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Unda F, Mottiar Y, Mahon EL, Karlen SD, Kim KH, Loqué D, Eudes A, Ralph J, Mansfield SD. A new approach to zip-lignin: 3,4-dihydroxybenzoate is compatible with lignification. New Phytol 2022; 235:234-246. [PMID: 35377486 PMCID: PMC9325543 DOI: 10.1111/nph.18136] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/17/2022] [Indexed: 06/02/2023]
Abstract
Renewed interests in the development of bioenergy, biochemicals, and biomaterials have elicited new strategies for engineering the lignin of biomass feedstock plants. This study shows, for the first time, that 3,4-dihydroxybenzoate (DHB) is compatible with the radical coupling reactions that assemble polymeric lignin in plants. We introduced a bacterial 3-dehydroshikimate dehydratase into hybrid poplar (Populus alba × grandidentata) to divert carbon flux away from the shikimate pathway, which lies upstream of lignin biosynthesis. Transgenic poplar wood had up to 33% less lignin with p-hydroxyphenyl units comprising as much as 10% of the lignin. Mild alkaline hydrolysis of transgenic wood released fewer ester-linked p-hydroxybenzoate groups than control trees, and revealed the novel incorporation of cell-wall-bound DHB, as well as glycosides of 3,4-dihydroxybenzoic acid (DHBA). Two-dimensional nuclear magnetic resonance (2D-NMR) analysis uncovered DHBA-derived benzodioxane structures suggesting that DHB moieties were integrated into the lignin polymer backbone. In addition, up to 40% more glucose was released from transgenic wood following ionic liquid pretreatment and enzymatic hydrolysis. This work highlights the potential of diverting carbon flux from the shikimate pathway for lignin engineering and describes a new type of 'zip-lignin' derived from the incorporation of DHB into poplar lignin.
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Affiliation(s)
- Faride Unda
- Department of Wood ScienceUniversity of British Columbia2424 Main MallVancouverBCV6T 1Z4Canada
- Department of EnergyGreat Lakes Bioenergy Research CenterWisconsin Energy InstituteUniversity of Wisconsin‐Madison1552 University AvenueMadisonWI53726USA
| | - Yaseen Mottiar
- Department of Wood ScienceUniversity of British Columbia2424 Main MallVancouverBCV6T 1Z4Canada
- Department of EnergyGreat Lakes Bioenergy Research CenterWisconsin Energy InstituteUniversity of Wisconsin‐Madison1552 University AvenueMadisonWI53726USA
| | - Elizabeth L. Mahon
- Department of Wood ScienceUniversity of British Columbia2424 Main MallVancouverBCV6T 1Z4Canada
- Department of EnergyGreat Lakes Bioenergy Research CenterWisconsin Energy InstituteUniversity of Wisconsin‐Madison1552 University AvenueMadisonWI53726USA
| | - Steven D. Karlen
- Department of EnergyGreat Lakes Bioenergy Research CenterWisconsin Energy InstituteUniversity of Wisconsin‐Madison1552 University AvenueMadisonWI53726USA
- Department of BiochemistryUniversity of Wisconsin‐Madison433 Babcock DriveMadisonWI53706USA
| | - Kwang Ho Kim
- Department of Wood ScienceUniversity of British Columbia2424 Main MallVancouverBCV6T 1Z4Canada
- Clean Energy Research CenterKorea Institute of Science and TechnologySeoul02792Korea
| | - Dominique Loqué
- Joint BioEnergy Institute5885 Hollis StreetEmeryvilleCA94608USA
| | - Aymerick Eudes
- Joint BioEnergy Institute5885 Hollis StreetEmeryvilleCA94608USA
- Environmental Genomics and Systems Biology DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - John Ralph
- Department of EnergyGreat Lakes Bioenergy Research CenterWisconsin Energy InstituteUniversity of Wisconsin‐Madison1552 University AvenueMadisonWI53726USA
- Department of BiochemistryUniversity of Wisconsin‐Madison433 Babcock DriveMadisonWI53706USA
| | - Shawn D. Mansfield
- Department of Wood ScienceUniversity of British Columbia2424 Main MallVancouverBCV6T 1Z4Canada
- Department of EnergyGreat Lakes Bioenergy Research CenterWisconsin Energy InstituteUniversity of Wisconsin‐Madison1552 University AvenueMadisonWI53726USA
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2
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Hao Z, Yogiswara S, Wei T, Benites VT, Sinha A, Wang G, Baidoo EEK, Ronald PC, Scheller HV, Loqué D, Eudes A. Expression of a bacterial 3-dehydroshikimate dehydratase (QsuB) reduces lignin and improves biomass saccharification efficiency in switchgrass (Panicum virgatum L.). BMC Plant Biol 2021; 21:56. [PMID: 33478381 PMCID: PMC7819203 DOI: 10.1186/s12870-021-02842-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/13/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND Lignin deposited in plant cell walls negatively affects biomass conversion into advanced bioproducts. There is therefore a strong interest in developing bioenergy crops with reduced lignin content or altered lignin structures. Another desired trait for bioenergy crops is the ability to accumulate novel bioproducts, which would enhance the development of economically sustainable biorefineries. As previously demonstrated in the model plant Arabidopsis, expression of a 3-dehydroshikimate dehydratase in plants offers the potential for decreasing lignin content and overproducing a value-added metabolic coproduct (i.e., protocatechuate) suitable for biological upgrading. RESULTS The 3-dehydroshikimate dehydratase QsuB from Corynebacterium glutamicum was expressed in the bioenergy crop switchgrass (Panicum virgatum L.) using the stem-specific promoter of an O-methyltransferase gene (pShOMT) from sugarcane. The activity of pShOMT was validated in switchgrass after observation in-situ of beta-glucuronidase (GUS) activity in stem nodes of plants carrying a pShOMT::GUS fusion construct. Under controlled growth conditions, engineered switchgrass lines containing a pShOMT::QsuB construct showed reductions of lignin content, improvements of biomass saccharification efficiency, and accumulated higher amount of protocatechuate compared to control plants. Attempts to generate transgenic switchgrass lines carrying the QsuB gene under the control of the constitutive promoter pZmUbi-1 were unsuccessful, suggesting possible toxicity issues associated with ectopic QsuB expression during the plant regeneration process. CONCLUSION This study validates the transfer of the QsuB engineering approach from a model plant to switchgrass. We have demonstrated altered expression of two important traits: lignin content and accumulation of a co-product. We found that the choice of promoter to drive QsuB expression should be carefully considered when deploying this strategy to other bioenergy crops. Field-testing of engineered QsuB switchgrass are in progress to assess the performance of the introduced traits and agronomic performances of the transgenic plants.
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Affiliation(s)
- Zhangying Hao
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Sasha Yogiswara
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Tong Wei
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616 USA
- Present address: State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518000 China
| | - Veronica Teixeira Benites
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Anagh Sinha
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - George Wang
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Edward E. K. Baidoo
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Pamela C. Ronald
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616 USA
| | - Henrik V. Scheller
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA 94720 USA
| | - Dominique Loqué
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Aymerick Eudes
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
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3
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Calgaro-Kozina A, Vuu KM, Keasling JD, Loqué D, Sattely ES, Shih PM. Engineering Plant Synthetic Pathways for the Biosynthesis of Novel Antifungals. ACS Cent Sci 2020; 6:1394-1400. [PMID: 32875080 PMCID: PMC7453567 DOI: 10.1021/acscentsci.0c00241] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Indexed: 05/21/2023]
Abstract
Plants produce a wealth of biologically active compounds, many of which are used to defend themselves from various pests and pathogens. We explore the possibility of expanding upon the natural chemical diversity of plants and create molecules that have enhanced properties, by engineering metabolic pathways new to nature. We rationally broaden the set of primary metabolites that can be utilized by the core biosynthetic pathway of the natural biopesticide, brassinin, producing in planta a novel class of compounds that we call crucifalexins. Two of our new-to-nature crucifalexins are more potent antifungals than brassinin and, in some instances, comparable to commercially used fungicides. Our findings highlight the potential to push the boundaries of plant metabolism for the biosynthesis of new biopesticides.
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Affiliation(s)
- Amy Calgaro-Kozina
- Department
of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Khanh M. Vuu
- Joint
BioEnergy Institute, Emeryville, California 94608, United States
- Environmental
Genomics and Systems Biology Division, Lawrence
Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Joint
BioEnergy Institute, Emeryville, California 94608, United States
- Department
of Chemical and Biomolecular Engineering, UC Berkeley, Berkeley, California 94720, United States
- Department
of Bioengineering, UC Berkeley, Berkeley, California 94720, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, One Cyclotron Road, Berkeley, California 94720, United States
| | - Dominique Loqué
- Joint
BioEnergy Institute, Emeryville, California 94608, United States
- Environmental
Genomics and Systems Biology Division, Lawrence
Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Elizabeth S. Sattely
- Department
of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- Howard
Hughes Medical Institute, Stanford University, Stanford, California 94305, United States
- E-mail:
| | - Patrick M. Shih
- Joint
BioEnergy Institute, Emeryville, California 94608, United States
- Environmental
Genomics and Systems Biology Division, Lawrence
Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
- Department
of Plant Biology, University of California,
Davis, Davis, California 95616, United States
- Genome
Center, University of California, Davis, Davis, California 95616, United States
- E-mail:
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4
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Belcher MS, Vuu KM, Zhou A, Mansoori N, Agosto Ramos A, Thompson MG, Scheller HV, Loqué D, Shih PM. Design of orthogonal regulatory systems for modulating gene expression in plants. Nat Chem Biol 2020; 16:857-865. [PMID: 32424304 DOI: 10.1038/s41589-020-0547-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 04/09/2020] [Indexed: 11/08/2022]
Abstract
Agricultural biotechnology strategies often require the precise regulation of multiple genes to effectively modify complex plant traits. However, most efforts are hindered by a lack of characterized tools that allow for reliable and targeted expression of transgenes. We have successfully engineered a library of synthetic transcriptional regulators that modulate expression strength in planta. By leveraging orthogonal regulatory systems from Saccharomyces spp., we have developed a strategy for the design of synthetic activators, synthetic repressors, and synthetic promoters and have validated their use in Nicotiana benthamiana and Arabidopsis thaliana. This characterization of contributing genetic elements that dictate gene expression represents a foundation for the rational design of refined synthetic regulators. Our findings demonstrate that these tools provide variation in transcriptional output while enabling the concerted expression of multiple genes in a tissue-specific and environmentally responsive manner, providing a basis for generating complex genetic circuits that process endogenous and environmental stimuli.
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Affiliation(s)
- Michael S Belcher
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Khanh M Vuu
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andy Zhou
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
| | - Nasim Mansoori
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Amanda Agosto Ramos
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mitchell G Thompson
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
| | - Henrik V Scheller
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Dominique Loqué
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Patrick M Shih
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Plant Biology, University of California, Davis, Davis, CA, USA.
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5
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Liang Y, Eudes A, Yogiswara S, Jing B, Benites VT, Yamanaka R, Cheng-Yue C, Baidoo EE, Mortimer JC, Scheller HV, Loqué D. A screening method to identify efficient sgRNAs in Arabidopsis, used in conjunction with cell-specific lignin reduction. Biotechnol Biofuels 2019; 12:130. [PMID: 31143243 PMCID: PMC6532251 DOI: 10.1186/s13068-019-1467-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/14/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Single guide RNA (sgRNA) selection is important for the efficiency of CRISPR/Cas9-mediated genome editing. However, in plants, the rules governing selection are not well established. RESULTS We developed a facile transient assay to screen sgRNA efficiency. We then used it to test top-performing bioinformatically predicted sgRNAs for two different Arabidopsis genes. In our assay, these sgRNAs had vastly different editing efficiencies, and these efficiencies were replicated in stably transformed Arabidopsis lines. One of the genes, hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase (HCT), is an essential gene, required for lignin biosynthesis. Previously, HCT function has been studied using gene silencing. Here, to avoid the negative growth effects that are due to the loss of HCT activity in xylem vessels, we used a fiber-specific promoter to drive CAS9 expression. Two independent transgenic lines showed the expected lignin decrease. Successful editing was confirmed via the observation of mutations at the HCT target loci, as well as an approximately 90% decrease in HCT activity. Histochemical analysis and a normal growth phenotype support the fiber-specific knockout of HCT. For the targeting of the second gene, Golgi-localized nucleotide sugar transporter2 (GONST2), a highly efficient sgRNA drastically increased the rate of germline editing in T1 generation. CONCLUSIONS This screening method is widely applicable, and the selection and use of efficient sgRNAs will accelerate the process of expanding germplasm for both molecular breeding and research. In addition, this, to the best of our knowledge, is the first application of constrained genome editing to obtain chimeric plants of essential genes, thereby providing a dominant method to avoid lethal growth phenotypes.
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Affiliation(s)
- Yan Liang
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Aymerick Eudes
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Sasha Yogiswara
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Beibei Jing
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Veronica T. Benites
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biological Systems Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Reo Yamanaka
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- School of Public Health, University of California, Berkeley, CA 94720 USA
| | - Clarabelle Cheng-Yue
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Edward E. Baidoo
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biological Systems Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Jenny C. Mortimer
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Henrik V. Scheller
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
| | - Dominique Loqué
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
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6
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Li G, Jones KC, Eudes A, Pidatala VR, Sun J, Xu F, Zhang C, Wei T, Jain R, Birdseye D, Canlas PE, Baidoo EEK, Duong PQ, Sharma MK, Singh S, Ruan D, Keasling JD, Mortimer JC, Loqué D, Bartley LE, Scheller HV, Ronald PC. Overexpression of a rice BAHD acyltransferase gene in switchgrass (Panicum virgatum L.) enhances saccharification. BMC Biotechnol 2018; 18:54. [PMID: 30180895 PMCID: PMC6123914 DOI: 10.1186/s12896-018-0464-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 08/27/2018] [Indexed: 11/10/2022] Open
Abstract
Background Switchgrass (Panicum virgatum L.) is a promising bioenergy feedstock because it can be grown on marginal land and produces abundant biomass. Recalcitrance of the lignocellulosic components of the switchgrass cell wall to enzymatic degradation into simple sugars impedes efficient biofuel production. We previously demonstrated that overexpression of OsAT10, a BAHD acyltransferase gene, enhances saccharification efficiency in rice. Results Here we show that overexpression of the rice OsAT10 gene in switchgrass decreased the levels of cell wall-bound ferulic acid (FA) in green leaf tissues and to a lesser extent in senesced tissues, and significantly increased levels of cell wall-bound p-coumaric acid (p-CA) in green leaves but decreased its level in senesced tissues of the T0 plants under greenhouse conditions. The engineered switchgrass lines exhibit an approximate 40% increase in saccharification efficiency in green tissues and a 30% increase in senesced tissues. Conclusion Our study demonstrates that overexpression of OsAT10, a rice BAHD acyltransferase gene, enhances saccharification of lignocellulosic biomass in switchgrass. Electronic supplementary material The online version of this article (10.1186/s12896-018-0464-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guotian Li
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Plant Pathology and the Genome Center, University of California, Davis, CA, 95616, USA
| | - Kyle C Jones
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Plant Pathology and the Genome Center, University of California, Davis, CA, 95616, USA
| | - Aymerick Eudes
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | | | - Jian Sun
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Biomass Science and Conversion Technology Department, Sandia National Laboratories, CA94551, Livermore, USA
| | - Feng Xu
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chengcheng Zhang
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Tong Wei
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Plant Pathology and the Genome Center, University of California, Davis, CA, 95616, USA
| | - Rashmi Jain
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Plant Pathology and the Genome Center, University of California, Davis, CA, 95616, USA
| | - Devon Birdseye
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Patrick E Canlas
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA, 95616, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Phat Q Duong
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA, 95616, USA
| | - Manoj K Sharma
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Plant Pathology and the Genome Center, University of California, Davis, CA, 95616, USA.,School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Seema Singh
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Biomass Science and Conversion Technology Department, Sandia National Laboratories, CA94551, Livermore, USA
| | - Deling Ruan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Plant Pathology and the Genome Center, University of California, Davis, CA, 95616, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Bioengineering and Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
| | - Jenny C Mortimer
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Dominique Loqué
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Laura E Bartley
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Henrik V Scheller
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Pamela C Ronald
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Department of Plant Pathology and the Genome Center, University of California, Davis, CA, 95616, USA.
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7
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Zhalnina K, Louie KB, Hao Z, Mansoori N, da Rocha UN, Shi S, Cho H, Karaoz U, Loqué D, Bowen BP, Firestone MK, Northen TR, Brodie EL. Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nat Microbiol 2018. [PMID: 29556109 DOI: 10.1016/b978-0-12-520920-5.50016-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Like all higher organisms, plants have evolved in the context of a microbial world, shaping both their evolution and their contemporary ecology. Interactions between plant roots and soil microorganisms are critical for plant fitness in natural environments. Given this co-evolution and the pivotal importance of plant-microbial interactions, it has been hypothesized, and a growing body of literature suggests, that plants may regulate the composition of their rhizosphere to promote the growth of microorganisms that improve plant fitness in a given ecosystem. Here, using a combination of comparative genomics and exometabolomics, we show that pre-programmed developmental processes in plants (Avena barbata) result in consistent patterns in the chemical composition of root exudates. This chemical succession in the rhizosphere interacts with microbial metabolite substrate preferences that are predictable from genome sequences. Specifically, we observed a preference by rhizosphere bacteria for consumption of aromatic organic acids exuded by plants (nicotinic, shikimic, salicylic, cinnamic and indole-3-acetic). The combination of these plant exudation traits and microbial substrate uptake traits interact to yield the patterns of microbial community assembly observed in the rhizosphere of an annual grass. This discovery provides a mechanistic underpinning for the process of rhizosphere microbial community assembly and provides an attractive direction for the manipulation of the rhizosphere microbiome for beneficial outcomes.
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Affiliation(s)
- Kateryna Zhalnina
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Katherine B Louie
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Zhao Hao
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nasim Mansoori
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Biosystems Engineering Division, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Ulisses Nunes da Rocha
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Shengjing Shi
- Lincoln Science Centre, AgResearch Ltd, Christchurch, New Zealand
| | - Heejung Cho
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Dominique Loqué
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Biosystems Engineering Division, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- INSA de Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Benjamin P Bowen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mary K Firestone
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Eoin L Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
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8
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Eudes A, Berthomieu R, Hao Z, Zhao N, Benites VT, Baidoo EEK, Loqué D. Production of muconic acid in plants. Metab Eng 2018; 46:13-19. [PMID: 29474840 DOI: 10.1016/j.ymben.2018.02.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 01/06/2018] [Accepted: 02/13/2018] [Indexed: 12/16/2022]
Abstract
Muconic acid (MA) is a dicarboxylic acid used for the production of industrially relevant chemicals such as adipic acid, terephthalic acid, and caprolactam. Because the synthesis of these polymer precursors generates toxic intermediates by utilizing petroleum-derived chemicals and corrosive catalysts, the development of alternative strategies for the bio-based production of MA has garnered significant interest. Plants produce organic carbon skeletons by harvesting carbon dioxide and energy from the sun, and therefore represent advantageous hosts for engineered metabolic pathways towards the manufacturing of chemicals. In this work, we engineered Arabidopsis to demonstrate that plants can serve as green factories for the bio-manufacturing of MA. In particular, dual expression of plastid-targeted bacterial salicylate hydroxylase (NahG) and catechol 1,2-dioxygenase (CatA) resulted in the conversion of the endogenous salicylic acid (SA) pool into MA via catechol. Sequential increase of SA derived from the shikimate pathway was achieved by expressing plastid-targeted versions of bacterial salicylate synthase (Irp9) and feedback-resistant 3-deoxy-D-arabino-heptulosonate synthase (AroG). Introducing this SA over-producing strategy into engineered plants that co-express NahG and CatA resulted in a 50-fold increase in MA titers. Considering that MA was easily recovered from senesced plant biomass after harvest, we envision the phytoproduction of MA as a beneficial option to add value to bioenergy crops.
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Affiliation(s)
- Aymerick Eudes
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
| | - Roland Berthomieu
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA; Ecole Polytechnique, Université Paris-Saclay, Palaiseau 91120, France
| | - Zhangying Hao
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Nanxia Zhao
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA; Department of Bioengineering, Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Veronica Teixeira Benites
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Dominique Loqué
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; Université Lyon 1, INSA de Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 rue Raphaël Dubois, F-69622, Villeurbanne, France.
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9
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Yan J, Aznar A, Chalvin C, Birdseye DS, Baidoo EEK, Eudes A, Shih PM, Loqué D, Zhang A, Scheller HV. Increased drought tolerance in plants engineered for low lignin and low xylan content. Biotechnol Biofuels 2018; 11:195. [PMID: 30026810 PMCID: PMC6050699 DOI: 10.1186/s13068-018-1196-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 07/06/2018] [Indexed: 05/08/2023]
Abstract
BACKGROUND We previously developed several strategies to engineer plants to produce cost-efficient biofuels from plant biomass. Engineered Arabidopsis plants with low xylan and lignin content showed normal growth and improved saccharification efficiency under standard growth conditions. However, it remains to be determined whether these engineered plants perform well under drought stress, which is the primary source of abiotic stress in the field. RESULTS Upon exposing engineered Arabidopsis plants to severe drought, we observed better survival rates in those with a low degree of xylan acetylation, low lignin, and low xylan content compared to those in wild-type plants. Increased pectic galactan content had no effect on drought tolerance. The drought-tolerant plants exhibited low water loss from leaves, and drought-responsive genes (RD29A, RD29B, DREB2A) were generally up-regulated under drought stress, which did not occur in the well-watered state. When compared with the wild type, plants with low lignin due to expression of QsuB, a 3-dehydroshikimate dehydratase, showed a stronger response to abscisic acid (ABA) in assays for seed germination and stomatal closure. The low-lignin plants also accumulated more ABA in response to drought than the wild-type plants. On the contrary, the drought tolerance in the engineered plants with low xylan content and low xylan acetylation was not associated with differences in ABA content or response compared to the wild type. Surprisingly, we found a significant increase in galactose levels and sugar released from the low xylan-engineered plants under drought stress. CONCLUSIONS This study shows that plants engineered to accumulate less lignin or xylan are more tolerant to drought and activate drought responses faster than control plants. This is an important finding because it demonstrates that modification of secondary cell walls does not necessarily render the plants less robust in the environment, and it shows that substantial changes in biomass composition can be achieved without compromising plant resilience.
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Affiliation(s)
- Jingwei Yan
- Joint BioEnergy Institute and Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Aude Aznar
- Joint BioEnergy Institute and Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Camille Chalvin
- Joint BioEnergy Institute and Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Ecole Normale Supérieure de Cachan, 94230 Cachan, France
| | - Devon S. Birdseye
- Joint BioEnergy Institute and Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Edward E. K. Baidoo
- Joint BioEnergy Institute and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Aymerick Eudes
- Joint BioEnergy Institute and Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Patrick M. Shih
- Joint BioEnergy Institute and Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Dominique Loqué
- Joint BioEnergy Institute and Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Aying Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Henrik V. Scheller
- Joint BioEnergy Institute and Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720 USA
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10
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Aznar A, Chalvin C, Shih PM, Maimann M, Ebert B, Birdseye DS, Loqué D, Scheller HV. Gene stacking of multiple traits for high yield of fermentable sugars in plant biomass. Biotechnol Biofuels 2018; 11:2. [PMID: 29321811 PMCID: PMC5759196 DOI: 10.1186/s13068-017-1007-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/23/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND Second-generation biofuels produced from biomass can help to decrease dependency on fossil fuels, bringing about many economic and environmental benefits. To make biomass more suitable for biorefinery use, we need a better understanding of plant cell wall biosynthesis. Increasing the ratio of C6 to C5 sugars in the cell wall and decreasing the lignin content are two important targets in engineering of plants that are more suitable for downstream processing for second-generation biofuel production. RESULTS We have studied the basic mechanisms of cell wall biosynthesis and identified genes involved in biosynthesis of pectic galactan, including the GALS1 galactan synthase and the UDP-galactose/UDP-rhamnose transporter URGT1. We have engineered plants with a more suitable biomass composition by applying these findings, in conjunction with synthetic biology and gene stacking tools. Plants were engineered to have up to fourfold more pectic galactan in stems by overexpressing GALS1, URGT1, and UGE2, a UDP-glucose epimerase. Furthermore, the increased galactan trait was engineered into plants that were already engineered to have low xylan content by restricting xylan biosynthesis to vessels where this polysaccharide is essential. Finally, the high galactan and low xylan traits were stacked with the low lignin trait obtained by expressing the QsuB gene encoding dehydroshikimate dehydratase in lignifying cells. CONCLUSION The results show that approaches to increasing C6 sugar content, decreasing xylan, and reducing lignin content can be combined in an additive manner. Thus, the engineered lines obtained by this trait-stacking approach have substantially improved properties from the perspective of biofuel production, and they do not show any obvious negative growth effects. The approach used in this study can be readily transferred to bioenergy crop plants.
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Affiliation(s)
- Aude Aznar
- Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Camille Chalvin
- Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Ecole Normale Supérieure de Cachan, 94230 Cachan, France
| | - Patrick M. Shih
- Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Michael Maimann
- Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Berit Ebert
- Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010 Australia
| | - Devon S. Birdseye
- Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Dominique Loqué
- Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- INSA de Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Claude Bernard Lyon 1, 69622 Villeurbanne, France
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720 USA
| | - Henrik V. Scheller
- Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720 USA
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11
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Liang Y, Richardson S, Yan J, Benites VT, Cheng-Yue C, Tran T, Mortimer J, Mukhopadhyay A, Keasling JD, Scheller HV, Loqué D. Endoribonuclease-Based Two-Component Repressor Systems for Tight Gene Expression Control in Plants. ACS Synth Biol 2017; 6:806-816. [PMID: 28094975 DOI: 10.1021/acssynbio.6b00295] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Tight control and multifactorial regulation of gene expression are important challenges in genetic engineering and are critical for the development of regulatory circuits. Meeting these challenges will facilitate transgene expression regulation and support the fine-tuning of metabolic pathways to avoid the accumulation of undesired intermediates. By employing the endoribonuclease Csy4 and its recognition sequence from Pseudomonas aeruginosa and manipulating 5'UTR of mRNA, we developed a two-component expression-repression system to tightly control synthesis of transgene products. We demonstrated that this regulatory device was functional in monocotyledonous and dicotyledonous plant species, and showed that it can be used to repress transgene expression by >400-fold and to synchronize transgene repression. In addition to tissue-specific transgene repression, this system offers stimuli-dependent expression control. Using a bioinformatics approach, we identified 54 orthologous systems from various bacteria, and then validated in planta the activity for a few of those systems, demonstrating the potential diversity of such a two-component repressor system.
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Affiliation(s)
- Yan Liang
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis Street, 4th Floor, Emeryville, California 94608, United States
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Sarah Richardson
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis Street, 4th Floor, Emeryville, California 94608, United States
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Jingwei Yan
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis Street, 4th Floor, Emeryville, California 94608, United States
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Veronica T. Benites
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis Street, 4th Floor, Emeryville, California 94608, United States
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Clarabelle Cheng-Yue
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis Street, 4th Floor, Emeryville, California 94608, United States
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Thu Tran
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis Street, 4th Floor, Emeryville, California 94608, United States
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Jenny Mortimer
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis Street, 4th Floor, Emeryville, California 94608, United States
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis Street, 4th Floor, Emeryville, California 94608, United States
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis Street, 4th Floor, Emeryville, California 94608, United States
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Henrik V. Scheller
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis Street, 4th Floor, Emeryville, California 94608, United States
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Dominique Loqué
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis Street, 4th Floor, Emeryville, California 94608, United States
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
- INSA de Lyon, CNRS, UMR5240, Microbiologie,
Adaptation et Pathogénie, Université Claude Bernard Lyon 1, 10 rue Raphaël Dubois, F-69622, Villeurbanne, France
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12
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Eudes A, Mouille M, Robinson DS, Benites VT, Wang G, Roux L, Tsai YL, Baidoo EEK, Chiu TY, Heazlewood JL, Scheller HV, Mukhopadhyay A, Keasling JD, Deutsch S, Loqué D. Exploiting members of the BAHD acyltransferase family to synthesize multiple hydroxycinnamate and benzoate conjugates in yeast. Microb Cell Fact 2016; 15:198. [PMID: 27871334 PMCID: PMC5117604 DOI: 10.1186/s12934-016-0593-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/06/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND BAHD acyltransferases, named after the first four biochemically characterized enzymes of the group, are plant-specific enzymes that catalyze the transfer of coenzyme A-activated donors onto various acceptor molecules. They are responsible for the synthesis in plants of a myriad of secondary metabolites, some of which are beneficial for humans either as therapeutics or as specialty chemicals such as flavors and fragrances. The production of pharmaceutical, nutraceutical and commodity chemicals using engineered microbes is an alternative, green route to energy-intensive chemical syntheses that consume petroleum-based precursors. However, identification of appropriate enzymes and validation of their functional expression in heterologous hosts is a prerequisite for the design and implementation of metabolic pathways in microbes for the synthesis of such target chemicals. RESULTS For the synthesis of valuable metabolites in the yeast Saccharomyces cerevisiae, we selected BAHD acyltransferases based on their preferred donor and acceptor substrates. In particular, BAHDs that use hydroxycinnamoyl-CoAs and/or benzoyl-CoA as donors were targeted because a large number of molecules beneficial to humans belong to this family of hydroxycinnamate and benzoate conjugates. The selected BAHD coding sequences were synthesized and cloned individually on a vector containing the Arabidopsis gene At4CL5, which encodes a promiscuous 4-coumarate:CoA ligase active on hydroxycinnamates and benzoates. The various S. cerevisiae strains obtained for co-expression of At4CL5 with the different BAHDs effectively produced a wide array of valuable hydroxycinnamate and benzoate conjugates upon addition of adequate combinations of donors and acceptor molecules. In particular, we report here for the first time the production in yeast of rosmarinic acid and its derivatives, quinate hydroxycinnamate esters such as chlorogenic acid, and glycerol hydroxycinnamate esters. Similarly, we achieved for the first time the microbial production of polyamine hydroxycinnamate amides; monolignol, malate and fatty alcohol hydroxycinnamate esters; tropane alkaloids; and benzoate/caffeate alcohol esters. In some instances, the additional expression of Flavobacterium johnsoniae tyrosine ammonia-lyase (FjTAL) allowed the synthesis of p-coumarate conjugates and eliminated the need to supplement the culture media with 4-hydroxycinnamate. CONCLUSION We demonstrate in this study the effectiveness of expressing members of the plant BAHD acyltransferase family in yeast for the synthesis of numerous valuable hydroxycinnamate and benzoate conjugates.
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Affiliation(s)
- Aymerick Eudes
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St., 4th Floor, Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Maxence Mouille
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St., 4th Floor, Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | | | - Veronica T Benites
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St., 4th Floor, Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Graduate Program, San Francisco State University, San Francisco, CA, 94132, USA
| | - George Wang
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St., 4th Floor, Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Lucien Roux
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St., 4th Floor, Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Master Program, Ecole Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Yi-Lin Tsai
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St., 4th Floor, Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St., 4th Floor, Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Tsan-Yu Chiu
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St., 4th Floor, Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Joshua L Heazlewood
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St., 4th Floor, Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Henrik V Scheller
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St., 4th Floor, Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St., 4th Floor, Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St., 4th Floor, Emeryville, CA, 94608, USA.,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,Department of Chemical & Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle´, 2970, Hørsholm, Denmark
| | | | - Dominique Loqué
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St., 4th Floor, Emeryville, CA, 94608, USA. .,Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA. .,CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Claude Bernard Lyon 1, INSA de Lyon, 10 rue Raphaël Dubois, 69622, Villeurbanne, France.
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13
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Eudes A, Zhao N, Sathitsuksanoh N, Baidoo EEK, Lao J, Wang G, Yogiswara S, Lee TS, Singh S, Mortimer JC, Keasling JD, Simmons BA, Loqué D. Expression of S-adenosylmethionine Hydrolase in Tissues Synthesizing Secondary Cell Walls Alters Specific Methylated Cell Wall Fractions and Improves Biomass Digestibility. Front Bioeng Biotechnol 2016; 4:58. [PMID: 27486577 PMCID: PMC4949269 DOI: 10.3389/fbioe.2016.00058] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 06/23/2016] [Indexed: 11/21/2022] Open
Abstract
Plant biomass is a large source of fermentable sugars for the synthesis of bioproducts using engineered microbes. These sugars are stored as cell wall polymers, mainly cellulose and hemicellulose, and are embedded with lignin, which makes their enzymatic hydrolysis challenging. One of the strategies to reduce cell wall recalcitrance is the modification of lignin content and composition. Lignin is a phenolic polymer of methylated aromatic alcohols and its synthesis in tissues developing secondary cell walls is a significant sink for the consumption of the methyl donor S-adenosylmethionine (AdoMet). In this study, we demonstrate in Arabidopsis stems that targeted expression of AdoMet hydrolase (AdoMetase, E.C. 3.3.1.2) in secondary cell wall synthesizing tissues reduces the AdoMet pool and impacts lignin content and composition. In particular, both NMR analysis and pyrolysis gas chromatography mass spectrometry of lignin in engineered biomass showed relative enrichment of non-methylated p-hydroxycinnamyl (H) units and a reduction of dimethylated syringyl (S) units. This indicates a lower degree of methylation compared to that in wild-type lignin. Quantification of cell wall-bound hydroxycinnamates revealed a reduction of ferulate in AdoMetase transgenic lines. Biomass from transgenic lines, in contrast to that in control plants, exhibits an enrichment of glucose content and a reduction in the degree of hemicellulose glucuronoxylan methylation. We also show that these modifications resulted in a reduction of cell wall recalcitrance, because sugar yield generated by enzymatic biomass saccharification was greater than that of wild-type plants. Considering that transgenic plants show no important diminution of biomass yields, and that heterologous expression of AdoMetase protein can be spatiotemporally optimized, this novel approach provides a valuable option for the improvement of lignocellulosic biomass feedstock.
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Affiliation(s)
- Aymerick Eudes
- Joint BioEnergy Institute, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nanxia Zhao
- Joint BioEnergy Institute, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Bioengineering, University of California, Berkeley, CA, USA; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Noppadon Sathitsuksanoh
- Joint BioEnergy Institute, Emeryville, CA, USA; Department of Bioengineering, University of California, Berkeley, CA, USA; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, USA; Department of Chemical Engineering, Conn Center for Renewable Energy, University of Louisville, Louisville, KY, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeemeng Lao
- Joint BioEnergy Institute, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - George Wang
- Joint BioEnergy Institute, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sasha Yogiswara
- Joint BioEnergy Institute, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Bioengineering, University of California, Berkeley, CA, USA; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Taek Soon Lee
- Joint BioEnergy Institute, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Seema Singh
- Joint BioEnergy Institute, Emeryville, CA, USA; Sandia National Laboratory, Livermore, CA, USA
| | - Jenny C Mortimer
- Joint BioEnergy Institute, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Bioengineering, University of California, Berkeley, CA, USA; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Sandia National Laboratory, Livermore, CA, USA
| | - Dominique Loqué
- Joint BioEnergy Institute, Emeryville, CA, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Université Claude Bernard Lyon 1, INSA de Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
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14
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Shih PM, Liang Y, Loqué D. Biotechnology and synthetic biology approaches for metabolic engineering of bioenergy crops. Plant J 2016; 87:103-17. [PMID: 27030440 DOI: 10.1111/tpj.13176] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 03/18/2016] [Accepted: 03/22/2016] [Indexed: 05/26/2023]
Abstract
The Green Revolution has fuelled an exponential growth in human population since the mid-20th century. Due to population growth, food and energy demands will soon surpass supply capabilities. To overcome these impending problems, significant improvements in genetic engineering will be needed to complement breeding efforts in order to accelerate the improvement of agronomical traits. The new field of plant synthetic biology has emerged in recent years and is expected to support rapid, precise, and robust engineering of plants. In this review, we present recent advances made in the field of plant synthetic biology, specifically in genome editing, transgene expression regulation, and bioenergy crop engineering, with a focus on traits related to lignocellulose, oil, and soluble sugars. Ultimately, progress and innovation in these fields may facilitate the development of beneficial traits in crop plants to meet society's bioenergy needs.
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Affiliation(s)
- Patrick M Shih
- Joint BioEnergy Institute, Emery Station East, 5885 Hollis St, 4th Floor, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Yan Liang
- Joint BioEnergy Institute, Emery Station East, 5885 Hollis St, 4th Floor, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Dominique Loqué
- Joint BioEnergy Institute, Emery Station East, 5885 Hollis St, 4th Floor, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Université Lyon 1, INSA de Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 rue Raphaël Dubois, F-69622, Villeurbanne, France
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15
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Eudes A, Pereira JH, Yogiswara S, Wang G, Teixeira Benites V, Baidoo EEK, Lee TS, Adams PD, Keasling JD, Loqué D. Exploiting the Substrate Promiscuity of Hydroxycinnamoyl-CoA:Shikimate Hydroxycinnamoyl Transferase to Reduce Lignin. Plant Cell Physiol 2016; 57:568-79. [PMID: 26858288 PMCID: PMC4790474 DOI: 10.1093/pcp/pcw016] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 01/13/2016] [Indexed: 05/19/2023]
Abstract
Lignin poses a major challenge in the processing of plant biomass for agro-industrial applications. For bioengineering purposes, there is a pressing interest in identifying and characterizing the enzymes responsible for the biosynthesis of lignin. Hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyl transferase (HCT; EC 2.3.1.133) is a key metabolic entry point for the synthesis of the most important lignin monomers: coniferyl and sinapyl alcohols. In this study, we investigated the substrate promiscuity of HCT from a bryophyte (Physcomitrella) and from five representatives of vascular plants (Arabidopsis, poplar, switchgrass, pine and Selaginella) using a yeast expression system. We demonstrate for these HCTs a conserved capacity to acylate with p-coumaroyl-CoA several phenolic compounds in addition to the canonical acceptor shikimate normally used during lignin biosynthesis. Using either recombinant HCT from switchgrass (PvHCT2a) or an Arabidopsis stem protein extract, we show evidence of the inhibitory effect of these phenolics on the synthesis of p-coumaroyl shikimate in vitro, which presumably occurs via a mechanism of competitive inhibition. A structural study of PvHCT2a confirmed the binding of a non-canonical acceptor in a similar manner to shikimate in the active site of the enzyme. Finally, we exploited in Arabidopsis the substrate flexibility of HCT to reduce lignin content and improve biomass saccharification by engineering transgenic lines that overproduce one of the HCT non-canonical acceptors. Our results demonstrate conservation of HCT substrate promiscuity and provide support for a new strategy for lignin reduction in the effort to improve the quality of plant biomass for forage and cellulosic biofuels.
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Affiliation(s)
- Aymerick Eudes
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Jose H Pereira
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Sasha Yogiswara
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA Department of Bioengineering & Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - George Wang
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Veronica Teixeira Benites
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA Graduate Program, San Francisco State University, San Francisco, CA 94132, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Taek Soon Lee
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Paul D Adams
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA Department of Bioengineering & Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Dominique Loqué
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
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16
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Eudes A, Sathitsuksanoh N, Baidoo EEK, George A, Liang Y, Yang F, Singh S, Keasling JD, Simmons BA, Loqué D. Expression of a bacterial 3-dehydroshikimate dehydratase reduces lignin content and improves biomass saccharification efficiency. Plant Biotechnol J 2015; 13:1241-50. [PMID: 25583257 PMCID: PMC6680230 DOI: 10.1111/pbi.12310] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 11/03/2014] [Accepted: 11/04/2014] [Indexed: 05/18/2023]
Abstract
Lignin confers recalcitrance to plant biomass used as feedstocks in agro-processing industries or as source of renewable sugars for the production of bioproducts. The metabolic steps for the synthesis of lignin building blocks belong to the shikimate and phenylpropanoid pathways. Genetic engineering efforts to reduce lignin content typically employ gene knockout or gene silencing techniques to constitutively repress one of these metabolic pathways. Recently, new strategies have emerged offering better spatiotemporal control of lignin deposition, including the expression of enzymes that interfere with the normal process for cell wall lignification. In this study, we report that expression of a 3-dehydroshikimate dehydratase (QsuB from Corynebacterium glutamicum) reduces lignin deposition in Arabidopsis cell walls. QsuB was targeted to the plastids to convert 3-dehydroshikimate - an intermediate of the shikimate pathway - into protocatechuate. Compared to wild-type plants, lines expressing QsuB contain higher amounts of protocatechuate, p-coumarate, p-coumaraldehyde and p-coumaryl alcohol, and lower amounts of coniferaldehyde, coniferyl alcohol, sinapaldehyde and sinapyl alcohol. 2D-NMR spectroscopy and pyrolysis-gas chromatography/mass spectrometry (pyro-GC/MS) reveal an increase of p-hydroxyphenyl units and a reduction of guaiacyl units in the lignin of QsuB lines. Size-exclusion chromatography indicates a lower degree of lignin polymerization in the transgenic lines. Therefore, our data show that the expression of QsuB primarily affects the lignin biosynthetic pathway. Finally, biomass from these lines exhibits more than a twofold improvement in saccharification efficiency. We conclude that the expression of QsuB in plants, in combination with specific promoters, is a promising gain-of-function strategy for spatiotemporal reduction of lignin in plant biomass.
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Affiliation(s)
- Aymerick Eudes
- Joint BioEnergy Institute, Emeryville, CA, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Noppadon Sathitsuksanoh
- Joint BioEnergy Institute, Emeryville, CA, USA
- Sandia National Laboratory, Livermore, CA, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, Emeryville, CA, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Anthe George
- Joint BioEnergy Institute, Emeryville, CA, USA
- Sandia National Laboratory, Livermore, CA, USA
| | - Yan Liang
- Joint BioEnergy Institute, Emeryville, CA, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Fan Yang
- Joint BioEnergy Institute, Emeryville, CA, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Seema Singh
- Joint BioEnergy Institute, Emeryville, CA, USA
- Sandia National Laboratory, Livermore, CA, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, Emeryville, CA, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA, USA
- Sandia National Laboratory, Livermore, CA, USA
| | - Dominique Loqué
- Joint BioEnergy Institute, Emeryville, CA, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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17
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Deng K, Guenther JM, Gao J, Bowen BP, Tran H, Reyes-Ortiz V, Cheng X, Sathitsuksanoh N, Heins R, Takasuka TE, Bergeman LF, Geertz-Hansen H, Deutsch S, Loqué D, Sale KL, Simmons BA, Adams PD, Singh AK, Fox BG, Northen TR. Development of a High Throughput Platform for Screening Glycoside Hydrolases Based on Oxime-NIMS. Front Bioeng Biotechnol 2015; 3:153. [PMID: 26528471 PMCID: PMC4603251 DOI: 10.3389/fbioe.2015.00153] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 09/21/2015] [Indexed: 12/26/2022] Open
Abstract
Cost-effective hydrolysis of biomass into sugars for biofuel production requires high-performance low-cost glycoside hydrolase (GH) cocktails that are active under demanding process conditions. Improving the performance of GH cocktails depends on knowledge of many critical parameters, including individual enzyme stabilities, optimal reaction conditions, kinetics, and specificity of reaction. With this information, rate- and/or yield-limiting reactions can be potentially improved through substitution, synergistic complementation, or protein engineering. Given the wide range of substrates and methods used for GH characterization, it is difficult to compare results across a myriad of approaches to identify high performance and synergistic combinations of enzymes. Here, we describe a platform for systematic screening of GH activities using automatic biomass handling, bioconjugate chemistry, robotic liquid handling, and nanostructure-initiator mass spectrometry (NIMS). Twelve well-characterized substrates spanning the types of glycosidic linkages found in plant cell walls are included in the experimental workflow. To test the application of this platform and substrate panel, we studied the reactivity of three engineered cellulases and their synergy of combination across a range of reaction conditions and enzyme concentrations. We anticipate that large-scale screening using the standardized platform and substrates will generate critical datasets to enable direct comparison of enzyme activities for cocktail design.
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Affiliation(s)
- Kai Deng
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Sandia National Laboratories , Livermore, CA , USA
| | - Joel M Guenther
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Sandia National Laboratories , Livermore, CA , USA
| | - Jian Gao
- Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | | | - Huu Tran
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Sandia National Laboratories , Livermore, CA , USA
| | - Vimalier Reyes-Ortiz
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Xiaoliang Cheng
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Noppadon Sathitsuksanoh
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Richard Heins
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Sandia National Laboratories , Livermore, CA , USA
| | - Taichi E Takasuka
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin , Madison, WI , USA
| | - Lai F Bergeman
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin , Madison, WI , USA
| | | | - Samuel Deutsch
- Lawrence Berkeley National Laboratory , Berkeley, CA , USA ; Joint Genome Institute , Walnut Creek, CA , USA
| | - Dominique Loqué
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Kenneth L Sale
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Sandia National Laboratories , Livermore, CA , USA
| | - Blake A Simmons
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Sandia National Laboratories , Livermore, CA , USA
| | - Paul D Adams
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Lawrence Berkeley National Laboratory , Berkeley, CA , USA ; Department of Bioengineering, University of California Berkeley , Berkeley, CA , USA
| | - Anup K Singh
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Sandia National Laboratories , Livermore, CA , USA
| | - Brian G Fox
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin , Madison, WI , USA ; Department of Biochemistry, University of Wisconsin , Madison, WI , USA
| | - Trent R Northen
- US Department of Energy Joint BioEnergy Institute , Emeryville, CA , USA ; Lawrence Berkeley National Laboratory , Berkeley, CA , USA
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18
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Eudes A, Teixeira Benites V, Wang G, Baidoo EEK, Lee TS, Keasling JD, Loqué D. Precursor-Directed Combinatorial Biosynthesis of Cinnamoyl, Dihydrocinnamoyl, and Benzoyl Anthranilates in Saccharomyces cerevisiae. PLoS One 2015; 10:e0138972. [PMID: 26430899 PMCID: PMC4591981 DOI: 10.1371/journal.pone.0138972] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 09/07/2015] [Indexed: 01/23/2023] Open
Abstract
Biological synthesis of pharmaceuticals and biochemicals offers an environmentally friendly alternative to conventional chemical synthesis. These alternative methods require the design of metabolic pathways and the identification of enzymes exhibiting adequate activities. Cinnamoyl, dihydrocinnamoyl, and benzoyl anthranilates are natural metabolites which possess beneficial activities for human health, and the search is expanding for novel derivatives that might have enhanced biological activity. For example, biosynthesis in Dianthus caryophyllus is catalyzed by hydroxycinnamoyl/benzoyl-CoA:anthranilate N-hydroxycinnamoyl/ benzoyltransferase (HCBT), which couples hydroxycinnamoyl-CoAs and benzoyl-CoAs to anthranilate. We recently demonstrated the potential of using yeast (Saccharomyces cerevisiae) for the biological production of a few cinnamoyl anthranilates by heterologous co-expression of 4-coumaroyl:CoA ligase from Arabidopsis thaliana (4CL5) and HCBT. Here we report that, by exploiting the substrate flexibility of both 4CL5 and HCBT, we achieved rapid biosynthesis of more than 160 cinnamoyl, dihydrocinnamoyl, and benzoyl anthranilates in yeast upon feeding with both natural and non-natural cinnamates, dihydrocinnamates, benzoates, and anthranilates. Our results demonstrate the use of enzyme promiscuity in biological synthesis to achieve high chemical diversity within a defined class of molecules. This work also points to the potential for the combinatorial biosynthesis of diverse and valuable cinnamoylated, dihydrocinnamoylated, and benzoylated products by using the versatile biological enzyme 4CL5 along with characterized cinnamoyl-CoA- and benzoyl-CoA-utilizing transferases.
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Affiliation(s)
- Aymerick Eudes
- Joint BioEnergy Institute, Emery Station East, 5885 Hollis St, 4 Floor, Emeryville, California, 94608, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, United States of America
| | - Veronica Teixeira Benites
- Joint BioEnergy Institute, Emery Station East, 5885 Hollis St, 4 Floor, Emeryville, California, 94608, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, United States of America
- Graduate Program, San Francisco State University, San Francisco, California, 94132, United States of America
| | - George Wang
- Joint BioEnergy Institute, Emery Station East, 5885 Hollis St, 4 Floor, Emeryville, California, 94608, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, United States of America
| | - Edward E. K. Baidoo
- Joint BioEnergy Institute, Emery Station East, 5885 Hollis St, 4 Floor, Emeryville, California, 94608, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, United States of America
| | - Taek Soon Lee
- Joint BioEnergy Institute, Emery Station East, 5885 Hollis St, 4 Floor, Emeryville, California, 94608, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, United States of America
| | - Jay D. Keasling
- Joint BioEnergy Institute, Emery Station East, 5885 Hollis St, 4 Floor, Emeryville, California, 94608, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, United States of America
- Department of Bioengineering & Department of Chemical & Biomolecular Engineering, University of California, Berkeley, California, 94720, United States of America
| | - Dominique Loqué
- Joint BioEnergy Institute, Emery Station East, 5885 Hollis St, 4 Floor, Emeryville, California, 94608, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, United States of America
- * E-mail:
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19
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Patron NJ, Orzaez D, Marillonnet S, Warzecha H, Matthewman C, Youles M, Raitskin O, Leveau A, Farré G, Rogers C, Smith A, Hibberd J, Webb AAR, Locke J, Schornack S, Ajioka J, Baulcombe DC, Zipfel C, Kamoun S, Jones JDG, Kuhn H, Robatzek S, Van Esse HP, Sanders D, Oldroyd G, Martin C, Field R, O'Connor S, Fox S, Wulff B, Miller B, Breakspear A, Radhakrishnan G, Delaux PM, Loqué D, Granell A, Tissier A, Shih P, Brutnell TP, Quick WP, Rischer H, Fraser PD, Aharoni A, Raines C, South PF, Ané JM, Hamberger BR, Langdale J, Stougaard J, Bouwmeester H, Udvardi M, Murray JAH, Ntoukakis V, Schäfer P, Denby K, Edwards KJ, Osbourn A, Haseloff J. Standards for plant synthetic biology: a common syntax for exchange of DNA parts. New Phytol 2015; 208:13-9. [PMID: 26171760 DOI: 10.1111/nph.13532] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Inventors in the field of mechanical and electronic engineering can access multitudes of components and, thanks to standardization, parts from different manufacturers can be used in combination with each other. The introduction of BioBrick standards for the assembly of characterized DNA sequences was a landmark in microbial engineering, shaping the field of synthetic biology. Here, we describe a standard for Type IIS restriction endonuclease-mediated assembly, defining a common syntax of 12 fusion sites to enable the facile assembly of eukaryotic transcriptional units. This standard has been developed and agreed by representatives and leaders of the international plant science and synthetic biology communities, including inventors, developers and adopters of Type IIS cloning methods. Our vision is of an extensive catalogue of standardized, characterized DNA parts that will accelerate plant bioengineering.
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Affiliation(s)
- Nicola J Patron
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7RG, UK
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Avda Tarongers SN, Valencia, Spain
| | | | - Heribert Warzecha
- Plant Biotechnology and Metabolic Engineering, Technische Universität Darmstadt, Schnittspahnstrasse 4, Darmstadt 64287, Germany
| | - Colette Matthewman
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Mark Youles
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7RG, UK
| | - Oleg Raitskin
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7RG, UK
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
| | - Aymeric Leveau
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Gemma Farré
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Christian Rogers
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Alison Smith
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Julian Hibberd
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Alex A R Webb
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - James Locke
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge, CB2 1LR, UK
| | - Sebastian Schornack
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The Sainsbury Laboratory, Cambridge University, Bateman Street, Cambridge, CB2 1LR, UK
| | - Jim Ajioka
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - David C Baulcombe
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Cyril Zipfel
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7RG, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7RG, UK
| | | | - Hannah Kuhn
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7RG, UK
| | - Silke Robatzek
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7RG, UK
| | - H Peter Van Esse
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7RG, UK
| | - Dale Sanders
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Giles Oldroyd
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Cathie Martin
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Rob Field
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sarah O'Connor
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Samantha Fox
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Brande Wulff
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ben Miller
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Andy Breakspear
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | | | - Dominique Loqué
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA, 94608, USA
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Avda Tarongers SN, Valencia, Spain
| | - Alain Tissier
- Leibniz-Institut für Pflanzenbiochemie, Weinberg 3, 06120, Halle (Saale), Germany
| | - Patrick Shih
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | | | - W Paul Quick
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Heiko Rischer
- VTT Technical Research Centre of Finland, Espoo 02044, Finland
| | - Paul D Fraser
- School of Biological Sciences, Royal Holloway, University of London, Egham Hill, Egham, TW20 0EX, UK
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Christine Raines
- School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, UK
| | - Paul F South
- United States Department of Agriculture, Global Change and Photosynthesis Research Unit, ARS 1206 West Gregory Drive, Urbana, IL 61801, USA
| | - Jean-Michel Ané
- Departments of Bacteriology and Agronomy, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706, USA
| | - Björn R Hamberger
- Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark
| | - Jane Langdale
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Jens Stougaard
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, Aarhus, Denmark
| | - Harro Bouwmeester
- Wageningen UR, Wageningen University, Wageningen 6700 AA, the Netherlands
| | - Michael Udvardi
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - James A H Murray
- School of Biosciences, Sir Martin Evans Building, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Vardis Ntoukakis
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Patrick Schäfer
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Katherine Denby
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Keith J Edwards
- BrisSynBio, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Anne Osbourn
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Jim Haseloff
- OpenPlant Consortium: The University of Cambridge, The John Innes Centre and The Sainsbury Laboratory, Norwich, NR4 7UH, UK
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
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20
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Vega-Sánchez ME, Loqué D, Lao J, Catena M, Verhertbruggen Y, Herter T, Yang F, Harholt J, Ebert B, Baidoo EEK, Keasling JD, Scheller HV, Heazlewood JL, Ronald PC. Engineering temporal accumulation of a low recalcitrance polysaccharide leads to increased C6 sugar content in plant cell walls. Plant Biotechnol J 2015; 13:903-14. [PMID: 25586315 DOI: 10.1111/pbi.12326] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 11/11/2014] [Accepted: 12/10/2014] [Indexed: 05/10/2023]
Abstract
Reduced cell wall recalcitrance and increased C6 monosaccharide content are desirable traits for future biofuel crops, as long as these biomass modifications do not significantly alter normal growth and development. Mixed-linkage glucan (MLG), a cell wall polysaccharide only present in grasses and related species among flowering plants, is comprised of glucose monomers linked by both β-1,3 and β-1,4 bonds. Previous data have shown that constitutive production of MLG in barley (Hordeum vulgare) severely compromises growth and development. Here, we used spatio-temporal strategies to engineer Arabidopsis thaliana plants to accumulate significant amounts of MLG in the cell wall by expressing the rice CslF6 MLG synthase using secondary cell wall and senescence-associated promoters. Results using secondary wall promoters were suboptimal. When the rice MLG synthase was expressed under the control of a senescence-associated promoter, we obtained up to four times more glucose in the matrix cell wall fraction and up to a 42% increase in saccharification compared to control lines. Importantly, these plants grew and developed normally. The induction of MLG deposition at senescence correlated with an increase of gluconic acid in cell wall extracts of transgenic plants in contrast to the other approaches presented in this study. MLG produced in Arabidopsis has an altered structure compared to the grass glucan, which likely affects its solubility, while its molecular size is unaffected. The induction of cell wall polysaccharide biosynthesis in senescing tissues offers a novel engineering alternative to enhance cell wall properties of lignocellulosic biofuel crops.
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Affiliation(s)
- Miguel E Vega-Sánchez
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Dominique Loqué
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeemeng Lao
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michela Catena
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yves Verhertbruggen
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Thomas Herter
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Fan Yang
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jesper Harholt
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Berit Ebert
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Edward E K Baidoo
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jay D Keasling
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Chemical and Biomolecular Engineering, and Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Henrik V Scheller
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Joshua L Heazlewood
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Pamela C Ronald
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA, USA
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21
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Gonzalez TL, Liang Y, Nguyen BN, Staskawicz BJ, Loqué D, Hammond MC. Tight regulation of plant immune responses by combining promoter and suicide exon elements. Nucleic Acids Res 2015; 43:7152-61. [PMID: 26138488 PMCID: PMC4538838 DOI: 10.1093/nar/gkv655] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 06/12/2015] [Accepted: 06/16/2015] [Indexed: 11/20/2022] Open
Abstract
Effector-triggered immunity (ETI) is activated when plant disease resistance (R) proteins recognize the presence of pathogen effector proteins delivered into host cells. The ETI response generally encompasses a defensive 'hypersensitive response' (HR) that involves programmed cell death at the site of pathogen recognition. While many R protein and effector protein pairs are known to trigger HR, other components of the ETI signaling pathway remain elusive. Effector genes regulated by inducible promoters cause background HR due to leaky protein expression, preventing the generation of relevant transgenic plant lines. By employing the HyP5SM suicide exon, we have developed a strategy to tightly regulate effector proteins such that HR is chemically inducible and non-leaky. This alternative splicing-based gene regulation system was shown to successfully control Bs2/AvrBs2-dependent and RPP1/ATR1Δ51-dependent HR in Nicotiana benthamiana and Nicotiana tabacum, respectively. It was also used to generate viable and healthy transgenic Arabidopsis thaliana plants that inducibly initiate HR. Beyond enabling studies on the ETI pathway, our regulatory strategy is generally applicable to reduce or eliminate undesired background expression of transgenes.
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Affiliation(s)
- Tania L Gonzalez
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Yan Liang
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA 94608, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Bao N Nguyen
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Brian J Staskawicz
- Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Dominique Loqué
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA 94608, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ming C Hammond
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA Department of Chemistry, University of California, Berkeley, CA 94720, USA
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22
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Loqué D, Scheller HV, Pauly M. Engineering of plant cell walls for enhanced biofuel production. Curr Opin Plant Biol 2015; 25:151-61. [PMID: 26051036 DOI: 10.1016/j.pbi.2015.05.018] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 05/07/2015] [Accepted: 05/16/2015] [Indexed: 05/17/2023]
Abstract
The biomass of plants consists predominately of cell walls, a sophisticated composite material composed of various polymer networks including numerous polysaccharides and the polyphenol lignin. In order to utilize this renewable, highly abundant resource for the production of commodity chemicals such as biofuels, major hurdles have to be surpassed to reach economical viability. Recently, major advances in the basic understanding of the synthesis of the various wall polymers and its regulation has enabled strategies to alter the qualitative composition of wall materials. Such emerging strategies include a reduction/alteration of the lignin network to enhance polysaccharide accessibility, reduction of polymer derived processing inhibitors, and increases in polysaccharides with a high hexose/pentose ratio.
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Affiliation(s)
- Dominique Loqué
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94702, USA
| | - Henrik V Scheller
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94702, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94702, USA
| | - Markus Pauly
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94702, USA.
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23
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De Michele R, Ast C, Loqué D, Ho CH, Andrade SLA, Lanquar V, Grossmann G, Gehne S, Kumke MU, Frommer WB. Correction: Fluorescent sensors reporting the activity of ammonium transceptors in live cells. eLife 2015; 4. [PMID: 25692497 PMCID: PMC4337722 DOI: 10.7554/elife.06986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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24
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Gondolf VM, Stoppel R, Ebert B, Rautengarten C, Liwanag AJM, Loqué D, Scheller HV. A gene stacking approach leads to engineered plants with highly increased galactan levels in Arabidopsis. BMC Plant Biol 2014; 14:344. [PMID: 25492673 PMCID: PMC4268804 DOI: 10.1186/s12870-014-0344-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 11/20/2014] [Indexed: 05/17/2023]
Abstract
BACKGROUND Engineering of plants with a composition of lignocellulosic biomass that is more suitable for downstream processing is of high interest for next-generation biofuel production. Lignocellulosic biomass contains a high proportion of pentose residues, which are more difficult to convert into fuels than hexoses. Therefore, increasing the hexose/pentose ratio in biomass is one approach for biomass improvement. A genetic engineering approach was used to investigate whether the amount of pectic galactan can be specifically increased in cell walls of Arabidopsis fiber cells, which in turn could provide a potential source of readily fermentable galactose. RESULTS First it was tested if overexpression of various plant UDP-glucose 4-epimerases (UGEs) could increase the availability of UDP-galactose and thereby increase the biosynthesis of galactan. Constitutive and tissue-specific expression of a poplar UGE and three Arabidopsis UGEs in Arabidopsis plants could not significantly increase the amount of cell wall bound galactose. We then investigated co-overexpression of AtUGE2 together with the β-1,4-galactan synthase GalS1. Co-overexpression of AtUGE2 and GalS1 led to over 80% increase in cell wall galactose levels in Arabidopsis stems, providing evidence that these proteins work synergistically. Furthermore, AtUGE2 and GalS1 overexpression in combination with overexpression of the NST1 master regulator for secondary cell wall biosynthesis resulted in increased thickness of fiber cell walls in addition to the high cell wall galactose levels. Immunofluorescence microscopy confirmed that the increased galactose was present as β-1,4-galactan in secondary cell walls. CONCLUSIONS This approach clearly indicates that simultaneous overexpression of AtUGE2 and GalS1 increases the cell wall galactose to much higher levels than can be achieved by overexpressing either one of these proteins alone. Moreover, the increased galactan content in fiber cells while improving the biomass composition had no impact on plant growth and development and hence on the overall biomass amount. Thus, we could show that the gene stacking approach described here is a promising method to engineer advanced feedstocks for biofuel production.
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Affiliation(s)
- Vibe M Gondolf
- />Feedstocks Division, Joint BioEnergy Institute, Emeryville, California 94608 USA
- />Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 USA
- />Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Rhea Stoppel
- />Feedstocks Division, Joint BioEnergy Institute, Emeryville, California 94608 USA
- />Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 USA
| | - Berit Ebert
- />Feedstocks Division, Joint BioEnergy Institute, Emeryville, California 94608 USA
- />Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 USA
- />Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Carsten Rautengarten
- />Feedstocks Division, Joint BioEnergy Institute, Emeryville, California 94608 USA
- />Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 USA
| | - April JM Liwanag
- />Feedstocks Division, Joint BioEnergy Institute, Emeryville, California 94608 USA
- />Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 USA
| | - Dominique Loqué
- />Feedstocks Division, Joint BioEnergy Institute, Emeryville, California 94608 USA
- />Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 USA
| | - Henrik V Scheller
- />Feedstocks Division, Joint BioEnergy Institute, Emeryville, California 94608 USA
- />Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 USA
- />Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 USA
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25
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Lao J, Oikawa A, Bromley JR, McInerney P, Suttangkakul A, Smith-Moritz AM, Plahar H, Chiu TY, González Fernández-Niño SM, Ebert B, Yang F, Christiansen KM, Hansen SF, Stonebloom S, Adams PD, Ronald PC, Hillson NJ, Hadi MZ, Vega-Sánchez ME, Loqué D, Scheller HV, Heazlewood JL. The plant glycosyltransferase clone collection for functional genomics. Plant J 2014. [PMID: 24905498 DOI: 10.1111/tpj.12577/0960-7412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The glycosyltransferases (GTs) are an important and functionally diverse family of enzymes involved in glycan and glycoside biosynthesis. Plants have evolved large families of GTs which undertake the array of glycosylation reactions that occur during plant development and growth. Based on the Carbohydrate-Active enZymes (CAZy) database, the genome of the reference plant Arabidopsis thaliana codes for over 450 GTs, while the rice genome (Oryza sativa) contains over 600 members. Collectively, GTs from these reference plants can be classified into over 40 distinct GT families. Although these enzymes are involved in many important plant specific processes such as cell-wall and secondary metabolite biosynthesis, few have been functionally characterized. We have sought to develop a plant GTs clone resource that will enable functional genomic approaches to be undertaken by the plant research community. In total, 403 (88%) of CAZy defined Arabidopsis GTs have been cloned, while 96 (15%) of the GTs coded by rice have been cloned. The collection resulted in the update of a number of Arabidopsis GT gene models. The clones represent full-length coding sequences without termination codons and are Gateway® compatible. To demonstrate the utility of this JBEI GT Collection, a set of efficient particle bombardment plasmids (pBullet) was also constructed with markers for the endomembrane. The utility of the pBullet collection was demonstrated by localizing all members of the Arabidopsis GT14 family to the Golgi apparatus or the endoplasmic reticulum (ER). Updates to these resources are available at the JBEI GT Collection website http://www.addgene.org/.
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Affiliation(s)
- Jeemeng Lao
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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26
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Lao J, Oikawa A, Bromley JR, McInerney P, Suttangkakul A, Smith-Moritz AM, Plahar H, Chiu TY, González Fernández-Niño SM, Ebert B, Yang F, Christiansen KM, Hansen SF, Stonebloom S, Adams PD, Ronald PC, Hillson NJ, Hadi MZ, Vega-Sánchez ME, Loqué D, Scheller HV, Heazlewood JL. The plant glycosyltransferase clone collection for functional genomics. Plant J 2014; 79:517-29. [PMID: 24905498 DOI: 10.1111/tpj.12577] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/25/2014] [Accepted: 05/28/2014] [Indexed: 05/18/2023]
Abstract
The glycosyltransferases (GTs) are an important and functionally diverse family of enzymes involved in glycan and glycoside biosynthesis. Plants have evolved large families of GTs which undertake the array of glycosylation reactions that occur during plant development and growth. Based on the Carbohydrate-Active enZymes (CAZy) database, the genome of the reference plant Arabidopsis thaliana codes for over 450 GTs, while the rice genome (Oryza sativa) contains over 600 members. Collectively, GTs from these reference plants can be classified into over 40 distinct GT families. Although these enzymes are involved in many important plant specific processes such as cell-wall and secondary metabolite biosynthesis, few have been functionally characterized. We have sought to develop a plant GTs clone resource that will enable functional genomic approaches to be undertaken by the plant research community. In total, 403 (88%) of CAZy defined Arabidopsis GTs have been cloned, while 96 (15%) of the GTs coded by rice have been cloned. The collection resulted in the update of a number of Arabidopsis GT gene models. The clones represent full-length coding sequences without termination codons and are Gateway® compatible. To demonstrate the utility of this JBEI GT Collection, a set of efficient particle bombardment plasmids (pBullet) was also constructed with markers for the endomembrane. The utility of the pBullet collection was demonstrated by localizing all members of the Arabidopsis GT14 family to the Golgi apparatus or the endoplasmic reticulum (ER). Updates to these resources are available at the JBEI GT Collection website http://www.addgene.org/.
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Affiliation(s)
- Jeemeng Lao
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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27
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Abstract
Arabidopsis thaliana is a model organism commonly used to understand and manipulate various cellular processes in plants, and it has been used extensively in the study of secondary cell wall formation. Secondary cell wall deposition occurs after the primary cell wall is laid down, a process carried out exclusively by specialized cells such as those forming vessel and fiber tissues. Most secondary cell walls are composed of cellulose (40-50%), hemicellulose (25-30%), and lignin (20-30%). Several mutations affecting secondary cell wall biosynthesis have been isolated, and the corresponding mutants may or may not exhibit obvious biochemical composition changes or visual phenotypes since these mutations could be masked by compensatory responses. Staining procedures have historically been used to show differences on a cellular basis. These methods are exclusively visual means of analysis; nevertheless their role in rapid and critical analysis is of great importance. Congo red and calcofluor white are stains used to detect polysaccharides, whereas Mäule and phloroglucinol are commonly used to determine differences in lignin, and toluidine blue O is used to differentially stain polysaccharides and lignin. The seemingly simple techniques of sectioning, staining, and imaging can be a challenge for beginners. Starting with sample preparation using the A. thaliana model, this study details the protocols of a variety of staining methodologies that can be easily implemented for observation of cell and tissue organization in secondary cell walls of plants.
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Affiliation(s)
- Prajakta Pradhan Mitra
- Feedstocks Division, Joint Bioenergy Institute; Physical Biosciences Division, Lawrence Berkeley National Laboratory
| | - Dominique Loqué
- Feedstocks Division, Joint Bioenergy Institute; Physical Biosciences Division, Lawrence Berkeley National Laboratory;
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28
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Eudes A, Liang Y, Mitra P, Loqué D. Lignin bioengineering. Curr Opin Biotechnol 2014. [PMID: 24607805 DOI: 10.1016/j.copbio.2014.01.00] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Lignin is one of the most abundant aromatic biopolymers and a major component of plant cell walls. It occurs via oxidative coupling of monolignols, which are synthesized from the phenylpropanoid pathway. Lignin is the primary material responsible for biomass recalcitrance, has almost no industrial utility, and cannot be simply removed from growing plants without causing serious developmental defects. Fortunately, recent studies report that lignin composition and distribution can be manipulated to a certain extent by using tissue-specific promoters to reduce its recalcitrance, change its biophysical properties, and increase its commercial value. Moreover, the emergence of novel synthetic biology tools to achieve biological control using genome bioediting technologies and tight regulation of transgene expression opens new doors for engineering. This review focuses on lignin bioengineering strategies and describes emerging technologies that could be used to generate tomorrow's bioenergy and biochemical crops.
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Affiliation(s)
- Aymerick Eudes
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA 94608, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Rd, Berkeley, CA 94720, USA
| | - Yan Liang
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA 94608, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Rd, Berkeley, CA 94720, USA
| | - Prajakta Mitra
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA 94608, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Rd, Berkeley, CA 94720, USA
| | - Dominique Loqué
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA 94608, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Rd, Berkeley, CA 94720, USA.
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29
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Eudes A, Juminaga D, Baidoo EEK, Collins FW, Keasling JD, Loqué D. Erratum to: Production of hydroxycinnamoyl anthranilates from glucose in Escherichia coli. Microb Cell Fact 2014. [PMCID: PMC3897996 DOI: 10.1186/1475-2859-13-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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30
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De Michele R, Ast C, Loqué D, Ho CH, Andrade SLA, Lanquar V, Grossmann G, Gehne S, Kumke MU, Frommer WB. Fluorescent sensors reporting the activity of ammonium transceptors in live cells. eLife 2013; 2:e00800. [PMID: 23840931 PMCID: PMC3699834 DOI: 10.7554/elife.00800] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 05/18/2013] [Indexed: 01/14/2023] Open
Abstract
Ammonium serves as key nitrogen source and metabolic intermediate, yet excess causes toxicity. Ammonium uptake is mediated by ammonium transporters, whose regulation is poorly understood. While transport can easily be characterized in heterologous systems, measuring transporter activity in vivo remains challenging. Here we developed a simple assay for monitoring activity in vivo by inserting circularly-permutated GFP into conformation-sensitive positions of two plant and one yeast ammonium transceptors (‘AmTrac’ and ‘MepTrac’). Addition of ammonium to yeast cells expressing the sensors triggered concentration-dependent fluorescence intensity (FI) changes that strictly correlated with the activity of the transporter. Fluorescence-based activity sensors present a novel technology for monitoring the interaction of the transporters with their substrates, the activity of transporters and their regulation in vivo, which is particularly valuable in the context of analytes for which no radiotracers exist, as well as for cell-specific and subcellular transport processes that are otherwise difficult to track. DOI:http://dx.doi.org/10.7554/eLife.00800.001 Ammonium provides a vital source of nitrogen for bacteria, fungi and plants, and is produced by animals as a waste product of metabolism. High levels of ammonium can be toxic, so all organisms need to control their uptake or excretion of this substance. Ammonium transporters, which are highly conserved from bacteria to plants to humans, are essential for this process but, along with transporters in general, they are hard to study. Their activity can be examined in vitro by expressing them in heterologous systems—that is, in cells other than those in which they are naturally found. But in vivo studies must rely on indirect techniques such as monitoring radioactive isotopes or membrane potentials, and these cannot distinguish between the activity of ammonium transporters and uptake of ammonium through other routes. One approach that has been successful in other fields is the use of fluorescent proteins that can signal conformational changes—such as those that occur when a transporter is activated—by a shift in fluorescence. Green fluorescent protein (GFP) is a commonly used fluorescent indicator, and a particularly useful variant is ‘circularly permutated GFP’. This is GFP in which parts of the amino acid sequence have been rearranged without fundamentally changing the overall structure or function of the protein. Circularly permutated GFP can be fused to another protein in such a way that a conformational change in the second protein triggers a change in fluorescence that can be detected by fluorescence spectroscopy or microscopy. Now, De Michele et al. have applied this approach to the study of both plant and yeast ammonium transporters. They constructed a library of fusion proteins made up of circularly permutated GFP and an ammonium transporter from the plant Arabidopsis thaliana—and found one version that functioned normally as a transporter but also produced a detectable change in fluorescence that correlated precisely with transporter activity. De Michele et al. then used the same method to produce fluorescent indicator fusion proteins of two more ammonium transporters—a second isoform from Arabidopsis and one from yeast. These fluorescent sensors should be a great boon to researchers studying the ammonium transport system. Moreover, this approach could in theory be applied to other transporter proteins that are currently difficult to study, and so could help to open up research into a variety of transport processes. DOI:http://dx.doi.org/10.7554/eLife.00800.002
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Affiliation(s)
- Roberto De Michele
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States.,Institute of Plant Genetics, Italian National Research Council (CNR-IGV), Palermo, Italy
| | - Cindy Ast
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States.,NanoPolyPhotonik, Fraunhofer Institute for Applied Polymer Research, Potsdam-Golm, Germany
| | - Dominique Loqué
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, United States
| | - Cheng-Hsun Ho
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Susana LA Andrade
- Department of Biochemistry, Institute for Organic Chemistry and Biochemistry, and BIOSS Center for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Viviane Lanquar
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Guido Grossmann
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Sören Gehne
- Department of Physical Chemistry, Institute of Chemistry, University of Potsdam, Potsdam, Germany
| | - Michael U Kumke
- Department of Physical Chemistry, Institute of Chemistry, University of Potsdam, Potsdam, Germany
| | - Wolf B Frommer
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
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31
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De Michele R, Ast C, Loqué D, Ho CH, Andrade SLA, Lanquar V, Grossmann G, Gehne S, Kumke MU, Frommer WB. Fluorescent sensors reporting the activity of ammonium transceptors in live cells. eLife 2013; 2:e00800. [PMID: 23840931 DOI: 10.7554/elife.00800.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 05/18/2013] [Indexed: 05/26/2023] Open
Abstract
Ammonium serves as key nitrogen source and metabolic intermediate, yet excess causes toxicity. Ammonium uptake is mediated by ammonium transporters, whose regulation is poorly understood. While transport can easily be characterized in heterologous systems, measuring transporter activity in vivo remains challenging. Here we developed a simple assay for monitoring activity in vivo by inserting circularly-permutated GFP into conformation-sensitive positions of two plant and one yeast ammonium transceptors ('AmTrac' and 'MepTrac'). Addition of ammonium to yeast cells expressing the sensors triggered concentration-dependent fluorescence intensity (FI) changes that strictly correlated with the activity of the transporter. Fluorescence-based activity sensors present a novel technology for monitoring the interaction of the transporters with their substrates, the activity of transporters and their regulation in vivo, which is particularly valuable in the context of analytes for which no radiotracers exist, as well as for cell-specific and subcellular transport processes that are otherwise difficult to track. DOI:http://dx.doi.org/10.7554/eLife.00800.001.
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Affiliation(s)
- Roberto De Michele
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
- Institute of Plant Genetics, Italian National Research Council (CNR-IGV), Palermo, Italy
| | - Cindy Ast
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
- NanoPolyPhotonik, Fraunhofer Institute for Applied Polymer Research, Potsdam-Golm, Germany
| | - Dominique Loqué
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, United States
| | - Cheng-Hsun Ho
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Susana LA Andrade
- Department of Biochemistry, Institute for Organic Chemistry and Biochemistry, and BIOSS Center for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Viviane Lanquar
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Guido Grossmann
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Sören Gehne
- Department of Physical Chemistry, Institute of Chemistry, University of Potsdam, Potsdam, Germany
| | - Michael U Kumke
- Department of Physical Chemistry, Institute of Chemistry, University of Potsdam, Potsdam, Germany
| | - Wolf B Frommer
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
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Yang F, Mitra P, Zhang L, Prak L, Verhertbruggen Y, Kim JS, Sun L, Zheng K, Tang K, Auer M, Scheller HV, Loqué D. Engineering secondary cell wall deposition in plants. Plant Biotechnol J 2013; 11:325-35. [PMID: 23140549 PMCID: PMC3644865 DOI: 10.1111/pbi.12016] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 09/21/2012] [Accepted: 09/25/2012] [Indexed: 05/17/2023]
Abstract
Lignocellulosic biomass was used for thousands of years as animal feed and is now considered a great sugar source for biofuels production. It is composed mostly of secondary cell walls built with polysaccharide polymers that are embedded in lignin to reinforce the cell wall structure and maintain its integrity. Lignin is the primary material responsible for biomass recalcitrance to enzymatic hydrolysis. During plant development, deep reductions of lignin cause growth defects and often correlate with the loss of vessel integrity that adversely affects water and nutrient transport in plants. The work presented here describes a new approach to decrease lignin content while preventing vessel collapse and introduces a new strategy to boost transcription factor expression in native tissues. We used synthetic biology tools in Arabidopsis to rewire the secondary cell network by changing promoter-coding sequence associations. The result was a reduction in lignin and an increase in polysaccharide depositions in fibre cells. The promoter of a key lignin gene, C4H, was replaced by the vessel-specific promoter of transcription factor VND6. This rewired lignin biosynthesis specifically for vessel formation while disconnecting C4H expression from the fibre regulatory network. Secondly, the promoter of the IRX8 gene, secondary cell wall glycosyltransferase, was used to express a new copy of the fibre transcription factor NST1, and as the IRX8 promoter is induced by NST1, this also created an artificial positive feedback loop (APFL). The combination of strategies-lignin rewiring with APFL insertion-enhances polysaccharide deposition in stems without over-lignifying them, resulting in higher sugar yields after enzymatic hydrolysis.
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Affiliation(s)
- Fan Yang
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National LaboratoryOne Cyclotron Road, Berkeley, CA, USA
| | - Prajakta Mitra
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National LaboratoryOne Cyclotron Road, Berkeley, CA, USA
| | - Ling Zhang
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National LaboratoryOne Cyclotron Road, Berkeley, CA, USA
- FSN Plant Biotechnology R&D Centre, Shanghai Jiaotong UniversityShanghai, China
| | - Lina Prak
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National LaboratoryOne Cyclotron Road, Berkeley, CA, USA
| | - Yves Verhertbruggen
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National LaboratoryOne Cyclotron Road, Berkeley, CA, USA
| | - Jin-Sun Kim
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National LaboratoryOne Cyclotron Road, Berkeley, CA, USA
| | - Lan Sun
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National LaboratoryOne Cyclotron Road, Berkeley, CA, USA
| | - Kejian Zheng
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National LaboratoryOne Cyclotron Road, Berkeley, CA, USA
| | - Kexuan Tang
- FSN Plant Biotechnology R&D Centre, Shanghai Jiaotong UniversityShanghai, China
| | - Manfred Auer
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National LaboratoryOne Cyclotron Road, Berkeley, CA, USA
| | - Henrik V Scheller
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National LaboratoryOne Cyclotron Road, Berkeley, CA, USA
| | - Dominique Loqué
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National LaboratoryOne Cyclotron Road, Berkeley, CA, USA
- *Correspondence (fax 510 486 4252; email )
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Yuan L, Gu R, Xuan Y, Smith-Valle E, Loqué D, Frommer WB, von Wirén N. Allosteric regulation of transport activity by heterotrimerization of Arabidopsis ammonium transporter complexes in vivo. Plant Cell 2013; 25:974-84. [PMID: 23463773 PMCID: PMC3634700 DOI: 10.1105/tpc.112.108027] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Ammonium acquisition by plant roots is mediated by AMMONIUM TRANSPORTERs (AMTs), ubiquitous membrane proteins with essential roles in nitrogen nutrition in all organisms. In microbial and plant cells, ammonium transport activity is controlled by ammonium-triggered feedback inhibition to prevent cellular ammonium toxicity. Data from heterologous expression in yeast indicate that oligomerization of plant AMTs is critical for allosteric regulation of transport activity, in which the conserved cytosolic C terminus functions as a trans-activator. Employing the coexpressed transporters AMT1;1 and AMT1;3 from Arabidopsis thaliana as a model, we show here that these two isoforms form functional homo- and heterotrimers in yeast and plant roots and that AMT1;3 carrying a phosphomimic residue in its C terminus regulates both homo- and heterotrimers in a dominant-negative fashion in vivo. (15)NH4(+) influx studies further indicate that allosteric inhibition represses ammonium transport activity in roots of transgenic Arabidopsis expressing a phosphomimic mutant together with functional AMT1;3 or AMT1;1. Our study demonstrates in planta a regulatory role in transport activity of heterooligomerization of transporter isoforms, which may enhance their versatility for signal exchange in response to environmental triggers.
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Affiliation(s)
- Lixing Yuan
- Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Riliang Gu
- Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Yuanhu Xuan
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Erika Smith-Valle
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Dominique Loqué
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
- Joint Bioenergy Institute, Emeryville, California 94608
| | - Wolf B. Frommer
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Nicolaus von Wirén
- Molecular Plant Nutrition, Leibniz Institute for Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
- Address correspondence to
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Petersen PD, Lau J, Ebert B, Yang F, Verhertbruggen Y, Kim JS, Varanasi P, Suttangkakul A, Auer M, Loqué D, Scheller HV. Engineering of plants with improved properties as biofuels feedstocks by vessel-specific complementation of xylan biosynthesis mutants. Biotechnol Biofuels 2012; 5. [PMID: 23181474 PMCID: PMC3537538 DOI: 10.1186/1754-6834-5-84] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
BACKGROUND Cost-efficient generation of second-generation biofuels requires plant biomass that can easily be degraded into sugars and further fermented into fuels. However, lignocellulosic biomass is inherently recalcitrant toward deconstruction technologies due to the abundant lignin and cross-linked hemicelluloses. Furthermore, lignocellulosic biomass has a high content of pentoses, which are more difficult to ferment into fuels than hexoses. Engineered plants with decreased amounts of xylan in their secondary walls have the potential to render plant biomass a more desirable feedstock for biofuel production. RESULTS Xylan is the major non-cellulosic polysaccharide in secondary cell walls, and the xylan deficient irregular xylem (irx) mutants irx7, irx8 and irx9 exhibit severe dwarf growth phenotypes. The main reason for the growth phenotype appears to be xylem vessel collapse and the resulting impaired transport of water and nutrients. We developed a xylan-engineering approach to reintroduce xylan biosynthesis specifically into the xylem vessels in the Arabidopsis irx7, irx8 and irx9 mutant backgrounds by driving the expression of the respective glycosyltransferases with the vessel-specific promoters of the VND6 and VND7 transcription factor genes. The growth phenotype, stem breaking strength, and irx morphology was recovered to varying degrees. Some of the plants even exhibited increased stem strength compared to the wild type. We obtained Arabidopsis plants with up to 23% reduction in xylose levels and 18% reduction in lignin content compared to wild-type plants, while exhibiting wild-type growth patterns and morphology, as well as normal xylem vessels. These plants showed a 42% increase in saccharification yield after hot water pretreatment. The VND7 promoter yielded a more complete complementation of the irx phenotype than the VND6 promoter. CONCLUSIONS Spatial and temporal deposition of xylan in the secondary cell wall of Arabidopsis can be manipulated by using the promoter regions of vessel-specific genes to express xylan biosynthetic genes. The expression of xylan specifically in the xylem vessels is sufficient to complement the irx phenotype of xylan deficient mutants, while maintaining low overall amounts of xylan and lignin in the cell wall. This engineering approach has the potential to yield bioenergy crop plants that are more easily deconstructed and fermented into biofuels.
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Affiliation(s)
- Pia Damm Petersen
- Feedstocks Division, Joint Bioenergy Institute, 5885 Hollis St, Emeryville, CA, 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
- Department of Plant Biology and Biotechnology, University of Copenhagen, 40 Thorvaldsensvej, Frederiksberg C, DK-1871, Denmark
| | - Jane Lau
- Feedstocks Division, Joint Bioenergy Institute, 5885 Hollis St, Emeryville, CA, 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Berit Ebert
- Feedstocks Division, Joint Bioenergy Institute, 5885 Hollis St, Emeryville, CA, 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Fan Yang
- Feedstocks Division, Joint Bioenergy Institute, 5885 Hollis St, Emeryville, CA, 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Yves Verhertbruggen
- Feedstocks Division, Joint Bioenergy Institute, 5885 Hollis St, Emeryville, CA, 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Jin Sun Kim
- Feedstocks Division, Joint Bioenergy Institute, 5885 Hollis St, Emeryville, CA, 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Patanjali Varanasi
- Technology Division, Joint Bioenergy Institute, 5885 Hollis St, Emeryville, CA, 94608, USA
- Sandia National Laboratories, 7011 East Avenue, Livermore, CA, 94550, USA
| | - Anongpat Suttangkakul
- Feedstocks Division, Joint Bioenergy Institute, 5885 Hollis St, Emeryville, CA, 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Manfred Auer
- Technology Division, Joint Bioenergy Institute, 5885 Hollis St, Emeryville, CA, 94608, USA
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Dominique Loqué
- Feedstocks Division, Joint Bioenergy Institute, 5885 Hollis St, Emeryville, CA, 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Henrik Vibe Scheller
- Feedstocks Division, Joint Bioenergy Institute, 5885 Hollis St, Emeryville, CA, 94608, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
- Department of Plant & Microbial Biology, University of California, Berkeley, CA, 94720, USA
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Chiu TY, Christiansen K, Moreno I, Lao J, Loqué D, Orellana A, Heazlewood JL, Clark G, Roux SJ. AtAPY1 and AtAPY2 function as Golgi-localized nucleoside diphosphatases in Arabidopsis thaliana. Plant Cell Physiol 2012; 53:1913-25. [PMID: 23034877 DOI: 10.1093/pcp/pcs131] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Nucleoside triphosphate diphosphohydrolases (NTPDases; apyrases) (EC 3.6.1.5) hydrolyze di- and triphosphate nucleotides, but not monophosphate nucleotides. They are categorized as E-type ATPases, have a broad divalent cation (Mg(2+), Ca(2+)) requirement for activation and are insensitive to inhibitors of F-type, P-type and V-type ATPases. Among the seven NTPDases identified in Arabidopsis, only APYRASE 1 (AtAPY1) and APYRASE 2 (AtAPY2) have been previously characterized. In this work, either AtAPY1 or AtAPY2 tagged with C-terminal green fluorescent protein (GFP) driven by their respective native promoter can rescue the apy1 apy2 double knockout (apy1 apy2 dKO) successfully, and confocal microscopy reveals that these two Arabidopsis apyrases reside in the Golgi apparatus. In Saccharomyces cerevisiae, both AtAPY1 and AtAPY2 can complement the Golgi-localized GDA1 mutant, rescuing its aberrant protein glycosylation phenotype. In Arabidopsis, microsomes of the wild type show higher substrate preferences toward UDP compared with other NDP substrates. Loss-of-function Arabidopsis AtAPY1 mutants exhibit reduced microsomal UDPase activity, and this activity is even more significantly reduced in the loss-of-function AtAPY2 mutant and in the AtAPY1/AtAPY2 RNA interference (RNAi) technology repressor lines. Microsomes from wild-type plants also have detectable GDPase activity, which is significantly reduced in apy2 but not apy1 mutants. The GFP-tagged AtAPY1 or AtAPY2 constructs in the apy1 apy2 dKO plants can restore microsomal UDP/GDPase activity, confirming that they both also have functional competency. The cell walls of apy1, apy2 and the RNAi-silenced lines all have an increased composition of galactose, but the transport efficiency of UDP-galactose across microsomal membranes was not altered. Taken together, these results reveal that AtAPY1 and AtAPY2 are Golgi-localized nucleotide diphosphatases and are likely to have roles in regulating UDP/GDP concentrations in the Golgi lumen.
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Affiliation(s)
- Tsan-Yu Chiu
- Section of Molecular Cell and Developmental Biology, University of Texas, Austin, TX 78712, USA
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36
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Eudes A, George A, Mukerjee P, Kim JS, Pollet B, Benke PI, Yang F, Mitra P, Sun L, Cetinkol OP, Chabout S, Mouille G, Soubigou-Taconnat L, Balzergue S, Singh S, Holmes BM, Mukhopadhyay A, Keasling JD, Simmons BA, Lapierre C, Ralph J, Loqué D. Biosynthesis and incorporation of side-chain-truncated lignin monomers to reduce lignin polymerization and enhance saccharification. Plant Biotechnol J 2012; 10:609-20. [PMID: 22458713 DOI: 10.1111/j.1467-7652.2012.00692.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Lignocellulosic biomass is utilized as a renewable feedstock in various agro-industrial activities. Lignin is an aromatic, hydrophobic and mildly branched polymer integrally associated with polysaccharides within the biomass, which negatively affects their extraction and hydrolysis during industrial processing. Engineering the monomer composition of lignins offers an attractive option towards new lignins with reduced recalcitrance. The presented work describes a new strategy developed in Arabidopsis for the overproduction of rare lignin monomers to reduce lignin polymerization degree (DP). Biosynthesis of these 'DP reducers' is achieved by expressing a bacterial hydroxycinnamoyl-CoA hydratase-lyase (HCHL) in lignifying tissues of Arabidopsis inflorescence stems. HCHL cleaves the propanoid side-chain of hydroxycinnamoyl-CoA lignin precursors to produce the corresponding hydroxybenzaldehydes so that plant stems expressing HCHL accumulate in their cell wall higher amounts of hydroxybenzaldehyde and hydroxybenzoate derivatives. Engineered plants with intermediate HCHL activity levels show no reduction in total lignin, sugar content or biomass yield compared with wild-type plants. However, cell wall characterization of extract-free stems by thioacidolysis and by 2D-NMR revealed an increased amount of unusual C₆C₁ lignin monomers most likely linked with lignin as end-groups. Moreover the analysis of lignin isolated from these plants using size-exclusion chromatography revealed a reduced molecular weight. Furthermore, these engineered lines show saccharification improvement of pretreated stem cell walls. Therefore, we conclude that enhancing the biosynthesis and incorporation of C₆C₁ monomers ('DP reducers') into lignin polymers represents a promising strategy to reduce lignin DP and to decrease cell wall recalcitrance to enzymatic hydrolysis.
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Affiliation(s)
- Aymerick Eudes
- Joint BioEnergy Institute, EmeryStation East, Emeryville, CA, USA
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37
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Parsons HT, Christiansen K, Knierim B, Carroll A, Ito J, Batth TS, Smith-Moritz AM, Morrison S, McInerney P, Hadi MZ, Auer M, Mukhopadhyay A, Petzold CJ, Scheller HV, Loqué D, Heazlewood JL. Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components involved in plant cell wall biosynthesis. Plant Physiol 2012; 159:12-26. [PMID: 22430844 PMCID: PMC3375956 DOI: 10.1104/pp.111.193151] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 03/04/2012] [Indexed: 05/17/2023]
Abstract
The plant Golgi plays a pivotal role in the biosynthesis of cell wall matrix polysaccharides, protein glycosylation, and vesicle trafficking. Golgi-localized proteins have become prospective targets for reengineering cell wall biosynthetic pathways for the efficient production of biofuels from plant cell walls. However, proteomic characterization of the Golgi has so far been limited, owing to the technical challenges inherent in Golgi purification. In this study, a combination of density centrifugation and surface charge separation techniques have allowed the reproducible isolation of Golgi membranes from Arabidopsis (Arabidopsis thaliana) at sufficiently high purity levels for in-depth proteomic analysis. Quantitative proteomic analysis, immunoblotting, enzyme activity assays, and electron microscopy all confirm high purity levels. A composition analysis indicated that approximately 19% of proteins were likely derived from contaminating compartments and ribosomes. The localization of 13 newly assigned proteins to the Golgi using transient fluorescent markers further validated the proteome. A collection of 371 proteins consistently identified in all replicates has been proposed to represent the Golgi proteome, marking an appreciable advancement in numbers of Golgi-localized proteins. A significant proportion of proteins likely involved in matrix polysaccharide biosynthesis were identified. The potential within this proteome for advances in understanding Golgi processes has been demonstrated by the identification and functional characterization of the first plant Golgi-resident nucleoside diphosphatase, using a yeast complementation assay. Overall, these data show key proteins involved in primary cell wall synthesis and include a mixture of well-characterized and unknown proteins whose biological roles and importance as targets for future research can now be realized.
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Wipf D, Loqué D, Lalonde S, Frommer WB. Amino Acid transporter inventory of the selaginella genome. Front Plant Sci 2012; 3:36. [PMID: 22639646 PMCID: PMC3355638 DOI: 10.3389/fpls.2012.00036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 02/10/2012] [Indexed: 05/05/2023]
Abstract
Amino acids play fundamental roles in a multitude of functions including protein synthesis, hormone metabolism, nerve transmission, cell growth, production of metabolic energy, nucleobase synthesis, nitrogen metabolism, and urea biosynthesis. Selaginella as a member of the lycophytes is part of an ancient lineage of vascular plants that had arisen ∼400 million years ago. In angiosperms, which have attracted most of the attention for nutrient transport so far, we have been able to identify many of the key transporters for nitrogen. Their role is not always fully clear, thus an analysis of Selaginella as a representative of an ancient vascular plant may help shed light on the evolution and function of these diverse transporters. Here we annotated and analyzed the genes encoding putative transporters involved in cellular uptake of amino acids present in the Selaginella genome.
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Affiliation(s)
- Daniel Wipf
- UMR INRA 1088, CNRS 5184, Université de Bourgogne Plante-Microbe-EnvironnementDijon, France
- *Correspondence: Daniel Wipf, UMR INRA 1088, CNRS 5184, Université de Bourgogne Plante-Microbe-Environnement, BP 86510, 21065 Dijon Cedex, France. e-mail:
| | | | - Sylvie Lalonde
- Department of Plant Biology, Carnegie Institution for ScienceStanford, CA, USA
| | - Wolf B. Frommer
- Department of Plant Biology, Carnegie Institution for ScienceStanford, CA, USA
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De Michele R, Loqué D, Lalonde S, Frommer WB. Ammonium and urea transporter inventory of the selaginella and physcomitrella genomes. Front Plant Sci 2012; 3:62. [PMID: 22639655 PMCID: PMC3355718 DOI: 10.3389/fpls.2012.00062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 03/14/2012] [Indexed: 05/05/2023]
Abstract
Ammonium and urea are important nitrogen sources for autotrophic organisms. Plant genomes encode several families of specific transporters for these molecules, plus other uptake mechanisms such as aquaporins and ABC transporters. Selaginella and Physcomitrella are representatives of lycophytes and bryophytes, respectively, and the recent completion of their genome sequences provided us with an opportunity for comparative genome studies, with special emphasis on the adaptive processes that accompanied the conquest of dry land and the evolution of a vascular system. Our phylogenetic analysis revealed that the number of genes encoding urea transporters underwent a progressive reduction during evolution, eventually down to a single copy in vascular plants. Conversely, no clear evolutionary pattern was found for ammonium transporters, and their number and distribution in families varies between species. In particular Selaginella, similar to rice, favors the AMT2/MEP family of ammonium transporters over the plant-specific AMT1 type. In comparison, Physcomitrella presents several members belonging to both families.
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Affiliation(s)
- Roberto De Michele
- Department of Plant Biology, Carnegie Institution for ScienceStanford, CA, USA
- Plant Genetics Institute, National Research Council of ItalyPalermo, Italy
| | | | - Sylvie Lalonde
- Department of Plant Biology, Carnegie Institution for ScienceStanford, CA, USA
| | - Wolf B. Frommer
- Department of Plant Biology, Carnegie Institution for ScienceStanford, CA, USA
- *Correspondence: Wolf B. Frommer, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA. e-mail:
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40
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Sun L, Varanasi P, Yang F, Loqué D, Simmons BA, Singh S. Rapid determination of syringyl: guaiacyl ratios using FT-Raman spectroscopy. Biotechnol Bioeng 2011; 109:647-56. [PMID: 22012706 DOI: 10.1002/bit.24348] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 09/15/2011] [Accepted: 10/10/2011] [Indexed: 11/09/2022]
Abstract
Lignin composition in relation to its basic phenylpropanoid units, particularly the syringyl to guaiacyl (S/G) ratio, is an important property for biomass characterization and varies greatly as a function of species, genotype and environment. A rapid screening method is highly desirable to assess lignin composition in a large number of samples. We have developed a nondestructive and label-free Fourier transform Raman (FT-Raman) spectroscopic method that is capable of rapidly and reliably measuring the S/G ratio with minimal sample preparation. A variety of feedstocks, including hardwood (Eucalyptus globulus), softwood (Pinus radiata), herbaceous plants (Zea mays, Panicum virgatum, and Sorghum bicolor), and a model dicot (Arabidopsis thaliana) were measured using this technique and the corresponding S/G ratio was calculated after spectral deconvolution based on the S and G bands identified using a known library of model compounds. The results obtained using this technique were successfully validated by pyrolysis-gas chromatography/mass spectrometry (pyro-GC/MS). This technique holds significant promise in the rapid screening of engineered feedstocks as part of a comprehensive screening methodology that is correlated with biomass recalcitrance.
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Affiliation(s)
- Lan Sun
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, California 94608, USA
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Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, Albert VA, Aono N, Aoyama T, Ambrose BA, Ashton NW, Axtell MJ, Barker E, Barker MS, Bennetzen JL, Bonawitz ND, Chapple C, Cheng C, Correa LGG, Dacre M, DeBarry J, Dreyer I, Elias M, Engstrom EM, Estelle M, Feng L, Finet C, Floyd SK, Frommer WB, Fujita T, Gramzow L, Gutensohn M, Harholt J, Hattori M, Heyl A, Hirai T, Hiwatashi Y, Ishikawa M, Iwata M, Karol KG, Koehler B, Kolukisaoglu U, Kubo M, Kurata T, Lalonde S, Li K, Li Y, Litt A, Lyons E, Manning G, Maruyama T, Michael TP, Mikami K, Miyazaki S, Morinaga SI, Murata T, Mueller-Roeber B, Nelson DR, Obara M, Oguri Y, Olmstead RG, Onodera N, Petersen BL, Pils B, Prigge M, Rensing SA, Riaño-Pachón DM, Roberts AW, Sato Y, Scheller HV, Schulz B, Schulz C, Shakirov EV, Shibagaki N, Shinohara N, Shippen DE, Sørensen I, Sotooka R, Sugimoto N, Sugita M, Sumikawa N, Tanurdzic M, Theissen G, Ulvskov P, Wakazuki S, Weng JK, Willats WWGT, Wipf D, Wolf PG, Yang L, Zimmer AD, Zhu Q, Mitros T, Hellsten U, Loqué D, Otillar R, Salamov A, Schmutz J, Shapiro H, Lindquist E, Lucas S, Rokhsar D, Grigoriev IV. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science 2011; 332:960-3. [PMID: 21551031 PMCID: PMC3166216 DOI: 10.1126/science.1203810] [Citation(s) in RCA: 582] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Vascular plants appeared ~410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.
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Affiliation(s)
- Jo Ann Banks
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA.
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Graff L, Obrdlik P, Yuan L, Loqué D, Frommer WB, von Wirén N. N-terminal cysteines affect oligomer stability of the allosterically regulated ammonium transporter LeAMT1;1. J Exp Bot 2011; 62:1361-73. [PMID: 21127027 DOI: 10.1093/jxb/erq379] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
AMMONIUM TRANSPORTER (AMT) proteins are conserved in all domains of life and mediate the transport of ammonium or ammonia across cell membranes. AMTs form trimers and use intermolecular interaction between subunits to regulate activity. So far, binding forces that stabilize AMT protein complexes are not well characterized. High temperature or reducing agents released mono- and dimeric forms from trimeric complexes formed by AMT1;1 from Arabidopsis and tomato. However, in the paralogue LeAMT1;3, trimeric complexes were not detected. LeAMT1;3 differs from the other AMTs by an unusually short N-terminus, suggesting a role for the N-terminus in oligomer stability. Truncation of the N-terminus in LeAMT1;1 destabilized the trimer and led to loss of functionality when expressed in yeast. Swapping of the N-terminus between LeAMT1;1 and LeAMT1;3 showed that sequences in the N-terminus of LeAMT1;1 are necessary and sufficient for stabilization of the interaction among the subunits. Two N-terminal cysteine residues are highly conserved among AMT1 transporters in plants but are lacking in LeAMT1;3. C3S or C27S variants of LeAMT1;1 showed reduced complex stability, which coincided with lower transport capacity for the substrate analogue methylammonium. Both cysteine-substituted LeAMT1;1 variants showed weaker interactions with the wildtype as determined by a quantitative analysis of the complex stability using the mating-based split-ubiquitin assay. These data indicate that the binding affinity of AMT1 subunits is stabilized by cysteines in the N-terminus and suggest a role for disulphide bridge formation via apoplastic N-terminal cysteine residues.
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Affiliation(s)
- Lucile Graff
- Institute for Plant Nutrition, University of Hohenheim, D-70593 Stuttgart, Germany
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Eudes A, Baidoo EEK, Yang F, Burd H, Hadi MZ, Collins FW, Keasling JD, Loqué D. Production of tranilast [N-(3′,4′-dimethoxycinnamoyl)-anthranilic acid] and its analogs in yeast Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2010; 89:989-1000. [DOI: 10.1007/s00253-010-2939-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 10/06/2010] [Accepted: 10/07/2010] [Indexed: 10/18/2022]
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Lalonde S, Sero A, Pratelli R, Pilot G, Chen J, Sardi MI, Parsa SA, Kim DY, Acharya BR, Stein EV, Hu HC, Villiers F, Takeda K, Yang Y, Han YS, Schwacke R, Chiang W, Kato N, Loqué D, Assmann SM, Kwak JM, Schroeder JI, Rhee SY, Frommer WB. A membrane protein/signaling protein interaction network for Arabidopsis version AMPv2. Front Physiol 2010; 1:24. [PMID: 21423366 PMCID: PMC3059934 DOI: 10.3389/fphys.2010.00024] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Accepted: 07/20/2010] [Indexed: 01/15/2023] Open
Abstract
Interactions between membrane proteins and the soluble fraction are essential for signal transduction and for regulating nutrient transport. To gain insights into the membrane-based interactome, 3,852 open reading frames (ORFs) out of a target list of 8,383 representing membrane and signaling proteins from Arabidopsis thaliana were cloned into a Gateway-compatible vector. The mating-based split ubiquitin system was used to screen for potential protein-protein interactions (pPPIs) among 490 Arabidopsis ORFs. A binary robotic screen between 142 receptor-like kinases (RLKs), 72 transporters, 57 soluble protein kinases and phosphatases, 40 glycosyltransferases, 95 proteins of various functions, and 89 proteins with unknown function detected 387 out of 90,370 possible PPIs. A secondary screen confirmed 343 (of 386) pPPIs between 179 proteins, yielding a scale-free network (r(2) = 0.863). Eighty of 142 transmembrane RLKs tested positive, identifying 3 homomers, 63 heteromers, and 80 pPPIs with other proteins. Thirty-one out of 142 RLK interactors (including RLKs) had previously been found to be phosphorylated; thus interactors may be substrates for respective RLKs. None of the pPPIs described here had been reported in the major interactome databases, including potential interactors of G-protein-coupled receptors, phospholipase C, and AMT ammonium transporters. Two RLKs found as putative interactors of AMT1;1 were independently confirmed using a split luciferase assay in Arabidopsis protoplasts. These RLKs may be involved in ammonium-dependent phosphorylation of the C-terminus and regulation of ammonium uptake activity. The robotic screening method established here will enable a systematic analysis of membrane protein interactions in fungi, plants and metazoa.
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Affiliation(s)
- Sylvie Lalonde
- Department of Plant Biology, Carnegie Institution for Science Stanford, CA, USA.
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Simmons BA, Loqué D, Ralph J. Advances in modifying lignin for enhanced biofuel production. Curr Opin Plant Biol 2010; 13:313-20. [PMID: 20359939 DOI: 10.1016/j.pbi.2010.03.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Revised: 02/24/2010] [Accepted: 03/01/2010] [Indexed: 05/02/2023]
Abstract
Renewable and sustainable liquid transportation biofuels based on lignocellulosics conversion face several obstacles that must be overcome in order for them to become commercially viable and cost-competitive. The presence of lignin is one of the most significant contributors to biomass recalcitrance and consequently increases the costs associated with conversion. Lignins are complex aromatic biopolymers, derived from hydroxyphenylpropanoids, that vary in composition and structure as a function of genotype, phenotype, and environment, as well as with the cell type and maturity of the plant tissue. Lignins consist of (mainly) syringyl (S), guaiacyl (G), and p-hydroxyphenyl (H) units, derived from sinapyl, coniferyl, and p-coumaryl alcohols. These units are not discrete within either the cell or a given lignin molecule, and the compositional ratios of these three moieties can vary significantly. This inherent complexity and heterogeneity of lignin, both in structure and composition, make it extremely difficult to develop a conversion technology that can efficiently process a wide range of sustainable feedstocks cost-effectively. There is a growing body of work that has demonstrated several genetic engineering strategies that, when coupled with an integrated approach to conversion, hold significant promise for the development of tailored feedstocks designed for biofuel production. The knowledgebase is at the point where researchers are also able to contemplate strategies to 'design' the lignin polymer for easier processing. The realization of advanced analytical techniques and an increasing number of plant genomes are enabling researchers to take a systems approach towards understanding and engineering lignin to develop these optimal feedstocks.
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Lanquar V, Loqué D, Hörmann F, Yuan L, Bohner A, Engelsberger WR, Lalonde S, Schulze WX, von Wirén N, Frommer WB. Feedback inhibition of ammonium uptake by a phospho-dependent allosteric mechanism in Arabidopsis. Plant Cell 2009; 21:3610-22. [PMID: 19948793 PMCID: PMC2798313 DOI: 10.1105/tpc.109.068593] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 09/23/2009] [Accepted: 11/06/2009] [Indexed: 05/18/2023]
Abstract
The acquisition of nutrients requires tight regulation to ensure optimal supply while preventing accumulation to toxic levels. Ammonium transporter/methylamine permease/rhesus (AMT/Mep/Rh) transporters are responsible for ammonium acquisition in bacteria, fungi, and plants. The ammonium transporter AMT1;1 from Arabidopsis thaliana uses a novel regulatory mechanism requiring the productive interaction between a trimer of subunits for function. Allosteric regulation is mediated by a cytosolic C-terminal trans-activation domain, which carries a conserved Thr (T460) in a critical position in the hinge region of the C terminus. When expressed in yeast, mutation of T460 leads to inactivation of the trimeric complex. This study shows that phosphorylation of T460 is triggered by ammonium in a time- and concentration-dependent manner. Neither Gln nor l-methionine sulfoximine-induced ammonium accumulation were effective in inducing phosphorylation, suggesting that roots use either the ammonium transporter itself or another extracellular sensor to measure ammonium concentrations in the rhizosphere. Phosphorylation of T460 in response to an increase in external ammonium correlates with inhibition of ammonium uptake into Arabidopsis roots. Thus, phosphorylation appears to function in a feedback loop restricting ammonium uptake. This novel autoregulatory mechanism is capable of tuning uptake capacity over a wide range of supply levels using an extracellular sensory system, potentially mediated by a transceptor (i.e., transporter and receptor).
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Affiliation(s)
- Viviane Lanquar
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Dominique Loqué
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Friederike Hörmann
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Lixing Yuan
- Key Lab of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Anne Bohner
- Molecular Plant Nutrition, Leibniz-Institute for Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | | | - Sylvie Lalonde
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | | | - Nicolaus von Wirén
- Molecular Plant Nutrition, Leibniz-Institute for Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany
| | - Wolf B. Frommer
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
- Address correspondence to
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Loqué D, Mora SI, Andrade SLA, Pantoja O, Frommer WB. Pore mutations in ammonium transporter AMT1 with increased electrogenic ammonium transport activity. J Biol Chem 2009; 284:24988-95. [PMID: 19581303 DOI: 10.1074/jbc.m109.020842] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
AMT/Mep ammonium transporters mediate high affinity ammonium/ammonia uptake in bacteria, fungi, and plants. The Arabidopsis AMT1 proteins mediate uptake of the ionic form of ammonium. AMT transport activity is controlled allosterically via a highly conserved cytosolic C terminus that interacts with neighboring subunits in a trimer. The C terminus is thus capable of modulating the conductivity of the pore. To gain insight into the underlying mechanism, pore mutants suppressing the inhibitory effect of mutations in the C-terminal trans-activation domain were characterized. AMT1;1 carrying the mutation Q57H in transmembrane helix I (TMH I) showed increased ammonium uptake but reduced capacity to take up methylammonium. To explore whether the transport mechanism was altered, the AMT1;1-Q57H mutant was expressed in Xenopus oocytes and analyzed electrophysiologically. AMT1;1-Q57H was characterized by increased ammonium-induced and reduced methylammonium-induced currents. AMT1;1-Q57H possesses a 100x lower affinity for ammonium (K(m)) and a 10-fold higher V(max) as compared with the wild type form. To test whether the trans-regulatory mechanism is conserved in archaeal homologs, AfAmt-2 from Archaeoglobus fulgidus was expressed in yeast. The transport function of AfAmt-2 also depends on trans-activation by the C terminus, and mutations in pore-residues corresponding to Q57H of AMT1;1 suppress nonfunctional AfAmt-2 mutants lacking the activating C terminus. Altogether, our data suggest that bacterial and plant AMTs use a conserved allosteric mechanism to control ammonium flux, potentially using a gating mechanism that limits flux to protect against ammonium toxicity.
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Affiliation(s)
- Dominique Loqué
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
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Yuan L, Graff L, Loqué D, Kojima S, Tsuchiya YN, Takahashi H, von Wirén N. AtAMT1;4, a pollen-specific high-affinity ammonium transporter of the plasma membrane in Arabidopsis. Plant Cell Physiol 2009; 50:13-25. [PMID: 19073648 PMCID: PMC2638712 DOI: 10.1093/pcp/pcn186] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Accepted: 11/27/2008] [Indexed: 05/19/2023]
Abstract
Pollen represents an important nitrogen sink in flowers to ensure pollen viability. Since pollen cells are symplasmically isolated during maturation and germination, membrane transporters are required for nitrogen import across the pollen plasma membrane. This study describes the characterization of the ammonium transporter AtAMT1;4, a so far uncharacterized member of the Arabidopsis AMT1 family, which is suggested to be involved in transporting ammonium into pollen. The AtAMT1;4 gene encodes a functional ammonium transporter when heterologously expressed in yeast or when overexpressed in Arabidopsis roots. Concentration-dependent analysis of (15)N-labeled ammonium influx into roots of AtAMT1;4-transformed plants allowed characterization of AtAMT1;4 as a high-affinity transporter with a K(m) of 17 microM. RNA and protein gel blot analysis showed expression of AtAMT1;4 in flowers, and promoter-gene fusions to the green fluorescent protein (GFP) further defined its exclusive expression in pollen grains and pollen tubes. The AtAMT1;4 protein appeared to be localized to the plasma membrane as indicated by protein gel blot analysis of plasma membrane-enriched membrane fractions and by visualization of GFP-tagged AtAMT1;4 protein in pollen grains and pollen tubes. However, no phenotype related to pollen function could be observed in a transposon-tagged line, in which AtAMT1;4 expression is disrupted. These results suggest that AtAMT1;4 mediates ammonium uptake across the plasma membrane of pollen to contribute to nitrogen nutrition of pollen via ammonium uptake or retrieval.
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Affiliation(s)
- Lixing Yuan
- Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, PR China
- Molecular Plant Nutrition, Institute of Plant Nutrition, University of Hohenheim, D-70593 Stuttgart, Germany
| | - Lucile Graff
- Molecular Plant Nutrition, Institute of Plant Nutrition, University of Hohenheim, D-70593 Stuttgart, Germany
| | - Dominique Loqué
- Molecular Plant Nutrition, Institute of Plant Nutrition, University of Hohenheim, D-70593 Stuttgart, Germany
| | - Soichi Kojima
- Molecular Plant Nutrition, Institute of Plant Nutrition, University of Hohenheim, D-70593 Stuttgart, Germany
| | | | | | - Nicolaus von Wirén
- Molecular Plant Nutrition, Institute of Plant Nutrition, University of Hohenheim, D-70593 Stuttgart, Germany
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Lalonde S, Ehrhardt DW, Loqué D, Chen J, Rhee SY, Frommer WB. Molecular and cellular approaches for the detection of protein-protein interactions: latest techniques and current limitations. Plant J 2008; 53:610-635. [PMID: 18269572 DOI: 10.1111/j.1365-313x.2007.03332.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Homotypic and heterotypic protein interactions are crucial for all levels of cellular function, including architecture, regulation, metabolism, and signaling. Therefore, protein interaction maps represent essential components of post-genomic toolkits needed for understanding biological processes at a systems level. Over the past decade, a wide variety of methods have been developed to detect, analyze, and quantify protein interactions, including surface plasmon resonance spectroscopy, NMR, yeast two-hybrid screens, peptide tagging combined with mass spectrometry and fluorescence-based technologies. Fluorescence techniques range from co-localization of tags, which may be limited by the optical resolution of the microscope, to fluorescence resonance energy transfer-based methods that have molecular resolution and can also report on the dynamics and localization of the interactions within a cell. Proteins interact via highly evolved complementary surfaces with affinities that can vary over many orders of magnitude. Some of the techniques described in this review, such as surface plasmon resonance, provide detailed information on physical properties of these interactions, while others, such as two-hybrid techniques and mass spectrometry, are amenable to high-throughput analysis using robotics. In addition to providing an overview of these methods, this review emphasizes techniques that can be applied to determine interactions involving membrane proteins, including the split ubiquitin system and fluorescence-based technologies for characterizing hits obtained with high-throughput approaches. Mass spectrometry-based methods are covered by a review by Miernyk and Thelen (2008; this issue, pp. 597-609). In addition, we discuss the use of interaction data to construct interaction networks and as the basis for the exciting possibility of using to predict interaction surfaces.
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Affiliation(s)
- Sylvie Lalonde
- Carnegie Institution, 260 Panama Street, Stanford, CA 94305, USA.
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Yuan L, Loqué D, Kojima S, Rauch S, Ishiyama K, Inoue E, Takahashi H, von Wirén N. The organization of high-affinity ammonium uptake in Arabidopsis roots depends on the spatial arrangement and biochemical properties of AMT1-type transporters. Plant Cell 2007; 19:2636-52. [PMID: 17693533 PMCID: PMC2002620 DOI: 10.1105/tpc.107.052134] [Citation(s) in RCA: 213] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The AMMONIUM TRANSPORTER (AMT) family comprises six isoforms in Arabidopsis thaliana. Here, we describe the complete functional organization of root-expressed AMTs for high-affinity ammonium uptake. High-affinity influx of (15)N-labeled ammonium in two transposon-tagged amt1;2 lines was reduced by 18 to 26% compared with wild-type plants. Enrichment of the AMT1;2 protein in the plasma membrane and localization of AMT1;2 promoter activity in the endodermis and root cortex indicated that AMT1;2 mediates the uptake of ammonium entering the root via the apoplasmic transport route. An amt1;1 amt1;2 amt1;3 amt2;1 quadruple mutant (qko) showed severe growth depression under ammonium supply and maintained only 5 to 10% of wild-type high-affinity ammonium uptake capacity. Transcriptional upregulation of AMT1;5 in nitrogen-deficient rhizodermal and root hair cells and the ability of AMT1;5 to transport ammonium in yeast suggested that AMT1;5 accounts for the remaining uptake capacity in qko. Triple and quadruple amt insertion lines revealed in vivo ammonium substrate affinities of 50, 234, 61, and 4.5 muM for AMT1;1, AMT1;2, AMT1;3, and AMT1;5, respectively, but no ammonium influx activity for AMT2;1. These data suggest that two principle means of achieving effective ammonium uptake in Arabidopsis roots are the spatial arrangement of AMT1-type ammonium transporters and the distribution of their transport capacities at different substrate affinities.
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Affiliation(s)
- Lixing Yuan
- Molecular Plant Nutrition, Institute of Plant Nutrition, University of Hohenheim, D-70593 Stuttgart, Germany
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