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Reyer A, Bazihizina N, Jaślan J, Scherzer S, Schäfer N, Jaślan D, Becker D, Müller TD, Pommerrenig B, Neuhaus HE, Marten I, Hedrich R. Sugar beet PMT5a and STP13 carriers suitable for proton-driven plasma membrane sucrose and glucose import in taproots. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2219-2232. [PMID: 38602250 DOI: 10.1111/tpj.16740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/26/2024] [Accepted: 03/18/2024] [Indexed: 04/12/2024]
Abstract
Sugar beet (Beta vulgaris) is the major sugar-producing crop in Europe and Northern America, as the taproot stores sucrose at a concentration of around 20%. Genome sequence analysis together with biochemical and electrophysiological approaches led to the identification and characterization of the TST sucrose transporter driving vacuolar sugar accumulation in the taproot. However, the sugar transporters mediating sucrose uptake across the plasma membrane of taproot parenchyma cells remained unknown. As with glucose, sucrose stimulation of taproot parenchyma cells caused inward proton fluxes and plasma membrane depolarization, indicating a sugar/proton symport mechanism. To decipher the nature of the corresponding proton-driven sugar transporters, we performed taproot transcriptomic profiling and identified the cold-induced PMT5a and STP13 transporters. When expressed in Xenopus laevis oocytes, BvPMT5a was characterized as a voltage- and H+-driven low-affinity glucose transporter, which does not transport sucrose. In contrast, BvSTP13 operated as a high-affinity H+/sugar symporter, transporting glucose better than sucrose, and being more cold-tolerant than BvPMT5a. Modeling of the BvSTP13 structure with bound mono- and disaccharides suggests plasticity of the binding cleft to accommodate the different saccharides. The identification of BvPMT5a and BvSTP13 as taproot sugar transporters could improve breeding of sugar beet to provide a sustainable energy crop.
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Affiliation(s)
- Antonella Reyer
- Department of Molecular Plant Physiology and Biophysics, Biocenter, Julius-Maximilians-Universität (JMU), Würzburg, 97082, Germany
| | - Nadia Bazihizina
- Department of Molecular Plant Physiology and Biophysics, Biocenter, Julius-Maximilians-Universität (JMU), Würzburg, 97082, Germany
- Department of Agrifood Production and Environmental Sciences, Università degli Studi di Firenze, Florence, 50019, Sesto Fiorentino, Italy
| | - Justyna Jaślan
- Department of Molecular Plant Physiology and Biophysics, Biocenter, Julius-Maximilians-Universität (JMU), Würzburg, 97082, Germany
| | - Sönke Scherzer
- Department of Molecular Plant Physiology and Biophysics, Biocenter, Julius-Maximilians-Universität (JMU), Würzburg, 97082, Germany
| | - Nadine Schäfer
- Department of Molecular Plant Physiology and Biophysics, Biocenter, Julius-Maximilians-Universität (JMU), Würzburg, 97082, Germany
| | - Dawid Jaślan
- Department of Molecular Plant Physiology and Biophysics, Biocenter, Julius-Maximilians-Universität (JMU), Würzburg, 97082, Germany
- Faculty of Medicine, Walther Straub Institute of Pharmacology and Toxicology, Ludwig Maximilians-Universität, 80336, Munich, Germany
| | - Dirk Becker
- Department of Molecular Plant Physiology and Biophysics, Biocenter, Julius-Maximilians-Universität (JMU), Würzburg, 97082, Germany
| | - Thomas D Müller
- Department of Molecular Plant Physiology and Biophysics, Biocenter, Julius-Maximilians-Universität (JMU), Würzburg, 97082, Germany
| | - Benjamin Pommerrenig
- Plant Physiology, University of Kaiserslautern, 67663, Kaiserslautern, Germany
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, 06484, Germany
| | - H Ekkehard Neuhaus
- Plant Physiology, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Irene Marten
- Department of Molecular Plant Physiology and Biophysics, Biocenter, Julius-Maximilians-Universität (JMU), Würzburg, 97082, Germany
| | - Rainer Hedrich
- Department of Molecular Plant Physiology and Biophysics, Biocenter, Julius-Maximilians-Universität (JMU), Würzburg, 97082, Germany
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2
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Li C, Krishnan S, Zhang M, Hu D, Meng D, Riedelsberger J, Dougherty L, Xu K, Piñeros MA, Cheng L. Alternative Splicing Underpins the ALMT9 Transporter Function for Vacuolar Malic Acid Accumulation in Apple. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310159. [PMID: 38514904 PMCID: PMC11165477 DOI: 10.1002/advs.202310159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 03/08/2024] [Indexed: 03/23/2024]
Abstract
Vacuolar malic acid accumulation largely determines fruit acidity, a key trait for the taste and flavor of apple and other fleshy fruits. Aluminum-activated malate transporter 9 (ALMT9/Ma1) underlies a major genetic locus, Ma, for fruit acidity in apple, but how the protein transports malate across the tonoplast is unclear. Here, it is shown that overexpression of the coding sequence of Ma1 (Ma1α) drastically decreases fruit acidity in "Royal Gala" apple, leading to uncovering alternative splicing underpins Ma1's function. Alternative splicing generates two isoforms: Ma1β is 68 amino acids shorter with much lower expression than the full-length protein Ma1α. Ma1β does not transport malate itself but interacts with the functional Ma1α to form heterodimers, creating synergy with Ma1α for malate transport in a threshold manner (When Ma1β/Ma1α ≥ 1/8). Overexpression of Ma1α triggers feedback inhibition on the native Ma1 expression via transcription factor MYB73, decreasing the Ma1β level well below the threshold that leads to significant reductions in Ma1 function and malic acid accumulation in fruit. Overexpression of Ma1α and Ma1β or genomic Ma1 increases both isoforms proportionally and enhances fruit malic acid accumulation. These findings reveal an essential role of alternative splicing in ALMT9-mediated malate transport underlying apple fruit acidity.
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Affiliation(s)
- Chunlong Li
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural CropsCollege of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhan430070China
| | | | - Mengxia Zhang
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
| | - Dagang Hu
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
| | - Dong Meng
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
| | - Janin Riedelsberger
- Center for Bioinformatics, Simulation and Modeling, Department of Bioinformatics, Faculty of EngineeringUniversity of TalcaTalca3460000Chile
| | - Laura Dougherty
- Horticulture Section, School of Integrative Plant Science, New York State Agricultural Experiment StationCornell UniversityGenevaNY14456USA
| | - Kenong Xu
- Horticulture Section, School of Integrative Plant Science, New York State Agricultural Experiment StationCornell UniversityGenevaNY14456USA
| | - Miguel A. Piñeros
- Plant Biology Section, School of Integrative Plant Science and Robert W. Holley Center for Agriculture and HealthUSDA‐ARS Cornell UniversityIthacaNY14853USA
| | - Lailiang Cheng
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityIthacaNY14853USA
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3
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Bradley SA, Hansson FG, Lehka BJ, Rago D, Pinho P, Peng H, Adhikari KB, Haidar AK, Hansen LG, Volkova D, Holtz M, Muyo Abad S, Ma X, Koudounas K, Besseau S, Gautron N, Mélin C, Marc J, Birer Williams C, Courdavault V, Jensen ED, Keasling JD, Zhang J, Jensen MK. Yeast Platforms for Production and Screening of Bioactive Derivatives of Rauwolscine. ACS Synth Biol 2024; 13:1498-1512. [PMID: 38635307 DOI: 10.1021/acssynbio.4c00039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Monoterpene indole alkaloids (MIAs) make up a highly bioactive class of metabolites produced by a range of tropical and subtropical plants. The corynanthe-type MIAs are a stereochemically complex subclass with therapeutic potential against a large number of indications including cancer, psychotic disorders, and erectile dysfunction. Here, we report yeast-based cell factories capable of de novo production of corynanthe-type MIAs rauwolscine, yohimbine, tetrahydroalstonine, and corynanthine. From this, we demonstrate regioselective biosynthesis of 4 fluorinated derivatives of these compounds and de novo biosynthesis of 7-chlororauwolscine by coexpression of a halogenase with the biosynthetic pathway. Finally, we capitalize on the ability of these cell factories to produce derivatives of these bioactive scaffolds to establish a proof-of-principle drug discovery pipeline in which the corynanthe-type MIAs are screened for bioactivity on human drug targets, expressed in yeast. In doing so, we identify antagonistic and agonistic behavior against the human adrenergic G protein-coupled receptors ADRA2A and ADRA2B, and the serotonergic receptor 5HT4b, respectively. This study thus demonstrates a proto-drug discovery pipeline for bioactive plant-inspired small molecules based on one-pot biocatalysis of natural and new-to-nature corynanthe-type MIAs in yeast.
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Affiliation(s)
- Samuel A Bradley
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Frederik G Hansson
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Beata J Lehka
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Daniela Rago
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Pedro Pinho
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Huadong Peng
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Khem B Adhikari
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Ahmad K Haidar
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Lea G Hansen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
- Biomia ApS, DK-2100 Copenhagen, Denmark
| | - Daria Volkova
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Maxence Holtz
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Sergi Muyo Abad
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Xin Ma
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Konstantinos Koudounas
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, F-37200 Tours, France
| | - Sébastien Besseau
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, F-37200 Tours, France
| | - Nicolas Gautron
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, F-37200 Tours, France
| | - Céline Mélin
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, F-37200 Tours, France
| | - Jillian Marc
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, F-37200 Tours, France
| | - Caroline Birer Williams
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, F-37200 Tours, France
| | - Vincent Courdavault
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, F-37200 Tours, France
| | - Emil D Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Jay D Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
- Joint BioEnergy Institute, Emeryville, California 94608,United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720,United States
- Department of Chemical and Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, California 94720, United States
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen 518055, China
| | - Jie Zhang
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
- Biomia ApS, DK-2100 Copenhagen, Denmark
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
- Biomia ApS, DK-2100 Copenhagen, Denmark
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4
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Cachera P, Kurt NC, Røpke A, Strucko T, Mortensen UH, Jensen MK. Genome-wide host-pathway interactions affecting cis-cis-muconic acid production in yeast. Metab Eng 2024; 83:75-85. [PMID: 38428729 DOI: 10.1016/j.ymben.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/11/2024] [Accepted: 02/23/2024] [Indexed: 03/03/2024]
Abstract
The success of forward metabolic engineering depends on a thorough understanding of the behaviour of a heterologous metabolic pathway within its host. We have recently described CRI-SPA, a high-throughput gene editing method enabling the delivery of a metabolic pathway to all strains of the Saccharomyces cerevisiae knock-out library. CRI-SPA systematically quantifies the effect of each modified gene present in the library on product synthesis, providing a complete map of host:pathway interactions. In its first version, CRI-SPA relied on the colour of the product betaxanthins to quantify strains synthesis ability. However, only a few compounds produce a visible or fluorescent phenotype limiting the scope of our approach. Here, we adapt CRI-SPA to onboard a biosensor reporting the interactions between host genes and the synthesis of the colourless product cis-cis-muconic acid (CCM). We phenotype >9,000 genotypes, including both gene knock-out and overexpression, by quantifying the fluorescence of yeast colonies growing in high-density agar arrays. We identify novel metabolic targets belonging to a broad range of cellular functions and confirm their positive impact on CCM biosynthesis. In particular, our data suggests a new interplay between CCM biosynthesis and cytosolic redox through their common interaction with the oxidative pentose phosphate pathway. Our genome-wide exploration of host:pathway interaction opens novel strategies for improved production of CCM in yeast cell factories.
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Affiliation(s)
- Paul Cachera
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Nikolaj Can Kurt
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Andreas Røpke
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Tomas Strucko
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Uffe H Mortensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.
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5
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Møller-Hansen I, Sáez-Sáez J, van der Hoek SA, Dyekjær JD, Christensen HB, Wright Muelas M, O’Hagan S, Kell DB, Borodina I. Deorphanizing solute carriers in Saccharomyces cerevisiae for secondary uptake of xenobiotic compounds. Front Microbiol 2024; 15:1376653. [PMID: 38680917 PMCID: PMC11045925 DOI: 10.3389/fmicb.2024.1376653] [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: 01/25/2024] [Accepted: 03/25/2024] [Indexed: 05/01/2024] Open
Abstract
The exchange of small molecules between the cell and the environment happens through transporter proteins. Besides nutrients and native metabolic products, xenobiotic molecules are also transported, however it is not well understood which transporters are involved. In this study, by combining exo-metabolome screening in yeast with transporter characterization in Xenopus oocytes, we mapped the activity of 30 yeast transporters toward six small non-toxic substrates. Firstly, using LC-MS, we determined 385 compounds from a chemical library that were imported and exported by S. cerevisiae. Of the 385 compounds transported by yeast, we selected six compounds (viz. sn-glycero-3-phosphocholine, 2,5-furandicarboxylic acid, 2-methylpyrazine, cefadroxil, acrylic acid, 2-benzoxazolol) for characterization against 30 S. cerevisiae xenobiotic transport proteins expressed in Xenopus oocytes. The compounds were selected to represent a diverse set of chemicals with a broad interest in applied microbiology. Twenty transporters showed activity toward one or more of the compounds. The tested transporter proteins were mostly promiscuous in equilibrative transport (i.e., facilitated diffusion). The compounds 2,5-furandicarboxylic acid, 2-methylpyrazine, cefadroxil, and sn-glycero-3-phosphocholine were transported equilibratively by transporters that could transport up to three of the compounds. In contrast, the compounds acrylic acid and 2-benzoxazolol, were strictly transported by dedicated transporters. The prevalence of promiscuous equilibrative transporters of non-native substrates has significant implications for strain development in biotechnology and offers an explanation as to why transporter engineering has been a challenge in metabolic engineering. The method described here can be generally applied to study the transport of other small non-toxic molecules. The yeast transporter library is available at AddGene (ID 79999).
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Affiliation(s)
- Iben Møller-Hansen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Javier Sáez-Sáez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Steven A. van der Hoek
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Jane D. Dyekjær
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Hanne B. Christensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Marina Wright Muelas
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Steve O’Hagan
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Douglas B. Kell
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
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6
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Nomura K, Onda K, Murase H, Hashiya F, Ono Y, Terai G, Oka N, Asai K, Suzuki D, Takahashi N, Hiraoka H, Inagaki M, Kimura Y, Shimizu Y, Abe N, Abe H. Development of PCR primers enabling the design of flexible sticky ends for efficient concatenation of long DNA fragments. RSC Chem Biol 2024; 5:360-371. [PMID: 38576723 PMCID: PMC10989509 DOI: 10.1039/d3cb00212h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/19/2024] [Indexed: 04/06/2024] Open
Abstract
We developed chemically modified PCR primers that allow the design of flexible sticky ends by introducing a photo-cleavable group at the phosphate moiety. Nucleic acid derivatives containing o-nitrobenzyl photo-cleavable groups with a tert-butyl group at the benzyl position were stable during strong base treatment for oligonucleotide synthesis and thermal cycling in PCR reactions. PCR using primers incorporating these nucleic acid derivatives confirmed that chain extension reactions completely stopped at position 1 before and after the site of the photo-cleavable group was introduced. DNA fragments of 2 and 3 kbp, with sticky ends of 50 bases, were successfully concatenated with a high yield of 77%. A plasmid was constructed using this method. Finally, we applied this approach to construct a 48.5 kbp lambda phage DNA, which is difficult to achieve using restriction enzyme-based methods. After 7 days, we were able to confirm the generation of DNA of the desired length. Although the efficiency is yet to be improved, the chemically modified PCR primer offers potential to complement enzymatic methods and serve as a DNA concatenation technique.
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Affiliation(s)
- Kohei Nomura
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Kaoru Onda
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Hirotaka Murase
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Fumitaka Hashiya
- Research Center for Materials Science, Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
- CREST, Japan Science and Technology Agency 7 Gobancho Chiyoda-ku Tokyo 102-0076 Japan
| | - Yukiteru Ono
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo Kashiwanoha, Kashiwa Chiba 277-8561 Japan
| | - Goro Terai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo Kashiwanoha, Kashiwa Chiba 277-8561 Japan
| | - Natsuhisa Oka
- Department of Chemistry and Biomolecular Science Faculty of Engineering, Gifu University Gifu 501-1193 Japan
| | - Kiyoshi Asai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo Kashiwanoha, Kashiwa Chiba 277-8561 Japan
| | - Daisuke Suzuki
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Naho Takahashi
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Haruka Hiraoka
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Masahito Inagaki
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Yasuaki Kimura
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Yoshihiro Shimizu
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research Suita Osaka 565-0874 Japan
| | - Naoko Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
| | - Hiroshi Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
- Research Center for Materials Science, Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8602 Japan
- CREST, Japan Science and Technology Agency 7 Gobancho Chiyoda-ku Tokyo 102-0076 Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University Furo-cho, Chikusa-ku Nagoya Aichi 464-8601 Japan
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7
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Zhao H, Li D, Liu Y, Zhang T, Zhao X, Su H, Li J. Flavin-containing monooxygenases FMO GS-OXs integrate flowering transition and salt tolerance in Arabidopsis thaliana. PHYSIOLOGIA PLANTARUM 2024; 176:e14287. [PMID: 38606719 DOI: 10.1111/ppl.14287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/27/2024] [Indexed: 04/13/2024]
Abstract
Salt stress substantially leads to flowering delay. The regulation of salt-induced late flowering has been studied at the transcriptional and protein levels; however, the involvement of secondary metabolites has rarely been investigated. Here, we report that FMOGS-OXs (EC 1.14.13.237), the enzymes that catalyze the biosynthesis of glucosinolates (GSLs), promote flowering transition in Arabidopsis thaliana. It has been reported that WRKY75 is a positive regulator, and MAF4 is a negative regulator of flowering transition. The products of FMOGS-OXs, methylsulfinylalkyl GSLs (MS GSLs), facilitate flowering by inducing WRKY75 and repressing the MAS-MAF4 module. We further show that the degradation of MS GSLs is involved in salt-induced late flowering and salt tolerance. Salt stress induces the expression of myrosinase genes, resulting in the degradation of MS GSLs, thereby relieving the promotion of WRKY75 and inhibition of MAF4, leading to delayed flowering. In addition, the degradation products derived from MS GSLs enhance salt tolerance. Previous studies have revealed that FMOGS-OXs exhibit alternative catalytic activity to form trimethylamine N-oxide (TMAO) under salt stress, which activates multiple stress-related genes to promote salt tolerance. Therefore, FMOGS-OXs integrate flowering transition and salt tolerance in various ways. Our study shed light on the functional diversity of GSLs and established a connection between flowering transition, salt resistance, and GSL metabolism.
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Affiliation(s)
- Haiyan Zhao
- College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Dong Li
- College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Yuqi Liu
- College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Tianqi Zhang
- College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Xiaofei Zhao
- College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Hongzhu Su
- College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Jing Li
- College of Life Sciences, Northeast Agricultural University, Harbin, China
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8
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Petersen SD, Levassor L, Pedersen CM, Madsen J, Hansen LG, Zhang J, Haidar AK, Frandsen RJN, Keasling JD, Weber T, Sonnenschein N, K. Jensen M. teemi: An open-source literate programming approach for iterative design-build-test-learn cycles in bioengineering. PLoS Comput Biol 2024; 20:e1011929. [PMID: 38457467 PMCID: PMC10954146 DOI: 10.1371/journal.pcbi.1011929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 03/20/2024] [Accepted: 02/17/2024] [Indexed: 03/10/2024] Open
Abstract
Synthetic biology dictates the data-driven engineering of biocatalysis, cellular functions, and organism behavior. Integral to synthetic biology is the aspiration to efficiently find, access, interoperate, and reuse high-quality data on genotype-phenotype relationships of native and engineered biosystems under FAIR principles, and from this facilitate forward-engineering strategies. However, biology is complex at the regulatory level, and noisy at the operational level, thus necessitating systematic and diligent data handling at all levels of the design, build, and test phases in order to maximize learning in the iterative design-build-test-learn engineering cycle. To enable user-friendly simulation, organization, and guidance for the engineering of biosystems, we have developed an open-source python-based computer-aided design and analysis platform operating under a literate programming user-interface hosted on Github. The platform is called teemi and is fully compliant with FAIR principles. In this study we apply teemi for i) designing and simulating bioengineering, ii) integrating and analyzing multivariate datasets, and iii) machine-learning for predictive engineering of metabolic pathway designs for production of a key precursor to medicinal alkaloids in yeast. The teemi platform is publicly available at PyPi and GitHub.
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Affiliation(s)
- Søren D. Petersen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lucas Levassor
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Christine M. Pedersen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jan Madsen
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lea G. Hansen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jie Zhang
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Ahmad K. Haidar
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Rasmus J. N. Frandsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jay D. Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Chemical and Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, California, United States of America
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen, China
| | - Tilmann Weber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Nikolaus Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michael K. Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
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9
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Kruse LH, Sunstrum FG, Garcia D, López Pérez G, Jancsik S, Bohlmann J, Irmisch S. Improved production of the antidiabetic metabolite montbretin A in Nicotiana benthamiana: discovery, characterization, and use of Crocosmia shikimate shunt genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:766-785. [PMID: 37960967 DOI: 10.1111/tpj.16528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/20/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023]
Abstract
The plant-specialized metabolite montbretin A (MbA) is being developed as a new treatment option for type-2 diabetes, which is among the ten leading causes of premature death and disability worldwide. MbA is a complex acylated flavonoid glycoside produced in small amounts in below-ground organs of the perennial plant Montbretia (Crocosmia × crocosmiiflora). The lack of a scalable production system limits the development and potential application of MbA as a pharmaceutical or nutraceutical. Previous efforts to reconstruct montbretin biosynthesis in Nicotiana benthamiana (Nb) resulted in low yields of MbA and higher levels of montbretin B (MbB) and montbretin C (MbC). MbA, MbB, and MbC are nearly identical metabolites differing only in their acyl moieties, derived from caffeoyl-CoA, coumaroyl-CoA, and feruloyl-CoA, respectively. In contrast to MbA, MbB and MbC are not pharmaceutically active. To utilize the montbretia caffeoyl-CoA biosynthesis for improved MbA engineering in Nb, we cloned and characterized enzymes of the shikimate shunt of the general phenylpropanoid pathway, specifically hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (CcHCT), p-coumaroylshikimate 3'-hydroxylase (CcC3'H), and caffeoylshikimate esterase (CcCSE). Gene expression patterns suggest that CcCSE enables the predominant formation of MbA, relative to MbB and MbC, in montbretia. This observation is supported by results from in vitro characterization of CcCSE and reconstruction of the shikimate shunt in yeast. Using CcHCT together with montbretin biosynthetic genes in multigene constructs resulted in a 30-fold increase of MbA in Nb. This work advances our understanding of the phenylpropanoid pathway and features a critical step towards improved MbA production in bioengineered Nb.
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Affiliation(s)
- Lars H Kruse
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Frederick G Sunstrum
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Daniela Garcia
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Guillermo López Pérez
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Sharon Jancsik
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Department of Forest and Conservation Science, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Sandra Irmisch
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Plant Sciences, Institute of Biology, Leiden University, Leiden, 2333 BE, Netherlands
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10
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Sands C, Hedin KA, Vazquez-Uribe R, Sommer MOA. Saccharomyces boulardii promoters for control of gene expression in vivo. Microb Cell Fact 2024; 23:16. [PMID: 38185666 PMCID: PMC10771652 DOI: 10.1186/s12934-023-02288-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 12/26/2023] [Indexed: 01/09/2024] Open
Abstract
BACKGROUND Interest in the use of engineered microbes to deliver therapeutic activities has increased in recent years. The probiotic yeast Saccharomyces boulardii has been investigated for production of therapeutics in the gastrointestinal tract. Well-characterised promoters are a prerequisite for robust therapeutic expression in the gut; however, S. boulardii promoters have not yet been thoroughly characterised in vitro and in vivo. RESULTS We present a thorough characterisation of the expression activities of 12 S. boulardii promoters in vitro in glucose, fructose, sucrose, inulin and acetate, under both aerobic and anaerobic conditions, as well as in the murine gastrointestinal tract. Green fluorescent protein was used to report on promoter activity. Promoter expression was found to be carbon-source dependent, with inulin emerging as a favourable carbon source. Furthermore, relative promoter expression in vivo was highly correlated with expression in sucrose (R = 0.99). CONCLUSIONS These findings provide insights into S. boulardii promoter activity and aid in promoter selection in future studies utilising S. boulardii to produce therapeutics in the gut.
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Affiliation(s)
- Carmen Sands
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Karl Alex Hedin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Ruben Vazquez-Uribe
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
| | - Morten Otto Alexander Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
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11
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Huang S, Shen L, Roelfsema MRG, Becker D, Hedrich R. Light-gated channelrhodopsin sparks proton-induced calcium release in guard cells. Science 2023; 382:1314-1318. [PMID: 38096275 DOI: 10.1126/science.adj9696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/10/2023] [Indexed: 12/18/2023]
Abstract
Although there has been long-standing recognition that stimuli-induced cytosolic pH alterations coincide with changes in calcium ion (Ca2+) levels, the interdependence between protons (H+) and Ca2+ remains poorly understood. We addressed this topic using the light-gated channelrhodopsin HcKCR2 from the pseudofungus Hyphochytrium catenoides, which operates as a H+ conductive, Ca2+ impermeable ion channel on the plasma membrane of plant cells. Light activation of HcKCR2 in Arabidopsis guard cells evokes a transient cytoplasmic acidification that sparks Ca2+ release from the endoplasmic reticulum. A H+-induced cytosolic Ca2+ signal results in membrane depolarization through the activation of Ca2+-dependent SLAC1/SLAH3 anion channels, which enabled us to remotely control stomatal movement. Our study suggests a H+-induced Ca2+ release mechanism in plant cells and establishes HcKCR2 as a tool to dissect the molecular basis of plant intracellular pH and Ca2+ signaling.
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Affiliation(s)
- Shouguang Huang
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, Würzburg University, Julius-von-Sachs-Platz 2, D-97082 Würzburg, Germany
| | - Like Shen
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, Würzburg University, Julius-von-Sachs-Platz 2, D-97082 Würzburg, Germany
- College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - M Rob G Roelfsema
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, Würzburg University, Julius-von-Sachs-Platz 2, D-97082 Würzburg, Germany
| | - Dirk Becker
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, Würzburg University, Julius-von-Sachs-Platz 2, D-97082 Würzburg, Germany
| | - Rainer Hedrich
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, Würzburg University, Julius-von-Sachs-Platz 2, D-97082 Würzburg, Germany
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12
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Due Tankmar M, Reichel M, Arribas-Hernández L, Brodersen P. A YTHDF-PABP interaction is required for m 6 A-mediated organogenesis in plants. EMBO Rep 2023; 24:e57741. [PMID: 38009565 DOI: 10.15252/embr.202357741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/29/2023] Open
Abstract
N6-methyladenosine (m6 A) in mRNA is key to eukaryotic gene regulation. Many m6 A functions involve RNA-binding proteins that recognize m6 A via a YT521-B Homology (YTH) domain. YTH domain proteins contain long intrinsically disordered regions (IDRs) that may mediate phase separation and interaction with protein partners, but whose precise biochemical functions remain largely unknown. The Arabidopsis thaliana YTH domain proteins ECT2, ECT3, and ECT4 accelerate organogenesis through stimulation of cell division in organ primordia. Here, we use ECT2 to reveal molecular underpinnings of this function. We show that stimulation of leaf formation requires the long N-terminal IDR, and we identify two short IDR elements required for ECT2-mediated organogenesis. Of these two, a 19-amino acid region containing a tyrosine-rich motif conserved in both plant and metazoan YTHDF proteins is necessary for binding to the major cytoplasmic poly(A)-binding proteins PAB2, PAB4, and PAB8. Remarkably, overexpression of PAB4 in leaf primordia partially rescues the delayed leaf formation in ect2 ect3 ect4 mutants, suggesting that the ECT2-PAB2/4/8 interaction on target mRNAs of organogenesis-related genes may overcome limiting PAB concentrations in primordial cells.
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Affiliation(s)
| | - Marlene Reichel
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Peter Brodersen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
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13
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Bradley SA, Lehka BJ, Hansson FG, Adhikari KB, Rago D, Rubaszka P, Haidar AK, Chen L, Hansen LG, Gudich O, Giannakou K, Lengger B, Gill RT, Nakamura Y, de Bernonville TD, Koudounas K, Romero-Suarez D, Ding L, Qiao Y, Frimurer TM, Petersen AA, Besseau S, Kumar S, Gautron N, Melin C, Marc J, Jeanneau R, O'Connor SE, Courdavault V, Keasling JD, Zhang J, Jensen MK. Biosynthesis of natural and halogenated plant monoterpene indole alkaloids in yeast. Nat Chem Biol 2023; 19:1551-1560. [PMID: 37932529 PMCID: PMC10667104 DOI: 10.1038/s41589-023-01430-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/25/2023] [Indexed: 11/08/2023]
Abstract
Monoterpenoid indole alkaloids (MIAs) represent a large class of plant natural products with marketed pharmaceutical activities against a wide range of indications, including cancer, malaria and hypertension. Halogenated MIAs have shown improved pharmaceutical properties; however, synthesis of new-to-nature halogenated MIAs remains a challenge. Here we demonstrate a platform for de novo biosynthesis of two MIAs, serpentine and alstonine, in baker's yeast Saccharomyces cerevisiae and deploy it to systematically explore the biocatalytic potential of refactored MIA pathways for the production of halogenated MIAs. From this, we demonstrate conversion of individual haloindole derivatives to a total of 19 different new-to-nature haloserpentine and haloalstonine analogs. Furthermore, by process optimization and heterologous expression of a modified halogenase in the microbial MIA platform, we document de novo halogenation and biosynthesis of chloroalstonine. Together, this study highlights a microbial platform for enzymatic exploration and production of complex natural and new-to-nature MIAs with therapeutic potential.
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Affiliation(s)
- Samuel A Bradley
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Beata J Lehka
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Frederik G Hansson
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Khem B Adhikari
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Daniela Rago
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Paulina Rubaszka
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Ahmad K Haidar
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Ling Chen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Lea G Hansen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Olga Gudich
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Konstantina Giannakou
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Bettina Lengger
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Ryan T Gill
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Yoko Nakamura
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | | | | | - David Romero-Suarez
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Ling Ding
- Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Yijun Qiao
- Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Thomas M Frimurer
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Anja A Petersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Sébastien Besseau
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Sandeep Kumar
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Nicolas Gautron
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Celine Melin
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Jillian Marc
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | | | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Vincent Courdavault
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Jay D Keasling
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen, China
| | - Jie Zhang
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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14
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Jia B, Cui H, Zhang D, Hu B, Li Y, Shen Y, Cai X, Sun X, Sun M. The conserved evolution of plant H +-ATPase family and the involvement of soybean H +-ATPases in sodium bicarbonate stress responses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108133. [PMID: 37883915 DOI: 10.1016/j.plaphy.2023.108133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/11/2023] [Accepted: 10/21/2023] [Indexed: 10/28/2023]
Abstract
Plant plasma membrane (PM) H+-ATPases are essential pumps involved in multiple physiological processes. They play a significant role in regulating pH homeostasis and membrane potential by generating the electrochemical gradient of the proton across the plasma membrane. However, information on soybean PM H+-ATPase is still limited. In this study, we conducted the evolutionary analysis of PM H+-ATPases in land plants and investigated the subfamily classification and whole genome duplication of PM H+-ATPases in angiosperms. We further characterized the extremely high conservation of the soybean PM H+-ATPase family in terms of gene structure, domain architecture, and protein sequence identity. Using the yeast system, we confirmed the highly conserved biochemical characteristics (14-3-3 binding affinity and pump activity) of soybean PM H+-ATPases and their conserved function in enhancing tolerance to high pH and NaHCO3 stresses. Meanwhile, our results also revealed their divergence in the transcriptional expression in different tissues and under sodium bicarbonate stress. Finally, the function of soybean PM H+-ATPases in conferring sodium bicarbonate tolerance was validated using transgenic Arabidopsis. Together, these results conclude that the soybean PM H+-ATPase is evolutionarily conserved and positively regulates the response to sodium bicarbonate stress.
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Affiliation(s)
- Bowei Jia
- Crop Stress Molecular Biology Laboratory, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China; Key Laboratory of Germplasm Enhancement, Physiology, and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hongli Cui
- Crop Stress Molecular Biology Laboratory, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Dajian Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Bingshuang Hu
- Crop Stress Molecular Biology Laboratory, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Yuan Li
- Crop Stress Molecular Biology Laboratory, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Yang Shen
- Crop Stress Molecular Biology Laboratory, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Xiaoxi Cai
- Crop Stress Molecular Biology Laboratory, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Xiaoli Sun
- Crop Stress Molecular Biology Laboratory, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China.
| | - Mingzhe Sun
- Crop Stress Molecular Biology Laboratory, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China.
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15
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Flores-Téllez D, Tankmar MD, von Bülow S, Chen J, Lindorff-Larsen K, Brodersen P, Arribas-Hernández L. Insights into the conservation and diversification of the molecular functions of YTHDF proteins. PLoS Genet 2023; 19:e1010980. [PMID: 37816028 PMCID: PMC10617740 DOI: 10.1371/journal.pgen.1010980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 10/31/2023] [Accepted: 09/17/2023] [Indexed: 10/12/2023] Open
Abstract
YT521-B homology (YTH) domain proteins act as readers of N6-methyladenosine (m6A) in mRNA. Members of the YTHDF clade determine properties of m6A-containing mRNAs in the cytoplasm. Vertebrates encode three YTHDF proteins whose possible functional specialization is debated. In land plants, the YTHDF clade has expanded from one member in basal lineages to eleven so-called EVOLUTIONARILY CONSERVED C-TERMINAL REGION1-11 (ECT1-11) proteins in Arabidopsis thaliana, named after the conserved YTH domain placed behind a long N-terminal intrinsically disordered region (IDR). ECT2, ECT3 and ECT4 show genetic redundancy in stimulation of primed stem cell division, but the origin and implications of YTHDF expansion in higher plants are unknown, as it is unclear whether it involves acquisition of fundamentally different molecular properties, in particular of their divergent IDRs. Here, we use functional complementation of ect2/ect3/ect4 mutants to test whether different YTHDF proteins can perform the same function when similarly expressed in leaf primordia. We show that stimulation of primordial cell division relies on an ancestral molecular function of the m6A-YTHDF axis in land plants that is present in bryophytes and is conserved over YTHDF diversification, as it appears in all major clades of YTHDF proteins in flowering plants. Importantly, although our results indicate that the YTH domains of all arabidopsis ECT proteins have m6A-binding capacity, lineage-specific neo-functionalization of ECT1, ECT9 and ECT11 happened after late duplication events, and involves altered properties of both the YTH domains, and, especially, of the IDRs. We also identify two biophysical properties recurrent in IDRs of YTHDF proteins able to complement ect2 ect3 ect4 mutants, a clear phase separation propensity and a charge distribution that creates electric dipoles. Human and fly YTHDFs do not have IDRs with this combination of properties and cannot replace ECT2/3/4 function in arabidopsis, perhaps suggesting different molecular activities of YTHDF proteins between major taxa.
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Affiliation(s)
- Daniel Flores-Téllez
- University of Copenhagen, Biology Department. Copenhagen, Denmark
- Universidad Francisco de Vitoria, Facultad de Ciencias Experimentales. Pozuelo de Alarcón (Madrid), Spain
| | | | - Sören von Bülow
- University of Copenhagen, Biology Department. Copenhagen, Denmark
| | - Junyu Chen
- University of Copenhagen, Biology Department. Copenhagen, Denmark
| | | | - Peter Brodersen
- University of Copenhagen, Biology Department. Copenhagen, Denmark
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16
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Wassano NS, da Silva GB, Reis AH, Gerhardt JA, Antoniel EP, Akiyama D, Rezende CP, Neves LX, Vasconcelos E, Figueiredo FL, Almeida F, de Castro PA, Pinzan CF, Goldman GH, Leme AFP, Fill TP, Moretti NS, Damasio A. Deacetylation by sirtuins is important for Aspergillus fumigatus pathogenesis and virulence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.558961. [PMID: 37808717 PMCID: PMC10557594 DOI: 10.1101/2023.09.25.558961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Protein acetylation is a crucial post-translational modification that controls gene expression and a variety of biological processes. Sirtuins, a prominent class of NAD + -dependent lysine deacetylases, serve as key regulators of protein acetylation and gene expression in eukaryotes. In this study, six single knockout strains of fungal pathogen Aspergillus fumigatus were constructed, in addition to a strain lacking all predicted sirtuins (SIRTKO). Phenotypic assays suggest that sirtuins are involved in cell wall integrity, secondary metabolite production, thermotolerance, and virulence. AfsirE deletion resulted in attenuation of virulence, as demonstrated in murine and Galleria infection models. The absence of AfSirE leads to altered acetylation status of proteins, including histones and non-histones, resulting in significant changes in the expression of genes associated with secondary metabolism, cell wall biosynthesis, and virulence factors. These findings encourage testing sirtuin inhibitors as potential therapeutic strategies to combat A. fumigatus infections or in combination therapy with available antifungals.
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17
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Cachera P, Olsson H, Coumou H, Jensen ML, Sánchez B, Strucko T, van den Broek M, Daran JM, Jensen M, Sonnenschein N, Lisby M, Mortensen U. CRI-SPA: a high-throughput method for systematic genetic editing of yeast libraries. Nucleic Acids Res 2023; 51:e91. [PMID: 37572348 PMCID: PMC10516668 DOI: 10.1093/nar/gkad656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 07/07/2023] [Accepted: 08/10/2023] [Indexed: 08/14/2023] Open
Abstract
Biological functions are orchestrated by intricate networks of interacting genetic elements. Predicting the interaction landscape remains a challenge for systems biology and new research tools allowing simple and rapid mapping of sequence to function are desirable. Here, we describe CRI-SPA, a method allowing the transfer of chromosomal genetic features from a CRI-SPA Donor strain to arrayed strains in large libraries of Saccharomyces cerevisiae. CRI-SPA is based on mating, CRISPR-Cas9-induced gene conversion, and Selective Ploidy Ablation. CRI-SPA can be massively parallelized with automation and can be executed within a week. We demonstrate the power of CRI-SPA by transferring four genes that enable betaxanthin production into each strain of the yeast knockout collection (≈4800 strains). Using this setup, we show that CRI-SPA is highly efficient and reproducible, and even allows marker-free transfer of genetic features. Moreover, we validate a set of CRI-SPA hits by showing that their phenotypes correlate strongly with the phenotypes of the corresponding mutant strains recreated by reverse genetic engineering. Hence, our results provide a genome-wide overview of the genetic requirements for betaxanthin production. We envision that the simplicity, speed, and reliability offered by CRI-SPA will make it a versatile tool to forward systems-level understanding of biological processes.
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Affiliation(s)
- Paul Cachera
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Helén Olsson
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Hilde Coumou
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Denmark
| | - Mads L Jensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Denmark
| | - Benjamín J Sánchez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Denmark
| | - Tomas Strucko
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Denmark
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Michael K Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Nikolaus Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Denmark
| | - Michael Lisby
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Uffe H Mortensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Denmark
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18
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Martínez‐Pérez M, Aparicio F, Arribas‐Hernández L, Tankmar MD, Rennie S, von Bülow S, Lindorff‐Larsen K, Brodersen P, Pallas V. Plant YTHDF proteins are direct effectors of antiviral immunity against an N6-methyladenosine-containing RNA virus. EMBO J 2023; 42:e113378. [PMID: 37431920 PMCID: PMC10505913 DOI: 10.15252/embj.2022113378] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/31/2023] [Accepted: 06/15/2023] [Indexed: 07/12/2023] Open
Abstract
In virus-host interactions, nucleic acid-directed first lines of defense that allow viral clearance without compromising growth are of paramount importance. Plants use the RNA interference pathway as a basal antiviral immune system, but additional RNA-based mechanisms of defense also exist. The infectivity of a plant positive-strand RNA virus, alfalfa mosaic virus (AMV), relies on the demethylation of viral RNA by the recruitment of the cellular N6-methyladenosine (m6 A) demethylase ALKBH9B, but how demethylation of viral RNA promotes AMV infection remains unknown. Here, we show that inactivation of the Arabidopsis cytoplasmic YT521-B homology domain (YTH)-containing m6 A-binding proteins ECT2, ECT3, and ECT5 is sufficient to restore AMV infectivity in partially resistant alkbh9b mutants. We further show that the antiviral function of ECT2 is distinct from its previously demonstrated function in the promotion of primordial cell proliferation: an ect2 mutant carrying a small deletion in its intrinsically disordered region is partially compromised for antiviral defense but not for developmental functions. These results indicate that the m6 A-YTHDF axis constitutes a novel branch of basal antiviral immunity in plants.
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Affiliation(s)
- Mireya Martínez‐Pérez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValènciaValenciaSpain
| | - Frederic Aparicio
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValènciaValenciaSpain
| | | | | | - Sarah Rennie
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Sören von Bülow
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | | | - Peter Brodersen
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Vicente Pallas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValènciaValenciaSpain
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19
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Sun M, Gao AX, Liu X, Yang Y, Ledesma-Amaro R, Bai Z. High-throughput process development from gene cloning to protein production. Microb Cell Fact 2023; 22:182. [PMID: 37715258 PMCID: PMC10503041 DOI: 10.1186/s12934-023-02184-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/19/2023] [Indexed: 09/17/2023] Open
Abstract
In the post-genomic era, the demand for faster and more efficient protein production has increased, both in public laboratories and industry. In addition, with the expansion of protein sequences in databases, the range of possible enzymes of interest for a given application is also increasing. Faced with peer competition, budgetary, and time constraints, companies and laboratories must find ways to develop a robust manufacturing process for recombinant protein production. In this review, we explore high-throughput technologies for recombinant protein expression and present a holistic high-throughput process development strategy that spans from genes to proteins. We discuss the challenges that come with this task, the limitations of previous studies, and future research directions.
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Affiliation(s)
- Manman Sun
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214112, China
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - Alex Xiong Gao
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Xiuxia Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214112, China
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Yankun Yang
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214112, China
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.
| | - Zhonghu Bai
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214112, China.
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China.
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20
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Yang S, Zhou Z, Zhang T, Zhang Q, Li R, Li J. Overexpression of BoLSU1 and BoLSU2 Confers Tolerance to Sulfur Deficiency in Arabidopsis by Manipulating Glucosinolate Metabolism. Int J Mol Sci 2023; 24:13520. [PMID: 37686325 PMCID: PMC10487721 DOI: 10.3390/ijms241713520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/17/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
Sulfur is an essential element for plant growth, development and resistance to environmental stresses. Glucosinolates (GSLs), a group of sulfur rich secondary metabolites found in Brassicaceae plants, are known for their defensive properties against pathogens and herbivores. Due to their integration of a large proportion of total sulfur, their biosynthesis and degradation are closely linked to sulfur metabolism. It has been demonstrated that GSLs can be broken down to release sulfur and facilitate the production of other thio-metabolites when the plant is under stress. However, the regulation of this process is still not fully understood. In this study, we constructed two broccoli LSU (low sulfur responsive) gene overexpressing lines, 35S::BoLSU1 and 35S::BoLSU2, to detect changes in GSL metabolism after sulfur deficiency treatment. The results showed that BoLSU1 and BoLSU2 inhibit the biosynthesis of aliphatic GSLs, while also promoting their degradation and increasing the content of glutathione (GSH), leading to the reallocation of sulfur from the GSL pool to other thio-metabolites such as GSH. Furthermore, this regulation of GSL metabolism mediated by BoLSU1 and BoLSU2 is found to be dependent on myrosinases BGLU28 and BGLU30. Our study provides insight into the physiological role of LSU proteins and their regulation of sulfur metabolism.
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Affiliation(s)
| | | | | | | | - Rui Li
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (S.Y.)
| | - Jing Li
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (S.Y.)
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21
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Liao R, Wei X, Zhao Y, Xie Z, Nath UK, Yang S, Su H, Wang Z, Li L, Tian B, Wei F, Yuan Y, Zhang X. bra-miR167a Targets ARF8 and Negatively Regulates Arabidopsis thaliana Immunity against Plasmodiophora brassicae. Int J Mol Sci 2023; 24:11850. [PMID: 37511608 PMCID: PMC10380745 DOI: 10.3390/ijms241411850] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/14/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Clubroot is a soil-borne disease caused by Plasmodiophora brassicae, which can seriously affect the growth and production of cruciferous crops, especially Chinese cabbage crops, worldwide. At present, few studies have been conducted on the molecular mechanism of this disease's resistance response. In this experiment, we analyzed the bioinformation of bra-miR167a, constructed a silencing vector (STTM167a) and an overexpression vector (OE-miR167a), and transformed them to Arabidopsis to confirm the role of miR167a in the clubroot resistance mechanism of Arabidopsis. Afterwards, phenotype analysis and expression level analysis of key genes were conducted on transgenic plants. From the result, we found that the length and number of lateral roots of silence transgenic Arabidopsis STTM167a was higher than that of WT and OE-miR167a. In addition, the STTM167a transgenic Arabidopsis induced up-regulation of disease resistance-related genes (PR1, PR5, MPK3, and MPK6) at 3 days after inoculation. On the other hand, the auxin pathway genes (TIR1, AFB2, and AFB3), which are involved in maintaining the balance of auxin/IAA and auxin response factor (ARF), were down-regulated. These results indicate that bra-miR167a is negative to the development of lateral roots and auxins, but positive to the expression of resistance-related genes. This also means that the STTM167a can improve the resistance of clubroot by promoting lateral root development and the level of auxin, and can induce resistance-related genes by regulating its target genes. We found a positive correlation between miR167a and clubroot disease, which is a new clue for the prevention and treatment of clubroot disease.
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Affiliation(s)
- Rujiao Liao
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China; (R.L.); (X.W.); (Y.Z.); (S.Y.); (H.S.); (Z.W.); (L.L.); (F.W.)
- Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.X.); (B.T.)
| | - Xiaochun Wei
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China; (R.L.); (X.W.); (Y.Z.); (S.Y.); (H.S.); (Z.W.); (L.L.); (F.W.)
- Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.X.); (B.T.)
| | - Yanyan Zhao
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China; (R.L.); (X.W.); (Y.Z.); (S.Y.); (H.S.); (Z.W.); (L.L.); (F.W.)
| | - Zhengqing Xie
- Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.X.); (B.T.)
| | - Ujjal Kumar Nath
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh;
| | - Shuangjuan Yang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China; (R.L.); (X.W.); (Y.Z.); (S.Y.); (H.S.); (Z.W.); (L.L.); (F.W.)
| | - Henan Su
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China; (R.L.); (X.W.); (Y.Z.); (S.Y.); (H.S.); (Z.W.); (L.L.); (F.W.)
| | - Zhiyong Wang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China; (R.L.); (X.W.); (Y.Z.); (S.Y.); (H.S.); (Z.W.); (L.L.); (F.W.)
| | - Lin Li
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China; (R.L.); (X.W.); (Y.Z.); (S.Y.); (H.S.); (Z.W.); (L.L.); (F.W.)
| | - Baoming Tian
- Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.X.); (B.T.)
| | - Fang Wei
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China; (R.L.); (X.W.); (Y.Z.); (S.Y.); (H.S.); (Z.W.); (L.L.); (F.W.)
- Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.X.); (B.T.)
| | - Yuxiang Yuan
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China; (R.L.); (X.W.); (Y.Z.); (S.Y.); (H.S.); (Z.W.); (L.L.); (F.W.)
| | - Xiaowei Zhang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China; (R.L.); (X.W.); (Y.Z.); (S.Y.); (H.S.); (Z.W.); (L.L.); (F.W.)
- Henan International Joint Laboratory of Crop Gene Resources and Improvement, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.X.); (B.T.)
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22
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Meyer L, Crocoll C, Halkier BA, Mirza OA, Xu D. Identification of key amino acid residues in AtUMAMIT29 for transport of glucosinolates. FRONTIERS IN PLANT SCIENCE 2023; 14:1219783. [PMID: 37528977 PMCID: PMC10388549 DOI: 10.3389/fpls.2023.1219783] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/08/2023] [Indexed: 08/03/2023]
Abstract
Glucosinolates are key defense compounds of plants in Brassicales order, and their accumulation in seeds is essential for the protection of the next generation. Recently, members of the Usually Multiple Amino acids Move In and Out Transporter (UMAMIT) family were shown to be essential for facilitating transport of seed-bound glucosinolates from site of synthesis within the reproductive organ to seeds. Here, we set out to identify amino acid residues responsible for glucosinolate transport activity of the main seed glucosinolate exporter UMAMIT29 in Arabidopsis thaliana. Based on a predicted model of UMAMIT29, we propose that the substrate transporting cavity consists of 51 residues, of which four are highly conserved residues across all the analyzed homologs of UMAMIT29. A comparison of the putative substrate binding site of homologs within the brassicaceous-specific, glucosinolate-transporting clade with the non-brassicaceous-specific, non-glucosinolate-transporting UMAMIT32 clade identified 11 differentially conserved sites. When each of the 11 residues of UMAMIT29 was individually mutated into the corresponding residue in UMAMIT32, five mutant variants (UMAMIT29#V27F, UMAMIT29#M86V, UMAMIT29#L109V, UMAMIT29#Q263S, and UMAMIT29#T267Y) reduced glucosinolate transport activity over 75% compared to wild-type UMAMIT29. This suggests that these residues are key for UMAMIT29-mediated glucosinolate transport activity and thus potential targets for blocking the transport of glucosinolates to the seeds.
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Affiliation(s)
- Lasse Meyer
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Christoph Crocoll
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Barbara Ann Halkier
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Osman Asghar Mirza
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Deyang Xu
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
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23
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Bressendorff S, Kausika S, Sjøgaard IMZ, Oksbjerg ED, Michels A, Poulsen C, Brodersen P. The N-coil and the globular N-terminal domain of plant ARGONAUTE1 are interaction hubs for regulatory factors. Biochem J 2023; 480:957-974. [PMID: 37278687 DOI: 10.1042/bcj20230025] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 06/06/2023] [Accepted: 06/06/2023] [Indexed: 06/07/2023]
Abstract
The effector complex of RNA interference (RNAi) contains at its core an ARGONAUTE (AGO) protein bound to a small guide RNA. AGO proteins adopt a two-lobed structure in which the N-terminal (N) and Piwi-Argonaute-Zwille (PAZ) domains make up one lobe, while the middle (MID) and Piwi domains make up the other. Specific biochemical functions of PAZ, MID and Piwi domains of eukaryotic AGO proteins have been described, but the functions of the N domain remain less clear. Here, we use yeast two-hybrid screening with the N domain of the founding member of the AGO protein family, Arabidopsis AGO1, to reveal that it interacts with many factors involved in regulated proteolysis. Interaction with a large group of proteins, including the autophagy cargo receptors ATI1 and ATI2, requires residues in a short, linear region, the N-coil, that joins the MID-Piwi lobe in the three-dimensional structure of AGO. In contrast, the F-box protein AUF1 interacts with AGO1 independently of the N-coil and requires distinct residues in the globular N domain itself. Mutation of AGO1 residues necessary for interaction with protein degradation factors in yeast stabilizes reporters fused to the AGO1 N domain in plants, supporting their in vivo relevance. Our results define distinct regions of the N domain implicated in protein-protein interaction, and point to a particular importance of the AGO1 N-coil as a site of interaction with regulatory factors.
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Affiliation(s)
- Simon Bressendorff
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Swathi Kausika
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Ida Marie Zobbe Sjøgaard
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Emilie Duus Oksbjerg
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Alec Michels
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Christian Poulsen
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Peter Brodersen
- Copenhagen Plant Science Center, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
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24
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Xiong X, Lu Z, Ma L, Zhai C. Applications of Programmable Endonucleases in Sequence- and Ligation-Independent Seamless DNA Assembly. Biomolecules 2023; 13:1022. [PMID: 37509059 PMCID: PMC10377497 DOI: 10.3390/biom13071022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/02/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Programmable endonucleases, such as Cas (Clustered Regularly-Interspaced Short Repeats-associated proteins) and prokaryotic Argonaute (pAgo), depend on base pairing of the target DNA with the guide RNA or DNA to cleave DNA strands. Therefore, they are capable of recognizing and cleaving DNA sequences at virtually any arbitrary site. The present review focuses on the commonly used in vivo and in vitro recombination-based gene cloning methods and the application of programmable endonucleases in these sequence- and ligation-independent DNA assembly methods. The advantages and shortcomings of the programmable endonucleases utilized as tools for gene cloning are also discussed in this review.
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Affiliation(s)
- Xingchen Xiong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Zhiwen Lu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Chao Zhai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
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25
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Miller S, Rønager A, Holm R, Fontanet-Manzaneque JB, Caño-Delgado AI, Bjarnholt N. New methods for sorghum transformation in temperate climates. AOB PLANTS 2023; 15:plad030. [PMID: 37396498 PMCID: PMC10308921 DOI: 10.1093/aobpla/plad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 06/02/2023] [Indexed: 07/04/2023]
Abstract
Sorghum (Sorghum bicolor) is an emerging cereal crop in temperate climates due to its high drought tolerance and other valuable traits. Genetic transformation is an important tool for the improvement of cereals. However, sorghum is recalcitrant to genetic transformation which is almost only successful in warmer climates. Here, we test the application of two new techniques for sorghum transformation in temperate climates, namely transient transformation by Agrobacterium tumefaciens-mediated agroinfiltration and stable transformation using gold particle bombardment and leaf whorls as explants. We optimized the transient transformation method, including post-infiltration incubation of plants in the dark and using Agrobacterium grown on plates with a high cell density (OD600 = 2.0). Expression of the green fluorescence protein (GFP)-tagged endogenous sorghum gene SbDHR2 was achieved with low transformation efficiency, and our results point out a potential weakness in using this approach for localization studies. Furthermore, we succeeded in the production of callus and somatic embryos from leaf whorls, although no genetic transformation was accomplished with this method. Both methods show potential, even if they seem to be influenced by climatic conditions and therefore need further optimization to be applied routinely in temperate climates.
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Affiliation(s)
- Sara Miller
- Section for Plant Biochemistry, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksbergs, Denmark
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Asta Rønager
- Section for Plant Biochemistry, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksbergs, Denmark
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Rose Holm
- Section for Plant Biochemistry, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksbergs, Denmark
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Juan B Fontanet-Manzaneque
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - Ana I Caño-Delgado
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB (Cerdanyola del Vallès), 08193 Barcelona, Spain
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26
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Driessen JL, Johnsen J, Pogrebnyakov I, Mohamed ET, Mussatto SI, Feist AM, Jensen SI, Nielsen AT. Adaptive laboratory evolution of Bacillus subtilis to overcome toxicity of lignocellulosic hydrolysate derived from Distiller's dried grains with solubles (DDGS). Metab Eng Commun 2023; 16:e00223. [PMID: 37234932 PMCID: PMC10206485 DOI: 10.1016/j.mec.2023.e00223] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/03/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Microbial tolerance to toxic compounds formed during biomass pretreatment is a significant challenge to produce bio-based products from lignocellulose cost effectively. Rational engineering can be problematic due to insufficient prerequisite knowledge of tolerance mechanisms. Therefore, adaptive laboratory evolution was applied to obtain 20 tolerant lineages of Bacillus subtilis strains able to utilize Distiller's Dried Grains with Solubles-derived (DDGS) hydrolysate. Evolved strains showed both improved growth performance and retained heterologous enzyme production using 100% hydrolysate-based medium, whereas growth of the starting strains was essentially absent. Whole-genome resequencing revealed that evolved isolates acquired mutations in the global regulator codY in 15 of the 19 sequenced isolates. Furthermore, mutations in genes related to oxidative stress (katA, perR) and flagella function appeared in both tolerance and control evolution experiments without toxic compounds. Overall, tolerance adaptive laboratory evolution yielded strains able to utilize DDGS-hydrolysate to produce enzymes and hence proved to be a valuable tool for the valorization of lignocellulose.
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Affiliation(s)
- Jasper L.S.P. Driessen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220, 2800, Kongens Lyngby, Denmark
| | - Josefin Johnsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220, 2800, Kongens Lyngby, Denmark
| | - Ivan Pogrebnyakov
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220, 2800, Kongens Lyngby, Denmark
| | - Elsayed T.T. Mohamed
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220, 2800, Kongens Lyngby, Denmark
| | - Solange I. Mussatto
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, 2800, Kongens Lyngby, Denmark
| | - Adam M. Feist
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220, 2800, Kongens Lyngby, Denmark
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0412, USA
| | - Sheila I. Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220, 2800, Kongens Lyngby, Denmark
| | - Alex T. Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 220, 2800, Kongens Lyngby, Denmark
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27
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Radchuk V, Belew ZM, Gündel A, Mayer S, Hilo A, Hensel G, Sharma R, Neumann K, Ortleb S, Wagner S, Muszynska A, Crocoll C, Xu D, Hoffie I, Kumlehn J, Fuchs J, Peleke FF, Szymanski JJ, Rolletschek H, Nour-Eldin HH, Borisjuk L. SWEET11b transports both sugar and cytokinin in developing barley grains. THE PLANT CELL 2023; 35:2186-2207. [PMID: 36857316 DOI: 10.1093/plcell/koad055] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/17/2023] [Accepted: 02/17/2023] [Indexed: 05/30/2023]
Abstract
Even though Sugars Will Eventually be Exported Transporters (SWEETs) have been found in every sequenced plant genome, a comprehensive understanding of their functionality is lacking. In this study, we focused on the SWEET family of barley (Hordeum vulgare). A radiotracer assay revealed that expressing HvSWEET11b in African clawed frog (Xenopus laevis) oocytes facilitated the bidirectional transfer of not only just sucrose and glucose, but also cytokinin. Barley plants harboring a loss-of-function mutation of HvSWEET11b could not set viable grains, while the distribution of sucrose and cytokinin was altered in developing grains of plants in which the gene was knocked down. Sucrose allocation within transgenic grains was disrupted, which is consistent with the changes to the cytokinin gradient across grains, as visualized by magnetic resonance imaging and Fourier transform infrared spectroscopy microimaging. Decreasing HvSWEET11b expression in developing grains reduced overall grain size, sink strength, the number of endopolyploid endosperm cells, and the contents of starch and protein. The control exerted by HvSWEET11b over sugars and cytokinins likely predetermines their synergy, resulting in adjustments to the grain's biochemistry and transcriptome.
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Affiliation(s)
- Volodymyr Radchuk
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Zeinu M Belew
- Faculty of Science, Department of Plant and Environmental Sciences, DynaMo Center of Excellence, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Andre Gündel
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Simon Mayer
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
- Institute of Experimental Physics 5, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Alexander Hilo
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Goetz Hensel
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
- Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, 78371 Olomouc, Czech Republic
| | - Rajiv Sharma
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JGUK
| | - Kerstin Neumann
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Stefan Ortleb
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Steffen Wagner
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Aleksandra Muszynska
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Christoph Crocoll
- Faculty of Science, Department of Plant and Environmental Sciences, DynaMo Center of Excellence, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Deyang Xu
- Faculty of Science, Department of Plant and Environmental Sciences, DynaMo Center of Excellence, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Iris Hoffie
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Jochen Kumlehn
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Joerg Fuchs
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Fritz F Peleke
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Jedrzej J Szymanski
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Hardy Rolletschek
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
| | - Hussam H Nour-Eldin
- Faculty of Science, Department of Plant and Environmental Sciences, DynaMo Center of Excellence, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Ljudmilla Borisjuk
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany
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Yu X, Xie Y, Luo D, Liu H, de Oliveira MVV, Qi P, Kim SI, Ortiz-Morea FA, Liu J, Chen Y, Chen S, Rodrigues B, Li B, Xue S, He P, Shan L. A phospho-switch constrains BTL2-mediated phytocytokine signaling in plant immunity. Cell 2023; 186:2329-2344.e20. [PMID: 37192618 PMCID: PMC10281528 DOI: 10.1016/j.cell.2023.04.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 02/10/2023] [Accepted: 04/18/2023] [Indexed: 05/18/2023]
Abstract
Enabling and constraining immune activation is of fundamental importance in maintaining cellular homeostasis. Depleting BAK1 and SERK4, the co-receptors of multiple pattern recognition receptors (PRRs), abolishes pattern-triggered immunity but triggers intracellular NOD-like receptor (NLR)-mediated autoimmunity with an elusive mechanism. By deploying RNAi-based genetic screens in Arabidopsis, we identified BAK-TO-LIFE 2 (BTL2), an uncharacterized receptor kinase, sensing BAK1/SERK4 integrity. BTL2 induces autoimmunity through activating Ca2+ channel CNGC20 in a kinase-dependent manner when BAK1/SERK4 are perturbed. To compensate for BAK1 deficiency, BTL2 complexes with multiple phytocytokine receptors, leading to potent phytocytokine responses mediated by helper NLR ADR1 family immune receptors, suggesting phytocytokine signaling as a molecular link connecting PRR- and NLR-mediated immunity. Remarkably, BAK1 constrains BTL2 activation via specific phosphorylation to maintain cellular integrity. Thus, BTL2 serves as a surveillance rheostat sensing the perturbation of BAK1/SERK4 immune co-receptors in promoting NLR-mediated phytocytokine signaling to ensure plant immunity.
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Affiliation(s)
- Xiao Yu
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843, USA; National Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Plant Pathology, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yingpeng Xie
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Dexian Luo
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843, USA; State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Hai Liu
- College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Marcos V V de Oliveira
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Peipei Qi
- National Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Plant Pathology, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Sung-Il Kim
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843, USA
| | | | - Jun Liu
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Yafei Chen
- National Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Plant Pathology, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Sixue Chen
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA
| | - Bárbara Rodrigues
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Bo Li
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843, USA; National Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Plant Pathology, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Shaowu Xue
- College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Ping He
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843, USA.
| | - Libo Shan
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843, USA.
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29
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Li R, Zhou Z, Zhang T, Su H, Li J. Overexpression of LSU1 and LSU2 confers cadmium tolerance by manipulating sulfur metabolism in Arabidopsis. CHEMOSPHERE 2023; 334:139046. [PMID: 37244555 DOI: 10.1016/j.chemosphere.2023.139046] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/13/2023] [Accepted: 05/25/2023] [Indexed: 05/29/2023]
Abstract
Phytoremediation using plants is an environmentally friendly and cost-effective strategy for removing cadmium (Cd) from soil. Plants used for phytoremediation must have a high Cd accumulation capacity and strong Cd tolerance. Therefore, understanding the molecular mechanism of Cd tolerance and accumulation in plants is of great interest. In response to Cd exposure, plants produce various thio-rich compounds, such as glutathione, phytochelatins, and metallothioneins, which play important roles in Cd immobilization, sequestration, and detoxification. Therefore, sulfur (S) metabolism is crucial for Cd tolerance and accumulation. In this study, we report that the overexpression of low-S responsive genes, LSU1 and LSU2, confers Cd tolerance in Arabidopsis. First, LSU1 and LSU2 promoted S assimilation under Cd stress. Second, LSU1 and LSU2 inhibited the biosynthesis and promoted the degradation of aliphatic glucosinolates, which could limit the consumption and enhance the release of S, thus, facilitating the production of the S-rich metabolites, glutathione, phytochelatins, and metallothioneins. We further demonstrated that the Cd tolerance mediated by LSU1 and LSU2 was dependent on the myrosinases BGLU28 and BGLU30, which catalyze the degradation of aliphatic glucosinolates. In addition, the overexpression of LSU1 and LSU2 improved Cd accumulation, which has great potential for the phytoremediation of Cd-contaminated soil.
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Affiliation(s)
- Rui Li
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Zihuan Zhou
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Tianqi Zhang
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Hongzhu Su
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Jing Li
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China.
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30
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Alejandro S, Meier B, Hoang MTT, Peiter E. Cation diffusion facilitator proteins of Beta vulgaris reveal diversity of metal handling in dicotyledons. PLANT, CELL & ENVIRONMENT 2023; 46:1629-1652. [PMID: 36698321 DOI: 10.1111/pce.14544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 01/17/2023] [Indexed: 06/17/2023]
Abstract
Manganese (Mn), iron (Fe), and zinc (Zn) are essential for diverse processes in plants, but their availability is often limiting or excessive. Cation diffusion facilitator (CDF) proteins have been implicated in the allocation of those metals in plants, whereby most of our mechanistic understanding has been obtained in Arabidopsis. It is unclear to what extent this can be generalized to other dicots. We characterized all CDFs/metal tolerance proteins of sugar beet (Beta vulgaris spp. vulgaris), which is phylogenetically distant from Arabidopsis. Analysis of subcellular localization, substrate selectivities, and transcriptional regulation upon exposure to metal deficiencies and toxicities revealed unexpected deviations from their Arabidopsis counterparts. Localization and selectivity of some members were modulated by alternative splicing. Notably, unlike in Arabidopsis, Mn- and Zn-sequestrating members were not induced in Fe-deficient roots, pointing to differences in the Fe acquisition machinery. This was supported by low Zn and Mn accumulation under Fe deficiency and a strikingly increased Fe accumulation under Mn and Zn excess, coinciding with an induction of BvIRT1. High Zn load caused a massive upregulation of Zn-BvMTPs. The results suggest that the employment of the CDF toolbox is highly diverse amongst dicots, which questions the general applicability of metal homeostasis models derived from Arabidopsis.
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Affiliation(s)
- Santiago Alejandro
- Plant Nutrition Laboratory, Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Bastian Meier
- Plant Nutrition Laboratory, Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Minh Thi Thanh Hoang
- Plant Nutrition Laboratory, Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Edgar Peiter
- Plant Nutrition Laboratory, Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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31
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Yu MM, Wang R, Xia JQ, Li C, Xu QH, Cang J, Wang YY, Zhang D. JA-induced TaMPK6 enhanced the freeze tolerance of Arabidopsis thaliana through regulation of ICE-CBF-COR module and antioxidant enzyme system. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 329:111621. [PMID: 36736462 DOI: 10.1016/j.plantsci.2023.111621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
Mitogen-activated protein kinases (MAPKs) play important roles in the stress response of plants. However, the function of MPK proteins in freeze-resistance in wheat remains unclear. Dongnongdongmai No.1 (Dn1) is a winter wheat variety with a strong freezing resistance at extremely low temperature. In this study, we demonstrated that TaMPK6 is induced by JA signaling and is involved in the modulation of Dn1 freeze resistance. Overexpression of TaMPK6 in Arabidopsis increased the survival rate of plant at -10 ℃. The scavenging ability of reactive oxygen species (ROS) and the expression of cold-responsive genes CBFs and CORs were significantly enhanced in TaMPK6-overexpressed Arabidopsis, suggesting a role of TaMPK6 in activating the ICE-CBF-COR module and antioxidant enzyme system to resist freezing stress. Furthermore, TaMPK6 is localized in the nucleus and TaMPK6 interacts with TaICE41, TaCBF14, and TaMYC2 proteins, the key components in JA signaling and the ICE-CBF-COR pathway. These results suggest that JA-induced TaMPK6 may regulate freezing-resistance in wheat by interacting with the TaICE41, TaCBF14, and TaMYC2 proteins, which in turn enhances the ICE-CBF-COR pathway. Our study revealed the molecular mechanism of TaMPK6 involvement in the cold resistance pathway in winter wheat under cold stress, which provides a basis for enriching the theory of wheat cold resistance.
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Affiliation(s)
- Meng-Meng Yu
- College of Life Science, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Rui Wang
- College of Life Science, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Jing-Qiu Xia
- College of Life Science, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Chang Li
- College of Life Science, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Qing-Hua Xu
- College of Life Science, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Jing Cang
- College of Life Science, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Yu-Ying Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Da Zhang
- College of Life Science, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
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32
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Huang S, Maierhofer T, Hashimoto K, Xu X, Karimi SM, Müller H, Geringer MA, Wang Y, Kudla J, De Smet I, Hedrich R, Geiger D, Roelfsema MRG. The CIPK23 protein kinase represses SLAC1-type anion channels in Arabidopsis guard cells and stimulates stomatal opening. THE NEW PHYTOLOGIST 2023; 238:270-282. [PMID: 36597715 DOI: 10.1111/nph.18708] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Guard cells control the opening of stomatal pores in the leaf surface, with the use of a network of protein kinases and phosphatases. Loss of function of the CBL-interacting protein kinase 23 (CIPK23) was previously shown to decrease the stomatal conductance, but the molecular mechanisms underlying this response still need to be clarified. CIPK23 was specifically expressed in Arabidopsis guard cells, using an estrogen-inducible system. Stomatal movements were linked to changes in ion channel activity, determined with double-barreled intracellular electrodes in guard cells and with the two-electrode voltage clamp technique in Xenopus oocytes. Expression of the phosphomimetic variant CIPK23T190D enhanced stomatal opening, while the natural CIPK23 and a kinase-inactive CIPK23K60N variant did not affect stomatal movements. Overexpression of CIPK23T190D repressed the activity of S-type anion channels, while their steady-state activity was unchanged by CIPK23 and CIPK23K60N . We suggest that CIPK23 enhances the stomatal conductance at favorable growth conditions, via the regulation of several ion transport proteins in guard cells. The inhibition of SLAC1-type anion channels is an important facet of this response.
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Affiliation(s)
- Shouguang Huang
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, Würzburg University, Julius-von-Sachs-Platz 2, D-97082, Würzburg, Germany
| | - Tobias Maierhofer
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, Würzburg University, Julius-von-Sachs-Platz 2, D-97082, Würzburg, Germany
| | - Kenji Hashimoto
- Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, 278-8510, Japan
| | - Xiangyu Xu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark Zwijnaarde 71, 9052, Ghent, Belgium
| | - Sohail M Karimi
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, Würzburg University, Julius-von-Sachs-Platz 2, D-97082, Würzburg, Germany
| | - Heike Müller
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, Würzburg University, Julius-von-Sachs-Platz 2, D-97082, Würzburg, Germany
| | - Michael A Geringer
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, Würzburg University, Julius-von-Sachs-Platz 2, D-97082, Würzburg, Germany
| | - Yi Wang
- State Key Laboratory of Plant Physiology and Biochemistry (SKLPPB), College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jörg Kudla
- Institut für Biologie und Biotechnologie der Pflanzen, Universität Münster, Schlossplatz 7, 48149, Münster, Germany
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark Zwijnaarde 71, 9052, Ghent, Belgium
| | - Rainer Hedrich
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, Würzburg University, Julius-von-Sachs-Platz 2, D-97082, Würzburg, Germany
| | - Dietmar Geiger
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, Würzburg University, Julius-von-Sachs-Platz 2, D-97082, Würzburg, Germany
| | - M Rob G Roelfsema
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, Würzburg University, Julius-von-Sachs-Platz 2, D-97082, Würzburg, Germany
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33
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Hu Y, Patra P, Pisanty O, Shafir A, Belew ZM, Binenbaum J, Ben Yaakov S, Shi B, Charrier L, Hyams G, Zhang Y, Trabulsky M, Caldararu O, Weiss D, Crocoll C, Avni A, Vernoux T, Geisler M, Nour-Eldin HH, Mayrose I, Shani E. Multi-Knock-a multi-targeted genome-scale CRISPR toolbox to overcome functional redundancy in plants. NATURE PLANTS 2023; 9:572-587. [PMID: 36973414 PMCID: PMC7615256 DOI: 10.1038/s41477-023-01374-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Plant genomes are characterized by large and complex gene families that often result in similar and partially overlapping functions. This genetic redundancy severely hampers current efforts to uncover novel phenotypes, delaying basic genetic research and breeding programmes. Here we describe the development and validation of Multi-Knock, a genome-scale clustered regularly interspaced short palindromic repeat toolbox that overcomes functional redundancy in Arabidopsis by simultaneously targeting multiple gene-family members, thus identifying genetically hidden components. We computationally designed 59,129 optimal single-guide RNAs that each target two to ten genes within a family at once. Furthermore, partitioning the library into ten sublibraries directed towards a different functional group allows flexible and targeted genetic screens. From the 5,635 single-guide RNAs targeting the plant transportome, we generated over 3,500 independent Arabidopsis lines that allowed us to identify and characterize the first known cytokinin tonoplast-localized transporters in plants. With the ability to overcome functional redundancy in plants at the genome-scale level, the developed strategy can be readily deployed by scientists and breeders for basic research and to expedite breeding efforts.
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Affiliation(s)
- Yangjie Hu
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Priyanka Patra
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, Lyon, France
| | - Odelia Pisanty
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Anat Shafir
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Zeinu Mussa Belew
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jenia Binenbaum
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Shir Ben Yaakov
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Bihai Shi
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, Lyon, France
| | - Laurence Charrier
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Gal Hyams
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Yuqin Zhang
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Maor Trabulsky
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Omer Caldararu
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Daniela Weiss
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Christoph Crocoll
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Adi Avni
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, Lyon, France
| | - Markus Geisler
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Hussam Hassan Nour-Eldin
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Itay Mayrose
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.
| | - Eilon Shani
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.
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34
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Wei L, Liu L, Chen Z, Huang Y, Yang L, Wang P, Xue S, Bie Z. CmCNIH1 improves salt tolerance by influencing the trafficking of CmHKT1;1 in pumpkin. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 36942473 DOI: 10.1111/tpj.16197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 03/05/2023] [Accepted: 03/09/2023] [Indexed: 05/17/2023]
Abstract
Pumpkin is often used as a rootstock for other Cucurbitaceae crops due to its resistance to soil-borne diseases and abiotic stress. Pumpkin rootstocks use a sodium transporter (CmHKT1;1) to promote the transport of Na+ from the shoot to the root effectively and improve the salt tolerance of the scion. However, the molecular regulatory mechanisms that influence the activity of CmHKT1;1 during salt stress response remain unknown. In this study, CmCNIH1, a cornichon homolog, was identified as a potential cargo receptor for CmHKT1;1. Yeast two-hybrid, biomolecular fluorescence complementation and luciferase complementary assays demonstrated that CmCNIH1 and CmHKT1;1 could interact. CmCNIH1 was a key component of the cellular vesicle transport machinery located in the endoplasmic reticulum (ER), ER export site and Golgi apparatus. A CmCNIH1 knockout mutant was more sensitive to salt stress than the wild-type (WT). In addition, ion homeostasis was disrupted in cmcnih1 mutants, which had higher Na+ and lower K+ content in shoots and roots than the WT. Two-electrode voltage-clamp experiment displayed that CmCNIH1 could not influence the Na+ current that passed through the plasma membrane (PM) in CmHKT1;1-expressing Xenopus laevis oocytes. Data from co-localization assays indicated that intact CmCNIH1 protein could alter the subcellular localization of CmHKT1;1 in tobacco leaf, pumpkin root and yeast. In summary, CmCNIH1 may function as a cargo receptor that regulates the localization of CmHKT1;1 to the PM to improve salt tolerance in pumpkin.
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Affiliation(s)
- Lanxing Wei
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, 430070, Wuhan, China
| | - Liu Liu
- College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zhi Chen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, 430070, Wuhan, China
| | - Yuan Huang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, 430070, Wuhan, China
| | - Li Yang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, 430070, Wuhan, China
| | - Pengwei Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, 430070, Wuhan, China
| | - Shaowu Xue
- College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zhilong Bie
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, 430070, Wuhan, China
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35
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He J, Yang B, Hause G, Rössner N, Peiter-Volk T, Schattat MH, Voiniciuc C, Peiter E. The trans-Golgi-localized protein BICAT3 regulates manganese allocation and matrix polysaccharide biosynthesis. PLANT PHYSIOLOGY 2022; 190:2579-2600. [PMID: 35993897 PMCID: PMC9706472 DOI: 10.1093/plphys/kiac387] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/18/2022] [Indexed: 05/11/2023]
Abstract
Manganese (Mn2+) is essential for a diversity of processes, including photosynthetic water splitting and the transfer of glycosyl moieties. Various Golgi-localized glycosyltransferases that mediate cell wall matrix polysaccharide biosynthesis are Mn2+ dependent, but the supply of these enzymes with Mn2+ is not well understood. Here, we show that the BIVALENT CATION TRANSPORTER 3 (BICAT3) localizes specifically to trans-cisternae of the Golgi. In agreement with a role in Mn2+ and Ca2+ homeostasis, BICAT3 rescued yeast (Saccharomyces cerevisiae) mutants defective in their translocation. Arabidopsis (Arabidopsis thaliana) knockout mutants of BICAT3 were sensitive to low Mn2+ and high Ca2+ availability and showed altered accumulation of these cations. Despite reduced cell expansion and leaf size in Mn2+-deficient bicat3 mutants, their photosynthesis was improved, accompanied by an increased Mn content of chloroplasts. Growth defects of bicat3 corresponded with an impaired glycosidic composition of matrix polysaccharides synthesized in the trans-Golgi. In addition to the vegetative growth defects, pollen tube growth of bicat3 was heterogeneously aberrant. This was associated with a severely reduced and similarly heterogeneous pectin deposition and caused diminished seed set and silique length. Double mutant analyses demonstrated that the physiological relevance of BICAT3 is distinct from that of ER-TYPE CA2+-ATPASE 3, a Golgi-localized Mn2+/Ca2+-ATPase. Collectively, BICAT3 is a principal Mn2+ transporter in the trans-Golgi whose activity is critical for specific glycosylation reactions in this organelle and for the allocation of Mn2+ between Golgi apparatus and chloroplasts.
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Affiliation(s)
- Jie He
- Plant Nutrition Laboratory, Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Bo Yang
- Independent Junior Research Group—Designer Glycans, Leibniz Institute of Plant Biochemistry, Halle (Saale), 06120, Germany
| | - Gerd Hause
- Biocentre, Martin Luther University Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Nico Rössner
- Plant Nutrition Laboratory, Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Tina Peiter-Volk
- Plant Nutrition Laboratory, Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Martin H Schattat
- Plant Physiology, Institute of Biology, Faculty of Natural Sciences I, Martin Luther University Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Cătălin Voiniciuc
- Independent Junior Research Group—Designer Glycans, Leibniz Institute of Plant Biochemistry, Halle (Saale), 06120, Germany
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, USA
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36
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Norrild RK, Johansson KE, O’Shea C, Morth JP, Lindorff-Larsen K, Winther JR. Increasing protein stability by inferring substitution effects from high-throughput experiments. CELL REPORTS METHODS 2022; 2:100333. [PMID: 36452862 PMCID: PMC9701609 DOI: 10.1016/j.crmeth.2022.100333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/22/2022] [Accepted: 10/19/2022] [Indexed: 06/17/2023]
Abstract
We apply a computational model, global multi-mutant analysis (GMMA), to inform on effects of most amino acid substitutions from a randomly mutated gene library. Using a high mutation frequency, the method can determine mutations that increase the stability of even very stable proteins for which conventional selection systems have reached their limit. As a demonstration of this, we screened a mutant library of a highly stable and computationally redesigned model protein using an in vivo genetic sensor for folding and assigned a stability effect to 374 of 912 possible single amino acid substitutions. Combining the top 9 substitutions increased the unfolding energy 47 to 69 kJ/mol in a single engineering step. Crystal structures of stabilized variants showed small perturbations in helices 1 and 2, which rendered them closer in structure to the redesign template. This case study illustrates the capability of the method, which is applicable to any screen for protein function.
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Affiliation(s)
- Rasmus Krogh Norrild
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Kristoffer Enøe Johansson
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Charlotte O’Shea
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Jens Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Jakob Rahr Winther
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
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37
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Malcı K, Jonguitud-Borrego N, van der Straten Waillet H, Puodžiu̅naitė U, Johnston EJ, Rosser SJ, Rios-Solis L. ACtivE: Assembly and CRISPR-Targeted in Vivo Editing for Yeast Genome Engineering Using Minimum Reagents and Time. ACS Synth Biol 2022; 11:3629-3643. [PMID: 36252276 PMCID: PMC9680028 DOI: 10.1021/acssynbio.2c00175] [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] [Indexed: 01/27/2023]
Abstract
Thanks to its sophistication, the CRISPR/Cas system has been a widely used yeast genome editing method. However, CRISPR methods generally rely on preassembled DNAs and extra cloning steps to deliver gRNA, Cas protein, and donor DNA. These laborious steps might hinder its usefulness. Here, we propose an alternative method, Assembly and CRISPR-targeted in vivo Editing (ACtivE), that only relies on in vivo assembly of linear DNA fragments for plasmid and donor DNA construction. Thus, depending on the user's need, these parts can be easily selected and combined from a repository, serving as a toolkit for rapid genome editing without any expensive reagent. The toolkit contains verified linear DNA fragments, which are easy to store, share, and transport at room temperature, drastically reducing expensive shipping costs and assembly time. After optimizing this technique, eight loci proximal to autonomously replicating sequences (ARS) in the yeast genome were also characterized in terms of integration and gene expression efficiencies and the impacts of the disruptions of these regions on cell fitness. The flexibility and multiplexing capacity of the ACtivE were shown by constructing a β-carotene pathway. In only a few days, >80% integration efficiency for single gene integration and >50% integration efficiency for triplex integration were achieved on Saccharomyces cerevisiae BY4741 from scratch without using in vitro DNA assembly methods, restriction enzymes, or extra cloning steps. This study presents a standardizable method to be readily employed to accelerate yeast genome engineering and provides well-defined genomic location alternatives for yeast synthetic biology and metabolic engineering purposes.
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Affiliation(s)
- Koray Malcı
- Institute
for Bioengineering, School of Engineering, University of Edinburgh, EdinburghEH9 3BF, U.K.,Centre
for Synthetic and Systems Biology (SynthSys), University of Edinburgh, EdinburghEH9 3BD, U.K.
| | - Nestor Jonguitud-Borrego
- Institute
for Bioengineering, School of Engineering, University of Edinburgh, EdinburghEH9 3BF, U.K.,Centre
for Synthetic and Systems Biology (SynthSys), University of Edinburgh, EdinburghEH9 3BD, U.K.
| | | | - Urtė Puodžiu̅naitė
- Institute
for Bioengineering, School of Engineering, University of Edinburgh, EdinburghEH9 3BF, U.K.,Centre
for Synthetic and Systems Biology (SynthSys), University of Edinburgh, EdinburghEH9 3BD, U.K.,School
of Biological Sciences, University of Edinburgh, EdinburghEH9 3FF, U.K.
| | - Emily J. Johnston
- Centre
for Synthetic and Systems Biology (SynthSys), University of Edinburgh, EdinburghEH9 3BD, U.K.,School
of Biological Sciences, University of Edinburgh, EdinburghEH9 3FF, U.K.
| | - Susan J. Rosser
- Centre
for Synthetic and Systems Biology (SynthSys), University of Edinburgh, EdinburghEH9 3BD, U.K.,School
of Biological Sciences, University of Edinburgh, EdinburghEH9 3FF, U.K.
| | - Leonardo Rios-Solis
- Institute
for Bioengineering, School of Engineering, University of Edinburgh, EdinburghEH9 3BF, U.K.,Centre
for Synthetic and Systems Biology (SynthSys), University of Edinburgh, EdinburghEH9 3BD, U.K.,School
of Natural and Environmental Sciences, Newcastle
University, Newcastle upon TyneNE1 7RU, U.K.,
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38
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Comparison of Genome and Plasmid-Based Engineering of Multigene Benzylglucosinolate Pathway in Saccharomyces cerevisiae. Appl Environ Microbiol 2022; 88:e0097822. [PMID: 36326240 PMCID: PMC9680641 DOI: 10.1128/aem.00978-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Intake of brassicaceous vegetables such as cabbage is associated with numerous health benefits. The major defense compounds in the Brassicales order are the amino acid-derived glucosinolates that have been associated with the health-promoting effects.
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39
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Olt P, Alejandro-Martinez S, Fermum J, Ramos E, Peiter E, Ludewig U. The vacuolar transporter LaMTP8.1 detoxifies manganese in leaves of Lupinus albus. PHYSIOLOGIA PLANTARUM 2022; 174:e13807. [PMID: 36270730 DOI: 10.1111/ppl.13807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 10/10/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Manganese (Mn) is an essential microelement, but overaccumulation is harmful to many plant species. Most plants have similar minimal Mn requirements, but the tolerance to elevated Mn varies considerably. Mobilization of phosphate (P) by plant roots leads to increased Mn uptake, and shoot Mn levels have been reported to serve as an indicator for P mobilization efficiency in the presence of P deficiency. White lupin (Lupinus albus L.) mobilizes P and Mn with outstanding efficiency due to the formation of determinate cluster roots that release carboxylates. The high Mn tolerance of L. albus goes along with shoot Mn accumulation, but the molecular basis of this detoxification mechanism has been unknown. In this study, we identify LaMTP8.1 as the transporter mediating vacuolar sequestration of Mn in the shoot of white lupin. The function of Mn transport was demonstrated by yeast complementation analysis, in which LaMTP8.1 detoxified Mn in pmr1∆ mutant cells upon elevated Mn supply. In addition, LaMTP8.1 also functioned as an iron (Fe) transporter in yeast assays. The expression of LaMTP8.1 was particularly high in old leaves under high Mn stress. However, low P availability per se did not result in transcriptional upregulation of LaMTP8.1. Moreover, LaMTP8.1 expression was strongly upregulated under Fe deficiency, where it was accompanied by Mn accumulation, indicating a role in the interaction of these micronutrients in L. albus. In conclusion, the tonoplast-localized Mn transporter LaMTP8.1 mediates Mn detoxification in leaf vacuoles, providing a mechanistic explanation for the high Mn accumulation and Mn tolerance in this species.
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Affiliation(s)
- Philipp Olt
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Stuttgart, Germany
| | - Santiago Alejandro-Martinez
- Plant Nutrition Laboratory, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Johann Fermum
- Plant Nutrition Laboratory, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Edith Ramos
- Plant Nutrition Laboratory, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Edgar Peiter
- Plant Nutrition Laboratory, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Uwe Ludewig
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Stuttgart, Germany
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40
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Mimata Y, Munemasa S, Nakamura T, Nakamura Y, Murata Y. Extracellular malate induces stomatal closure via direct activation of guard-cell anion channel SLAC1 and stimulation of Ca 2+ signalling. THE NEW PHYTOLOGIST 2022; 236:852-863. [PMID: 35879859 DOI: 10.1111/nph.18400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/17/2022] [Indexed: 06/15/2023]
Abstract
Plants secrete malate from guard cells to apoplast under stress conditions and exogenous malate induces stomatal closure. Malate is considered an extracellular chemical signal of stomatal closure. However, the molecular mechanism of malate-induced stomatal closure is not fully elucidated. We investigated responses of stomatal aperture, ion channels, and cytosolic Ca2+ to malate. A treatment with malate induced stomatal closure in Arabidopsis thaliana wild-type plants, but not in the mutants deficient in the slow (S-type) anion channel gene SLOW ANION CHANNEL-ASSOCIATED 1 (SLAC1). The treatment with malate increased S-type anion currents in guard-cell protoplasts of wild-type plants but not in the slac1 mutant. In addition, extracellular rather than intracellular application of malate increased the S-type currents of constitutively active mutants of SLAC1, which have kinase-independent activities, in a heterologous expression system using Xenopus oocytes. The treatment with malate transiently increased cytosolic Ca2+ concentration in the wild-type Arabidopsis guard cells and the malate-induced stomatal closure was inhibited by the Ca2+ channel blocker and the Ca2+ chelator. These results indicate that extracellular malate directly activates SLAC1 and simultaneously stimulates Ca2+ signalling in guard cells, resulting in steady and solid activation of SLAC1 for stomatal closure.
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Affiliation(s)
- Yoshiharu Mimata
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-Naka 1-1-1, 700-8530, Okayama, Japan
| | - Shintaro Munemasa
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-Naka 1-1-1, 700-8530, Okayama, Japan
| | - Toshiyuki Nakamura
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-Naka 1-1-1, 700-8530, Okayama, Japan
| | - Yoshimasa Nakamura
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-Naka 1-1-1, 700-8530, Okayama, Japan
| | - Yoshiyuki Murata
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-Naka 1-1-1, 700-8530, Okayama, Japan
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41
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Scherzer S, Böhm J, Huang S, Iosip AL, Kreuzer I, Becker D, Heckmann M, Al-Rasheid KAS, Dreyer I, Hedrich R. A unique inventory of ion transporters poises the Venus flytrap to fast-propagating action potentials and calcium waves. Curr Biol 2022; 32:4255-4263.e5. [PMID: 36087579 DOI: 10.1016/j.cub.2022.08.051] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/20/2022] [Accepted: 08/17/2022] [Indexed: 12/14/2022]
Abstract
Since the 19th century, it has been known that the carnivorous Venus flytrap is electrically excitable. Nevertheless, the mechanism and the molecular entities of the flytrap action potential (AP) remain unknown. When entering the electrically excitable stage, the trap expressed a characteristic inventory of ion transporters, among which the increase in glutamate receptor GLR3.6 RNA was most pronounced. Trigger hair stimulation or glutamate application evoked an AP and a cytoplasmic Ca2+ transient that both propagated at the same speed from the site of induction along the entire trap lobe surface. A priming Ca2+ moiety entering the cytoplasm in the context of the AP was further potentiated by an organelle-localized calcium-induced calcium release (CICR)-like system prolonging the Ca2+ signal. While the Ca2+ transient persisted, SKOR K+ channels and AHA H+-ATPases repolarized the AP already. By counting the number of APs and long-lasting Ca2+ transients, the trap directs the different steps in the carnivorous plant's hunting cycle. VIDEO ABSTRACT.
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Affiliation(s)
- Sönke Scherzer
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, Wuerzburg University, Julius-von-Sachs-Platz 2, 97070 Wuerzburg, Germany.
| | - Jennifer Böhm
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, Wuerzburg University, Julius-von-Sachs-Platz 2, 97070 Wuerzburg, Germany
| | - Shouguang Huang
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, Wuerzburg University, Julius-von-Sachs-Platz 2, 97070 Wuerzburg, Germany
| | - Anda L Iosip
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, Wuerzburg University, Julius-von-Sachs-Platz 2, 97070 Wuerzburg, Germany
| | - Ines Kreuzer
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, Wuerzburg University, Julius-von-Sachs-Platz 2, 97070 Wuerzburg, Germany
| | - Dirk Becker
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, Wuerzburg University, Julius-von-Sachs-Platz 2, 97070 Wuerzburg, Germany
| | - Manfred Heckmann
- Department of Neurophysiology, Institute of Physiology, Wuerzburg University, Röntgenring 9, 97070 Wuerzburg, Germany
| | - Khaled A S Al-Rasheid
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ingo Dreyer
- Center of Bioinformatics, Simulation and Modeling (CBSM), Faculty of Engineering, Universidad de Talca, 2 Norte 685, Talca 3460000, Chile
| | - Rainer Hedrich
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, Wuerzburg University, Julius-von-Sachs-Platz 2, 97070 Wuerzburg, Germany.
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42
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A microbial supply chain for production of the anti-cancer drug vinblastine. Nature 2022; 609:341-347. [PMID: 36045295 PMCID: PMC9452304 DOI: 10.1038/s41586-022-05157-3] [Citation(s) in RCA: 141] [Impact Index Per Article: 70.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/27/2022] [Indexed: 12/05/2022]
Abstract
Monoterpene indole alkaloids (MIAs) are a diverse family of complex plant secondary metabolites with many medicinal properties, including the essential anti-cancer therapeutics vinblastine and vincristine1. As MIAs are difficult to chemically synthesize, the world’s supply chain for vinblastine relies on low-yielding extraction and purification of the precursors vindoline and catharanthine from the plant Catharanthus roseus, which is then followed by simple in vitro chemical coupling and reduction to form vinblastine at an industrial scale2,3. Here, we demonstrate the de novo microbial biosynthesis of vindoline and catharanthine using a highly engineered yeast, and in vitro chemical coupling to vinblastine. The study showcases a very long biosynthetic pathway refactored into a microbial cell factory, including 30 enzymatic steps beyond the yeast native metabolites geranyl pyrophosphate and tryptophan to catharanthine and vindoline. In total, 56 genetic edits were performed, including expression of 34 heterologous genes from plants, as well as deletions, knock-downs and overexpression of ten yeast genes to improve precursor supplies towards de novo production of catharanthine and vindoline, from which semisynthesis to vinblastine occurs. As the vinblastine pathway is one of the longest MIA biosynthetic pathways, this study positions yeast as a scalable platform to produce more than 3,000 natural MIAs and a virtually infinite number of new-to-nature analogues. De novo microbial biosynthesis of vindoline and catharanthine using a highly engineered yeast and in vitro chemical coupling to vinblastine is carried out, positioning yeast as a scalable platform to produce many monoterpene indole alkaloids.
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43
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Hansen NL, Kjaerulff L, Heck QK, Forman V, Staerk D, Møller BL, Andersen-Ranberg J. Tripterygium wilfordii cytochrome P450s catalyze the methyl shift and epoxidations in the biosynthesis of triptonide. Nat Commun 2022; 13:5011. [PMID: 36008399 PMCID: PMC9411204 DOI: 10.1038/s41467-022-32667-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022] Open
Abstract
The diterpenoid triepoxides triptolide and triptonide from Tripterygium wilfordii (thunder god wine) exhibit unique bioactivities with potential uses in disease treatment and as a non-hormonal male contraceptives. Here, we show that cytochrome P450s (CYPs) from the CYP71BE subfamily catalyze an unprecedented 18(4→3) methyl shift required for biosynthesis of the abeo-abietane core structure present in diterpenoid triepoxides and in several other plant diterpenoids. In combination with two CYPs of the CYP82D subfamily, four CYPs from T. wilfordii are shown to constitute the minimal set of biosynthetic genes that enables triptonide biosynthesis using Nicotiana benthamiana and Saccharomyces cerevisiae as heterologous hosts. In addition, co-expression of a specific T. wilfordii cytochrome b5 (Twcytb5-A) increases triptonide output more than 9-fold in S. cerevisiae and affords isolation and structure elucidation by NMR spectroscopic analyses of 18 diterpenoids, providing insights into the biosynthesis of diterpenoid triepoxides. Our findings pave the way for diterpenoid triepoxide production via fermentation. How triptonide is made in the medicinal plant Tripterygium wilfordii is largely unknown. Here, the authors report the identification and characterization of a suite of cytochrome P450s and show their function in catalyzing the formation of triptonide from miltriadiene in tobacco and baker’s yeast.
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Affiliation(s)
- Nikolaj Lervad Hansen
- Plant Biochemistry Laboratory, Department of Plant and Environment Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Louise Kjaerulff
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Quinn Kalby Heck
- Plant Biochemistry Laboratory, Department of Plant and Environment Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Victor Forman
- Plant Biochemistry Laboratory, Department of Plant and Environment Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Dan Staerk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environment Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
| | - Johan Andersen-Ranberg
- Plant Biochemistry Laboratory, Department of Plant and Environment Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark.
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44
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Malcı K, Watts E, Roberts TM, Auxillos JY, Nowrouzi B, Boll HO, Nascimento CZSD, Andreou A, Vegh P, Donovan S, Fragkoudis R, Panke S, Wallace E, Elfick A, Rios-Solis L. Standardization of Synthetic Biology Tools and Assembly Methods for Saccharomyces cerevisiae and Emerging Yeast Species. ACS Synth Biol 2022; 11:2527-2547. [PMID: 35939789 PMCID: PMC9396660 DOI: 10.1021/acssynbio.1c00442] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
As redesigning organisms using engineering principles
is one of
the purposes of synthetic biology (SynBio), the standardization of
experimental methods and DNA parts is becoming increasingly a necessity.
The synthetic biology community focusing on the engineering of Saccharomyces cerevisiae has been in the foreground in this
area, conceiving several well-characterized SynBio toolkits widely
adopted by the community. In this review, the molecular methods and
toolkits developed for S. cerevisiae are discussed
in terms of their contributions to the required standardization efforts.
In addition, the toolkits designed for emerging nonconventional yeast
species including Yarrowia lipolytica, Komagataella
phaffii, and Kluyveromyces marxianus are
also reviewed. Without a doubt, the characterized DNA parts combined
with the standardized assembly strategies highlighted in these toolkits
have greatly contributed to the rapid development of many metabolic
engineering and diagnostics applications among others. Despite the
growing capacity in deploying synthetic biology for common yeast genome
engineering works, the yeast community has a long journey to go to
exploit it in more sophisticated and delicate applications like bioautomation.
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Affiliation(s)
- Koray Malcı
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, EH9 3BF Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom
| | - Emma Watts
- School of Biological Sciences, University of Edinburgh, Kings Buildings, EH9 3JW Edinburgh, United Kingdom
| | | | - Jamie Yam Auxillos
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom.,Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Kings Buildings, EH9 3FF Edinburgh, United Kingdom
| | - Behnaz Nowrouzi
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, EH9 3BF Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom
| | - Heloísa Oss Boll
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília, Brasília, Federal District 70910-900, Brazil
| | | | - Andreas Andreou
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom
| | - Peter Vegh
- Edinburgh Genome Foundry, University of Edinburgh, Kings Buildings, Edinburgh EH9 3BF, United Kingdom
| | - Sophie Donovan
- Edinburgh Genome Foundry, University of Edinburgh, Kings Buildings, Edinburgh EH9 3BF, United Kingdom
| | - Rennos Fragkoudis
- Edinburgh Genome Foundry, University of Edinburgh, Kings Buildings, Edinburgh EH9 3BF, United Kingdom
| | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Edward Wallace
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom.,Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Kings Buildings, EH9 3FF Edinburgh, United Kingdom
| | - Alistair Elfick
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, EH9 3BF Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Kings Buildings, EH9 3BF Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Kings Buildings, EH9 3BD Edinburgh, United Kingdom.,School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
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45
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Evolution of plasmid-construction. Int J Biol Macromol 2022; 209:1319-1326. [PMID: 35452702 DOI: 10.1016/j.ijbiomac.2022.04.094] [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: 02/20/2022] [Revised: 04/06/2022] [Accepted: 04/13/2022] [Indexed: 11/23/2022]
Abstract
Developing for almost half a century, plasmid-construction has explored more than 37 methods. Some methods have evolved into new versions. From a global and evolutionary viewpoint, a review will make a clear understand and an easy practice for plasmid-construction. The 37 methods employ three principles as creating single-strand overhang, recombining homology arms, or serving amplified insert as mega-primer, and are classified into three groups as single strand overhang cloning, homologous recombination cloning, and mega-primer cloning. The methods evolve along a route for easy, efficient, or/and seamless cloning. Mechanism of plasmid-construction is primer annealing or/and primer invasion. Scar junction is a must-be faced scientific problem in plasmid-construction.
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46
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Yang S, Zhang T, Wang Z, Zhao X, Li R, Li J. Nitrilases NIT1/2/3 Positively Regulate Flowering by Inhibiting MAF4 Expression in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:889460. [PMID: 35665187 PMCID: PMC9157433 DOI: 10.3389/fpls.2022.889460] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/18/2022] [Indexed: 06/15/2023]
Abstract
Three of the nitrilases (NITs), NIT1, NIT2, and NIT3, are ubiquitously existing in plant kingdom, which catalyze indole-3-acetonitrile into the most important auxin indole-3-acetic acid. Auxin is an indispensable hormone, which plays the important roles in almost all processes of plant growth and development. However, there are few reports on the regulation of flowering-time mediated by auxin. Here, we found that in Arabidopsis, nit1/2/3 showed a late flowering phenotype in short days. To explore the molecular mechanism by which NIT1/2/3 regulate flowering time, we performed transcriptome sequencing of nit1/2/3. The results showed that the expression of a MADS-box transcription factor gene MADS AFFECTING FLOWERING4 (MAF4) was dramatically increased in nit1/2/3 comparing to wild type (WT). MAF4 is one of the paralogs of the potent flowering inhibitor FLOWERING LOCUS C (FLC). There are four other paralogs in FLC clade in Arabidopsis, including FLOWERING LOCUS M (FLM/MAF1), MAF2, MAF3, and MAF5. The late flowering phenotype of nit1/2/3 could not be observed in the maf4 background, indicating that the phenotype was specifically dependent on MAF4 rather than other FLC clade members. Interestingly, the expression of a lncRNA gene MAS, which is transcribed in the opposite direction of MAF4, was found significantly increased in nit1/2/3. Also, MAS has been reported to activate MAF4 transcription by promoting histone 3 lysine 4 trimethylation (H3K4me3). As expected, H3K4me3 deposition at MAF4 locus in nit1/2/3 was highly enriched and significantly higher than that of WT. In summary, we show that NITs, NIT1/2/3, positively regulate flowering by repressing MAF4 through manipulating H3K4me3 modification. Further study needs to be performed to explore the largely unknown mechanisms behind it.
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PlasmidMaker is a versatile, automated, and high throughput end-to-end platform for plasmid construction. Nat Commun 2022; 13:2697. [PMID: 35577775 PMCID: PMC9110713 DOI: 10.1038/s41467-022-30355-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/28/2022] [Indexed: 01/01/2023] Open
Abstract
Plasmids are used extensively in basic and applied biology. However, design and construction of plasmids, specifically the ones carrying complex genetic information, remains one of the most time-consuming, labor-intensive, and rate-limiting steps in performing sophisticated biological experiments. Here, we report the development of a versatile, robust, automated end-to-end platform named PlasmidMaker that allows error-free construction of plasmids with virtually any sequences in a high throughput manner. This platform consists of a most versatile DNA assembly method using Pyrococcus furiosus Argonaute (PfAgo)-based artificial restriction enzymes, a user-friendly frontend for plasmid design, and a backend that streamlines the workflow and integration with a robotic system. As a proof of concept, we used this platform to generate 101 plasmids from six different species ranging from 5 to 18 kb in size from up to 11 DNA fragments. PlasmidMaker should greatly expand the potential of synthetic biology. Despite their broad utility, design and construction of plasmids remains laborious and time-consuming. Here the authors report a robust, versatile, and automated end-to-end platform that enables scarless construction of virtually any plasmid.
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48
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Marker-free CRISPR-Cas9 based genetic engineering of the phytopathogenic fungus, Penicillium expansum. Fungal Genet Biol 2022; 160:103689. [PMID: 35339702 DOI: 10.1016/j.fgb.2022.103689] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 01/12/2023]
Abstract
Filamentous fungi are prolific producers of secondary metabolites (SecMets), including compounds with antibiotic properties, like penicillin, that allows the producing fungus to combat competitors in a shared niche. However, the biological function of the majority of these small complex metabolites for the producing fungi remains unclear (Macheleidt et al., 2016). In an effort to address this lack of knowledge, we have chosen to study the microbial community of moldy apples in the hope of shedding more light on the role of SecMets for the dynamics of the microbial community. Penicillium expansum is one of the prevalent fungal species in this system, and in co-culture experiments with other apple fungal pathogens, we have observed up- and downregulation of several SecMets when compared to monocultures. However, molecular genetic dissection of the observed changes is challenging, and new methodologies for targeted genetic engineering in P. expansum are needed. In the current study, we have established a CRISPR-Cas9 dependent genetic engineering toolbox for the targeted genetic manipulation of P. expansum to allow for single-step construction of marker-free strains. The method and effect of different combinations of a Cas9-sgRNA expressing plasmids and repair template substrates in the NHEJ-proficient WT strain is tested by targeted deletion of melA, encoding a PKS responsible for pigment formation, which upon deletion resulted in white mutants. Co-transformation with a linear double-stranded DNA fragment consisting of two 2 kb homology arms flanking the PKS gene proved to be the most efficient strategy with 100% confirmed deletions by diagnostic PCR. Shorter homology arms (500-1000bp) resulted in 20-30% deletion efficiency. Furthermore, we demonstrate the application of the CRISPR-Cas9 method for targeted deletion of biosynthetic genes without a visible phenotype, insertion of a visual reporter-encoding gene (mRFP), and overexpression of biosynthetic genes. Combined, these tools will advance in enabling the deciphering of SecMet biosynthetic pathways, provide in situ insight into when and where SecMets are produced, and provide an avenue to study the role of P. expansum SecMets in shaping the microbial community development on moldy apples via marker-free targeted genetic engineering of P. expansum.
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49
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Dickinson MS, Lu J, Gupta M, Marten I, Hedrich R, Stroud RM. Molecular basis of multistep voltage activation in plant two-pore channel 1. Proc Natl Acad Sci U S A 2022; 119:e2110936119. [PMID: 35210362 PMCID: PMC8892357 DOI: 10.1073/pnas.2110936119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/29/2021] [Indexed: 12/26/2022] Open
Abstract
Voltage-gated ion channels confer excitability to biological membranes, initiating and propagating electrical signals across large distances on short timescales. Membrane excitation requires channels that respond to changes in electric field and couple the transmembrane voltage to gating of a central pore. To address the mechanism of this process in a voltage-gated ion channel, we determined structures of the plant two-pore channel 1 at different stages along its activation coordinate. These high-resolution structures of activation intermediates, when compared with the resting-state structure, portray a mechanism in which the voltage-sensing domain undergoes dilation and in-membrane plane rotation about the gating charge-bearing helix, followed by charge translocation across the charge transfer seal. These structures, in concert with patch-clamp electrophysiology, show that residues in the pore mouth sense inhibitory Ca2+ and are allosterically coupled to the voltage sensor. These conformational changes provide insight into the mechanism of voltage-sensor domain activation in which activation occurs vectorially over a series of elementary steps.
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Affiliation(s)
- Miles Sasha Dickinson
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, CA 94143
| | - Jinping Lu
- Department of Molecular Plant Physiology and Biophysics, University of Würzburg, D-97082 Würzburg, Germany
| | - Meghna Gupta
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143
| | - Irene Marten
- Department of Molecular Plant Physiology and Biophysics, University of Würzburg, D-97082 Würzburg, Germany
| | - Rainer Hedrich
- Department of Molecular Plant Physiology and Biophysics, University of Würzburg, D-97082 Würzburg, Germany
| | - Robert M Stroud
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143;
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50
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Peña-Varas C, Kanstrup C, Vergara-Jaque A, González-Avendaño M, Crocoll C, Mirza O, Dreyer I, Nour-Eldin H, Ramírez D. Structural Insights into the Substrate Transport Mechanisms in GTR Transporters through Ensemble Docking. Int J Mol Sci 2022; 23:ijms23031595. [PMID: 35163519 PMCID: PMC8836200 DOI: 10.3390/ijms23031595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/11/2022] [Accepted: 01/19/2022] [Indexed: 02/04/2023] Open
Abstract
Glucosinolate transporters (GTRs) are part of the nitrate/peptide transporter (NPF) family, members of which also transport specialized secondary metabolites as substrates. Glucosinolates are defense compounds derived from amino acids. We selected 4-methylthiobutyl (4MTB) and indol-3-ylmethyl (I3M) glucosinolates to study how GTR1 from Arabidopsis thaliana transports these substrates in computational simulation approaches. The designed pipeline reported here includes massive docking of 4MTB and I3M in an ensemble of GTR1 conformations (in both inward and outward conformations) extracted from molecular dynamics simulations, followed by clustered and substrate–protein interactions profiling. The identified key residues were mutated, and their role in substrate transport was tested. We were able to identify key residues that integrate a major binding site of these substrates, which is critical for transport activity. In silico approaches employed here represent a breakthrough in the plant transportomics field, as the identification of key residues usually takes a long time if performed from a purely wet-lab experimental perspective. The inclusion of structural bioinformatics in the analyses of plant transporters significantly speeds up the knowledge-gaining process and optimizes valuable time and resources.
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Affiliation(s)
- Carlos Peña-Varas
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Llano Subercaseaux 2801-piso 6, Santiago 8900000, Chile;
| | - Christa Kanstrup
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (C.K.); (C.C.); (H.N.-E.)
| | - Ariela Vergara-Jaque
- Center for Bioinformatics, Simulation and Modeling (CBSM), Faculty of Engineering, Campus Talca, Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca 3460000, Chile; (A.V.-J.); (M.G.-A.); (I.D.)
| | - Mariela González-Avendaño
- Center for Bioinformatics, Simulation and Modeling (CBSM), Faculty of Engineering, Campus Talca, Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca 3460000, Chile; (A.V.-J.); (M.G.-A.); (I.D.)
| | - Christoph Crocoll
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (C.K.); (C.C.); (H.N.-E.)
| | - Osman Mirza
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark;
| | - Ingo Dreyer
- Center for Bioinformatics, Simulation and Modeling (CBSM), Faculty of Engineering, Campus Talca, Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca 3460000, Chile; (A.V.-J.); (M.G.-A.); (I.D.)
| | - Hussam Nour-Eldin
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (C.K.); (C.C.); (H.N.-E.)
| | - David Ramírez
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Llano Subercaseaux 2801-piso 6, Santiago 8900000, Chile;
- Research Center for the Development of Novel Therapeutic Alternatives for Alcohol Use Disorders, Santiago 8900000, Chile
- Correspondence: ; Tel.: +56-(22)-3036667
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