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Dijokaite-Guraliuc A, Das R, Zhou D, Ginn HM, Liu C, Duyvesteyn HME, Huo J, Nutalai R, Supasa P, Selvaraj M, de Silva TI, Plowright M, Newman TAH, Hornsby H, Mentzer AJ, Skelly D, Ritter TG, Temperton N, Klenerman P, Barnes E, Dunachie SJ, Roemer C, Peacock TP, Paterson NG, Williams MA, Hall DR, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses. Cell Rep 2023; 42:112271. [PMID: 36995936 PMCID: PMC9988707 DOI: 10.1016/j.celrep.2023.112271] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/21/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023] Open
Abstract
In November 2021, Omicron BA.1, containing a raft of new spike mutations, emerged and quickly spread globally. Intense selection pressure to escape the antibody response produced by vaccines or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection then led to a rapid succession of Omicron sub-lineages with waves of BA.2 and then BA.4/5 infection. Recently, many variants have emerged such as BQ.1 and XBB, which carry up to 8 additional receptor-binding domain (RBD) amino acid substitutions compared with BA.2. We describe a panel of 25 potent monoclonal antibodies (mAbs) generated from vaccinees suffering BA.2 breakthrough infections. Epitope mapping shows potent mAb binding shifting to 3 clusters, 2 corresponding to early-pandemic binding hotspots. The RBD mutations in recent variants map close to these binding sites and knock out or severely knock down neutralization activity of all but 1 potent mAb. This recent mAb escape corresponds with large falls in neutralization titer of vaccine or BA.1, BA.2, or BA.4/5 immune serum.
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Key Words
- CP: Immunology
- CP: Microbiology
- SARS-CoV-2, BA.2, variant, mutation, RBD, antibodies, binding site, breakthrough, neutralizing, structure, COVID-19
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Affiliation(s)
- Aiste Dijokaite-Guraliuc
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Raksha Das
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daming Zhou
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Helen M Ginn
- Diamond Light Source, Ltd., Harwell Science & Innovation Campus, Didcot, UK
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Jiandong Huo
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Rungtiwa Nutalai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Muneeswaran Selvaraj
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Thushan I de Silva
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Megan Plowright
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Thomas A H Newman
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Hailey Hornsby
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Donal Skelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Thomas G Ritter
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and Greenwich Chatham Maritime, Kent, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand; Department of Medicine, University of Oxford, Oxford, UK
| | - Cornelius Roemer
- Biozentrum, University of Basel, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
| | - Neil G Paterson
- Diamond Light Source, Ltd., Harwell Science & Innovation Campus, Didcot, UK
| | - Mark A Williams
- Diamond Light Source, Ltd., Harwell Science & Innovation Campus, Didcot, UK
| | - David R Hall
- Diamond Light Source, Ltd., Harwell Science & Innovation Campus, Didcot, UK
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Diamond Light Source, Ltd., Harwell Science & Innovation Campus, Didcot, UK.
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
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52
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Strand DD, Karcher D, Ruf S, Schadach A, Schöttler MA, Sandoval-Ibañez O, Hall D, Kramer DM, Bock R. Characterization of mutants deficient in N-terminal phosphorylation of the chloroplast ATP synthase subunit β. PLANT PHYSIOLOGY 2023; 191:1818-1835. [PMID: 36635853 PMCID: PMC10022623 DOI: 10.1093/plphys/kiad013] [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: 11/08/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Understanding the regulation of photosynthetic light harvesting and electron transfer is of great importance to efforts to improve the ability of the electron transport chain to supply downstream metabolism. A central regulator of the electron transport chain is ATP synthase, the molecular motor that harnesses the chemiosmotic potential generated from proton-coupled electron transport to synthesize ATP. ATP synthase is regulated both thermodynamically and post-translationally, with proposed phosphorylation sites on multiple subunits. In this study we focused on two N-terminal serines on the catalytic subunit β in tobacco (Nicotiana tabacum), previously proposed to be important for dark inactivation of the complex to avoid ATP hydrolysis at night. Here we show that there is no clear role for phosphorylation in the dark inactivation of ATP synthase. Instead, mutation of one of the two phosphorylated serine residues to aspartate to mimic constitutive phosphorylation strongly decreased ATP synthase abundance. We propose that the loss of N-terminal phosphorylation of ATPβ may be involved in proper ATP synthase accumulation during complex assembly.
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Affiliation(s)
| | - Daniel Karcher
- Max-Planck-Institut für Molecular Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Stephanie Ruf
- Max-Planck-Institut für Molecular Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Anne Schadach
- Max-Planck-Institut für Molecular Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Mark A Schöttler
- Max-Planck-Institut für Molecular Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Omar Sandoval-Ibañez
- Max-Planck-Institut für Molecular Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - David Hall
- DOE Plant Research Laboratory, Michigan State University, 612 Wilson Rd 106, East Lansing, Michigan, 48824, USA
| | - David M Kramer
- DOE Plant Research Laboratory, Michigan State University, 612 Wilson Rd 106, East Lansing, Michigan, 48824, USA
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53
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Kurashina M, Mizumoto K. Targeting endogenous proteins for spatial and temporal knockdown using auxin-inducible degron in Caenorhabditis elegans. STAR Protoc 2023; 4:102028. [PMID: 36640369 PMCID: PMC9860162 DOI: 10.1016/j.xpro.2022.102028] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/21/2022] [Accepted: 12/27/2022] [Indexed: 01/15/2023] Open
Abstract
The auxin-inducible degron (AID) provides reversible, spatiotemporal control for the knockdown of target proteins. Here, we present a protocol for AID-mediated protein knockdown in Caenorhabditis elegans. We describe steps for generating the knock-in mutants using two CRISPR-Cas9 genome editing techniques and preparing the auxin-containing nematode growth media (NGM) plates. We also detail AID-mediated spatiotemporal protein knockdown. For complete details on the use and execution of this protocol, please refer to Kurashina et al. (2021).1.
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Affiliation(s)
- Mizuki Kurashina
- Department of Zoology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Graduate Program in Cell & Developmental Biology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; The Life Sciences Institute, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Kota Mizumoto
- Department of Zoology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Graduate Program in Cell & Developmental Biology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; The Life Sciences Institute, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Djavad Mowafaghian Centre for Brain Health, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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54
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Yan P, Tuo D, Shen W, Deng H, Zhou P, Gao X. A Nimble Cloning-compatible vector system for high-throughput gene functional analysis in plants. PLANT COMMUNICATIONS 2023; 4:100471. [PMID: 36352791 PMCID: PMC10030367 DOI: 10.1016/j.xplc.2022.100471] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 05/04/2023]
Abstract
Plant expression vectors are essential tools for gene functional analysis and molecular plant breeding. The gene of interest is transferred to the vector by molecular cloning technology. Nimble Cloning is a newly developed molecular cloning method with the advantages of simplicity, efficiency, and standardization. In this study, we developed a "pNC" vector system that contains 55 Nimble Cloning-compatible vectors for functional analysis of genes in plants. These vectors contain the NC frame flanked by unique adapters for one-step and standardized Nimble Cloning. We demonstrate that the pNC vectors are convenient and effective for the functional analysis of plant genes, including the study of gene ectopic expression, protein subcellular localization, protein-protein interaction, gene silencing (RNAi), virus-induced gene silencing, promoter activity, and CRISPR-Cas9-mediated genome editing. The "pNC" vector system represents a high-throughput toolkit that can facilitate the large-scale analysis of plant functional genomics.
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Affiliation(s)
- Pu Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Sanya Research Institute, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Science & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute of Tropical Agricultural Resources, Haikou 571101, China.
| | - Decai Tuo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Sanya Research Institute, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Science & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute of Tropical Agricultural Resources, Haikou 571101, China
| | - Wentao Shen
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Sanya Research Institute, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Science & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute of Tropical Agricultural Resources, Haikou 571101, China
| | - Haida Deng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Sanya Research Institute, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Science & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute of Tropical Agricultural Resources, Haikou 571101, China
| | - Peng Zhou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Sanya Research Institute, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Science & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute of Tropical Agricultural Resources, Haikou 571101, China.
| | - Xinzheng Gao
- Department of Biology, Hainan Medical University, Haikou, China.
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55
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Lee SN, Cho HJ, Jeong H, Ryu B, Lee HJ, Kim M, Yoo J, Woo JS, Lee HH. Cryo-EM structures of human Cx36/GJD2 neuronal gap junction channel. Nat Commun 2023; 14:1347. [PMID: 36906653 PMCID: PMC10008584 DOI: 10.1038/s41467-023-37040-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 02/28/2023] [Indexed: 03/13/2023] Open
Abstract
Connexin 36 (Cx36) is responsible for signal transmission in electrical synapses by forming interneuronal gap junctions. Despite the critical role of Cx36 in normal brain function, the molecular architecture of the Cx36 gap junction channel (GJC) is unknown. Here, we determine cryo-electron microscopy structures of Cx36 GJC at 2.2-3.6 Å resolutions, revealing a dynamic equilibrium between its closed and open states. In the closed state, channel pores are obstructed by lipids, while N-terminal helices (NTHs) are excluded from the pore. In the open state with pore-lining NTHs, the pore is more acidic than those in Cx26 and Cx46/50 GJCs, explaining its strong cation selectivity. The conformational change during channel opening also includes the α-to-π-helix transition of the first transmembrane helix, which weakens the protomer-protomer interaction. Our structural analyses provide high resolution information on the conformational flexibility of Cx36 GJC and suggest a potential role of lipids in the channel gating.
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Affiliation(s)
- Seu-Na Lee
- Department of Life Sciences, Korea University, Seoul, 02841, Republic of Korea
| | - Hwa-Jin Cho
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Korea
| | - Hyeongseop Jeong
- Center for Research Equipment, Korea Basic Science Institute, Chungcheongbuk-do, 28119, Korea
| | - Bumhan Ryu
- Research Solution Center, Institute for Basic Science, Daejeon, 34126, Republic of Korea
| | - Hyuk-Joon Lee
- Department of Life Sciences, Korea University, Seoul, 02841, Republic of Korea
| | - Minsoo Kim
- Department of Physics, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Jejoong Yoo
- Department of Physics, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Jae-Sung Woo
- Department of Life Sciences, Korea University, Seoul, 02841, Republic of Korea.
| | - Hyung Ho Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Korea.
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56
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Escobedo-Hinojosa W, Vila MA, Wissner JL, Härterich N, Horz P, Iglesias C, Hauer B. Exploring the substrate scope of glycerol dehydrogenase GldA from E. coli BW25113 towards cis-dihydrocatechol derivatives. J Biotechnol 2023; 366:19-24. [PMID: 36870480 DOI: 10.1016/j.jbiotec.2023.02.010] [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: 12/04/2022] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023]
Abstract
Glycerol dehydrogenase (GldA) from Escherichia coli BW25113, naturally catalyzes the oxidation of glycerol to dihydroxyacetone. It is known that GldA exhibits promiscuity towards short-chain C2-C4 alcohols. However, there are no reports regarding the substrate scope of GldA towards larger substrates. Herein we demonstrate that GldA can accept bulkier C6-C8 alcohols than previously anticipated. Overexpression of the gldA gene in the knockout background, E. coli BW25113 ΔgldA, was strikingly effective converting 2 mM of the compounds: cis-dihydrocatetechol, cis-(1 S,2 R)- 3-methylcyclohexa-3,5-diene-1,2-diol and cis-(1 S,2 R)- 3-ethylcyclohexa-3,5-diene-1,2-diol, into 2.04 ± 0.21 mM of catechol, 0.62 ± 0.11 mM 3-methylcatechol, and 0.16 ± 0.02 mM 3-ethylcatechol, respectively. In-silico studies on the active site of GldA enlightened the decrease in product formation as the steric substrate demand increased. These results are of high interests for E. coli-based cell factories expressing Rieske non-heme iron dioxygenases, producing cis-dihydrocatechols, since such sough-after valuable products can be immediately degraded by GldA, substantially hampering the expected performance of the recombinant platform.
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Affiliation(s)
- Wendy Escobedo-Hinojosa
- Unidad de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Puerto de abrigo s/n, 97356 Sisal, Yucatán, Mexico
| | - María Agustina Vila
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Química Orgánica y Departamento de Biociencias, Facultad de Química Universidad de la República, Av General Flores 2124, CP 11800 Montevideo, Uruguay
| | - Julian L Wissner
- Unidad de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Puerto de abrigo s/n, 97356 Sisal, Yucatán, Mexico; Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Natalie Härterich
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Philip Horz
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - César Iglesias
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Química Orgánica y Departamento de Biociencias, Facultad de Química Universidad de la República, Av General Flores 2124, CP 11800 Montevideo, Uruguay
| | - Bernhard Hauer
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
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57
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Zhou K, Yu C, Liang N, Xiao W, Wang Y, Yao M, Yuan Y. Adaptive Evolution and Metabolic Engineering Boost Lycopene Production in Saccharomyces cerevisiae via Enhanced Precursors Supply and Utilization. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:3821-3831. [PMID: 36802623 DOI: 10.1021/acs.jafc.2c08579] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Lycopene is a red carotenoid with remarkable antioxidant activity, which has been widely used in food, cosmetics, medicine, and other industries. Production of lycopene in Saccharomyces cerevisiae provides an economic and sustainable means. Many efforts have been done in recent years, but the titer of lycopene seems to reach a ceiling. Enhancing the supply and utilization of farnesyl diphosphate (FPP) is generally regarded as an efficient strategy for terpenoid production. Herein, an integrated strategy by means of atmospheric and room-temperature plasma (ARTP) mutagenesis combined with H2O2-induced adaptive laboratory evolution (ALE) was proposed to improve the supply of upstream metabolic flux toward FPP. Enhancing the expression of CrtE and introducing an engineered CrtI mutant (Y160F&N576S) increased the utilization of FPP toward lycopene. Consequently, the titer of lycopene in the strain harboring the Ura3 marker was increased by 60% to 703 mg/L (89.3 mg/g DCW) at the shake-flask level. Eventually, the highest reported titer of 8.15 g/L of lycopene in S. cerevisiae was achieved in a 7 L bioreactor. The study highlights an effective strategy that the synergistic complementarity of metabolic engineering and adaptive evolution facilitates natural product synthesis.
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Affiliation(s)
- Kui Zhou
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Chao Yu
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- CABIO Biotech (Wuhan) Co., Ltd, Wuhan 430075, China
| | - Nan Liang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Wenhai Xiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Georgia Tech Shenzhen Institute, Tianjin University, Shenzhen 518071, China
| | - Ying Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Mingdong Yao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yingjin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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58
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Herring CD, Ajie MP, Lynd LR. Growth-uncoupled propanediol production in a Thermoanaerobacterium thermosaccharolyticum strain engineered for high ethanol yield. Sci Rep 2023; 13:2394. [PMID: 36765076 PMCID: PMC9918460 DOI: 10.1038/s41598-023-29220-9] [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: 09/30/2022] [Accepted: 01/31/2023] [Indexed: 02/12/2023] Open
Abstract
Cocultures of engineered thermophilic bacteria can ferment lignocellulose without costly pretreatment or added enzymes, an ability that can be exploited for low cost biofuel production from renewable feedstocks. The hemicellulose-fermenting species Thermoanaerobacterium thermosaccharolyticum was engineered for high ethanol yield, but we found that the strains switched from growth-coupled production of ethanol to growth uncoupled production of acetate and 1,2-propanediol upon growth cessation, producing up to 6.7 g/L 1,2-propanediol from 60 g/L cellobiose. The unique capability of this species to make 1,2-propanediol from sugars was described decades ago, but the genes responsible were not identified. Here we deleted genes encoding methylglyoxal reductase, methylglyoxal synthase and glycerol dehydrogenase. Deletion of the latter two genes eliminated propanediol production. To understand how carbon flux is redirected in this species, we hypothesized that high ATP levels during growth cessation downregulate the activity of alcohol and aldehyde dehydrogenase activities. Measurements with cell free extracts show approximately twofold and tenfold inhibition of these activities by 10 mM ATP, supporting the hypothesized mechanism of metabolic redirection. This result may have implications for efforts to direct and maximize flux through alcohol dehydrogenase in other species.
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Affiliation(s)
- Christopher D Herring
- Terragia Biofuel Incorporated, Hanover, New Hampshire, United States. .,Dartmouth College, Thayer School of Engineering, Hanover, New Hampshire, United States. .,Center for Bioenergy Innovation, Oak Ridge, Tennessee, United States.
| | - Maulana Permana Ajie
- Technical University of Munich, Munich, Germany.,Bioengineering, Rhine-Waal University of Applied Sciences, Kleve, Germany
| | - Lee R Lynd
- Terragia Biofuel Incorporated, Hanover, New Hampshire, United States.,Dartmouth College, Thayer School of Engineering, Hanover, New Hampshire, United States.,Center for Bioenergy Innovation, Oak Ridge, Tennessee, United States
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59
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Acuña ML, García-Morin A, Orozco-Sepúlveda R, Ontiveros C, Flores A, Diaz AV, Gutiérrez-Zubiate I, Patil AR, Alvarado LA, Roy S, Russell WK, Rosas-Acosta G. Alternative splicing of the SUMO1/2/3 transcripts affects cellular SUMOylation and produces functionally distinct SUMO protein isoforms. Sci Rep 2023; 13:2309. [PMID: 36759644 PMCID: PMC9911741 DOI: 10.1038/s41598-023-29357-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 02/02/2023] [Indexed: 02/11/2023] Open
Abstract
Substantial increases in the conjugation of the main human SUMO paralogs, SUMO1, SUMO2, and SUMO3, are observed upon exposure to different cellular stressors, and such increases are considered important to facilitate cell survival to stress. Despite their critical cellular role, little is known about how the levels of the SUMO modifiers are regulated in the cell, particularly as it relates to the changes observed upon stress. Here we characterize the contribution of alternative splicing towards regulating the expression of the main human SUMO paralogs under normalcy and three different stress conditions, heat-shock, cold-shock, and Influenza A Virus infection. Our data reveal that the normally spliced transcript variants are the predominant mature mRNAs produced from the SUMO genes and that the transcript coding for SUMO2 is by far the most abundant of all. We also provide evidence that alternatively spliced transcripts coding for protein isoforms of the prototypical SUMO proteins, which we refer to as the SUMO alphas, are also produced, and that their abundance and nuclear export are affected by stress in a stress- and cell-specific manner. Additionally, we provide evidence that the SUMO alphas are actively synthesized in the cell as their coding mRNAs are found associated with translating ribosomes. Finally, we provide evidence that the SUMO alphas are functionally different from their prototypical counterparts, with SUMO1α and SUMO2α being non-conjugatable to protein targets, SUMO3α being conjugatable but targeting a seemingly different subset of protein from those targeted by SUMO3, and all three SUMO alphas displaying different cellular distributions from those of the prototypical SUMOs. Thus, alternative splicing appears to be an important contributor to the regulation of the expression of the SUMO proteins and the cellular functions of the SUMOylation system.
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Affiliation(s)
- Myriah L Acuña
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Andrea García-Morin
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Rebeca Orozco-Sepúlveda
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Carlos Ontiveros
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, 79968, USA
- Graduate School of Biomedical Sciences, University of Texas Health, San Antonio, TX, 78229, USA
| | - Alejandra Flores
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, 79968, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Arely V Diaz
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, 79968, USA
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | | | - Abhijeet R Patil
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Luis A Alvarado
- Biostatistics and Epidemiology Consulting Lab, Texas Tech University Health Sciences Center, El Paso, TX, 79905, USA
| | - Sourav Roy
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, 79968, USA
- Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX, 79968, USA
| | - William K Russell
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Germán Rosas-Acosta
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX, 79968, USA.
- Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX, 79968, USA.
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60
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Rollins MR, Raynor JF, Miller EA, Butler JZ, Spartz EJ, Lahr WS, You Y, Burrack AL, Moriarity BS, Webber BR, Stromnes IM. Germline T cell receptor exchange results in physiological T cell development and function. Nat Commun 2023; 14:528. [PMID: 36726009 PMCID: PMC9892040 DOI: 10.1038/s41467-023-36180-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 01/18/2023] [Indexed: 02/03/2023] Open
Abstract
T cell receptor (TCR) transgenic mice represent an invaluable tool to study antigen-specific immune responses. In the pre-existing models, a monoclonal TCR is driven by a non-physiologic promoter and randomly integrated into the genome. Here, we create a highly efficient methodology to develop T cell receptor exchange (TRex) mice, in which TCRs, specific to the self/tumor antigen mesothelin (Msln), are integrated into the Trac locus, with concomitant Msln disruption to circumvent T cell tolerance. We show that high affinity TRex thymocytes undergo all sequential stages of maturation, express the exogenous TCR at DN4, require MHC class I for positive selection and undergo negative selection only when both Msln alleles are present. By comparison of TCRs with the same specificity but varying affinity, we show that Trac targeting improves functional sensitivity of a lower affinity TCR and confers resistance to T cell functional loss. By generating P14 TRex mice with the same specificity as the widely used LCMV-P14 TCR transgenic mouse, we demonstrate increased avidity of Trac-targeted TCRs over transgenic TCRs, while preserving physiologic T cell development. Together, our results support that the TRex methodology is an advanced tool to study physiological antigen-specific T cell behavior.
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Affiliation(s)
- Meagan R Rollins
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Jackson F Raynor
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Ebony A Miller
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Jonah Z Butler
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Ellen J Spartz
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA
- Department of Medicine, UCLA Health, Los Angeles, CA, USA
| | - Walker S Lahr
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Yun You
- Mouse Genetics Laboratory, University of Minnesota, Minneapolis, MN, USA
| | - Adam L Burrack
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Branden S Moriarity
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Beau R Webber
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Ingunn M Stromnes
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA.
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA.
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.
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61
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Functional Analysis of Variants in BRCA1 Using CRISPR Base Editors. Methods Mol Biol 2023; 2606:73-85. [PMID: 36592309 DOI: 10.1007/978-1-0716-2879-9_7] [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: 01/03/2023]
Abstract
To date, methods such as fluorescent reporter assays, embryonic stem cell viability assays, and therapeutic drug-based sensitivity assays have been used to evaluate the function of the variants of uncertain significance (VUS) of the BRCA genes. However, these methods have limitations as they are associated with overexpression and do not apply to post-transcriptional regulation. Therefore, there are several VUS whose functions are unclear. Recently, we devised a new way to assess the functionality of variants in BRCA1 via a CRISPR-mediated base editor to overcome these limitations. We precisely introduced the target nucleotide substitution in living cells and identified variants whose functions were not defined. Here, we describe the methods for the functional appraisal of BRCA1 variants using CRISPR-based base editors.
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62
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Im J, Hillenaar T, Yeoh HY, Sahasrabudhe P, Mijnders M, van Willigen M, Hagos A, de Mattos E, van der Sluijs P, Braakman I. ABC-transporter CFTR folds with high fidelity through a modular, stepwise pathway. Cell Mol Life Sci 2023; 80:33. [PMID: 36609925 PMCID: PMC9825563 DOI: 10.1007/s00018-022-04671-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/01/2022] [Accepted: 11/28/2022] [Indexed: 01/09/2023]
Abstract
The question how proteins fold is especially pointed for large multi-domain, multi-spanning membrane proteins with complex topologies. We have uncovered the sequence of events that encompass proper folding of the ABC transporter CFTR in live cells by combining kinetic radiolabeling with protease-susceptibility assays. We found that CFTR folds in two clearly distinct stages. The first, co-translational, stage involves folding of the 2 transmembrane domains TMD1 and TMD2, plus one nucleotide-binding domain, NBD1. The second stage is a simultaneous, post-translational increase in protease resistance for both TMDs and NBD2, caused by assembly of these domains onto NBD1. Our assays probe every 2-3 residues (on average) in CFTR. This in-depth analysis at amino-acid level allows detailed analysis of domain folding and importantly also the next level: assembly of the domains into native, folded CFTR. Defects and changes brought about by medicines, chaperones, or mutations also are amenable to analysis. We here show that the well-known disease-causing mutation F508del, which established cystic fibrosis as protein-folding disease, caused co-translational misfolding of NBD1 but not TMD1 nor TMD2 in stage 1, leading to absence of stage-2 folding. Corrector drugs rescued stage 2 without rescuing NBD1. Likewise, the DxD motif in NBD1 that was identified to be required for export of CFTR from the ER we found to be required already upstream of export as CFTR mutated in this motif phenocopies F508del CFTR. The highly modular and stepwise folding process of such a large, complex protein explains the relatively high fidelity and correctability of its folding.
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Affiliation(s)
- Jisu Im
- Cellular Protein Chemistry, Faculty of Science, Bijvoet Centre for Biomolecular Research, Science for Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Tamara Hillenaar
- Cellular Protein Chemistry, Faculty of Science, Bijvoet Centre for Biomolecular Research, Science for Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Hui Ying Yeoh
- Cellular Protein Chemistry, Faculty of Science, Bijvoet Centre for Biomolecular Research, Science for Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands ,Present Address: Center of Translational Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Priyanka Sahasrabudhe
- Cellular Protein Chemistry, Faculty of Science, Bijvoet Centre for Biomolecular Research, Science for Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands ,Present Address: Navigo Proteins GmbH, 06120 Halle, Germany
| | - Marjolein Mijnders
- Cellular Protein Chemistry, Faculty of Science, Bijvoet Centre for Biomolecular Research, Science for Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands ,Present Address: Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Marcel van Willigen
- Cellular Protein Chemistry, Faculty of Science, Bijvoet Centre for Biomolecular Research, Science for Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands ,Present Address: Julius Clinical Ltd, 3703 CD Zeist, The Netherlands
| | - Azib Hagos
- Cellular Protein Chemistry, Faculty of Science, Bijvoet Centre for Biomolecular Research, Science for Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Eduardo de Mattos
- Cellular Protein Chemistry, Faculty of Science, Bijvoet Centre for Biomolecular Research, Science for Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Peter van der Sluijs
- Cellular Protein Chemistry, Faculty of Science, Bijvoet Centre for Biomolecular Research, Science for Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Ineke Braakman
- Cellular Protein Chemistry, Faculty of Science, Bijvoet Centre for Biomolecular Research, Science for Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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63
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Onodera H, Niwa T, Taguchi H, Chadani Y. Prophage excision switches the primary ribosome rescue pathway and rescue-associated gene regulations in Escherichia coli. Mol Microbiol 2023; 119:44-58. [PMID: 36471624 PMCID: PMC10107115 DOI: 10.1111/mmi.15003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/07/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022]
Abstract
Escherichia coli has multiple pathways to release nonproductive ribosome complexes stalled at the 3' end of nonstop mRNA: tmRNA (SsrA RNA)-mediated trans-translation and stop codon-independent termination by ArfA/RF2 or ArfB (YaeJ). The arfA mRNA lacks a stop codon and its expression is repressed by trans-translation. Therefore, ArfA is considered to complement the ribosome rescue activity of trans-translation, but the physiological situations in which ArfA is expressed have not been elucidated. Here, we found that the excision of CP4-57 prophage adjacent to E. coli ssrA leads to the inactivation of tmRNA and switches the primary rescue pathway from trans-translation to ArfA/RF2. This "rescue-switching" rearranges not only the proteome landscape in E. coli but also the phenotype such as motility. Furthermore, among the proteins with significantly increased abundance in the ArfA+ cells, we found ZntR, whose mRNA is transcribed together as the upstream part of nonstop arfA mRNA. Repression of ZntR and reconstituted model genes depends on the translation of the downstream nonstop ORFs that trigger the trans-translation-coupled exonucleolytic degradation by polynucleotide phosphorylase (PNPase). Namely, our studies provide a novel example of trans-translation-dependent regulation and re-define the physiological roles of prophage excision.
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Affiliation(s)
- Haruka Onodera
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Tatsuya Niwa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Hideki Taguchi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yuhei Chadani
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
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64
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Peiter N, Rother M. In vivo probing of SECIS-dependent selenocysteine translation in Archaea. Life Sci Alliance 2023; 6:6/1/e202201676. [PMID: 36316034 PMCID: PMC9622424 DOI: 10.26508/lsa.202201676] [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: 08/17/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/05/2022] Open
Abstract
Cotranslational insertion of selenocysteine (Sec) proceeds by recoding UGA to a sense codon. This recoding is governed by the Sec insertion sequence (SECIS) element, an RNA structure on the mRNA, but size, location, structure determinants, and mechanism differ for Bacteria, Eukarya, and Archaea. For Archaea, the structure-function relation of the SECIS is poorly understood, as only rather laborious experimental approaches are established. Furthermore, these methods do not allow for quantitative probing of Sec insertion. In order to overcome these limitations, we engineered bacterial β-lactamase into an archaeal selenoprotein, thereby establishing a reporter system, which correlates enzyme activity to Sec insertion. Using this system, in vivo Sec insertion depending on the availability of selenium and the presence of a SECIS element was assessed in Methanococcus maripaludis Furthermore, a minimal SECIS element required for Sec insertion in M. maripaludis was defined and a conserved structural motif shown to be essential for function. Besides developing a convenient tool for selenium research, converting a bacterial enzyme into an archaeal selenoprotein provides proof of concept that novel selenoproteins can be engineered in Archaea.
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Affiliation(s)
- Nils Peiter
- Fakultät Biologie, Technische Universität Dresden, Dresden, Germany
| | - Michael Rother
- Fakultät Biologie, Technische Universität Dresden, Dresden, Germany
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65
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Nishiguchi R, Tanaka T, Hayashida J, Nakagita T, Zhou W, Takeda H. Evaluation of Cell-Free Synthesized Human Channel Proteins for In Vitro Channel Research. MEMBRANES 2022; 13:48. [PMID: 36676855 PMCID: PMC9861611 DOI: 10.3390/membranes13010048] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
Despite channel proteins being important drug targets, studies on channel proteins remain limited, as the proteins are difficult to express and require correct complex formation within membranes. Although several in vitro synthesized recombinant channels have been reported, considering the vast diversity of the structures and functions of channel proteins, it remains unclear which classes of channels cell-free synthesis can be applied to. In this study, we synthesized 250 clones of human channels, including ion channel pore-forming subunits, gap junction proteins, porins, and regulatory subunits, using a wheat cell-free membrane protein production system, and evaluated their synthetic efficiency and function. Western blotting confirmed that 95% of the channels were successfully synthesized, including very large channels with molecular weights of over 200 kDa. A subset of 47 voltage-gated potassium ion channels was further analyzed using a planar lipid bilayer assay, out of which 80% displayed a voltage-dependent opening in the assay. We co-synthesized KCNB1 and KCNS3, a known heteromeric complex pair, and demonstrated that these channels interact on a liposome. These results indicate that cell-free protein synthesis provides a promising solution for channel studies to overcome the bottleneck of in vitro protein production.
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Affiliation(s)
- Rei Nishiguchi
- Proteo-Science Center, Ehime University, Bunkyocho 3, Matsuyama 790-8577, Ehime, Japan
| | - Toyohisa Tanaka
- Proteo-Science Center, Ehime University, Bunkyocho 3, Matsuyama 790-8577, Ehime, Japan
| | - Jun Hayashida
- Nissan Chemical Corporation, Shiraoka 1470, Shiraoka 349-0294, Saitama, Japan
| | - Tomoya Nakagita
- Proteo-Science Center, Ehime University, Bunkyocho 3, Matsuyama 790-8577, Ehime, Japan
| | - Wei Zhou
- Proteo-Science Center, Ehime University, Bunkyocho 3, Matsuyama 790-8577, Ehime, Japan
| | - Hiroyuki Takeda
- Proteo-Science Center, Ehime University, Bunkyocho 3, Matsuyama 790-8577, Ehime, Japan
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66
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An Optimized Transformation Protocol for Escherichia coli BW3KD with Supreme DNA Assembly Efficiency. Microbiol Spectr 2022; 10:e0249722. [PMID: 36317996 PMCID: PMC9769673 DOI: 10.1128/spectrum.02497-22] [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: 11/07/2022] Open
Abstract
DNA cloning requires two steps: the assembly of recombinant DNA molecules and the transformation of the product into a host organism for replication. High efficiencies in both processes can increase the success rate. Recently, we developed an Escherichia coli BW3KD strain with higher transformation efficiency than commonly used cloning strains. Here, we further developed a simple method named TSS-HI (transformation storage solution optimized by Hannahan and Inoue method) for competent cell preparation, which combined the advantages of three common methods for operational simplicity and high transformation efficiency. When competent BW3KD cells were prepared using this developed method, the transformation efficiency reached up to (7.21 ± 1.85) × 109 CFU/μg DNA, which exceeded the levels of commercial chemically competent cells and homemade electrocompetent cells. BW3KD cells formed colonies within 7 h on lysogeny broth agar plates, quicker than the well-known fast-growing E. coli cloning strain Mach1. The competent cells worked effectively for the transformation of assembled DNA of 1 to 7 fragments in one step and promoted efficiencies of transformation or cloning with large plasmids. The cloning efficiency of BW3KD cells prepared by this method increased up to 828-fold over that of E. coli XL1-Blue MRF' cells prepared by a common method. Thus, competent cells are suitable for different cloning jobs and should help with the increased demand for DNA assembly in biological studies and biotechnology. IMPORTANCE DNA transformation is commonly used in cloning; however, high transformation efficiency becomes a limiting factor in many applications, such as the construction of CRISPR and DNA libraries, the assembly of multiple fragments, and the transformation of large plasmids. We developed a new competent cell preparation method with unmatched transformation efficiency. When the BW3KD strain, derived from Escherichia coli BW25113 cells, was prepared by this method, its transformation efficiency reached up to (7.21 ± 1.85) × 109 CFU/μg DNA, which broke the record for chemically prepared competent cells. Routine cloning could be completed in 1 day due to the high growth rate of this strain. The competent cells were shown to be highly efficient for transformation or cloning with large plasmids and for the assembly of multiple fragments. The results highlight the effectiveness of the new protocol and the usefulness of the BW3KD strain as the host.
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67
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Poláchová E, Bach K, Heuten E, Stanchev S, Tichá A, Lampe P, Majer P, Langer T, Lemberg MK, Stříšovský K. Chemical Blockage of the Mitochondrial Rhomboid Protease PARL by Novel Ketoamide Inhibitors Reveals Its Role in PINK1/Parkin-Dependent Mitophagy. J Med Chem 2022; 66:251-265. [PMID: 36540942 PMCID: PMC9841525 DOI: 10.1021/acs.jmedchem.2c01092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The mitochondrial rhomboid protease PARL regulates mitophagy by balancing intramembrane proteolysis of PINK1 and PGAM5. It has been implicated in the pathogenesis of Parkinson's disease, but its investigation as a possible therapeutic target is challenging in this context because genetic deficiency of PARL may result in compensatory mechanisms. To address this problem, we undertook a hitherto unavailable chemical biology strategy. We developed potent PARL-targeting ketoamide inhibitors and investigated the effects of acute PARL suppression on the processing status of PINK1 intermediates and on Parkin activation. This approach revealed that PARL inhibition leads to a robust activation of the PINK1/Parkin pathway without major secondary effects on mitochondrial properties, which demonstrates that the pharmacological blockage of PARL to boost PINK1/Parkin-dependent mitophagy is a feasible approach to examine novel therapeutic strategies for Parkinson's disease. More generally, this study showcases the power of ketoamide inhibitors for cell biological studies of rhomboid proteases.
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Affiliation(s)
- Edita Poláchová
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 160 00, Czech Republic,First
Faculty of Medicine, Charles University, Kateřinská 32, Prague 121 08, Czech Republic
| | - Kathrin Bach
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 160 00, Czech Republic,Department
of Molecular Genetics, Faculty of Science, Charles University, Viničná 5, Prague 128 44, Czech Republic
| | - Elena Heuten
- Center
for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer
Feld 282, Heidelberg 69120, Germany,Center
for Biochemistry and Cologne Excellence Cluster on Cellular Stress
Responses in Aging-Associated Diseases (CECAD), Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 52, Cologne 50931, Germany
| | - Stancho Stanchev
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 160 00, Czech Republic
| | - Anežka Tichá
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 160 00, Czech Republic
| | - Philipp Lampe
- Institute
for Genetics and Cologne Excellence Cluster on Cellular Stress Responses
in Aging-Associated Diseases (CECAD), Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 52, Cologne 50931, Germany
| | - Pavel Majer
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 160 00, Czech Republic
| | - Thomas Langer
- Institute
for Genetics and Cologne Excellence Cluster on Cellular Stress Responses
in Aging-Associated Diseases (CECAD), Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 52, Cologne 50931, Germany,Center
for Molecular Medicine (CMMC), Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 52, Cologne 50931, Germany,Max-Planck-Institute
for Biology of Ageing, Joseph-Stelzmann-Str. 9b, Cologne 50931, Germany
| | - Marius K. Lemberg
- Center
for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer
Feld 282, Heidelberg 69120, Germany,Center
for Biochemistry and Cologne Excellence Cluster on Cellular Stress
Responses in Aging-Associated Diseases (CECAD), Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 52, Cologne 50931, Germany,
| | - Kvido Stříšovský
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 160 00, Czech Republic,
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Schmollack M, Werner F, Huber J, Kiefer D, Merkel M, Hausmann R, Siebert D, Blombach B. Metabolic engineering of Corynebacterium glutamicum for acetate-based itaconic acid production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:139. [PMID: 36517879 PMCID: PMC9753420 DOI: 10.1186/s13068-022-02238-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Itaconic acid is a promising platform chemical for a bio-based polymer industry. Today, itaconic acid is biotechnologically produced with Aspergillus terreus at industrial scale from sugars. The production of fuels but also of chemicals from food substrates is a dilemma since future processes should rely on carbon sources which do not compete for food or feed. Therefore, the production of chemicals from alternative substrates such as acetate is desirable to develop novel value chains in the bioeconomy. RESULTS In this study, Corynebacterium glutamicum ATCC 13032 was engineered to efficiently produce itaconic acid from the non-food substrate acetate. Therefore, we rewired the central carbon and nitrogen metabolism by inactivating the transcriptional regulator RamB, reducing the activity of isocitrate dehydrogenase, deletion of the gdh gene encoding glutamate dehydrogenase and overexpression of cis-aconitate decarboxylase (CAD) from A. terreus optimized for expression in C. glutamicum. The final strain C. glutamicum ΔramB Δgdh IDHR453C (pEKEx2-malEcadopt) produced 3.43 ± 0.59 g itaconic acid L-1 with a product yield of 81 ± 9 mmol mol-1 during small-scale cultivations in nitrogen-limited minimal medium containing acetate as sole carbon and energy source. Lowering the cultivation temperature from 30 °C to 25 °C improved CAD activity and further increased the titer and product yield to 5.01 ± 0.67 g L-1 and 116 ± 15 mmol mol-1, respectively. The latter corresponds to 35% of the theoretical maximum and so far represents the highest product yield for acetate-based itaconic acid production. Further, the optimized strain C. glutamicum ΔramB Δgdh IDHR453C (pEKEx2-malEcadopt), produced 3.38 ± 0.28 g itaconic acid L-1 at 25 °C from an acetate-containing aqueous side-stream of fast pyrolysis. CONCLUSION As shown in this study, acetate represents a suitable non-food carbon source for itaconic acid production with C. glutamicum. Tailoring the central carbon and nitrogen metabolism enabled the efficient production of itaconic acid from acetate and therefore this study offers useful design principles to genetically engineer C. glutamicum for other products from acetate.
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Affiliation(s)
- Marc Schmollack
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Uferstraße 53, 94315, Straubing, Germany
| | - Felix Werner
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Uferstraße 53, 94315, Straubing, Germany
| | - Janine Huber
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Uferstraße 53, 94315, Straubing, Germany
| | - Dirk Kiefer
- Institute of Food Science and Biotechnology, Department of Bioprocess Engineering, University of Hohenheim, Stuttgart, Germany
| | - Manuel Merkel
- Institute of Food Science and Biotechnology, Department of Bioprocess Engineering, University of Hohenheim, Stuttgart, Germany
| | - Rudolf Hausmann
- Institute of Food Science and Biotechnology, Department of Bioprocess Engineering, University of Hohenheim, Stuttgart, Germany
| | - Daniel Siebert
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Uferstraße 53, 94315, Straubing, Germany
- SynBiofoundry@TUM, Technical University of Munich, Straubing, Germany
| | - Bastian Blombach
- Microbial Biotechnology, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Uferstraße 53, 94315, Straubing, Germany.
- SynBiofoundry@TUM, Technical University of Munich, Straubing, Germany.
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69
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DeLuca KF, Mick JE, DeLuca JG. Production and purification of recombinant monoclonal antibodies from human cells based on a primary sequence. STAR Protoc 2022; 3:101915. [PMID: 36595892 PMCID: PMC9763751 DOI: 10.1016/j.xpro.2022.101915] [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: 09/15/2022] [Revised: 10/26/2022] [Accepted: 11/16/2022] [Indexed: 12/14/2022] Open
Abstract
There are challenges to using commercially available antibodies generated in animals, including concerns with reproducibility, high costs, and ethical issues. Here, we present a protocol for generating and purifying recombinant antibodies from human HEK293 suspension culture cells from a primary sequence. We describe the steps to generate antibody heavy and light chain plasmids, followed by transfection of the plasmids into cells and purification of antibodies. This protocol can produce high-yield recombinant monoclonal antibodies at a relatively low cost. For complete details on the use and execution of this protocol, please refer to DeLuca et al. (2021).1.
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Affiliation(s)
- Keith F DeLuca
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Jeanne E Mick
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Jennifer G DeLuca
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA.
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70
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Garcia PK, Martinez Borrero R, Annamalai T, Diaz E, Balarezo S, Tiwari PB, Tse-Dinh YC. Localization of Mycobacterium tuberculosis topoisomerase I C-terminal sequence motif required for inhibition by endogenous toxin MazF4. Front Microbiol 2022; 13:1032320. [PMID: 36545199 PMCID: PMC9760754 DOI: 10.3389/fmicb.2022.1032320] [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: 08/30/2022] [Accepted: 11/17/2022] [Indexed: 12/08/2022] Open
Abstract
Only about half the multi-drug resistant tuberculosis (MDR-TB) cases are successfully cured. Thus, there is an urgent need of new TB treatment against a novel target. Mycobacterium tuberculosis (Mtb) topoisomerase I (TopA) is the only type IA topoisomerase in this organism and has been validated as an essential target for TB drug discovery. Toxin-antitoxin (TA) systems participate as gene regulators within bacteria. The TA systems contribute to the long-term dormancy of Mtb within the host-cell environment. Mtb's toxin MazF4 (Rv1495) that is part of the MazEF4 TA system has been shown to have dual activities as endoribonuclease and topoisomerase I inhibitor. We have developed a complementary assay using an Escherichia coli strain with temperature-sensitive topA mutation to provide new insights into the MazF4 action. The assay showed that E. coli is not sensitive to the endoribonuclease activity of Mtb MazF4 but became vulnerable to MazF4 growth inhibition when recombinant Mtb TopA relaxation activity is required for growth. Results from the complementation by Mtb TopA mutants with C-terminal deletions showed that the lysine-rich C-terminal tail is required for interaction with MazF4. Site-directed mutagenesis is utilized to identify two lysine residues within a conserved motif in this C-terminal tail that are critical for MazF4 inhibition. We performed molecular dynamics simulations to predict the Mtb TopA-MazF4 complex. Our simulation results show that the complex is stabilized by hydrogen bonds and electrostatic interactions established by residues in the TopA C-terminal tail including the two conserved lysines. The mechanism of Mtb TopA inhibition by MazF4 could be useful for the discovery of novel inhibitors against a new antibacterial target in pathogenic mycobacteria for treatment of both TB and diseases caused by the non-tuberculosis mycobacteria (NTM).
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Affiliation(s)
- Pamela K. Garcia
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States
| | | | - Thirunavukkarasu Annamalai
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States,Biomolecular Sciences Institute, Florida International University, Miami, FL, United States
| | - Esnel Diaz
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States
| | - Steve Balarezo
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States
| | | | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, United States,Biomolecular Sciences Institute, Florida International University, Miami, FL, United States,*Correspondence: Yuk-Ching Tse-Dinh,
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71
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Ito Y, Chadani Y, Niwa T, Yamakawa A, Machida K, Imataka H, Taguchi H. Nascent peptide-induced translation discontinuation in eukaryotes impacts biased amino acid usage in proteomes. Nat Commun 2022; 13:7451. [PMID: 36460666 PMCID: PMC9718836 DOI: 10.1038/s41467-022-35156-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 11/18/2022] [Indexed: 12/04/2022] Open
Abstract
Robust translation elongation of any given amino acid sequence is required to shape proteomes. Nevertheless, nascent peptides occasionally destabilize ribosomes, since consecutive negatively charged residues in bacterial nascent chains can stochastically induce discontinuation of translation, in a phenomenon termed intrinsic ribosome destabilization (IRD). Here, using budding yeast and a human factor-based reconstituted translation system, we show that IRD also occurs in eukaryotic translation. Nascent chains enriched in aspartic acid (D) or glutamic acid (E) in their N-terminal regions alter canonical ribosome dynamics, stochastically aborting translation. Although eukaryotic ribosomes are more robust to ensure uninterrupted translation, we find many endogenous D/E-rich peptidyl-tRNAs in the N-terminal regions in cells lacking a peptidyl-tRNA hydrolase, indicating that the translation of the N-terminal D/E-rich sequences poses an inherent risk of failure. Indeed, a bioinformatics analysis reveals that the N-terminal regions of ORFs lack D/E enrichment, implying that the translation defect partly restricts the overall amino acid usage in proteomes.
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Affiliation(s)
- Yosuke Ito
- grid.32197.3e0000 0001 2179 2105School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8503 Japan
| | - Yuhei Chadani
- grid.32197.3e0000 0001 2179 2105Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503 Japan
| | - Tatsuya Niwa
- grid.32197.3e0000 0001 2179 2105School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8503 Japan ,grid.32197.3e0000 0001 2179 2105Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503 Japan
| | - Ayako Yamakawa
- grid.32197.3e0000 0001 2179 2105School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8503 Japan
| | - Kodai Machida
- grid.266453.00000 0001 0724 9317Graduate School of Engineering, University of Hyogo, Himeji, Hyogo 671-2280 Japan
| | - Hiroaki Imataka
- grid.266453.00000 0001 0724 9317Graduate School of Engineering, University of Hyogo, Himeji, Hyogo 671-2280 Japan
| | - Hideki Taguchi
- grid.32197.3e0000 0001 2179 2105School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8503 Japan ,grid.32197.3e0000 0001 2179 2105Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503 Japan
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72
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Hendi A, Niu LG, Snow AW, Ikegami R, Wang ZW, Mizumoto K. Channel-independent function of UNC-9/Innexin in spatial arrangement of GABAergic synapses in C. elegans. eLife 2022; 11:80555. [PMID: 36378164 PMCID: PMC9665852 DOI: 10.7554/elife.80555] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 11/03/2022] [Indexed: 11/16/2022] Open
Abstract
Precise synaptic connection of neurons with their targets is essential for the proper functioning of the nervous system. A plethora of signaling pathways act in concert to mediate the precise spatial arrangement of synaptic connections. Here we show a novel role for a gap junction protein in controlling tiled synaptic arrangement in the GABAergic motor neurons in Caenorhabditis elegans, in which their axons and synapses overlap minimally with their neighboring neurons within the same class. We found that while EGL-20/Wnt controls axonal tiling, their presynaptic tiling is mediated by a gap junction protein UNC-9/Innexin, that is localized at the presynaptic tiling border between neighboring dorsal D-type GABAergic motor neurons. Strikingly, the gap junction channel activity of UNC-9 is dispensable for its function in controlling tiled presynaptic patterning. While gap junctions are crucial for the proper functioning of the nervous system as channels, our finding uncovered the novel channel-independent role of UNC-9 in synapse patterning.
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Affiliation(s)
- Ardalan Hendi
- Department of Zoology, University of British Columbia
- Life Sciences Institute, University of British Columbia
| | - Long-Gang Niu
- Department of Neuroscience, University of Connecticut Health Center
| | - Andrew William Snow
- Graduate Program in Cell and Developmental Biology, University of British Columbia
| | | | - Zhao-Wen Wang
- Department of Neuroscience, University of Connecticut Health Center
| | - Kota Mizumoto
- Department of Zoology, University of British Columbia
- Life Sciences Institute, University of British Columbia
- Graduate Program in Cell and Developmental Biology, University of British Columbia
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia
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73
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Zheng Y, Zhang S, Luo Y, Li F, Tan J, Wang B, Zhao Z, Lin H, Zhang T, Liu J, Liu X, Guo J, Xie X, Chen L, Liu YG, Chu Z. Rice OsUBR7 modulates plant height by regulating histone H2B monoubiquitination and cell proliferation. PLANT COMMUNICATIONS 2022; 3:100412. [PMID: 35836378 PMCID: PMC9700165 DOI: 10.1016/j.xplc.2022.100412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/20/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Plant height is an important agronomic trait for lodging resistance and yield. Here, we report a new plant-height-related gene, OsUBR7 in rice (Oryza sativa L.); knockout of OsUBR7 caused fewer cells in internodes, resulting in a semi-dwarf phenotype. OsUBR7 encodes a putative E3 ligase containing a plant homeodomain finger and a ubiquitin protein ligase E3 component N-recognin 7 (UBR7) domain. OsUBR7 interacts with histones and monoubiquitinates H2B (H2Bub1) at lysine148 in coordination with the E2 conjugase OsUBC18. OsUBR7 mediates H2Bub1 at a number of chromatin loci for the normal expression of target genes, including cell-cycle-related and pleiotropic genes, consistent with the observation that cell-cycle progression was suppressed in the osubr7 mutant owing to reductions in H2Bub1 and expression levels at these loci. The genetic divergence of OsUBR7 alleles among japonica and indica cultivars affects their transcriptional activity, and these alleles may have undergone selection during rice domestication. Overall, our results reveal a novel mechanism that mediates H2Bub1 in plants, and UBR7 orthologs could be utilized as an untapped epigenetic resource for crop improvement.
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Affiliation(s)
- Yangyi Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Sensen Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yanqiu Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Fuquan Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jiantao Tan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Bin Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Zhe Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Huifang Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Tingting Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jianhong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xupeng Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jingxin Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xianrong Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
| | - Zhizhan Chu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou 510642, China.
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74
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Mukherjee M, Blair RH, Wang ZQ. Machine-learning guided elucidation of contribution of individual steps in the mevalonate pathway and construction of a yeast platform strain for terpenoid production. Metab Eng 2022; 74:139-149. [DOI: 10.1016/j.ymben.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 10/16/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022]
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75
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Increasing the Thermodynamic Driving Force of the Phosphofructokinase Reaction in
Clostridium thermocellum. Appl Environ Microbiol 2022; 88:e0125822. [PMID: 36286488 PMCID: PMC9680637 DOI: 10.1128/aem.01258-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ability to control the distribution of thermodynamic driving force throughout a metabolic pathway is likely to be an important tool for metabolic engineering. The phosphofructokinase reaction is a key enzyme in Embden-Mayerhof-Parnas glycolysis and therefore improving the thermodynamic driving force of this reaction in
C. thermocellum
is believed to enable higher product titers.
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76
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Ramachandran RP, Nandi I, Haritan N, Zlotkin-Rivkin E, Keren Y, Danieli T, Lebendiker M, Melamed-Book N, Breuer W, Reichmann D, Aroeti B. EspH interacts with the host active Bcr related (ABR) protein to suppress RhoGTPases. Gut Microbes 2022; 14:2130657. [PMID: 36219160 PMCID: PMC9559323 DOI: 10.1080/19490976.2022.2130657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Enteropathogenic Escherichia coli are bacterial pathogens that colonize the gut and cause severe diarrhea in humans. Upon intimate attachment to the intestinal epithelium, these pathogens translocate via a type III secretion system virulent proteins, termed effectors, into the host cells. These effectors manipulate diverse host cell organelles and functions for the pathogen's benefit. However, the precise mechanisms underlying their activities are not fully understood despite intensive research. EspH, a critical effector protein, has been previously reported to disrupt the host cell actin cytoskeleton by suppressing RhoGTPase guanine exchange factors. However, native host proteins targeted by EspH to mediate these activities remained unknown. Here, we identified the active Bcr related (ABR), a protein previously characterized to possess dual Rho guanine nucleotide exchange factor and GTPase activating protein (GAP) domains, as a native EspH interacting partner. These interactions are mediated by the effector protein's C-terminal 38 amino acid segment. The effector primarily targets the GAP domain of ABR to suppress Rac1 and Cdc42, host cell cytotoxicity, bacterial invasion, and filopodium formation at infection sites. Knockdown of ABR expression abolished the ability of EspH to suppress Rac1, Cdc42. Our studies unravel a novel mechanism by which host RhoGTPases are hijacked by bacterial effectors.
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Affiliation(s)
- Rachana Pattani Ramachandran
- Department of Cell and Developmental Biology, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ipsita Nandi
- Department of Cell and Developmental Biology, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nir Haritan
- Department of Cell and Developmental Biology, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Efrat Zlotkin-Rivkin
- Department of Cell and Developmental Biology, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yael Keren
- The Protein Production Facility, Wolfson Centre for Applied Structural Biology, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tsafi Danieli
- The Protein Production Facility, Wolfson Centre for Applied Structural Biology, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mario Lebendiker
- The Protein Production Facility, Wolfson Centre for Applied Structural Biology, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Naomi Melamed-Book
- Bioimaging Unit, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - William Breuer
- Proteomics and Mass Spectrometry Unit, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dana Reichmann
- Proteomics and Mass Spectrometry Unit, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel,Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Benjamin Aroeti
- Department of Cell and Developmental Biology, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel,CONTACT Benjamin Aroeti Department of Cell and Developmental Biology, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem91904, Israel
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77
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Zhao Y, Han J, Tan J, Yang Y, Li S, Gou Y, Luo Y, Li T, Xiao W, Xue Y, Hao Y, Xie X, Liu Y, Zhu Q. Efficient assembly of long DNA fragments and multiple genes with improved nickase-based cloning and Cre/loxP recombination. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1983-1995. [PMID: 35767383 PMCID: PMC9491458 DOI: 10.1111/pbi.13882] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/14/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Functional genomics, synthetic biology and metabolic engineering require efficient tools to deliver long DNA fragments or multiple gene constructs. Although numerous DNA assembly methods exist, most are complicated, time-consuming and expensive. Here, we developed a simple and flexible strategy, unique nucleotide sequence-guided nicking endonuclease (UNiE)-mediated DNA assembly (UNiEDA), for efficient cloning of long DNAs and multigene stacking. In this system, a set of unique 15-nt 3' single-strand overhangs were designed and produced by nicking endonucleases (nickases) in vectors and insert sequences. We introduced UNiEDA into our modified Cre/loxP recombination-mediated TransGene Stacking II (TGSII) system to generate an improved multigene stacking system we call TGSII-UNiE. Using TGSII-UNiE, we achieved efficient cloning of long DNA fragments of different sizes and assembly of multiple gene cassettes. Finally, we engineered and validated the biosynthesis of betanin in wild tobacco (Nicotiana benthamiana) leaves and transgenic rice (Oryza sativa) using multigene stacking constructs based on TGSII-UNiE. In conclusion, UNiEDA is an efficient, convenient and low-cost method for DNA cloning and multigene stacking, and the TGSII-UNiE system has important application prospects for plant functional genomics, genetic engineering and synthetic biology research.
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Affiliation(s)
- Yanchang Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Jingluan Han
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Jiantao Tan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yaqian Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Shuangchun Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yajun Gou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yuyu Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Tie Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Wenyu Xiao
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yang Xue
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yu Hao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Xianrong Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yao‐Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Qinlong Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
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78
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Spero MA, Jones J, Lomenick B, Chou TF, Newman DK. Mechanisms of chlorate toxicity and resistance in Pseudomonas aeruginosa. Mol Microbiol 2022; 118:321-335. [PMID: 36271736 PMCID: PMC9589919 DOI: 10.1111/mmi.14972] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/31/2022] [Accepted: 08/04/2022] [Indexed: 11/28/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic bacterial pathogen that often encounters hypoxic/anoxic environments within the host, which increases its tolerance to many conventional antibiotics. Toward identifying novel treatments, we explored the therapeutic potential of chlorate, a pro-drug that kills hypoxic/anoxic, antibiotic-tolerant P. aeruginosa populations. While chlorate itself is relatively nontoxic, it is enzymatically reduced to the toxic oxidizing agent, chlorite, by hypoxically induced nitrate reductase. To better assess chlorate's therapeutic potential, we investigated mechanisms of chlorate toxicity and resistance in P. aeruginosa. We used transposon mutagenesis to identify genes that alter P. aeruginosa fitness during chlorate treatment, finding that methionine sulfoxide reductases (Msr), which repair oxidized methionine residues, support survival during chlorate stress. Chlorate treatment leads to proteome-wide methionine oxidation, which is exacerbated in a ∆msrA∆msrB strain. In response to chlorate, P. aeruginosa upregulates proteins involved in a wide range of functions, including metabolism, DNA replication/repair, protein repair, transcription, and translation, and these newly synthesized proteins are particularly vulnerable to methionine oxidation. The addition of exogenous methionine partially rescues P. aeruginosa survival during chlorate treatment, suggesting that widespread methionine oxidation contributes to death. Finally, we found that mutations that decrease nitrate reductase activity are a common mechanism of chlorate resistance.
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Affiliation(s)
- Melanie A. Spero
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Present address: Institute of Molecular Biology, University of Oregon, Eugene, OR, USA
| | - Jeff Jones
- Proteome Exploration Laboratory, Beckman Institute, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Brett Lomenick
- Proteome Exploration Laboratory, Beckman Institute, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tsui-Fen Chou
- Proteome Exploration Laboratory, Beckman Institute, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Dianne K. Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
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79
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Gong X, Li F, Liang Y, Han X, Wen M. Characteristics of NtCCD1-3 from tobacco, and protein engineering of the CCD1 to enhance β-ionone production in yeast. Front Microbiol 2022; 13:1011297. [PMID: 36212872 PMCID: PMC9539813 DOI: 10.3389/fmicb.2022.1011297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/09/2022] [Indexed: 11/19/2022] Open
Abstract
Biosynthesis of β-ionone by microbial cell factories has become a promising way to obtain natural β-ionone. The catalytic activity of carotenoid cleavage dioxygenase 1 (CCD1) in cleavage of β-carotene to β-ionone severely limits its biosynthesis. In this study, NtCCD1-3 from Nicotiana tabacum with high ability to cleave β-carotene was screened. Multiple strategies for improving the β-ionone yield in Saccharomyces cerevisiae were performed. The results showed that NtCCD1-3 could cleave a variety of caroteniods at the 9,10 (9′,10′) double bonds and lycopene at the 5,6 (5′,6′) positions. The insertion site delta for NtCCD1-3 gene was more suitable for enhancing the yield of β-ionone, showing 19.1-fold increase compared with the rox1 site. More importantly, mutant K38A of NtCCD1-3 in membrane-bonding domains could greatly promote β-ionone production by more than 3-fold. We also found that overexpression of the NADH kinase Pos5 could improve β-ionone yield up to 1.5 times. These results may provide valuable references for biosynthesis of β-ionone.
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Affiliation(s)
- Xiaowei Gong
- National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
- R&D Center, China Tobacco Yunnan Industrial Co., Ltd., Kunming, China
| | - Fan Li
- National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Yupeng Liang
- National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Xiulin Han
- National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
- *Correspondence: Xiulin Han,
| | - Mengliang Wen
- National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
- Mengliang Wen,
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80
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Brunet YR, Habib C, Brogan AP, Artzi L, Rudner DZ. Intrinsically disordered protein regions are required for cell wall homeostasis in Bacillus subtilis. Genes Dev 2022; 36:970-984. [PMID: 36265902 PMCID: PMC9732909 DOI: 10.1101/gad.349895.122] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/03/2022] [Indexed: 01/07/2023]
Abstract
Intrinsically disordered protein regions (IDRs) have been implicated in diverse nuclear and cytoplasmic functions in eukaryotes, but their roles in bacteria are less clear. Here, we report that extracytoplasmic IDRs in Bacillus subtilis are required for cell wall homeostasis. The B. subtilis σI transcription factor is activated in response to envelope stress through regulated intramembrane proteolysis (RIP) of its membrane-anchored anti-σ factor, RsgI. Unlike canonical RIP pathways, we show that ectodomain (site-1) cleavage of RsgI is constitutive, but the two cleavage products remain stably associated, preventing intramembrane (site-2) proteolysis. The regulated step in this pathway is their dissociation, which is triggered by impaired cell wall synthesis and requires RsgI's extracytoplasmic IDR. Intriguingly, the major peptidoglycan polymerase PBP1 also contains an extracytoplasmic IDR, and we show that this region is important for its function. Disparate IDRs can replace the native IDRs on both RsgI and PBP1, arguing that these unstructured regions function similarly. Our data support a model in which the RsgI-σI signaling system and PBP1 represent complementary pathways to repair gaps in the PG meshwork. The IDR on RsgI senses these gaps and activates σI, while the IDR on PBP1 directs the synthase to these sites to fortify them.
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Affiliation(s)
- Yannick R. Brunet
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Cameron Habib
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Anna P. Brogan
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Lior Artzi
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - David Z. Rudner
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, USA
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81
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Sun H, Zhang J, Liu W, E W, Wang X, Li H, Cui Y, Zhao D, Liu K, Du B, Ding Y, Wang C. Identification and combinatorial engineering of indole-3-acetic acid synthetic pathways in Paenibacillus polymyxa. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:81. [PMID: 35953838 PMCID: PMC9367139 DOI: 10.1186/s13068-022-02181-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 08/05/2022] [Indexed: 11/22/2022]
Abstract
Background Paenibacillus polymyxa is a typical plant growth-promoting rhizobacterium (PGPR), and synthesis of indole-3-acetic acid (IAA) is one of the reasons for its growth-promoting capacity. The synthetic pathways of IAA in P. polymyxa must be identified and modified. Results P. polymyxa SC2 and its spontaneous mutant SC2-M1 could promote plant growth by directly secreting IAA. Through metabonomic and genomic analysis, the genes patA, ilvB3, and fusE in the native IPyA pathway of IAA synthesis in strain SC2-M1 were predicted. A novel strong promoter P04420 was rationally selected, synthetically analyzed, and then evaluated on its ability to express IAA synthetic genes. Co-expression of three genes, patA, ilvB3, and fusE, increased IAA yield by 60% in strain SC2-M1. Furthermore, the heterogeneous gene iaam of the IAM pathway and two heterogeneous IPyA pathways of IAA synthesis were selected to improve the IAA yield of strain SC2-M1. The genes ELJP6_14505, ipdC, and ELJP6_00725 of the entire IPyA pathway from Enterobacter ludwigii JP6 were expressed well by promoter P04420 in strain SC2-M1 and increased IAA yield in the engineered strain SC2-M1 from 13 to 31 μg/mL, which was an increase of 138%. Conclusions The results of our study help reveal and enhance the IAA synthesis pathways of P. polymyxa and its future application. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02181-3. Verifying an entire native IPyA pathway of IAA synthesis in P. polymyxa. Introducing heterologous IAM and IPyA pathways of IAA synthesis to P. polymyxa. Selecting and analyzing a novel strong promoter P04420 to express IAA synthesis genes.
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82
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A fully automated high-throughput plasmid purification workstation for the generation of mammalian cell expression-quality DNA. SLAS Technol 2022; 27:227-236. [DOI: 10.1016/j.slast.2022.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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83
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Jost A, Pfeifer F. Interaction of the gas vesicle proteins GvpA, GvpC, GvpN, and GvpO of Halobacterium salinarum. Front Microbiol 2022; 13:971917. [PMID: 35966690 PMCID: PMC9372576 DOI: 10.3389/fmicb.2022.971917] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 07/07/2022] [Indexed: 11/23/2022] Open
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84
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Biallelic and gene-wide genomic substitution for endogenous intron and retroelement mutagenesis in human cells. Nat Commun 2022; 13:4219. [PMID: 35864085 PMCID: PMC9304424 DOI: 10.1038/s41467-022-31982-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 07/13/2022] [Indexed: 01/09/2023] Open
Abstract
Functional annotation of the vast noncoding landscape of the diploid human genome still remains a major challenge of genomic research. An efficient, scarless, biallelic, and gene-wide mutagenesis approach is needed for direct investigation of the functional significance of endogenous long introns in gene regulation. Here we establish a genome substitution platform, the Universal Knock-in System or UKiS, that meets these requirements. For proof of concept, we first used UKiS on the longest intron of TP53 in the pseudo-diploid cell line HCT116. Complete deletion of the intron, its substitution with mouse and zebrafish syntenic introns, and specific removal of retrotransposon-derived elements (retroelements) were all efficiently and accurately achieved in both alleles, revealing a suppressive role of intronic Alu elements in TP53 expression. We also used UKiS for TP53 intron deletion in human induced pluripotent stem cells without losing their stemness. Furthermore, UKiS enabled biallelic removal of all introns from three human gene loci of ~100 kb and longer to demonstrate that intron requirements for transcriptional activities vary among genes. UKiS is a standard platform with which to pursue the design of noncoding regions for genome writing in human cells.
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85
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Makela AV, Schott MA, Madsen CS, Greeson EM, Contag CH. Magnetic Particle Imaging of Magnetotactic Bacteria as Living Contrast Agents Is Improved by Altering Magnetosome Arrangement. NANO LETTERS 2022; 22:4630-4639. [PMID: 35686930 DOI: 10.1021/acs.nanolett.1c05042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Superparamagnetic iron oxide nanoparticles (SPIONs) can be used as imaging agents to differentiate between normal and diseased tissue or track cell movement. Magnetic particle imaging (MPI) detects the magnetic properties of SPIONs, providing quantitative and sensitive image data. MPI performance depends on the size, structure, and composition of nanoparticles. Magnetotactic bacteria produce magnetosomes with properties similar to those of synthetic nanoparticles, and these can be modified by mutating biosynthetic genes. The use of Magnetospirillum gryphiswaldense, MSR-1 with a mamJ deletion, containing clustered magnetosomes instead of typical linear chains, resulted in improved MPI signal and resolution. Bioluminescent MSR-1 with the mamJ deletion were administered into tumor-bearing and healthy mice. In vivo bioluminescence imaging revealed the viability of MSR-1, and MPI detected signals in livers and tumors. The development of living contrast agents offers opportunities for imaging and therapy with multimodality imaging guiding development of these agents by tracking the location, viability, and resulting biological effects.
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Affiliation(s)
- Ashley V Makela
- Institute for Quantitative Health Science and Engineering, Michigan State University, 775 Woodlot Drive, East Lansing, Michigan 48824, United States
| | - Melissa A Schott
- Institute for Quantitative Health Science and Engineering, Michigan State University, 775 Woodlot Drive, East Lansing, Michigan 48824, United States
| | - Cody S Madsen
- Institute for Quantitative Health Science and Engineering, Michigan State University, 775 Woodlot Drive, East Lansing, Michigan 48824, United States
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan 48824, United States
| | - Emily M Greeson
- Institute for Quantitative Health Science and Engineering, Michigan State University, 775 Woodlot Drive, East Lansing, Michigan 48824, United States
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Christopher H Contag
- Institute for Quantitative Health Science and Engineering, Michigan State University, 775 Woodlot Drive, East Lansing, Michigan 48824, United States
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
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86
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Weiss A, Murdoch CC, Edmonds KA, Jordan MR, Monteith AJ, Perera YR, Rodríguez Nassif AM, Petoletti AM, Beavers WN, Munneke MJ, Drury SL, Krystofiak ES, Thalluri K, Wu H, Kruse ARS, DiMarchi RD, Caprioli RM, Spraggins JM, Chazin WJ, Giedroc DP, Skaar EP. Zn-regulated GTPase metalloprotein activator 1 modulates vertebrate zinc homeostasis. Cell 2022; 185:2148-2163.e27. [PMID: 35584702 DOI: 10.1016/j.cell.2022.04.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/07/2022] [Accepted: 04/07/2022] [Indexed: 12/13/2022]
Abstract
Zinc (Zn) is an essential micronutrient and cofactor for up to 10% of proteins in living organisms. During Zn limitation, specialized enzymes called metallochaperones are predicted to allocate Zn to specific metalloproteins. This function has been putatively assigned to G3E GTPase COG0523 proteins, yet no Zn metallochaperone has been experimentally identified in any organism. Here, we functionally characterize a family of COG0523 proteins that is conserved across vertebrates. We identify Zn metalloprotease methionine aminopeptidase 1 (METAP1) as a COG0523 client, leading to the redesignation of this group of COG0523 proteins as the Zn-regulated GTPase metalloprotein activator (ZNG1) family. Using biochemical, structural, genetic, and pharmacological approaches across evolutionarily divergent models, including zebrafish and mice, we demonstrate a critical role for ZNG1 proteins in regulating cellular Zn homeostasis. Collectively, these data reveal the existence of a family of Zn metallochaperones and assign ZNG1 an important role for intracellular Zn trafficking.
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Affiliation(s)
- Andy Weiss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Caitlin C Murdoch
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Matthew R Jordan
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA; Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Andrew J Monteith
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Yasiru R Perera
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Aslin M Rodríguez Nassif
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Amber M Petoletti
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - William N Beavers
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Matthew J Munneke
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Sydney L Drury
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Evan S Krystofiak
- Cell Imaging Shared Resource, Vanderbilt University, Nashville, TN 37232, USA
| | - Kishore Thalluri
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Hongwei Wu
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Angela R S Kruse
- Departments of Chemistry and Biochemistry, Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA
| | | | - Richard M Caprioli
- Departments of Chemistry and Biochemistry, Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA
| | - Jeffrey M Spraggins
- Departments of Chemistry and Biochemistry, Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37235, USA; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Walter J Chazin
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA; Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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87
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Nutalai R, Zhou D, Tuekprakhon A, Ginn HM, Supasa P, Liu C, Huo J, Mentzer AJ, Duyvesteyn HME, Dijokaite-Guraliuc A, Skelly D, Ritter TG, Amini A, Bibi S, Adele S, Johnson SA, Constantinides B, Webster H, Temperton N, Klenerman P, Barnes E, Dunachie SJ, Crook D, Pollard AJ, Lambe T, Goulder P, Paterson NG, Williams MA, Hall DR, Mongkolsapaya J, Fry EE, Dejnirattisai W, Ren J, Stuart DI, Screaton GR. Potent cross-reactive antibodies following Omicron breakthrough in vaccinees. Cell 2022; 185:2116-2131.e18. [PMID: 35662412 PMCID: PMC9120130 DOI: 10.1016/j.cell.2022.05.014] [Citation(s) in RCA: 101] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/04/2022] [Accepted: 05/14/2022] [Indexed: 11/28/2022]
Abstract
Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1, and BA.2. BA.2 RBD has slightly higher ACE2 affinity than BA.1 and slightly reduced neutralization by vaccine serum, possibly associated with its increased transmissibility. Neutralization differences between sub-lineages for mAbs (including therapeutics) mostly arise from variation in residues bordering the ACE2 binding site; however, more distant mutations S371F (BA.2) and R346K (BA.1.1) markedly reduce neutralization by therapeutic antibody Vir-S309. In-depth structure-and-function analyses of 27 potent RBD-binding mAbs isolated from vaccinated volunteers following breakthrough Omicron-BA.1 infection reveals that they are focused in two main clusters within the RBD, with potent right-shoulder antibodies showing increased prevalence. Selection and somatic maturation have optimized antibody potency in less-mutated epitopes and recovered potency in highly mutated epitopes. All 27 mAbs potently neutralize early pandemic strains, and many show broad reactivity with variants of concern.
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Affiliation(s)
- Rungtiwa Nutalai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daming Zhou
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Aekkachai Tuekprakhon
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Helen M Ginn
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Jiandong Huo
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Aiste Dijokaite-Guraliuc
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Donal Skelly
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Thomas G Ritter
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Ali Amini
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Sagida Bibi
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Sandra Adele
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | | | - Hermione Webster
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and Greenwich, Chatham Maritime, Kent ME4 4TB, UK
| | - Paul Klenerman
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Eleanor Barnes
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Susanna J Dunachie
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK; Centre For Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Teresa Lambe
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Philip Goulder
- Peter Medawar Building for Pathogen Research, Oxford, UK; Department of Paediatrics, University of Oxford, Oxford, UK
| | - Neil G Paterson
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Mark A Williams
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - David R Hall
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - Wanwisa Dejnirattisai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
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88
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Han J, Ma K, Li H, Su J, Zhou L, Tang J, Zhang S, Hou Y, Chen L, Liu Y, Zhu Q. All-in-one: a robust fluorescent fusion protein vector toolbox for protein localization and BiFC analyses in plants. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1098-1109. [PMID: 35179286 PMCID: PMC9129086 DOI: 10.1111/pbi.13790] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 02/01/2022] [Accepted: 02/04/2022] [Indexed: 05/20/2023]
Abstract
Fluorescent tagging protein localization (FTPL) and bimolecular fluorescence complementation (BiFC) are popular tools for in vivo analyses of the subcellular localizations of proteins and protein-protein interactions in plant cells. The efficiency of fluorescent fusion protein (FFP) expression analyses is typically impaired when the FFP genes are co-transformed on separate plasmids compared to when all are cloned and transformed in a single vector. Functional genomics applications using FFPs such as a gene family studies also often require the generation of multiple plasmids. Here, to address these needs, we developed an efficient, modular all-in-one (Aio) FFP (AioFFP) vector toolbox, including a set of fluorescently labelled organelle markers, FTPL and BiFC plasmids and associated binary vectors. This toolbox uses Gibson assembly (GA) and incorporates multiple unique nucleotide sequences (UNSs) to facilitate efficient gene cloning. In brief, this system enables convenient cloning of a target gene into various FFP vectors or the insertion of two or more target genes into the same FFP vector in a single-tube GA reaction. This system also enables integration of organelle marker genes or fluorescently fused target gene expression units into a single transient expression plasmid or binary vector. We validated the AioFFP system by testing genes encoding proteins known to be functional in FTPL and BiFC assays. In addition, we performed a high-throughput assessment of the accurate subcellular localizations of an uncharacterized rice CBSX protein subfamily. This modular UNS-guided GA-mediated AioFFP vector toolkit is cost-effective, easy to use and will promote functional genomics research in plants.
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Affiliation(s)
- Jingluan Han
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- College of Life ScienceSouth China Agricultural UniversityGuangzhouChina
| | - Kun Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- College of Life ScienceSouth China Agricultural UniversityGuangzhouChina
| | - Huali Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
| | - Jing Su
- Guangdong Provincial Key Laboratory of High Technology for Plant ProtectionPlant Protection Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Lian Zhou
- Rice Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Jintao Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- College of Life ScienceSouth China Agricultural UniversityGuangzhouChina
| | - Shijuan Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- College of Life ScienceSouth China Agricultural UniversityGuangzhouChina
| | - Yuke Hou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- College of Life ScienceSouth China Agricultural UniversityGuangzhouChina
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- College of Life ScienceSouth China Agricultural UniversityGuangzhouChina
| | - Yao‐Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- College of Life ScienceSouth China Agricultural UniversityGuangzhouChina
| | - Qinlong Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- College of Life ScienceSouth China Agricultural UniversityGuangzhouChina
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89
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Abstract
In response to viral predation, bacteria have evolved a wide range of defense mechanisms, which rely mostly on proteins acting at the cellular level. Here, we show that aminoglycosides, a well-known class of antibiotics produced by Streptomyces, are potent inhibitors of phage infection in widely divergent bacterial hosts. We demonstrate that aminoglycosides block an early step of the viral life cycle, prior to genome replication. Phage inhibition was also achieved using supernatants from natural aminoglycoside producers, indicating a broad physiological significance of the antiviral properties of aminoglycosides. Strikingly, we show that acetylation of the aminoglycoside antibiotic apramycin abolishes its antibacterial effect but retains its antiviral properties. Altogether, our study expands the knowledge of aminoglycoside functions, suggesting that aminoglycosides not only are used by their producers as toxic molecules against their bacterial competitors but also could provide protection against the threat of phage predation at the community level. IMPORTANCE Predation by phages is a major driver of bacterial evolution. As a result, elucidating antiphage strategies is crucial from both fundamental and therapeutic standpoints. While protein-mediated defense mechanisms, like restriction-modification systems or CRISPR/Cas, have been extensively studied, much less is known about the potential antiphage activity of small molecules. Focusing on the model bacteria Escherichia coli and Streptomyces venezuelae, our findings revealed significant antiphage properties of aminoglycosides, a major class of translation-targeting antibiotics produced by Streptomyces. Further, we demonstrate that supernatants from natural aminoglycoside producers protect bacteria from phage propagation, highlighting the physiological relevance of this inhibition. Suppression of phage infection by aminoglycosides did not result from the indirect inhibition of bacterial translation, suggesting a direct interaction between aminoglycosides and phage components. This work highlights the molecular versatility of aminoglycosides, which have evolved to efficiently block protein synthesis in bacterial competitors and provide protection against phages.
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90
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Abstract
Herpesviruses assemble new viral particles in the nucleus. These nucleocapsids bud through the inner nuclear membrane to produce enveloped viral particles in the perinuclear space before fusing with the outer nuclear membrane to reach the cytoplasm. This unusual route is necessary since viral capsids are too large to pass through nuclear pores. However, the transient perinuclear nucleocapsids (250 nm in diameter) are also larger than the width of the perinuclear space (30 to 50 nm). Interestingly, linker of the nucleoskeleton and cytoskeleton (LINC) components SUN and KASH connect the inner and outer nuclear membranes and regulate their spacing. Previous work by others on the related pseudorabies virus and human cytomegalovirus showed that they functionally interact with SUN proteins. To clarify the role of SUN proteins, we explored their impact on herpes simplex virus 1 (HSV-1), another herpesvirus. Using dominant negative SUN mutants and RNA interference, we show that HSV-1 propagation is dependent on the LINC complex. In contrast to pseudorabies virus, SUN2 disruption by either approach led to increased HSV-1 extracellular viral yields. This SUN2 dependency may be linked to its greater impact on perinuclear spacing in infected cells compared to SUN1. Finally, the virus itself seems to modulate perinuclear spacing. IMPORTANCE The large size of herpesviruses prevents them from travelling across the nuclear pores, and they instead egress across the two nuclear membranes, generating short-lived enveloped perinuclear virions. This poses a challenge as the perinuclear space is smaller than the virions. This implies the separation (unzipping) of the two nuclear membranes to accommodate the viral particles. The LINC complex bridges the two nuclear membranes and is an important regulator of perinuclear spacing. Work by others hint at its functional implication during pseudorabies virus and cytomegalovirus propagation. The present study probes the importance for HSV-1 of the SUN proteins, the LINC components found in the inner nuclear membrane. Using dominant negative constructs and RNA interference (RNAi), the data reveal that SUN2 exhibits antiviral propriety toward HSV-1, as disrupting the protein leads to increased viral yields. This is in contrast with that reported for pseudorabies and suggests that differences among herpesviruses may, once again, prevail.
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91
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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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92
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Abstract
Bacterial small RNAs (sRNAs) contribute to a variety of regulatory mechanisms that modulate a wide range of pathways, including metabolism, virulence, and antibiotic resistance. We investigated the involvement of sRNAs in rifampicin resistance in the opportunistic pathogen Staphylococcus aureus. Using a competition assay with an sRNA mutant library, we identified 6S RNA as being required for protection against low concentrations of rifampicin, an RNA polymerase (RNAP) inhibitor. This effect applied to rifabutin and fidaxomicin, two other RNAP-targeting antibiotics. 6S RNA is highly conserved in bacteria, and its absence in two other major pathogens, Salmonella enterica and Clostridioides difficile, also impaired susceptibility to RNAP inhibitors. In S. aureus, 6S RNA is produced from an autonomous gene and accumulates in stationary phase. In contrast to what was reported for Escherichia coli, S. aureus 6S RNA does not appear to play a critical role in the transition from exponential to stationary phase but affects σB-regulated expression in prolonged stationary phase. Nevertheless, its protective effect against rifampicin is independent of alternative sigma factor σB activity. Our results suggest that 6S RNA helps maintain RNAP-σA integrity in S. aureus, which could in turn help bacteria withstand low concentrations of RNAP inhibitors.
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93
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Benavidez JM, Kim JH, Greenwald I. Influences of HLH-2 stability on anchor cell fate specification during Caenorhabditis elegans gonadogenesis. G3 GENES|GENOMES|GENETICS 2022; 12:6520806. [PMID: 35134193 PMCID: PMC8982380 DOI: 10.1093/g3journal/jkac028] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/24/2022] [Indexed: 11/25/2022]
Abstract
The Caenorhabditis elegans E protein ortholog HLH-2 is required for the specification and function of the anchor cell, a unique, terminally differentiated somatic gonad cell that organizes uterine and vulval development. Initially, 4 cells—2 α cells and their sisters, the β cells—have the potential to be the sole anchor cell. The β cells rapidly lose anchor cell potential and invariably become ventral uterine precursor cells, while the 2 α cells interact via LIN-12/Notch to resolve which will be the anchor cell and which will become another ventral uterine precursor cell. HLH-2 protein stability is dynamically regulated in cells with anchor cell potential; initially present in all 4 cells, HLH-2 is degraded in presumptive ventral uterine precursor cells while remaining stable in the anchor cell. Here, we demonstrate that stability of HLH-2 protein is regulated by the activity of lin-12/Notch in both α and β cells. Our analysis provides evidence that activation of LIN-12 promotes degradation of HLH-2 as part of a negative feedback loop during the anchor cell/ventral uterine precursor cell decision by the α cells, and that absence of lin-12 activity in β cells increases HLH-2 stability and may account for their propensity to adopt the anchor cell fate in a lin-12 null background. We also performed an RNA interference screen of 232 ubiquitin-related genes and identified 7 genes that contribute to HLH-2 degradation in ventral uterine precursor cells; however, stabilizing HLH-2 by depleting ubiquitin ligases in a lin-12(+) background does not result in supernumerary anchor cells, suggesting that LIN-12 activation does not oppose hlh-2 activity solely by causing HLH-2 protein degradation. Finally, we provide evidence for lin-12-independent transcriptional regulation of hlh-2 in β cells that correlates with known differences in POP-1/TCF levels and anchor cell potential between α and β cells. Together, our results indicate that hlh-2 activity is regulated at multiple levels to restrict the anchor cell fate to a single cell.
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Affiliation(s)
- Justin M Benavidez
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Jee Hun Kim
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Iva Greenwald
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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94
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Goldsmith SL, Shimell M, Tauscher P, Daly SM, Shimmi O, O’Connor MB, Newfeld SJ. New resources for the Drosophila 4th chromosome: FRT101F enabled mitotic clones and Bloom syndrome helicase enabled meiotic recombination. G3 GENES|GENOMES|GENETICS 2022; 12:6516016. [PMID: 35084488 PMCID: PMC8982423 DOI: 10.1093/g3journal/jkac019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 01/14/2022] [Indexed: 11/14/2022]
Abstract
Genes on the long arm of the Drosophila melanogaster 4th chromosome are difficult to study because the chromosome lacks mitotic and meiotic recombination. Without recombination numerous standard methods of genetic analysis are impossible. Here, we report new resources for the 4th. For mitotic recombination, we generated a chromosome with an FRT very near the centromere in 101F and a derivative that carries FRT101F with a distal ubiquitously expressed GAL80 transgene. This pair of chromosomes enables both unmarked and MARCM clones. For meiotic recombination, we demonstrate that a Bloom syndrome helicase and recombination defective double mutant genotype can create recombinant 4th chromosomes via female meiosis. All strains will be available to the community via the Bloomington Drosophila Stock Center. Additional resources for studies of the 4th are in preparation and will also be made available. The goal of the 4th Chromosome Resource Project is to accelerate the genetic analysis of protein-coding genes on the 4th, including the 44 genes with no demonstrated function. Studies of these previously inaccessible but largely conserved genes will close longstanding gaps in our knowledge of metazoan development and physiology.
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Affiliation(s)
- Samuel L Goldsmith
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
| | - MaryJane Shimell
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Petra Tauscher
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Samantha M Daly
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
| | - Osamu Shimmi
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Michael B O’Connor
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Stuart J Newfeld
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
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95
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Abstract
Guanidinoacetate (GAA) is a naturally occurring amino acid derivative and the direct precursor of creatine, which is widely used in feed additives and the pharmaceutical industry. The current industrial synthesis of GAA is based on chemical methods, which limits the application of GAA. Here, a biological approach is developed for food safety GAA production via whole-cell biocatalysis by the generally regarded as safe (GRAS) bacterium Bacillus subtilis. First, we introduced a heterologous arginine: glycine amidinotransferase (AgaT) from Amycolatopsis kentuckyensis into B. subtilis and optimized its expression level using strategies including: promoter optimization, ribosome binding site (RBS) and N-terminal coding sequence (NCS) screening. In order to alleviate the waste of arginine and the inhibition of AgaT by ornithine, we optimized the natural ornithine cycle in B. subtilis. At the same time, the first gene in the glycine degradation pathway was knocked out. After optimization using these strategies, the titer of GAA was 4.26 g/L with a productivity of 0.21 g/L/h in 20 h, which provides a new method for the biosynthesis of GAA.
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96
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Ye Z, Huang Y, Shi B, Xiang Z, Tian Z, Huang M, Wu L, Deng Z, Shen K, Liu T. Coupling cell growth and biochemical pathway induction in Saccharomyces cerevisiae for production of (+)-valencene and its chemical conversion to (+)-nootkatone. Metab Eng 2022; 72:107-115. [DOI: 10.1016/j.ymben.2022.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/05/2022] [Accepted: 03/10/2022] [Indexed: 11/29/2022]
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97
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Bloemen M, Rector A, Swinnen J, Ranst MV, Maes P, Vanmechelen B, Wollants E. Fast Detection of SARS-CoV-2 Variants including Omicron Using One-step RT-PCR and Sanger Sequencing. J Virol Methods 2022; 304:114512. [PMID: 35257682 PMCID: PMC8896866 DOI: 10.1016/j.jviromet.2022.114512] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/25/2022] [Accepted: 03/01/2022] [Indexed: 11/02/2022]
Abstract
SARS-CoV-2 has kept the world in suspense for almost 2 years now. The virus spread rapidly worldwide and several variants of concern have emerged: Alpha, Beta, Gamma, Delta and recently Omicron. A rapid method to detect key mutations is needed because these variants may jeopardize the effectiveness of immune protection following vaccination or past infection. This article describes an easy, cheap and fast method for the detection of mutations in the spike protein that are indicative for specific variants. This method can easily distinguish Omicron from other variants.
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98
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Amon JD, Artzi L, Rudner DZ. Genetic Evidence for Signal Transduction within the Bacillus subtilis GerA Germinant Receptor. J Bacteriol 2022; 204:e0047021. [PMID: 34780301 PMCID: PMC8846391 DOI: 10.1128/jb.00470-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/06/2021] [Indexed: 11/20/2022] Open
Abstract
Bacterial spores can rapidly exit dormancy through the process of germination. This process begins with the activation of nutrient receptors embedded in the spore membrane. The prototypical germinant receptor in Bacillus subtilis responds to l-alanine and is thought to be a complex of proteins encoded by the genes in the gerA operon: gerAA, gerAB, and gerAC. The GerAB subunit has recently been shown to function as the nutrient sensor, but beyond contributing to complex stability, no additional functions have been attributed to the other two subunits. Here, we investigate the role of GerAA. We resurrect a previously characterized allele of gerA (termed gerA*) that carries a mutation in gerAA and show that it constitutively activates germination even in the presence of a wild-type copy of gerA. Using an enrichment strategy to screen for suppressors of gerA*, we identified mutations in all three gerA genes that restore a functional receptor. Characterization of two distinct gerAB suppressors revealed that one (gerAB[E105K]) reduces the GerA complex's ability to respond to l-alanine, while another (gerAB[F259S]) disrupts the germinant signal downstream of l-alanine recognition. These data argue against models in which GerAA is directly or indirectly involved in germinant sensing. Rather, our data suggest that GerAA is responsible for transducing the nutrient signal sensed by GerAB. While the steps downstream of gerAA have yet to be uncovered, these results validate the use of a dominant-negative genetic approach in elucidating the gerA signal transduction pathway. IMPORTANCE Endospore formers are a broad group of bacteria that can enter dormancy upon starvation and exit dormancy upon sensing the return of nutrients. How dormant spores sense and respond to these nutrients is poorly understood. Here, we identify a key step in the signal transduction pathway that is activated after spores detect the amino acid l-alanine. We present a model that provides a more complete picture of this process that is critical for allowing dormant spores to germinate and resume growth.
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Affiliation(s)
- Jeremy D. Amon
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Lior Artzi
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - David Z. Rudner
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
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99
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Inferring protein function in an emerging virus: detection of the nucleoprotein in Tilapia Lake Virus. J Virol 2022; 96:e0175721. [PMID: 35107373 DOI: 10.1128/jvi.01757-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Emerging viruses impose global threats to animal and human populations and may bear novel genes with limited homology to known sequences, necessitating the development of novel approaches to infer and test protein functions. This challenge is dramatically evident in tilapia lake virus (TiLV), an emerging orthomyxo-like virus that threatens the global tilapia aquaculture and food security of millions of people. The majority of TiLV proteins have no homology to known sequences, impeding functionality assessments. Using a novel bioinformatics approach, we predicted that TiLV's Protein 4 encodes the nucleoprotein - a factor essential for viral RNA replication. Multiple methodologies revealed the expected properties of orthomyxoviral nucleoproteins. A modified yeast three-hybrid assay detected Protein 4-RNA interactions, which were independent of the RNA sequence, and identified specific positively charged residues involved. Protein 4-RNA interactions were uncovered by R-DeeP and XRNAX methodologies. Immunoelectron microscopy found that multiple Protein 4 copies localized along enriched ribonucleoproteins. TiLV RNA from cells and virions co-immunoprecipitated with Protein 4. Immunofluorescence microscopy detected Protein 4 in the cytoplasm and nuclei, and nuclear Protein 4 increased upon CRM1 inhibition, suggesting CRM1-dependent nuclear export of TiLV RNA. Together, these data reveal TiLV's nucleoprotein and highlight the ability to infer protein functionality, including novel RNA-binding proteins, in emerging pathogens. These are important in light of the expected discovery of many unknown viruses and the zoonotic potential of such pathogens. Importance Tilapia is an important source of dietary protein, especially in developing countries. Massive losses of tilapia were identified worldwide, risking the food security of millions of people. Tilapia lake virus (TiLV) is an emerging pathogen responsible for these disease outbreaks. TiLV's genome encodes ten major proteins, nine of which show no homology to other known viral or cellular proteins, hindering functionality assessment of these proteins. Here we describe a novel bioinformatics approach to infer the functionality of TiLV proteins, which predicted Protein 4 as the nucleoprotein - a factor essential for viral RNA replication. We provided experimental support for this prediction by applying multiple molecular, biochemical, and imaging approaches. Overall, we illustrate a strategy for functional analyses in viral discovery. The strategy is important in light of the expected discovery of many unknown viruses and the zoonotic potential of such pathogens.
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100
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Philipp M, Hussnaetter KP, Reindl M, Müntjes K, Feldbrügge M, Schipper K. A Novel Potent Carrier for Unconventional Protein Export in Ustilago maydis. Front Cell Dev Biol 2022; 9:816335. [PMID: 35083222 PMCID: PMC8784666 DOI: 10.3389/fcell.2021.816335] [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: 11/16/2021] [Accepted: 12/17/2021] [Indexed: 11/14/2022] Open
Abstract
Recombinant proteins are ubiquitously applied in fields like research, pharma, diagnostics or the chemical industry. To provide the full range of useful proteins, novel expression hosts need to be established for proteins that are not sufficiently produced by the standard platform organisms. Unconventional secretion in the fungal model Ustilago maydis is an attractive novel option for export of heterologous proteins without N-glycosylation using chitinase Cts1 as a carrier. Recently, a novel factor essential for unconventional Cts1 secretion termed Jps1 was identified. Here, we show that Jps1 is unconventionally secreted using a fusion to bacterial β-glucuronidase as an established reporter. Interestingly, the experiment also demonstrates that the protein functions as an alternative carrier for heterologous proteins, showing about 2-fold higher reporter activity than the Cts1 fusion in the supernatant. In addition, Jps1-mediated secretion even allowed for efficient export of functional firefly luciferase as a novel secretion target which could not be achieved with Cts1. As an application for a relevant pharmaceutical target, export of functional bi-specific synthetic nanobodies directed against the SARS-CoV2 spike protein was demonstrated. The establishment of an alternative efficient carrier thus constitutes an excellent expansion of the existing secretion platform.
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Affiliation(s)
- Magnus Philipp
- Institute for Microbiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Kai P Hussnaetter
- Institute for Microbiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Michèle Reindl
- Institute for Microbiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Kira Müntjes
- Institute for Microbiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Michael Feldbrügge
- Institute for Microbiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Kerstin Schipper
- Institute for Microbiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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