its target gasdermin over evolutionary time at speciation junctures, initially cleaving GSDME in fish, then GSDMA in amphibians/reptiles/birds, and finally GSDMD in mammals.
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Affiliation(s)
- Zachary P Billman
- Duke University School of Medicine
- National Institutes of Health University of North Carolina at Chapel Hill
- Departments of: Integrative Immunobiology; Molecular Genetics and Microbiology; Cell Biology; Pathology; Durham, NC, USA
- Department of Microbiology and Immunology; Chapel Hill, NC, USA
| | - Stephen B Kovacs
- Duke University School of Medicine
- National Institutes of Health University of North Carolina at Chapel Hill
- Departments of: Integrative Immunobiology; Molecular Genetics and Microbiology; Cell Biology; Pathology; Durham, NC, USA
- Department of Microbiology and Immunology; Chapel Hill, NC, USA
| | - Bo Wei
- Duke University School of Medicine
- Departments of: Integrative Immunobiology; Molecular Genetics and Microbiology; Cell Biology; Pathology; Durham, NC, USA
| | - Kidong Kang
- Duke University School of Medicine
- Departments of: Integrative Immunobiology; Molecular Genetics and Microbiology; Cell Biology; Pathology; Durham, NC, USA
| | - Ousmane H Cissé
- National Institutes of Health
- Critical Care Medicine Department; Bethesda, MD, USA
| | - Edward A Miao
- Duke University School of Medicine
- National Institutes of Health University of North Carolina at Chapel Hill
- Departments of: Integrative Immunobiology; Molecular Genetics and Microbiology; Cell Biology; Pathology; Durham, NC, USA
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10
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Su T, Pang Q, Qi Q. In Vivo DNA Assembly Using the PEDA Method. Methods Mol Biol 2024; 2760:437-445. [PMID: 38468102 DOI: 10.1007/978-1-0716-3658-9_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Simple and efficient DNA assembly methods have been widely used in synthetic biology. Here, we provide the protocol for the recently developed PEDA (phage enzyme-assisted in vivo DNA assembly) method for direct in vivo assembly of individual DNA parts in multiple microorganisms, such as Escherichia coli, Ralstonia eutropha, Pseudomonas putida, Lactobacillus plantarum, and Yarrowia lipolytica. PEDA allows in vivo assembly of DNA fragments with homologous sequences as short as 5 bp, and the efficiency is comparable to the prevailing in vitro DNA assembly, which will broadly boost the rapid progress of synthetic biology.
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Affiliation(s)
- Tianyuan Su
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Qingxiao Pang
- Shandong Lishan Biotechnology Co. LTD, Jinan, People's Republic of China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China.
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11
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Guo L, Yang G. Pioneering DNA assembling techniques and their applications in eukaryotic microalgae. Biotechnol Adv 2024; 70:108301. [PMID: 38101551 DOI: 10.1016/j.biotechadv.2023.108301] [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: 09/27/2023] [Revised: 11/12/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
Assembling DNA fragments is a fundamental manipulation of cloning microalgal genes and carrying out microalgal synthetic biological studies. From the earliest DNA recombination to current trait and metabolic pathway engineering, we are always accompanied by homology-based DNA assembling. The improvement and modification of pioneering DNA assembling techniques and the combinational applications of the available assembling techniques have diversified and complicated the literature environment and aggravated our identification of the core and pioneering methodologies. Identifying the core assembling methodologies and using them appropriately and flourishing them even are important for researchers. A group of microalgae have been evolving as the models for both industrial applications and biological studies. DNA assembling requires researchers to know the methods available and their improvements and evolvements. In this review, we summarized the pioneering (core; leading) DNA assembling techniques developed previously, extended these techniques to their modifications, improvements and their combinations, and highlighted their applications in eukaryotic microalgae. We predicted that the gene(s) will be assembled into a functional cluster (e.g., those involving in a metabolic pathway, and stacked on normal microalgal chromosomes, their artificial episomes and looming artificial chromosomes. It should be particularly pointed out that the techniques mentioned in this review are classified according to the strategy used to assemble the final construct.
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Affiliation(s)
- Li Guo
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Guanpin Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China; Institutes of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; MoE Laboratory of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao 266003, China.
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12
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Arroyo-Urea S, Nazarova AL, Carrión-Antolí Á, Bonifazi A, Battiti FO, Lam JH, Newman AH, Katritch V, García-Nafría J. Structure of the dopamine D3 receptor bound to a bitopic agonist reveals a new specificity site in an expanded allosteric pocket. RESEARCH SQUARE 2023:rs.3.rs-3433207. [PMID: 38196573 PMCID: PMC10775388 DOI: 10.21203/rs.3.rs-3433207/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Although aminergic GPCRs are the target for ~25% of approved drugs, developing subtype selective drugs is a major challenge due to the high sequence conservation at their orthosteric binding site. Bitopic ligands are covalently joined orthosteric and allosteric pharmacophores with the potential to boost receptor selectivity, driven by the binding of the secondary pharmacophore to non-conserved regions of the receptor. Although bitopic ligands have great potential to improve current medications by reducing off-target side effects, the lack of structural information on their binding mode impedes rational design. Here we determine the cryo-EM structure of the hD3R coupled to a GO heterotrimer and bound to the D3R selective bitopic agonist FOB02-04A. Structural, functional and computational analyses provide new insights into its binding mode and point to a new TM2-ECL1-TM1 region, which requires the N-terminal ordering of TM1, as a major determinant of subtype selectivity in aminergic GPCRs. This region is underexploited in drug development, expands the established secondary binding pocket in aminergic GPCRs and could potentially be used to design novel and subtype selective drugs.
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Affiliation(s)
- Sandra Arroyo-Urea
- Institute for Biocomputation and Physics of Complex Systems (BIFI) and Laboratorio de Microscopías Avanzadas (LMA), University of Zaragoza, 50018, Zaragoza, Spain
| | - Antonina L. Nazarova
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089
- Center for New Technologies in Drug Discovery and Development, Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
| | - Ángela Carrión-Antolí
- Institute for Biocomputation and Physics of Complex Systems (BIFI) and Laboratorio de Microscopías Avanzadas (LMA), University of Zaragoza, 50018, Zaragoza, Spain
| | - Alessandro Bonifazi
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Francisco O. Battiti
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Jordy Homing Lam
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089
- Center for New Technologies in Drug Discovery and Development, Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
| | - Amy Hauck Newman
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Vsevolod Katritch
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089
- Center for New Technologies in Drug Discovery and Development, Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Javier García-Nafría
- Institute for Biocomputation and Physics of Complex Systems (BIFI) and Laboratorio de Microscopías Avanzadas (LMA), University of Zaragoza, 50018, Zaragoza, Spain
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13
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Khananisho D, Cumming AJ, Kulakova D, Shilling PJ, Daley DO. Tips for efficiently maintaining pET expression plasmids. Curr Genet 2023; 69:277-287. [PMID: 37938343 PMCID: PMC10716060 DOI: 10.1007/s00294-023-01276-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/09/2023]
Abstract
pET expression plasmids are widely used for producing recombinant proteins in Escherichia coli. Selection and maintenance of cells harboring a pET plasmid are possible using either a Tn3.1-type genetic fragment (which encodes a ß-lactamase and confers resistance to ß-lactam antibiotics) or a Tn903.1-type genetic fragment (which encodes an aminoglycoside-3'-phosphotransferase and confers resistance aminoglycoside antibiotics). Herein we have investigated how efficiently pET plasmids are maintained using these two fragments. The study reveals that pET plasmids are efficiently maintained with both Tn3.1 and Tn903.1 genetic fragments prior to the induction of recombinant protein production, and over short induction times (i.e., 2 h). However, over longer induction times (i.e., 20 h), the efficiency of plasmid maintenance depends on the host strain used, and the type of antibiotic selection cassette used. Based on our collective observations, we have 2 general tips for efficiently maintaining pET plasmids during recombinant production experiments. Tip #1: Use a strain with lowered levels of the T7 RNA polymerase, such as C41(DE3). pET plasmids will be efficiently maintained over long induction times with both the Tn3.1 and Tn903.1 genetic fragments, regardless of whether antibiotics are present during cultivation. Tip #2: If a strain with higher levels of T7 RNA polymerase strain is necessary, such as BL21(DE3)), keep induction times short or use a plasmid containing a Tn903.1-type fragment and select with kanamycin.
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Affiliation(s)
- Diana Khananisho
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Alister J Cumming
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Daria Kulakova
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Patrick J Shilling
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Daniel O Daley
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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14
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Muñoz-Reyes D, McClelland LJ, Arroyo-Urea S, Sánchez-Yepes S, Sabín J, Pérez-Suárez S, Menendez M, Mansilla A, García-Nafría J, Sprang S, Sanchez-Barrena MJ. The neuronal calcium sensor NCS-1 regulates the phosphorylation state and activity of the Gα chaperone and GEF Ric-8A. eLife 2023; 12:e86151. [PMID: 38018500 PMCID: PMC10732572 DOI: 10.7554/elife.86151] [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: 01/12/2023] [Accepted: 11/24/2023] [Indexed: 11/30/2023] Open
Abstract
The neuronal calcium sensor 1 (NCS-1), an EF-hand Ca2+ binding protein, and Ric-8A coregulate synapse number and probability of neurotransmitter release. Recently, the structures of Ric-8A bound to Gα have revealed how Ric-8A phosphorylation promotes Gα recognition and activity as a chaperone and guanine nucleotide exchange factor. However, the molecular mechanism by which NCS-1 regulates Ric-8A activity and its interaction with Gα subunits is not well understood. Given the interest in the NCS-1/Ric-8A complex as a therapeutic target in nervous system disorders, it is necessary to shed light on this molecular mechanism of action at atomic level. We have reconstituted NCS-1/Ric-8A complexes to conduct a multimodal approach and determine the sequence of Ca2+ signals and phosphorylation events that promote the interaction of Ric-8A with Gα. Our data show that the binding of NCS-1 and Gα to Ric-8A are mutually exclusive. Importantly, NCS-1 induces a structural rearrangement in Ric-8A that traps the protein in a conformational state that is inaccessible to casein kinase II-mediated phosphorylation, demonstrating one aspect of its negative regulation of Ric-8A-mediated G-protein signaling. Functional experiments indicate a loss of Ric-8A guanine nucleotide exchange factor (GEF) activity toward Gα when complexed with NCS-1, and restoration of nucleotide exchange activity upon increasing Ca2+ concentration. Finally, the high-resolution crystallographic data reported here define the NCS-1/Ric-8A interface and will allow the development of therapeutic synapse function regulators with improved activity and selectivity.
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Affiliation(s)
- Daniel Muñoz-Reyes
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry 'Blas Cabrera', CSICMadridSpain
| | - Levi J McClelland
- Center for Biomolecular Structure and Dynamics, and Division of Biological Sciences, University of MontanaMissoulaUnited States
| | - Sandra Arroyo-Urea
- Institute for Biocomputation and Physics of Complex Systems (BIFI) and Laboratorio de Microscopías Avanzadas (LMA), University of ZaragozaZaragozaSpain
| | - Sonia Sánchez-Yepes
- Department of Neurobiology, Instituto Ramón y Cajal de Investigación Sanitaria, Hospital Universitario Ramón y CajalMadridSpain
| | - Juan Sabín
- AFFINImeter Scientific & Development team, Software 4 Science DevelopmentsSantiago de CompostelaSpain
- Departamento de Física Aplicada, Universidad de Santiago de CompostelaSantiago de CompostelaSpain
| | - Sara Pérez-Suárez
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry 'Blas Cabrera', CSICMadridSpain
| | - Margarita Menendez
- Department of Biological Physical-Chemisty, Institute of Physical-Chemistry 'Blas Cabrera', CSICMadridSpain
- Ciber of Respiratory Diseases, ISCIIIMadridSpain
| | - Alicia Mansilla
- Department of Neurobiology, Instituto Ramón y Cajal de Investigación Sanitaria, Hospital Universitario Ramón y CajalMadridSpain
- Department of Systems Biology, Universidad de AlcalaMadridSpain
| | - Javier García-Nafría
- Institute for Biocomputation and Physics of Complex Systems (BIFI) and Laboratorio de Microscopías Avanzadas (LMA), University of ZaragozaZaragozaSpain
| | - Stephen Sprang
- Center for Biomolecular Structure and Dynamics, and Division of Biological Sciences, University of MontanaMissoulaUnited States
| | - Maria Jose Sanchez-Barrena
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry 'Blas Cabrera', CSICMadridSpain
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15
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Schichler D, Konle A, Spath EM, Riegler S, Klein A, Seleznev A, Jung S, Wuppermann T, Wetterich N, Borges A, Meyer-Natus E, Havlicek K, Pérez Cabrera S, Niedermüller K, Sajko S, Dohn M, Malzer X, Riemer E, Tumurbaatar T, Djinovic-Carugo K, Dong G, Janzen CJ, Morriswood B. Characterisation of TbSmee1 suggests endocytosis allows surface-bound cargo to enter the trypanosome flagellar pocket. J Cell Sci 2023; 136:jcs261548. [PMID: 37737012 PMCID: PMC10652038 DOI: 10.1242/jcs.261548] [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: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 09/23/2023] Open
Abstract
All endocytosis and exocytosis in the African trypanosome Trypanosoma brucei occurs at a single subdomain of the plasma membrane. This subdomain, the flagellar pocket, is a small vase-shaped invagination containing the root of the single flagellum of the cell. Several cytoskeleton-associated multiprotein complexes are coiled around the neck of the flagellar pocket on its cytoplasmic face. One of these, the hook complex, was proposed to affect macromolecule entry into the flagellar pocket lumen. In previous work, knockdown of T. brucei (Tb)MORN1, a hook complex component, resulted in larger cargo being unable to enter the flagellar pocket. In this study, the hook complex component TbSmee1 was characterised in bloodstream form T. brucei and found to be essential for cell viability. TbSmee1 knockdown resulted in flagellar pocket enlargement and impaired access to the flagellar pocket membrane by surface-bound cargo, similar to depletion of TbMORN1. Unexpectedly, inhibition of endocytosis by knockdown of clathrin phenocopied TbSmee1 knockdown, suggesting that endocytic activity itself is a prerequisite for the entry of surface-bound cargo into the flagellar pocket.
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Affiliation(s)
- Daja Schichler
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Antonia Konle
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Eva-Maria Spath
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Sina Riegler
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Alexandra Klein
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Anna Seleznev
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Sisco Jung
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Timothy Wuppermann
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Noah Wetterich
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Alyssa Borges
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Elisabeth Meyer-Natus
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Katharina Havlicek
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | | | - Korbinian Niedermüller
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Sara Sajko
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Maximilian Dohn
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Xenia Malzer
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Emily Riemer
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Tuguldur Tumurbaatar
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Kristina Djinovic-Carugo
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), 1030 Vienna, Austria
- Department of Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
- European Molecular Biology Laboratory (EMBL) Grenoble, 38000 Grenoble, France
| | - Gang Dong
- Center for Medical Biochemistry, Max Perutz Labs, Medical University of Vienna, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Christian J. Janzen
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Brooke Morriswood
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
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16
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Scaletti ER, Pettersson P, Patrick J, Shilling PJ, Westergren RG, Daley DO, Mäler L, Widmalm G, Stenmark P. Structural and functional insights into the Pseudomonas aeruginosa glycosyltransferase WaaG and the implications for lipopolysaccharide biosynthesis. J Biol Chem 2023; 299:105256. [PMID: 37716703 PMCID: PMC10579960 DOI: 10.1016/j.jbc.2023.105256] [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: 07/11/2023] [Revised: 08/31/2023] [Accepted: 09/10/2023] [Indexed: 09/18/2023] Open
Abstract
The glycosyltransferase WaaG in Pseudomonas aeruginosa (PaWaaG) is involved in the synthesis of the core region of lipopolysaccharides. It is a promising target for developing adjuvants that could help in the uptake of antibiotics. Herein, we have determined structures of PaWaaG in complex with the nucleotide-sugars UDP-glucose, UDP-galactose, and UDP-GalNAc. Structural comparison with the homolog from Escherichia coli (EcWaaG) revealed five key differences in the sugar-binding pocket. Solution-state NMR analysis showed that WT PaWaaG specifically hydrolyzes UDP-GalNAc and unlike EcWaaG, does not hydrolyze UDP-glucose. Furthermore, we found that a PaWaaG mutant (Y97F/T208R/N282A/T283A/T285I) designed to resemble the EcWaaG sugar binding site, only hydrolyzed UDP-glucose, underscoring the importance of the identified amino acids in substrate specificity. However, neither WT PaWaaG nor the PaWaaG mutant capable of hydrolyzing UDP-glucose was able to complement an E. coli ΔwaaG strain, indicating that more remains to be uncovered about the function of PaWaaG in vivo. This structural and biochemical information will guide future structure-based drug design efforts targeting PaWaaG.
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Affiliation(s)
- Emma R Scaletti
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Pontus Pettersson
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Joan Patrick
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Patrick J Shilling
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | | | - Daniel O Daley
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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17
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Neville N, Lehotsky K, Yang Z, Klupt KA, Denoncourt A, Downey M, Jia Z. Modification of histidine repeat proteins by inorganic polyphosphate. Cell Rep 2023; 42:113082. [PMID: 37660293 DOI: 10.1016/j.celrep.2023.113082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/29/2023] [Accepted: 08/16/2023] [Indexed: 09/05/2023] Open
Abstract
Inorganic polyphosphate (polyP) is a linear polymer of orthophosphate that is present in nearly all organisms studied to date. A remarkable function of polyP involves its attachment to lysine residues via non-enzymatic post-translational modification (PTM), which is presumed to be covalent. Here, we show that proteins containing tracts of consecutive histidine residues exhibit a similar modification by polyP, which confers an electrophoretic mobility shift on NuPAGE gels. Our screen uncovers 30 human and yeast histidine repeat proteins that undergo histidine polyphosphate modification (HPM). This polyP modification is histidine dependent and non-covalent in nature, although remarkably it withstands harsh denaturing conditions-a hallmark of covalent PTMs. Importantly, we show that HPM disrupts phase separation and the phosphorylation activity of the human protein kinase DYRK1A, and inhibits the activity of the transcription factor MafB, highlighting HPM as a potential protein regulatory mechanism.
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Affiliation(s)
- Nolan Neville
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Kirsten Lehotsky
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Zhiyun Yang
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Kody A Klupt
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Alix Denoncourt
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Ottawa Institute of Systems Biology, Ottawa, ON K1H 8M5, Canada
| | - Michael Downey
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Ottawa Institute of Systems Biology, Ottawa, ON K1H 8M5, Canada
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
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18
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Du B, Sun M, Hui W, Xie C, Xu X. Recent Advances on Key Enzymes of Microbial Origin in the Lycopene Biosynthesis Pathway. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:12927-12942. [PMID: 37609695 DOI: 10.1021/acs.jafc.3c03942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Lycopene is a common carotenoid found mainly in ripe red fruits and vegetables that is widely used in the food industry due to its characteristic color and health benefits. Microbial synthesis of lycopene is gradually replacing the traditional methods of plant extraction and chemical synthesis as a more economical and productive manufacturing strategy. The biosynthesis of lycopene is a typical multienzyme cascade reaction, and it is important to understand the characteristics of each key enzyme involved and how they are regulated. In this paper, the catalytic characteristics of the key enzymes involved in the lycopene biosynthesis pathway and related studies are first discussed in detail. Then, the strategies applied to the key enzymes of lycopene synthesis, including fusion proteins, enzyme screening, combinatorial engineering, CRISPR/Cas9-based gene editing, DNA assembly, and scaffolding technologies are purposefully illustrated and compared in terms of both traditional and emerging multienzyme regulatory strategies. Finally, future developments and regulatory options for multienzyme synthesis of lycopene and similar secondary metabolites are also discussed.
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Affiliation(s)
- Bangmian Du
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046, Jiangsu Province, China
| | - Mengjuan Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046, Jiangsu Province, China
| | - Wenyang Hui
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046, Jiangsu Province, China
| | - Chengjia Xie
- School of Chemical Engineering, Yangzhou Polytechnic Institute, Yangzhou 225127, Jiangsu Province, China
| | - Xian Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046, Jiangsu Province, China
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19
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Sorida M, Bonasio R. An efficient cloning method to expand vector and restriction site compatibility of Golden Gate Assembly. CELL REPORTS METHODS 2023; 3:100564. [PMID: 37671021 PMCID: PMC10475842 DOI: 10.1016/j.crmeth.2023.100564] [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: 03/02/2023] [Revised: 06/13/2023] [Accepted: 07/28/2023] [Indexed: 09/07/2023]
Abstract
Golden Gate Assembly is an efficient and rapid cloning method but requires dedicated vectors. Here, we modified Golden Gate to expand its compatibility to a broader range of destination vectors while maintaining its strengths. Our Expanded Golden Gate (ExGG) assembly adds to the insert(s) type IIS restriction sites that generate protruding ends compatible with traditional type IIP sites on the recipient vector. The ligated product cannot be cleaved again, owing to a single-base change near the junction. This allows the reaction to proceed in a single tube without an intermediate purification step. ExGG can be used to introduce multiple fragments into a vector simultaneously, including shorter fragments (<100 bp) and fragments with shared sequences, which can be difficult to assemble with other fast cloning strategies. Thus, ExGG extends the convenience of Golden Gate to a much larger space of pre-existing vectors designed for conventional cloning.
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Affiliation(s)
- Masato Sorida
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Roberto Bonasio
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
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20
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McLean ZL, Gao D, Correia K, Roy JCL, Shibata S, Farnum IN, Valdepenas-Mellor Z, Rapuru M, Morini E, Ruliera J, Gillis T, Lucente D, Kleinstiver BP, Lee JM, MacDonald ME, Wheeler VC, Pinto RM, Gusella JF. PMS1 as a target for splice modulation to prevent somatic CAG repeat expansion in Huntington's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550489. [PMID: 37547003 PMCID: PMC10402039 DOI: 10.1101/2023.07.25.550489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Huntington's disease (HD) is a dominantly inherited neurodegenerative disorder whose motor, cognitive, and behavioral manifestations are caused by an expanded, somatically unstable CAG repeat in the first exon of HTT that lengthens a polyglutamine tract in huntingtin. Genome-wide association studies (GWAS) have revealed DNA repair genes that influence the age-at-onset of HD and implicate somatic CAG repeat expansion as the primary driver of disease timing. To prevent the consequent neuronal damage, small molecule splice modulators (e.g., branaplam) that target HTT to reduce the levels of huntingtin are being investigated as potential HD therapeutics. We found that the effectiveness of the splice modulators can be influenced by genetic variants, both at HTT and other genes where they promote pseudoexon inclusion. Surprisingly, in a novel hTERT-immortalized retinal pigment epithelial cell (RPE1) model for assessing CAG repeat instability, these drugs also reduced the rate of HTT CAG expansion. We determined that the splice modulators also affect the expression of the mismatch repair gene PMS1, a known modifier of HD age-at-onset. Genome editing at specific HTT and PMS1 sequences using CRISPR-Cas9 nuclease confirmed that branaplam suppresses CAG expansion by promoting the inclusion of a pseudoexon in PMS1, making splice modulation of PMS1 a potential strategy for delaying HD onset. Comparison with another splice modulator, risdiplam, suggests that other genes affected by these splice modulators also influence CAG instability and might provide additional therapeutic targets.
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Affiliation(s)
- Zachariah L. McLean
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
| | - Dadi Gao
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
| | - Kevin Correia
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jennie C. L. Roy
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Shota Shibata
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
| | - Iris N. Farnum
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Zoe Valdepenas-Mellor
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Manasa Rapuru
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Elisabetta Morini
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Jayla Ruliera
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Tammy Gillis
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Diane Lucente
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Benjamin P. Kleinstiver
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Jong-Min Lee
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
| | - Marcy E. MacDonald
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
| | - Vanessa C. Wheeler
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Ricardo Mouro Pinto
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
| | - James F. Gusella
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Medical and Population Genetics Program, the Broad Institute of M.I.T. and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
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21
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Xiong X, Lu Z, Ma L, Zhai C. Applications of Programmable Endonucleases in Sequence- and Ligation-Independent Seamless DNA Assembly. Biomolecules 2023; 13:1022. [PMID: 37509059 PMCID: PMC10377497 DOI: 10.3390/biom13071022] [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: 05/05/2023] [Revised: 06/02/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Programmable endonucleases, such as Cas (Clustered Regularly-Interspaced Short Repeats-associated proteins) and prokaryotic Argonaute (pAgo), depend on base pairing of the target DNA with the guide RNA or DNA to cleave DNA strands. Therefore, they are capable of recognizing and cleaving DNA sequences at virtually any arbitrary site. The present review focuses on the commonly used in vivo and in vitro recombination-based gene cloning methods and the application of programmable endonucleases in these sequence- and ligation-independent DNA assembly methods. The advantages and shortcomings of the programmable endonucleases utilized as tools for gene cloning are also discussed in this review.
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Affiliation(s)
- Xingchen Xiong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Zhiwen Lu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Chao Zhai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
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22
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Poon NY, Sinskey AJ, Zhou K. Engineering Escherichia coli to assimilate β-alanine as a major carbon source. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12574-5. [PMID: 37249589 DOI: 10.1007/s00253-023-12574-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 05/31/2023]
Abstract
The threat of global plastic waste accumulation has spurred the exploration of plastics derived from biological sources. A well-known example is polyester made of 1,3-propanediol (1,3-PDO). However, there is no known pathway to assimilate 1,3-PDO into the central carbon metabolism, posing a potential challenge to upcycling such plastic wastes. Here, we proposed that the 1,3-PDO assimilation pathway could pass through malonate semialdehyde (MSA) as an intermediate. Since MSA is a toxic aldehyde, β-alanine was chosen as a surrogate substrate in this study to construct the lower part of the proposed pathway. To this end, we successfully engineered E. coli MG1655 to assimilate β-alanine as the major carbon source. β-alanine could be easily converted into MSA using a β-alanine/pyruvate transaminase from Pseudomonas aeruginosa (PaBapt). However, the subsequent step to generate acetyl-CoA from MSA was unknown. After a series of phenotype screenings, adaptive laboratory evolution and transcriptomic analysis, two CoA-acylating MSA dehydrogenases from Vibrio natriegens (VnMmsD), were found to be able to complete the metabolic pathway. Optical density at 600 nm (OD600) of the resulting strain E. coli BA02 could reach 4.5 after 96 h. Two approaches were subsequently used to improve its performance. First, PaBapt and both VnMmsDs were expressed from a single plasmid to mitigate antibiotic stress. Second, a native 3-hydroxy acid dehydrogenase (EcYdfG) was disrupted to address the carbon loss to 3-hydroxypropionate (3-HP) production from MSA. OD600 of the best-performing strain E. coli BA07∆ could reach 6 within 24 h using 5 g/L β-alanine. The construction of E. coli BA07∆ lays a solid foundation to establishing a 1,3-PDO assimilation pathway. KEYPOINTS: • This study demonstrates the implementation of a metabolic pathway to assimilate β-alanine as the major carbon source in E. coli MG1655. • Two V. natriegens CoA-acylating methyl malonate semialdehyde dehydrogenases were used to complete the pathway in E. coli BA02. • The construction of E. coli BA02 also revealed the plasmid fusion event between two plasmids with the same replication origin.
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Affiliation(s)
- Nga Yu Poon
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore
| | - Anthony J Sinskey
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Kang Zhou
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore.
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23
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Farfán-Pira KJ, Martínez-Cuevas TI, Evans TA, Nahmad M. A cis-regulatory sequence of the selector gene vestigial drives the evolution of wing scaling in Drosophila species. J Exp Biol 2023; 226:jeb244692. [PMID: 37078652 PMCID: PMC10234621 DOI: 10.1242/jeb.244692] [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: 06/23/2022] [Accepted: 04/13/2023] [Indexed: 04/21/2023]
Abstract
Scaling between specific organs and overall body size has long fascinated biologists, being a primary mechanism by which organ shapes evolve. Yet, the genetic mechanisms that underlie the evolution of scaling relationships remain elusive. Here, we compared wing and fore tibia lengths (the latter as a proxy of body size) in Drosophila melanogaster, Drosophila simulans, Drosophila ananassae and Drosophila virilis, and show that the first three of these species have roughly a similar wing-to-tibia scaling behavior. In contrast, D. virilis exhibits much smaller wings relative to their body size compared with the other species and this is reflected in the intercept of the wing-to-tibia allometry. We then asked whether the evolution of this relationship could be explained by changes in a specific cis-regulatory region or enhancer that drives expression of the wing selector gene, vestigial (vg), whose function is broadly conserved in insects and contributes to wing size. To test this hypothesis directly, we used CRISPR/Cas9 to replace the DNA sequence of the predicted Quadrant Enhancer (vgQE) from D. virilis for the corresponding vgQE sequence in the genome of D. melanogaster. Strikingly, we discovered that D. melanogaster flies carrying the D. virilis vgQE sequence have wings that are significantly smaller with respect to controls, partially shifting the intercept of the wing-to-tibia scaling relationship towards that observed in D. virilis. We conclude that a single cis-regulatory element in D. virilis contributes to constraining wing size in this species, supporting the hypothesis that scaling could evolve through genetic variations in cis-regulatory elements.
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Affiliation(s)
- Keity J. Farfán-Pira
- Department of Physiology, Biophysics and Neurosciences, Centre for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav-IPN), Mexico City 07360, Mexico
| | - Teresa I. Martínez-Cuevas
- Department of Physiology, Biophysics and Neurosciences, Centre for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav-IPN), Mexico City 07360, Mexico
| | - Timothy A. Evans
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Marcos Nahmad
- Department of Physiology, Biophysics and Neurosciences, Centre for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav-IPN), Mexico City 07360, Mexico
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24
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Arroyo-Urea S, Watson JF, García-Nafría J. Molecular Cloning Using In Vivo DNA Assembly. Methods Mol Biol 2023; 2633:33-44. [PMID: 36853454 DOI: 10.1007/978-1-0716-3004-4_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Here we describe the in vivo DNA assembly approach, where molecular cloning procedures are performed using an E. coli recA-independent recombination pathway, which assembles linear fragments of DNA with short homologous termini. This pathway is present in all standard laboratory E. coli strains and, by bypassing the need for in vitro DNA assembly, allows simplified molecular cloning to be performed without the plasmid instability issues associated with specialized recombination-cloning bacterial strains. The methodology requires specific primer design and can perform all standard plasmid modifications (insertions, deletions, mutagenesis, and sub-cloning) in a rapid, simple, and cost-efficient manner, as it does not require commercial kits or specialized bacterial strains. Additionally, this approach can be used to perform complex procedures such as multiple modifications to a plasmid, as up to 6 linear fragments can be assembled in vivo by this recombination pathway. Procedures generally require less than 3 h, involving PCR amplification, DpnI digestion of template DNA, and transformation, upon which circular plasmids are assembled. In this chapter we describe the requirements, procedure, and potential pitfalls when using this technique, as well as protocol variations to overcome the most common issues.
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Affiliation(s)
- Sandra Arroyo-Urea
- Institute for Biocomputation and Physics of Complex Systems (BIFI) and Laboratorio de Microscopías Avanzadas (LMA), University of Zaragoza, Zaragoza, Spain
| | | | - Javier García-Nafría
- Institute for Biocomputation and Physics of Complex Systems (BIFI) and Laboratorio de Microscopías Avanzadas (LMA), University of Zaragoza, Zaragoza, Spain.
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25
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Cho G, Lee J, Kim J. Identification of a novel 5-aminomethyl-2-thiouridine methyltransferase in tRNA modification. Nucleic Acids Res 2023; 51:1971-1983. [PMID: 36762482 PMCID: PMC9976899 DOI: 10.1093/nar/gkad048] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/07/2023] [Accepted: 01/18/2023] [Indexed: 02/11/2023] Open
Abstract
The uridine at the 34th position of tRNA, which is able to base pair with the 3'-end codon on mRNA, is usually modified to influence many aspects of decoding properties during translation. Derivatives of 5-methyluridine (xm5U), which include methylaminomethyl (mnm-) or carboxymethylaminomethyl (cmnm-) groups at C5 of uracil base, are widely conserved at the 34th position of many prokaryotic tRNAs. In Gram-negative bacteria such as Escherichia coli, a bifunctional MnmC is involved in the last two reactions of the biosynthesis of mnm5(s2)U, in which the enzyme first converts cmnm5(s2)U to 5-aminomethyl-(2-thio)uridine (nm5(s2)U) and subsequently installs the methyl group to complete the formation of mnm5(s2)U. Although mnm5s2U has been identified in tRNAs of Gram-positive bacteria and plants as well, their genomes do not contain an mnmC ortholog and the gene(s) responsible for this modification is unknown. We discovered that MnmM, previously known as YtqB, is the methyltransferase that converts nm5s2U to mnm5s2U in Bacillus subtilis through comparative genomics, gene complementation experiments, and in vitro assays. Furthermore, we determined X-ray crystal structures of MnmM complexed with anticodon stem loop of tRNAGln. The structures provide the molecular basis underlying the importance of U33-nm5s2U34-U35 as the key determinant for the specificity of MnmM.
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Affiliation(s)
- Gyuhyeok Cho
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Jangmin Lee
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Jungwook Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
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26
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Tavares M, Sousa-Filho JC, Machado IA, Gonçales RA, Antunes D, Mendes-Frias A, Silvestre R, Carvalho A, Torrado E, Cunha C, Rodrigues F. Development of a Versatile Toolbox for Genetic Manipulation of Sporothrix brasiliensis. Microbiol Spectr 2023; 11:e0456422. [PMID: 36847570 PMCID: PMC10101026 DOI: 10.1128/spectrum.04564-22] [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: 11/08/2022] [Accepted: 02/06/2023] [Indexed: 03/01/2023] Open
Abstract
Sporothrix brasiliensis has emerged as the most virulent species in the Sporothrix schenckii complex, accounting for sporotrichosis. Albeit the new insights into the understanding of host-pathogen interactions and comparative genomics of this fungi, the lack of genetic tools has hindered significant advances in this field of research. Here, we established an Agrobacterium tumefaciens-mediated transformation (ATMT) system to transform different strains of S. brasiliensis. We report parameters that account for a transformation efficiency of 3,179 ± 1,171 transformants/co-cultivation, which include the use of A. tumefaciens AGL-1 in a 2:1 ratio (bacteria:fungi) during 72 h at 26°C. Our data show that a single-copy transgene is transferred to S. brasiliensis that is mitotically stable in 99% of cells after 10 generations without selective pressure. In addition, we created a plasmid toolkit that allows the establishment of fusion proteins of any S. brasiliensis gene of interest with sGFP or mCherry under the control of the GAPDH or H2A endogenous promoters. These modules allow different levels of expression of the desired fusion. Moreover, we successfully targeted these fluorescent proteins to the nucleus and used fluorescence-tagged strains to assess phagocytosis. Overall, our data show that the ATMT system is an easy-to-use and efficient genetic toolbox for studies on recombinant expression and gene function in S. brasiliensis. IMPORTANCE Sporotrichosis is the most prevalent subcutaneous mycosis worldwide and has recently become a public health concern. Although immunocompetent hosts are also prone to sporotrichosis, immunodeficient hosts often develop a more severe and disseminated form of disease. To date, the Rio de Janeiro state in Brazil is the most significant feline zoonotic transmission epicenter in the world, with more than 4,000 human and feline diagnosed cases. Cats play an essential role in the S. brasiliensis infection due to their high susceptibility and transmissibility to other felines and humans. S. brasiliensis is the most virulent etiological agent of sporotrichosis, causing the most severe clinical manifestations. Despite the increasing incidence of sporotrichosis, the identification of virulence traits important for disease establishment, development, and severity has been lacking. In this work, we established an efficient genetic toolbox to manipulate S. brasiliensis that will guide future studies to define new virulence mechanisms and a better understanding of host-pathogen interactions from a molecular perspective.
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Affiliation(s)
- Matheus Tavares
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Jorge Carlos Sousa-Filho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Ian Alves Machado
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Relber Aguiar Gonçales
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Daniela Antunes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Ana Mendes-Frias
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Ricardo Silvestre
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Agostinho Carvalho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Egídio Torrado
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Cristina Cunha
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Fernando Rodrigues
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Guimarães/Braga, Portugal
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27
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Amstrup SK, Ong SC, Sofos N, Karlsen JL, Skjerning RB, Boesen T, Enghild JJ, Hove-Jensen B, Brodersen DE. Structural remodelling of the carbon-phosphorus lyase machinery by a dual ABC ATPase. Nat Commun 2023; 14:1001. [PMID: 36813778 PMCID: PMC9947105 DOI: 10.1038/s41467-023-36604-y] [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: 05/03/2022] [Accepted: 02/08/2023] [Indexed: 02/24/2023] Open
Abstract
In Escherichia coli, the 14-cistron phn operon encoding carbon-phosphorus lyase allows for utilisation of phosphorus from a wide range of stable phosphonate compounds containing a C-P bond. As part of a complex, multi-step pathway, the PhnJ subunit was shown to cleave the C-P bond via a radical mechanism, however, the details of the reaction could not immediately be reconciled with the crystal structure of a 220 kDa PhnGHIJ C-P lyase core complex, leaving a significant gap in our understanding of phosphonate breakdown in bacteria. Here, we show using single-particle cryogenic electron microscopy that PhnJ mediates binding of a double dimer of the ATP-binding cassette proteins, PhnK and PhnL, to the core complex. ATP hydrolysis induces drastic structural remodelling leading to opening of the core complex and reconfiguration of a metal-binding and putative active site located at the interface between the PhnI and PhnJ subunits.
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Affiliation(s)
- Søren K Amstrup
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark.,Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen N, Denmark
| | - Sui Ching Ong
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark
| | - Nicholas Sofos
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark.,Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen N, Denmark
| | - Jesper L Karlsen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark
| | - Ragnhild B Skjerning
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark
| | - Thomas Boesen
- Interdisciplinary Nanoscience Centre (iNANO) Aarhus University, Gustav Wieds Vej 14, DK-8000, Aarhus C, Denmark
| | - Jan J Enghild
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark
| | - Bjarne Hove-Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark
| | - Ditlev E Brodersen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000, Aarhus C, Denmark.
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28
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Juan T, Ribeiro da Silva A, Cardoso B, Lim S, Charteau V, Stainier DYR. Multiple pkd and piezo gene family members are required for atrioventricular valve formation. Nat Commun 2023; 14:214. [PMID: 36639367 PMCID: PMC9839778 DOI: 10.1038/s41467-023-35843-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Abstract
Cardiac valves ensure unidirectional blood flow through the heart, and altering their function can result in heart failure. Flow sensing via wall shear stress and wall stretching through the action of mechanosensors can modulate cardiac valve formation. However, the identity and precise role of the key mechanosensors and their effectors remain mostly unknown. Here, we genetically dissect the role of Pkd1a and other mechanosensors in atrioventricular (AV) valve formation in zebrafish and identify a role for several pkd and piezo gene family members in this process. We show that Pkd1a, together with Pkd2, Pkd1l1, and Piezo2a, promotes AV valve elongation and cardiac morphogenesis. Mechanistically, Pkd1a, Pkd2, and Pkd1l1 all repress the expression of klf2a and klf2b, transcription factor genes implicated in AV valve development. Furthermore, we find that the calcium-dependent protein kinase Camk2g is required downstream of Pkd function to repress klf2a expression. Altogether, these data identify, and dissect the role of, several mechanosensors required for AV valve formation, thereby broadening our understanding of cardiac valvulogenesis.
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Affiliation(s)
- Thomas Juan
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany. .,German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Germany. .,Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany.
| | - Agatha Ribeiro da Silva
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Germany
| | - Bárbara Cardoso
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Germany
| | - SoEun Lim
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Germany
| | - Violette Charteau
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Germany.,Institute for Molecules and Materials (IMM), Department of Biomolecular Chemistry, Radboud University, Nijmegen, The Netherlands
| | - Didier Y R Stainier
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim, Germany. .,German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Bad Nauheim, Germany. .,Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany.
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29
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Wang X, Teng C, Wei H, Liu S, Xuan H, Peng W, Li Q, Hao H, Lyu Q, Lyu S, Fan Y. Development of a set of novel binary expression vectors for plant gene function analysis and genetic transformation. FRONTIERS IN PLANT SCIENCE 2023; 13:1104905. [PMID: 36714700 PMCID: PMC9877630 DOI: 10.3389/fpls.2022.1104905] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 12/21/2022] [Indexed: 05/29/2023]
Abstract
With the advent of multiple omics and Genome-Wide Association Studies (GWAS) technology, genome-scale functional analysis of candidate genes is to be conducted in diverse plant species. Construction of plant binary expression vectors is the prerequisite for gene function analysis. Therefore, it is of significance to develop a set of plant binary expression vectors with highly efficient, inexpensive, and convenient cloning method, and easy-to-use in screening of positive recombinant in Escherichia coli. In this study, we developed a set of plant binary expression vectors, termed pBTR vectors, based on Golden Gate cloning using BsaI restriction site. Foreign DNA fragment of interest (FDI) can be cloned into the destination pBTR by one-step digestion-ligation reaction in a single tube, and even the FDI contains internal BsaI site(s). Markedly, in one digestion-ligation reaction, multiple FDIs (exemplified by cloning four soybean Glyma.02g025400, Glyma.05g201700, Glyma.06g165700, and Glyma.17g095000 genes) can be cloned into the pBTR vector to generate multiple corresponding expression constructs (each expression vector carrying an FDI). In addition, the pBTR vectors carry the visual marker, a brightness monomeric red fluorescent protein mScarlet-I, that can be observed with the unaided eye in screening of positive recombinants without the use of additional reagents/equipment. The reliability of the pBTR vectors was validated in plants by overexpression of AtMyb75/PAP1 in tomato and GUSPlus in soybean roots via Agrobacterium rhizogenes-mediated transformation, promoter activity analysis of AtGCSpro in Arabidopsis via A. tumefaciens-mediated transformation, and protein subcellular localization of the Vitis vinifera VvCEB1opt in tobacco, respectively. These results demonstrated that the pBTR vectors can be used in analysis of gene (over)expression, promoter activity, and protein subcellular localization. These vectors will contribute to speeding up gene function analysis and the process of plant molecular breeding.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Shanhua Lyu
- *Correspondence: Shanhua Lyu, ; ; Yinglun Fan,
| | - Yinglun Fan
- *Correspondence: Shanhua Lyu, ; ; Yinglun Fan,
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30
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Sobeh AM, Eichhorn CD. C-terminal determinants for RNA binding motif 7 protein stability and RNA recognition. Biophys Chem 2023; 292:106928. [PMID: 36427363 PMCID: PMC9768861 DOI: 10.1016/j.bpc.2022.106928] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 10/13/2022] [Accepted: 10/30/2022] [Indexed: 11/09/2022]
Abstract
The 7SK ribonucleoprotein (RNP) is a critical regulator of eukaryotic transcription. Recently, RNA binding motif 7 (RBM7) containing an RNA recognition motif (RRM) was reported to associate with 7SK RNA and core 7SK RNP protein components in response to DNA damage. However, little is known about the mode of RBM7-7SK RNA recognition. Here, we found that RRM constructs containing extended C-termini have increased solubility compared to a minimal RRM construct, although these constructs aggregate in a temperature and concentration-dependent manner. Using solution NMR dynamics experiments, we identified additional structural features observed previously in crystal but not in solution structures. To identify potential RBM7-7SK RNA binding sites, we analyzed deposited data from in cellulo crosslinking experiments and found that RBM7 primarily crosslinks to the distal region of 7SK stem-loop 3 (SL3). Electrophoretic mobility shift assays and NMR chemical shift perturbation experiments showed weak binding to 7SK SL3 constructs in vitro. Together, these results provide new insights into RBM7 RRM folding and recognition of 7SK RNA.
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Affiliation(s)
- Amr M Sobeh
- Department of Chemistry, University of Nebraska, 639 North 12th St, Lincoln, NE 68588, USA
| | - Catherine D Eichhorn
- Department of Chemistry, University of Nebraska, 639 North 12th St, Lincoln, NE 68588, USA.
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31
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Jia H, Couto-Rodriguez R, Johnson S, Medina S, Novillo B, Huynh P, Kim M, Cooper C, Michalik M, Siew B, Turesson E, Maupin-Furlow JA. Highly efficient and simple SSPER and rrPCR approaches for the accurate site-directed mutagenesis of large and small plasmids. N Biotechnol 2022; 72:22-28. [PMID: 36007808 PMCID: PMC9742187 DOI: 10.1016/j.nbt.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/16/2022] [Accepted: 08/21/2022] [Indexed: 12/27/2022]
Abstract
Advances are needed in the site-directed mutagenesis of large plasmids for protein structure-function studies, as current methods are often inefficient, complicated and time-consuming. Here two new methods are reported that overcome these difficulties, namely the single primer extension reaction (SSPER) strategy that reaches 100% efficiency and the reduce recycle PCR (rrPCR) method that is advantageous in generating single and pairwise combinations of mutations. Both methods are distinguished from current technologies by the addition of a step that easily removes the oligonucleotide primer(s) after the first reaction, thus allowing for the addition of a second reaction in chronological sequence to generate and isolate the appropriate DNA product with the site-directed mutation(s). High efficiency of the methods is demonstrated by generating single and paired combinations of the 11 site-directed mutations targeted on 5 different plasmid DNA templates ranging from 10 to 12 kb and 57-60% GC-content at a rate of 50-100%. Overall, the methods are demonstrated to be (i) highly accurate, allowing for screening of plasmids by DNA sequencing, (ii) streamlined to generate the mutations within a single day, (iii) cost-effective in requiring only two primers and two enzymes (DpnI and a proofreading DNA polymerase), (iv) straightforward in primer design, (v) applicable for both large and small plasmids, and (vi) easily implemented by entry level researchers.
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Affiliation(s)
- Huiyong Jia
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.
| | - Ricardo Couto-Rodriguez
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.
| | - Sharon Johnson
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.
| | - Stephanie Medina
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.
| | - Brianna Novillo
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.
| | - Peter Huynh
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.
| | - Matt Kim
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.
| | - Cade Cooper
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.
| | - Meagan Michalik
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.
| | - Benjamin Siew
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.
| | - Elise Turesson
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32608, USA.
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32
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Nozaki S. Rapid and Accurate Assembly of Large DNA Assisted by In Vitro Packaging of Bacteriophage. ACS Synth Biol 2022; 11:4113-4122. [PMID: 36446634 PMCID: PMC9764419 DOI: 10.1021/acssynbio.2c00419] [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] [Indexed: 12/05/2022]
Abstract
Development of DNA assembly methods made it possible to construct large DNA. However, achieving a large DNA assembly easily, accurately, and at a low cost remains a challenge. This study shows that DNA assembled only by annealing of overlapping single-stranded DNA ends, which are generated by exonuclease treatment, without ligation can be packaged in phage particles and can also be transduced into bacterial cells. Based on this, I developed a simple method to construct long DNA of about 40-50 kb from five to ten PCR fragments using the bacteriophage in vitro packaging system. This method, namely, iPac (in vitro Packaging-assisted DNA assembly), allowed accurate and rapid construction of large plasmids and phage genomes. This simple method will accelerate research in molecular and synthetic biology, including the construction of gene circuits or the engineering of metabolic pathways.
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Affiliation(s)
- Shingo Nozaki
- Department
of Life Science, College of Science, Rikkyo
University, Tokyo 171-8501, Japan,Graduate
School of Advanced Science and Engineering, Hiroshima University, Hiroshima 739-8527, Japan,
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33
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Shilling PJ, Khananisho D, Cumming J, Söderström B, Daley DO. Signal Amplification of araC pBAD Using a Standardised Translation Initiation Region. Synth Biol (Oxf) 2022; 7:ysac009. [PMID: 35903559 PMCID: PMC9316229 DOI: 10.1093/synbio/ysac009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/11/2022] [Accepted: 07/04/2022] [Indexed: 11/16/2022] Open
Abstract
araC pBAD is a genetic fragment that regulates the expression of the araBAD operon in bacteria, which is required for the metabolism of L-arabinose. It is widely used in bioengineering applications because it can drive regulatable and titratable expression of genes and genetic pathways in microbial cell factories. A notable limitation of araC pBAD is that it generates a low signal when induced with high concentrations of L-arabinose (the maximum ON state). Herein we have amplified the maximum ON state of araC pBAD by coupling it to a synthetically evolved translation initiation region (TIREVOL). The coupling maintains regulatable and titratable expression from araC pBAD and yet increases the maximal ON state by >5-fold. The general principle demonstrated in the study can be applied to amplify the signal from similar genetic modules.
Graphical Abstract
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Affiliation(s)
- Patrick J Shilling
- Department of Biochemistry and Biophysics, Stockholm University , Stockholm, Sweden
| | - Diana Khananisho
- Department of Biochemistry and Biophysics, Stockholm University , Stockholm, Sweden
| | - James Cumming
- Department of Biochemistry and Biophysics, Stockholm University , Stockholm, Sweden
| | - Bill Söderström
- Australian Institute for Microbiology and Infection, University of Technology Sydney , Sydney, New South Wales, Australia
| | - Daniel O Daley
- Department of Biochemistry and Biophysics, Stockholm University , Stockholm, Sweden
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34
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Söderström B, Pittorino MJ, Daley DO, Duggin IG. Assembly dynamics of FtsZ and DamX during infection-related filamentation and division in uropathogenic E. coli. Nat Commun 2022; 13:3648. [PMID: 35752634 PMCID: PMC9233674 DOI: 10.1038/s41467-022-31378-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 06/15/2022] [Indexed: 11/09/2022] Open
Abstract
During infection of bladder epithelial cells, uropathogenic Escherichia coli (UPEC) can stop dividing and grow into highly filamentous forms. Here, we find that some filaments of E. coli UTI89 released from infected cells grow very rapidly and by more than 100 μm before initiating division, whereas others do not survive, suggesting that infection-related filamentation (IRF) is a stress response that promotes bacterial dispersal. IRF is accompanied by unstable, dynamic repositioning of FtsZ division rings. In contrast, DamX, which is associated with normal cell division and is also essential for IRF, is distributed uniformly around the cell envelope during filamentation. When filaments initiate division to regenerate rod cells, DamX condenses into stable rings prior to division. The DamX rings maintain consistent thickness during constriction and remain at the septum until after membrane fusion. Deletion of damX affects vegetative cell division in UTI89 (but not in the model E. coli K-12), and, during infection, blocks filamentation and reduces bacterial cell integrity. IRF therefore involves DamX distribution throughout the membrane and prevention of FtsZ ring stabilization, leading to cell division arrest. DamX then reassembles into stable division rings for filament division, promoting dispersal and survival during infection.
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Affiliation(s)
- Bill Söderström
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, 2007, NSW, Australia.
| | - Matthew J Pittorino
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, 2007, NSW, Australia
| | - Daniel O Daley
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, 106 91, Sweden
| | - Iain G Duggin
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, 2007, NSW, Australia
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35
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Pang Q, Ma S, Han H, Jin X, Liu X, Su T, Qi Q. Phage Enzyme-Assisted Direct In Vivo DNA Assembly in Multiple Microorganisms. ACS Synth Biol 2022; 11:1477-1487. [PMID: 35298132 DOI: 10.1021/acssynbio.1c00529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The assembly of DNA fragments is extremely important for molecular biology. Increasing numbers of studies have focused on streamlining the laborious and costly protocols via in vivo DNA assembly. However, the existing methods were mainly developed for Escherichia coli or Saccharomyces cerevisiae, whereas there are few direct in vivo DNA assembly methods for other microorganisms. The use of shuttle vectors and tedious plasmid extraction and transformation procedures make DNA cloning in other microorganisms laborious and inefficient, especially for DNA library construction. In this study, we developed a "phage enzyme-assisted in vivo DNA assembly" (PEDA) method via combinatorial expression of T5 exonuclease and T4 DNA ligase. PEDA facilitated the in vivo assembly of DNA fragments with homologous sequences as short as 5 bp, and it is applicable to multiple microorganisms, such as Ralstonia eutropha, Pseudomonas putida, Lactobacillus plantarum, and Yarrowia lipolytica. The cloning efficiency of optimized PEDA is much higher than that of the existing in vivo DNA assembly methods and comparable to that of in vitro DNA assembly, making it extremely suitable for DNA library cloning. Collectively, PEDA will boost the application of in vivo DNA assembly in various microorganisms.
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Affiliation(s)
- Qingxiao Pang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People’s Republic of China
| | - Shuai Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People’s Republic of China
| | - Hao Han
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People’s Republic of China
| | - Xin Jin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People’s Republic of China
| | - Xiaoqin Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People’s Republic of China
| | - Tianyuan Su
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People’s Republic of China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People’s Republic of China
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36
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Bowlin MQ, Long AR, Huffines JT, Gray MJ. The role of nitrogen-responsive regulators in controlling inorganic polyphosphate synthesis in Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2022; 168:001185. [PMID: 35482529 PMCID: PMC10233264 DOI: 10.1099/mic.0.001185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/10/2022] [Indexed: 12/22/2022]
Abstract
Inorganic polyphosphate (polyP) is synthesized by bacteria under stressful environmental conditions and acts by a variety of mechanisms to promote cell survival. While the kinase that synthesizes polyP (PPK, encoded by the ppk gene) is well known, ppk transcription is not activated by environmental stress and little is understood about how environmental stress signals lead to polyP accumulation. Previous work has shown that the transcriptional regulators DksA, RpoN (σ54) and RpoE (σ24) positively regulate polyP production, but not ppk transcription, in Escherichia coli. In this work, we examine the role of the alternative sigma factor RpoN and nitrogen starvation stress response pathways in controlling polyP synthesis. We show that the RpoN enhancer binding proteins GlnG and GlrR impact polyP production, and uncover a new role for the nitrogen phosphotransferase regulator PtsN (EIIANtr) as a positive regulator of polyP production, acting upstream of DksA, downstream of RpoN and apparently independently of RpoE. However, neither these regulatory proteins nor common nitrogen metabolites appear to act directly on PPK, and the precise mechanism(s) by which polyP production is modulated after stress remain(s) unclear. Unexpectedly, we also found that the genes that impact polyP production vary depending on the composition of the rich media in which the cells were grown before exposure to polyP-inducing stress. These results constitute progress towards deciphering the regulatory networks driving polyP production under stress, and highlight the remarkable complexity of this regulation and its connections to a broad range of stress-sensing pathways.
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Affiliation(s)
- Marvin Q. Bowlin
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Abagail Renee Long
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Joshua T. Huffines
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Michael Jeffrey Gray
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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37
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Golden Gate assembly of BioBrick-compliant parts using Type II restriction endonucleases. Biotechniques 2022; 72:185-193. [PMID: 35255734 DOI: 10.2144/btn-2021-0083] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Aims: New methods of DNA recombination that capture the principal advantages of the BioBrick standard (ease of design) and Golden Gate assembly (decreased labor) are demonstrated here. Methods & materials: Both methods employ DNA methyltransferase expression vectors, available from Addgene, that protect selected sites on different plasmids from particular Type II restriction endonucleases. No other reagents are required. Results: The 4R/2M discontinuous DNA assembly is more efficient (produces more desired recombinant plasmids) and as specific (produces few undesired recombination products) as conventional subcloning. The 5RM continuous DNA assembly is approximately as efficient and specific as conventional Golden Gate assembly, even though in vivo methylation of one plasmid is incomplete. Conclusion: Both methylase-assisted methods streamline BioBrick assembly workflows without complicating the design of synthetic parts.
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38
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Cumming A, Khananisho D, Harris R, Bayer CN, Nørholm MHH, Jamshidi S, Ilag LL, Daley DO. Antibiotic-Efficient Genetic Cassette for the TEM-1 β-Lactamase That Improves Plasmid Performance. ACS Synth Biol 2022; 11:241-253. [PMID: 34982550 PMCID: PMC8787818 DOI: 10.1021/acssynbio.1c00393] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Indexed: 11/30/2022]
Abstract
Antibiotic resistance cassettes are indispensable tools in recombinant DNA technology, synthetic biology, and metabolic engineering. The genetic cassette encoding the TEM-1 β-lactamase (denoted Tn3.1) is one of the most commonly used and can be found in more than 120 commercially available bacterial expression plasmids (e.g., the pET, pUC, pGEM, pQE, pGEX, pBAD, and pSEVA series). A widely acknowledged problem with the cassette is that it produces excessively high titers of β-lactamase that rapidly degrade β-lactam antibiotics in the culture media, leading to loss of selective pressure, and eventually a large percentage of cells that do not have a plasmid. To address these shortcomings, we have engineered a next-generation version that expresses minimal levels of β-lactamase (denoted Tn3.1MIN). We have also engineered a version that is compatible with the Standard European Vector Architecture (SEVA) (denoted Ap (pSEVA#1MIN--)). Expression plasmids containing either Tn3.1MIN or Ap (pSEVA#1MIN--) can be selected using a 5-fold lower concentration of β-lactam antibiotics and benefit from the increased half-life of the β-lactam antibiotics in the culture medium (3- to 10-fold). Moreover, more cells in the culture retain the plasmid. In summary, we present two antibiotic-efficient genetic cassettes encoding the TEM-1 β-lactamase that reduce antibiotic consumption (an integral part of antibiotic stewardship), reduce production costs, and improve plasmid performance in bacterial cell factories.
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Affiliation(s)
- Alister
J. Cumming
- Department
of Biochemistry and Biophysics, Stockholm
University, Stockholm SE106 91, Sweden
| | - Diana Khananisho
- Department
of Biochemistry and Biophysics, Stockholm
University, Stockholm SE106 91, Sweden
| | - Ramona Harris
- Department
of Biochemistry and Biophysics, Stockholm
University, Stockholm SE106 91, Sweden
| | - Carolyn N. Bayer
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Morten H. H. Nørholm
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
- CloneOpt
AB, Upplands Väsby SE194 68, Sweden
- Mycropt
ApS, Kongens Lyngby 2800, Denmark
| | - Sara Jamshidi
- Department
of Materials and Environmental Chemistry, Stockholm University, Stockholm SE106 91, Sweden
| | - Leopold L. Ilag
- Department
of Materials and Environmental Chemistry, Stockholm University, Stockholm SE106 91, Sweden
| | - Daniel O. Daley
- Department
of Biochemistry and Biophysics, Stockholm
University, Stockholm SE106 91, Sweden
- CloneOpt
AB, Upplands Väsby SE194 68, Sweden
- Mycropt
ApS, Kongens Lyngby 2800, Denmark
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39
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Gulyuk AV, LaJeunesse DR, Collazo R, Ivanisevic A. Tuning Microbial Activity via Programmatic Alteration of Cell/Substrate Interfaces. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2004655. [PMID: 34028885 PMCID: PMC10167751 DOI: 10.1002/adma.202004655] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 11/11/2020] [Indexed: 05/11/2023]
Abstract
A wide portfolio of advanced programmable materials and structures has been developed for biological applications in the last two decades. Particularly, due to their unique properties, semiconducting materials have been utilized in areas of biocomputing, implantable electronics, and healthcare. As a new concept of such programmable material design, biointerfaces based on inorganic semiconducting materials as substrates introduce unconventional paths for bioinformatics and biosensing. In particular, understanding how the properties of a substrate can alter microbial biofilm behavior enables researchers to better characterize and thus create programmable biointerfaces with necessary characteristics on demand. Herein, the current status of advanced microorganism-inorganic biointerfaces is summarized along with types of responses that can be observed in such hybrid systems. This work identifies promising inorganic material types along with target microorganisms that will be critical for future research on programmable biointerfacial structures.
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Affiliation(s)
- Alexey V Gulyuk
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Dennis R LaJeunesse
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina-Greensboro, Greensboro, NC, 27401, USA
| | - Ramon Collazo
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Albena Ivanisevic
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC, 27695, USA
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40
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Assessment of Phenotype Relevant Amino Acid Residues in TEM-β-Lactamases by Mathematical Modelling and Experimental Approval. Microorganisms 2021; 9:microorganisms9081726. [PMID: 34442804 PMCID: PMC8399295 DOI: 10.3390/microorganisms9081726] [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: 07/02/2021] [Revised: 07/26/2021] [Accepted: 08/10/2021] [Indexed: 11/24/2022] Open
Abstract
Single substitutions or combinations of them alter the hydrolytic activity towards specific β-lactam-antibiotics and β-lactamase inhibitors of TEM-β-lactamases. The sequences and phenotypic classification of allelic TEM variants, as provided by the NCBI National Database of Antibiotic Resistant Organisms, does not attribute phenotypes to all variants. Some entries are doubtful as the data assessment differs strongly between the studies or no data on the methodology are provided at all. This complicates mathematical and bioinformatic predictions of phenotypes that rely on the database. The present work aimed to prove the role of specific substitutions on the resistance phenotype of TEM variants in, to our knowledge, the most extensive mutagenesis study. In parallel, the predictive power of extrapolation algorithms was assessed. Most well-known substitutions with direct impact on the phenotype could be reproduced, both mathematically and experimentally. Most discrepancies were found for supportive substitutions, where some resulted in antagonistic effects in contrast to previously described synergism. The mathematical modelling proved to predict the strongest phenotype-relevant substitutions accurately but showed difficulties in identifying less prevalent but still phenotype transforming ones. In general, mutations increasing cephalosporin resistance resulted in increased sensitivity to β-lactamase inhibitors and vice versa. Combining substitutions related to cephalosporin and β-lactamase inhibitor resistance in almost all cases increased BLI susceptibility, indicating the rarity of the combined phenotype.
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41
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de Sousa Machado JN, Vollmar L, Schimpf J, Chaudhury P, Kumariya R, van der Does C, Hugel T, Albers SV. Autophosphorylation of the KaiC-like protein ArlH inhibits oligomerization and interaction with ArlI, the motor ATPase of the archaellum. Mol Microbiol 2021; 116:943-956. [PMID: 34219289 DOI: 10.1111/mmi.14781] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/02/2021] [Accepted: 07/02/2021] [Indexed: 12/27/2022]
Abstract
Motile archaea are propelled by the archaellum, whose motor complex consists of the membrane protein ArlJ, the ATPase ArlI, and the ATP-binding protein ArlH. Despite its essential function and the existence of structural and biochemical data on ArlH, the role of ArlH in archaellum assembly and function remains elusive. ArlH is a structural homolog of KaiC, the central component of the cyanobacterial circadian clock. Since autophosphorylation and dephosphorylation of KaiC are central properties for the function of KaiC, we asked whether autophosphorylation is also a property of ArlH proteins. We observed that both ArlH from the euryarchaeon Pyrococcus furiosus (PfArlH) and from the crenarchaeon Sulfolobus acidocaldarius (SaArlH) have autophosphorylation activity. Using a combination of single-molecule fluorescence measurements and biochemical assays, we show that autophosphorylation of ArlH is closely linked to its oligomeric state when bound to hexameric ArlI. These experiments also strongly suggest that ArlH is a hexamer in its ArlI-bound state. Mutagenesis of the putative catalytic residue (Glu-57 in SaArlH) in ArlH results in a reduced autophosphorylation activity and abolished archaellation and motility in S. acidocaldarius, indicating that optimum phosphorylation activity of ArlH is essential for archaellation and motility.
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Affiliation(s)
- J Nuno de Sousa Machado
- Molecular Biology of Archaea and Signaling Research Centre BIOSS, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Leonie Vollmar
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany.,Institute of Physical Chemistry and Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Julia Schimpf
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany.,Institute of Physical Chemistry and Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Paushali Chaudhury
- Molecular Biology of Archaea and Signaling Research Centre BIOSS, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Rashmi Kumariya
- Molecular Biology of Archaea and Signaling Research Centre BIOSS, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Chris van der Does
- Molecular Biology of Archaea and Signaling Research Centre BIOSS, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Thorsten Hugel
- Institute of Physical Chemistry and Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea and Signaling Research Centre BIOSS, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
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de Sousa Machado JN, Vollmar L, Schimpf J, Chaudhury P, Kumariya R, van der Does C, Hugel T, Albers S. Autophosphorylation of the KaiC-like protein ArlH inhibits oligomerisation and interaction with ArlI, the motor ATPase of the archaellum.. [DOI: 10.1101/2021.03.19.436134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
Abstract
Motile archaea are propelled by the archaellum, whose motor complex consists of the membrane protein ArlJ, the ATPase ArlI, and the ATP-binding protein ArlH. Despite its essential function and the existence of structural and biochemical data on ArlH, the role of ArlH in archaellum assembly and function remains elusive. ArlH is a structural homolog of KaiC, the central component of the cyanobacterial circadian clock. Similar to KaiC, ArlH exhibits autophosphorylation activity, which was observed for both ArlH of the euryarchaeonPyrococcus furiosus (PfArlH)and the crenarchaeonSulfolobus acidocaldarius(SaArlH). Using a combination of single molecule fluorescence measurements and biochemical assays, it is shown that autophosphorylation of ArlH is closely linked to the oligomeric state of ArlH bound to ArlI. These experiments also strongly suggest that ArlH is a hexamer in its functional ArlI bound state. Mutagenesis of the putative catalytic residue Glu-57 inSaArlH results in a reduced autophosphorylation activity and abolished archaellation and motility, suggesting that optimum phosphorylation activity of ArlH is essential for both archaellation and motility.
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43
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Chen F, Li YY, Yu YL, Dai J, Huang JL, Lin J. Simplified plasmid cloning with a universal MCS design and bacterial in vivo assembly. BMC Biotechnol 2021; 21:24. [PMID: 33722223 PMCID: PMC7962268 DOI: 10.1186/s12896-021-00679-6] [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: 11/28/2020] [Accepted: 02/17/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The ability to clone DNA sequences quickly and precisely into plasmids is essential for molecular biology studies. The recent development of seamless cloning technologies has made significant improvements in plasmid construction, but simple and reliable tools are always desirable for time- and labor-saving purposes. RESULTS We developed and standardized a plasmid cloning protocol based on a universal MCS (Multiple Cloning Site) design and bacterial in vivo assembly. With this method, the vector is linearized first by PCR (Polymerase Chain Reaction) or restriction digestion. Then a small amount (10 ~ 20 ng) of this linear vector can be mixed with a PCR-amplified insert (5× molar ratio against vector) and transformed directly into competent E. coli cells to obtain the desired clones through in vivo assembly. Since we used a 36-bp universal MCS as the homologous linker, any PCR-amplified insert with ~ 15 bp compatible termini can be cloned into the vector with high fidelity and efficiency. Thus, the need for redesigning insert-amplifying primers according to various vector sequences and the following PCR procedures was eliminated. CONCLUSIONS Our protocol significantly reduced hands-on time for preparing transformation reactions, had excellent reliability, and was confirmed to be a rapid and versatile plasmid cloning technique. The protocol contains mostly mixing steps, making it an extremely automation-friendly and promising tool in modern biology studies.
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Affiliation(s)
- Fan Chen
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, 363000, P.R. China.
| | - Yi-Ya Li
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, 363000, P.R. China
| | - Yan-Li Yu
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, 363000, P.R. China
| | - Jie Dai
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, 363000, P.R. China
| | - Jin-Ling Huang
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, 363000, P.R. China
| | - Jie Lin
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, 363000, P.R. China
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Park S, Prévost K, Heideman EM, Carrier MC, Azam MS, Reyer MA, Liu W, Massé E, Fei J. Dynamic interactions between the RNA chaperone Hfq, small regulatory RNAs, and mRNAs in live bacterial cells. eLife 2021; 10:64207. [PMID: 33616037 PMCID: PMC7987339 DOI: 10.7554/elife.64207] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/19/2021] [Indexed: 12/26/2022] Open
Abstract
RNA-binding proteins play myriad roles in regulating RNAs and RNA-mediated functions. In bacteria, the RNA chaperone Hfq is an important post-transcriptional gene regulator. Using live-cell super-resolution imaging, we can distinguish Hfq binding to different sizes of cellular RNAs. We demonstrate that under normal growth conditions, Hfq exhibits widespread mRNA-binding activity, with the distal face of Hfq contributing mostly to the mRNA binding in vivo. In addition, sRNAs can either co-occupy Hfq with the mRNA as a ternary complex, or displace the mRNA from Hfq in a binding face-dependent manner, suggesting mechanisms through which sRNAs rapidly access Hfq to induce sRNA-mediated gene regulation. Finally, our data suggest that binding of Hfq to certain mRNAs through its distal face can recruit RNase E to promote turnover of these mRNAs in a sRNA-independent manner, and such regulatory function of Hfq can be decoyed by sRNA competitors that bind strongly at the distal face. Messenger RNAs or mRNAs are molecules that the cell uses to transfer the information stored in the cell’s DNA so it can be used to make proteins. Bacteria can regulate their levels of mRNA molecules, and they can therefore control how many proteins are being made, by producing a different type of RNA called small regulatory RNAs or sRNAs. Each sRNA can bind to several specific mRNA targets, and lead to their degradation by an enzyme called RNase E. Certain bacterial RNA-binding proteins, such as Hfq, protect sRNAs from being degraded, and help them find their mRNA targets. Hfq is abundant in bacteria. It is critical for bacterial growth under harsh conditions and it is involved in the process through which pathogenic bacteria infect cells. However, it is outnumbered by the many different RNA molecules in the cell, which compete for binding to the protein. It is not clear how Hfq prioritizes the different RNAs, or how binding to Hfq alters RNA regulation. Park, Prévost et al. imaged live bacterial cells to see how Hfq binds to RNA strands of different sizes. The experiments revealed that, when bacteria are growing normally, Hfq is mainly bound to mRNA molecules, and it can recruit RNase E to speed up mRNA degradation without the need for sRNAs. Park, Prévost et al. also showed that sRNAs could bind to Hfq by either replacing the bound mRNA or co-binding alongside it. The sRNA molecules that strongly bind Hfq can compete against mRNA for binding, and thus slow down the degradation of certain mRNAs. Hfq could be a potential drug target for treating bacterial infections. Understanding how it interacts with other molecules in bacteria could provide help in the development of new therapeutics. These findings suggest that a designed RNA that binds strongly to Hfq could disrupt its regulatory roles in bacteria, killing them. This could be a feasible drug design opportunity to counter the emergence of antibiotic-resistant bacteria.
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Affiliation(s)
- Seongjin Park
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
| | - Karine Prévost
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Canada
| | - Emily M Heideman
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
| | - Marie-Claude Carrier
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Canada
| | - Muhammad S Azam
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
| | - Matthew A Reyer
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, United States
| | - Wei Liu
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States
| | - Eric Massé
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Canada
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, United States
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Matsumura I. Methylase-assisted subcloning for high throughput BioBrick assembly. PeerJ 2020; 8:e9841. [PMID: 32974095 PMCID: PMC7489255 DOI: 10.7717/peerj.9841] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/10/2020] [Indexed: 12/02/2022] Open
Abstract
The BioBrick standard makes possible iterated pairwise assembly of cloned parts without any depletion of unique restriction sites. Every part that conforms to the standard is compatible with every other part, thereby fostering a worldwide user community. The assembly methods, however, are labor intensive or inefficient compared to some newer ones so the standard may be falling out of favor. An easier way to assemble BioBricks is described herein. Plasmids encoding BioBrick parts are purified from Escherichia coli cells that express a foreign site-specific DNA methyltransferase, so that each is subsequently protected in vitro from the activity of a particular restriction endonuclease. Each plasmid is double-digested and all resulting restriction fragments are ligated together without gel purification. The ligation products are subsequently double-digested with another pair of restriction endonucleases so only the desired insert-recipient vector construct retains the capacity to transform E. coli. This 4R/2M BioBrick assembly protocol is more efficient and accurate than established workflows including 3A assembly. It is also much easier than gel purification to miniaturize, automate and perform more assembly reactions in parallel. As such, it should streamline DNA assembly for the existing community of BioBrick users, and possibly encourage others to join.
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Affiliation(s)
- Ichiro Matsumura
- Emory University School of Medicine, Department of Biochemistry, Atlanta, GA, United States of America
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Melnikova DN, Bogdanov IV, Ignatova AA, Ovchinnikova TV, Finkina EI. New insights into ligand binding by plant lipid transfer proteins: A case study of the lentil Lc-LTP2. Biochem Biophys Res Commun 2020; 528:39-45. [PMID: 32456792 DOI: 10.1016/j.bbrc.2020.04.139] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 04/27/2020] [Indexed: 11/25/2022]
Abstract
Lipid transfer proteins (LTPs) are an important class of plant proteins containing an internal cavity and binding hydrophobic ligands. Although LTP structures and functions are well studied, mechanisms of ligand binding remain unclear. Earlier, we discovered the lentil lipid transfer protein Lc-LTP2 capable of binding and transfer various ligands. We have shown that the "bottom" entrance of the Lc-LTP2 cavity takes part in attachment to the micelle surface and in lipids uptake. Here, we studied the role of Arg45 and Tyr80, located at the "bottom" entrance, in Lc-LTP2 ligand binding. We obtained recombinant mutant analogs of Lc-LTP2 (R45A, Y80A, R45A/Y80A), investigated their ability to bind fatty acids and lysolipids, as well as performed molecular modeling of the protein-ligand complexes. We showed that replacement of one or both residues led to a change of the internal hydrophobic cavity dimensions. As a result, lipids may change their orientation into the protein cavity, and thereby binding ability of mutant analogs may be affected as well. In the present work, we revealed an important role of Arg45 and Tyr80 in stabilization of the Lc-LTP2 complexes with both fatty acids and lysolipids with different ligand orientation.
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Affiliation(s)
- D N Melnikova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997, Moscow, Russia
| | - I V Bogdanov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997, Moscow, Russia
| | - A A Ignatova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997, Moscow, Russia
| | - T V Ovchinnikova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997, Moscow, Russia
| | - E I Finkina
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997, Moscow, Russia.
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