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Dokka N, Tyagi S, Ramkumar MK, Rathinam M, Senthil K, Sreevathsa R. Genome-wide identification and characterization of DIRIGENT gene family (CcDIR) in pigeonpea (Cajanus cajan L.) provide insights on their spatial expression pattern and relevance to stress response. Gene 2024; 914:148417. [PMID: 38555003 DOI: 10.1016/j.gene.2024.148417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/20/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
This study is a thorough characterization of pigeonpea dirigent gene (CcDIR) family, an important component of the lignin biosynthesis pathway. Genome-wide analysis identified 25 CcDIR genes followed by a range of analytical approaches employed to unravel their structural and functional characteristics. Structural examination revealed a classic single exon and no intron arrangement in CcDIRs contributing to our understanding on evolutionary dynamics. Phylogenetic analysis elucidated evolutionary relationships among CcDIR genes with six DIR sub-families, while motif distribution analysis displayed and highlighted ten conserved protein motifs in CcDIRs. Promoter analyses of all the dirigent genes detected 18 stress responsive cis-acting elements offering insights into transcriptional regulation. While spatial expression analyses across six plant tissues showed preferential expression of CcDIR genes, exposure to salt (CcDIR2 and CcDIR9) and herbivory (CcDIR1, CcDIR2, CcDIR3 and CcDIR11), demonstrated potential roles of specific DIRs in plant defense. Interestingly, increased gene expression during herbivory, also correlated with increased lignin content authenticating the specific response. Furthermore, exogenous application of stress hormones, SA and MeJA on leaves significantly induced the expression of CcDIRs that responded to herbivory. Taken together, these findings contribute to a comprehensive understanding of CcDIR genes impacting development and stress response in the important legume pigeonpea.
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Affiliation(s)
- Narasimham Dokka
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Shaily Tyagi
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - M K Ramkumar
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Maniraj Rathinam
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Kameshwaran Senthil
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Rohini Sreevathsa
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India.
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Kapoor P, Rakhra G, Kumar V, Joshi R, Gupta M, Rakhra G. Insights into the functional characterization of DIR proteins through genome-wide in silico and evolutionary studies: a systematic review. Funct Integr Genomics 2023; 23:166. [PMID: 37202648 DOI: 10.1007/s10142-023-01095-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/04/2023] [Accepted: 05/10/2023] [Indexed: 05/20/2023]
Abstract
Dirigent proteins (DIRs) are a new class of proteins that were identified during the 8-8' lignan biosynthetic pathway and involves the formation of ( +) or ( -)-pinoresinol through stereoselective coupling from E-coniferyl alcohol. These proteins are known to play a vital role in the development and stress response in plants. Various studies have reported the functional and structural characterization of dirigent gene family in different plants using in silico approaches. Here, we have summarized the importance of dirigent proteins in plants and their role in plant stress tolerance by analyzing the genome-wide analysis including gene structure, mapping of chromosomes, phylogenetic evolution, conserved motifs, gene structure, and gene duplications in important plants. Overall, this review would help to compare and clarify the molecular and evolutionary characteristics of dirigent gene family in different plants.
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Affiliation(s)
- Preedhi Kapoor
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Gurseen Rakhra
- Department of Nutrition and Dietetics, Faculty of Allied Health Sciences, Manav Rachna International Institute of Research and Studies, Faridabad, Haryana, India
| | - Vineet Kumar
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Ridhi Joshi
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Mahiti Gupta
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala, 133207, India
| | - Gurmeen Rakhra
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India.
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala, 133207, India.
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Li X, Liu Z, Zhao H, Deng X, Su Y, Li R, Chen B. Overexpression of Sugarcane ScDIR Genes Enhances Drought Tolerance in Nicotiana benthamiana. Int J Mol Sci 2022; 23:5340. [PMID: 35628151 PMCID: PMC9141896 DOI: 10.3390/ijms23105340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 12/15/2022] Open
Abstract
Dirigent proteins (DIRs) are known to function in lignin biogenesis and to be involved in stress resistance in plants. However, the sugarcane DIRs have not been functionally characterized. In this study, we investigated the DIR-protein-encoding genes in Saccharum spp. (ScDIR) by screening collections of sugarcane databases, monitoring the responses of these genes to drought stress by real-time quantitative PCR, and identifying their heterologous expression in tobacco. Of the 64 ScDIRs identified, four belonging to the DIR-b/d (ScDIR5 and ScDIR11) and DIR-c (ScDIR7 and ScDIR40) subfamilies showed a significant transcriptional response when subjected to drought stress. ScDIR5, ScDIR7, and ScDIR11 are localized in the cell membrane, whereas ScDIR40 is found in the cell wall. The overexpression of these ScDIR genes in tobacco generally increased the drought tolerance of the transgenic lines, with ScDIR7 conferring the highest degree of drought tolerance. The characterization of the physiological and biochemical indicators (superoxide dismutase, catalase, malondialdehyde, and H2O2) confirmed that the ScDIR-overexpressing lines outperformed the wild type. These results demonstrated that specific ScDIRs in sugarcane respond and contribute to tolerance of drought stress, shedding light on potential means of improving drought tolerance in this crop.
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Affiliation(s)
- Xiufang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro−Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (X.L.); (Z.L.); (X.D.); (Y.S.)
| | - Zongling Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro−Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (X.L.); (Z.L.); (X.D.); (Y.S.)
| | - Haiyun Zhao
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China;
| | - Xingli Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro−Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (X.L.); (Z.L.); (X.D.); (Y.S.)
| | - Yizu Su
- State Key Laboratory for Conservation and Utilization of Subtropical Agro−Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (X.L.); (Z.L.); (X.D.); (Y.S.)
| | - Ru Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro−Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (X.L.); (Z.L.); (X.D.); (Y.S.)
| | - Baoshan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro−Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (X.L.); (Z.L.); (X.D.); (Y.S.)
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China;
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Hodgson-Kratky K, Perlo V, Furtado A, Choudhary H, Gladden JM, Simmons BA, Botha F, Henry RJ. Association of gene expression with syringyl to guaiacyl ratio in sugarcane lignin. PLANT MOLECULAR BIOLOGY 2021; 106:173-192. [PMID: 33738678 DOI: 10.1007/s11103-021-01136-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/02/2021] [Indexed: 05/11/2023]
Abstract
A transcriptome analysis reveals the transcripts and alleles differentially expressed in sugarcane genotypes with contrasting lignin composition. Sugarcane bagasse is a highly abundant resource that may be used as a feedstock for the production of biofuels and bioproducts in order to meet increasing demands for renewable replacements for fossil carbon. However, lignin imparts rigidity to the cell wall that impedes the efficient breakdown of the biomass into fermentable sugars. Altering the ratio of the lignin units, syringyl (S) and guaiacyl (G), which comprise the native lignin polymer in sugarcane, may facilitate the processing of bagasse. This study aimed to identify genes and markers associated with S/G ratio in order to accelerate the development of sugarcane bioenergy varieties with modified lignin composition. The transcriptome sequences of 12 sugarcane genotypes that contrasted for S/G ratio were compared and there were 2019 transcripts identified as differentially expressed (DE) between the high and low S/G ratio groups. These included transcripts encoding possible monolignol biosynthetic pathway enzymes, transporters, dirigent proteins and transcriptional and post-translational regulators. Furthermore, the frequencies of single nucleotide polymorphisms (SNPs) were compared between the low and high S/G ratio groups to identify specific alleles expressed with the phenotype. There were 2063 SNP loci across 787 unique transcripts that showed group-specific expression. Overall, the DE transcripts and SNP alleles identified in this study may be valuable for breeding sugarcane varieties with altered S/G ratio that may provide desirable bioenergy traits.
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Affiliation(s)
- K Hodgson-Kratky
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia
| | - V Perlo
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia
| | - A Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia
| | - H Choudhary
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Sandia National Laboratories, Livermore, CA, 94550, USA
| | - J M Gladden
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Sandia National Laboratories, Livermore, CA, 94550, USA
| | - B A Simmons
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - F Botha
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia
| | - R J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia.
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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 BIOLOGY 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] [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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6
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Padilla CS, Damaj MB, Yang ZN, Molina J, Berquist BR, White EL, Solís-Gracia N, Da Silva J, Mandadi KK. High-Level Production of Recombinant Snowdrop Lectin in Sugarcane and Energy Cane. Front Bioeng Biotechnol 2020; 8:977. [PMID: 33015000 PMCID: PMC7461980 DOI: 10.3389/fbioe.2020.00977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/27/2020] [Indexed: 01/11/2023] Open
Abstract
Sugarcane and energy cane (Saccharum spp. hybrids) are ideal for plant-based production of recombinant proteins because their high resource-use efficiency, rapid growth and efficient photosynthesis enable extensive biomass production and protein accumulation at a cost-effective scale. Here, we aimed to develop these species as efficient platforms to produce recombinant Galanthus nivalis L. (snowdrop) agglutinin (GNA), a monocot-bulb mannose-specific lectin with potent antiviral, antifungal and antitumor activities. Initially, GNA levels of 0.04% and 0.3% total soluble protein (TSP) (0.3 and 3.8 mg kg–1 tissue) were recovered from the culms and leaves, respectively, of sugarcane lines expressing recombinant GNA under the control of the constitutive maize ubiquitin 1 (Ubi) promoter. Co-expression of recombinant GNA from stacked multiple promoters (pUbi and culm-regulated promoters from sugarcane dirigent5-1 and Sugarcane bacilliform virus) on separate expression vectors increased GNA yields up to 42.3-fold (1.8% TSP or 12.7 mg kg–1 tissue) and 7.7-fold (2.3% TSP or 29.3 mg kg–1 tissue) in sugarcane and energy cane lines, respectively. Moreover, inducing promoter activity in the leaves of GNA transgenic lines with stress-regulated hormones increased GNA accumulation to 2.7% TSP (37.2 mg kg–1 tissue). Purification by mannose-agarose affinity chromatography yielded a functional sugarcane recombinant GNA with binding substrate specificity similar to that of native snowdrop-bulb GNA, as shown by enzyme-linked lectin and mannose-binding inhibition assays. The size and molecular weight of recombinant GNA were identical to those of native GNA, as determined by size-exclusion chromatography and MALDI-TOF mass spectrometry. This work demonstrates the feasibility of producing recombinant GNA at high levels in Saccharum species, with the long-term goal of using it as a broad-spectrum antiviral carrier molecule for hemopurifiers and in related therapeutic applications.
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Affiliation(s)
- Carmen S Padilla
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
| | - Mona B Damaj
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
| | - Zhong-Nan Yang
- Institute for Plant Gene Function, Department of Biology, Shanghai Normal University, Shanghai, China
| | - Joe Molina
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
| | | | - Earl L White
- MDx BioAnalytical Laboratory, Inc., College Station, TX, United States
| | - Nora Solís-Gracia
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
| | - Jorge Da Silva
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States.,Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Kranthi K Mandadi
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States.,Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, United States
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Damaj MB, Jifon JL, Woodard SL, Vargas-Bautista C, Barros GOF, Molina J, White SG, Damaj BB, Nikolov ZL, Mandadi KK. Unprecedented enhancement of recombinant protein production in sugarcane culms using a combinatorial promoter stacking system. Sci Rep 2020; 10:13713. [PMID: 32792533 PMCID: PMC7426418 DOI: 10.1038/s41598-020-70530-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 07/21/2020] [Indexed: 11/09/2022] Open
Abstract
Plants represent a safe and cost-effective platform for producing high-value proteins with pharmaceutical properties; however, the ability to accumulate these in commercially viable quantities is challenging. Ideal crops to serve as biofactories would include low-input, fast-growing, high-biomass species such as sugarcane. The objective of this study was to develop an efficient expression system to enable large-scale production of high-value recombinant proteins in sugarcane culms. Bovine lysozyme (BvLz) is a potent broad-spectrum antimicrobial enzyme used in the food, cosmetics and agricultural industries. Here, we report a novel strategy to achieve high-level expression of recombinant proteins using a combinatorial stacked promoter system. We demonstrate this by co-expressing BvLz under the control of multiple constitutive and culm-regulated promoters on separate expression vectors and combinatorial plant transformation. BvLz accumulation reached 1.4% of total soluble protein (TSP) (10.0 mg BvLz/kg culm mass) in stacked multiple promoter:BvLz lines, compared to 0.07% of TSP (0.56 mg/kg) in single promoter:BvLz lines. BvLz accumulation was further boosted to 11.5% of TSP (82.5 mg/kg) through event stacking by re-transforming the stacked promoter:BvLz lines with additional BvLz expression vectors. The protein accumulation achieved with the combinatorial promoter stacking expression system was stable in multiple vegetative propagations, demonstrating the feasibility of using sugarcane as a biofactory for producing high-value proteins and bioproducts.
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Affiliation(s)
- Mona B Damaj
- Texas A&M AgriLife Research and Extension Center, 2415 East US Highway 83, Weslaco, TX, 78596, USA.
| | - John L Jifon
- Texas A&M AgriLife Research and Extension Center, 2415 East US Highway 83, Weslaco, TX, 78596, USA
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843-2133, USA
| | - Susan L Woodard
- National Center for Therapeutics Manufacturing, Texas A&M University, 100 Discovery Drive, College Station, TX, 77843-4482, USA
| | - Carol Vargas-Bautista
- Texas A&M AgriLife Research and Extension Center, 2415 East US Highway 83, Weslaco, TX, 78596, USA
- College of Medicine, Texas A&M University, 8447 Riverside Parkway, Bryan, TX, 77807, USA
| | - Georgia O F Barros
- BioSeparation Laboratory, Biological and Agricultural Engineering Department, College Station, TX, 77843-2117, USA
| | - Joe Molina
- Texas A&M AgriLife Research and Extension Center, 2415 East US Highway 83, Weslaco, TX, 78596, USA
| | - Steven G White
- BioSeparation Laboratory, Biological and Agricultural Engineering Department, College Station, TX, 77843-2117, USA
| | - Bassam B Damaj
- Innovus Pharmaceuticals, Inc., 8845 Rehco Road, San Diego, CA, 92121, USA
| | - Zivko L Nikolov
- BioSeparation Laboratory, Biological and Agricultural Engineering Department, College Station, TX, 77843-2117, USA
| | - Kranthi K Mandadi
- Texas A&M AgriLife Research and Extension Center, 2415 East US Highway 83, Weslaco, TX, 78596, USA.
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843-2132, USA.
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Song M, Peng X. Genome-Wide Identification and Characterization of DIR Genes in Medicago truncatula. Biochem Genet 2019; 57:487-506. [PMID: 30649641 DOI: 10.1007/s10528-019-09903-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 01/04/2019] [Indexed: 11/29/2022]
Abstract
Dirigent proteins (DIRs) are critically involved in the formation of lignans, a diverse and widely distributed class of secondary plant metabolites exhibiting interesting pharmacological activities and implicated in natural plant defense. However, no detailed information is available about DIR gene family in Medicago truncatula. In this study, a total of 45 DIR genes were identified in M. truncatula. DIR proteins have variability in sequence. Most MtDIR genes have no intron. All MtDIR proteins contain single dirigent domain. A large number of MtDIR genes were expanded via gene duplication, and 37 MtDIR genes were duplicated in tandem. Digital expression data showed that 40% MtDIR genes had a higher expression level in the root. Analysis of RNA-seq and microarray data indicated that more than 30% MtDIR genes were responsive to biotic and/or abiotic treatments. This study will facilitate further studies on DIR family and provide useful clues for functional validation of DIR genes in higher plants.
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Affiliation(s)
- Min Song
- College of Life Science, Qufu Normal University, Qufu, 273165, People's Republic of China.
| | - Xiangyong Peng
- College of Life Science, Qufu Normal University, Qufu, 273165, People's Republic of China
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9
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Ramasamy M, Mora V, Damaj MB, Padilla CS, Ramos N, Rossi D, Solís-Gracia N, Vargas-Bautista C, Irigoyen S, DaSilva JA, Mirkov TE, Mandadi KK. A biolistic-based genetic transformation system applicable to a broad-range of sugarcane and energycane varieties. GM CROPS & FOOD 2018; 9:211-227. [PMID: 30558472 DOI: 10.1080/21645698.2018.1553836] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Sugarcane and energycane (Saccharum spp. hybrids) are prominent sources of sugar, ethanol, as well as high-value bioproducts globally. Genetic analysis for trait improvement of sugarcane is greatly hindered by its complex genome, limited germplasm resources, long breeding cycle, as well as recalcitrance to genetic transformation. Here, we present a biolistic-based transformation and bioreactor-based micro-propagation system that has been utilized successfully to transform twelve elite cane genotypes, yielding transformation efficiencies of up to 39%. The system relies on the generation of embryogenic callus from sugarcane and energycane apical shoot tissue, followed by DNA bombardment of embryogenic leaf roll discs (approximately one week) or calli (approximately 4 weeks). We present optimal criteria and practices for selection and regeneration of independent transgenic lines, molecular characterization, as well as a bioreactor-based micro-propagation technique, which can aid in rapid multiplication and analysis of transgenic lines. The cane transformation and micro-propagation system described here, although built on our previous protocols, has significantly accelerated the process of producing and multiplying transgenic material, and it is applicable to other varieties. The system is highly reproducible and has been successfully used to engineer multiple commercial sugarcane and energycane varieties. It will benefit worldwide researchers interested in genomics and genetics of sugarcane photosynthesis, cell wall, and bioenergy related traits.
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Affiliation(s)
| | - Victoria Mora
- a Texas A&M AgriLife Research & Extension Center , Weslaco , TX , USA
| | - Mona B Damaj
- a Texas A&M AgriLife Research & Extension Center , Weslaco , TX , USA
| | - Carmen S Padilla
- a Texas A&M AgriLife Research & Extension Center , Weslaco , TX , USA
| | - Ninfa Ramos
- a Texas A&M AgriLife Research & Extension Center , Weslaco , TX , USA
| | - Denise Rossi
- a Texas A&M AgriLife Research & Extension Center , Weslaco , TX , USA
| | - Nora Solís-Gracia
- a Texas A&M AgriLife Research & Extension Center , Weslaco , TX , USA
| | | | - Sonia Irigoyen
- a Texas A&M AgriLife Research & Extension Center , Weslaco , TX , USA
| | - Jorge A DaSilva
- a Texas A&M AgriLife Research & Extension Center , Weslaco , TX , USA.,b Department of Soil & Crop Sciences , Texas A&M University , TX , USA
| | - T Erik Mirkov
- a Texas A&M AgriLife Research & Extension Center , Weslaco , TX , USA.,c Department of Plant Pathology & Microbiology , Texas A&M University , TX , USA
| | - Kranthi K Mandadi
- a Texas A&M AgriLife Research & Extension Center , Weslaco , TX , USA.,c Department of Plant Pathology & Microbiology , Texas A&M University , TX , USA
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10
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Wu Q, Gao S, Pan YB, Su Y, Grisham MP, Guo J, Xu L, Que Y. Heterologous expression of a Glyoxalase I gene from sugarcane confers tolerance to several environmental stresses in bacteria. PeerJ 2018; 6:e5873. [PMID: 30402355 PMCID: PMC6215438 DOI: 10.7717/peerj.5873] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 10/01/2018] [Indexed: 01/02/2023] Open
Abstract
Glyoxalase I belongs to the glyoxalase system that detoxifies methylglyoxal (MG), a cytotoxic by-product produced mainly from triose phosphates. The concentration of MG increases rapidly under stress conditions. In this study, a novel glyoxalase I gene, designated as SoGloI was identified from sugarcane. SoGloI had a size of 1,091 bp with one open reading frame (ORF) of 885 bp encoding a protein of 294 amino acids. SoGloI was predicted as a Ni2+-dependent GLOI protein with two typical glyoxalase domains at positions 28-149 and 159-283, respectively. SoGloI was cloned into an expression plasmid vector, and the Trx-His-S-tag SoGloI protein produced in Escherichia coli was about 51 kDa. The recombinant E. coli cells expressing SoGloI compared to the control grew faster and tolerated higher concentrations of NaCl, CuCl2, CdCl2, or ZnSO4. SoGloI ubiquitously expressed in various sugarcane tissues. The expression was up-regulated under the treatments of NaCl, CuCl2, CdCl2, ZnSO4 and abscisic acid (ABA), or under simulated biotic stress conditions upon exposure to salicylic acid (SA) and methyl jasmonate (MeJA). SoGloI activity steadily increased when sugarcane was subjected to NaCl, CuCl2, CdCl2, or ZnSO4 treatments. Sub-cellular observations indicated that the SoGloI protein was located in both cytosol and nucleus. These results suggest that the SoGloI gene may play an important role in sugarcane's response to various biotic and abiotic stresses.
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Affiliation(s)
- Qibin Wu
- Fujian Agriculture and Forestry University, Key Laboratory of Sugarcane Biology and Genetic Breeding, Fuzhou, Fujian, China
| | - Shiwu Gao
- Fujian Agriculture and Forestry University, Key Laboratory of Sugarcane Biology and Genetic Breeding, Fuzhou, Fujian, China
| | - Yong-Bao Pan
- USDA-ARS, Sugarcane Research Unit, Houma, LA, USA
| | - Yachun Su
- Fujian Agriculture and Forestry University, Key Laboratory of Sugarcane Biology and Genetic Breeding, Fuzhou, Fujian, China
| | | | - Jinlong Guo
- Fujian Agriculture and Forestry University, Key Laboratory of Sugarcane Biology and Genetic Breeding, Fuzhou, Fujian, China
| | - Liping Xu
- Fujian Agriculture and Forestry University, Key Laboratory of Sugarcane Biology and Genetic Breeding, Fuzhou, Fujian, China
| | - Youxiong Que
- Fujian Agriculture and Forestry University, Key Laboratory of Sugarcane Biology and Genetic Breeding, Fuzhou, Fujian, China
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11
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Sánchez-Elordi E, Contreras R, de Armas R, Benito MC, Alarcón B, de Oliveira E, Del Mazo C, Díaz-Peña EM, Santiago R, Vicente C, Legaz ME. Differential expression of SofDIR16 and SofCAD genes in smut resistant and susceptible sugarcane cultivars in response to Sporisorium scitamineum. JOURNAL OF PLANT PHYSIOLOGY 2018; 226:103-113. [PMID: 29753910 DOI: 10.1016/j.jplph.2018.04.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 04/27/2018] [Accepted: 04/30/2018] [Indexed: 05/25/2023]
Abstract
Proteomic profiling of the stalk of a smut resistant and a susceptible sugarcane cultivars revealed the presence of dirigent and dirigent-like proteins in abundance in the pool of high molecular mass (HMMG) and mid-molecular mass (MMMG) glycoproteins, produced as part of the defensive response to the fungal smut pathogen. Quantitative RT-PCR analysis showed that expression levels of SofDIR16 (sugarcane dirigent16) and SofCAD (sugarcane cinnamyl alcohol dehydrogenase) were higher in the smut resistant My 55-14 cultivar than in the sensitive B 42231 cultivar prior to infection. Inoculation with fungal sporidia or water decreased the level of SofCAD transcripts in My 55-14, indicating that regulation of SofCAD expression does not take part of the specific response to smut infection. In contrast, SofDIR16 expression was almost nullified in My 55-14 after inoculation with fungal sporidia, but not after water injection. It is proposed that the decreased expression of dirigent proteins induces the formation of lignans, which are involved in the defense response of the smut resistant My 55-14 cultivar.
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Affiliation(s)
- Elena Sánchez-Elordi
- Intercellular Communication in Plant Symbiosis Team, Faculty of Biology, Complutense University, 28040 Madrid, Spain
| | - Roberto Contreras
- Department of Genetics, Faculty of Biology, Complutense University, 28040 Madrid, Spain
| | | | - Mario C Benito
- Department of Genetics, Faculty of Biology, Complutense University, 28040 Madrid, Spain
| | - Borja Alarcón
- Intercellular Communication in Plant Symbiosis Team, Faculty of Biology, Complutense University, 28040 Madrid, Spain
| | - Eliandre de Oliveira
- Plataforma de Proteómica, Parc Cientific de Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Carlos Del Mazo
- Intercellular Communication in Plant Symbiosis Team, Faculty of Biology, Complutense University, 28040 Madrid, Spain
| | - Eva M Díaz-Peña
- Intercellular Communication in Plant Symbiosis Team, Faculty of Biology, Complutense University, 28040 Madrid, Spain
| | - Rocío Santiago
- Department of Biochemistry and Department of Geographical Sciences, Universidade Federal de Pernambuco, Recife, Brazil
| | - Carlos Vicente
- Intercellular Communication in Plant Symbiosis Team, Faculty of Biology, Complutense University, 28040 Madrid, Spain
| | - María E Legaz
- Intercellular Communication in Plant Symbiosis Team, Faculty of Biology, Complutense University, 28040 Madrid, Spain.
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12
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Cheng X, Su X, Muhammad A, Li M, Zhang J, Sun Y, Li G, Jin Q, Cai Y, Lin Y. Molecular Characterization, Evolution, and Expression Profiling of the Dirigent ( DIR) Family Genes in Chinese White Pear ( Pyrus bretschneideri). Front Genet 2018; 9:136. [PMID: 29713336 PMCID: PMC5911567 DOI: 10.3389/fgene.2018.00136] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 04/03/2018] [Indexed: 01/24/2023] Open
Abstract
Stone cells content and size are the key factors determining the internal quality of the pear fruit. Synthesis of lignin and thickening of secondary cell wall are the keys to the development of stone cells. The polymerization of monolignols and secondary cell wall formation requires the participation of dirigent proteins (DIRs). In recent years, DIR family have been studied in higher plants, but lack of comprehensive study in the pear DIR (PbDIR) family. This study focuses on the identification and analysis of PbDIR family for the first time. We identified 35 PbDIRs from the pear genome, 89% of which are intronless genes. Phylogenetic tree and chromosome localization analysis showed that 35 PbDIRs were divided into four subfamilies (DIR-a, -b/d, -e, and -g) and irregularly distributed among 10 chromosomes. In addition, we identified 29, 26, and 14 DIRs from the other three Rosids (peach, Mei, and grape), respectively. Interspecies microsynteny analysis revealed the collinear gene pairs between pear and peach are the most. Temporal expression analysis showed that the expression changes of seven PbDIRs (DIR-a subfamily: PbDIR4 and PbDIR5; DIR-b/d subfamily: PbDIR11; DIR-g subfamily: PbDIR19; DIR-e subfamily: PbDIR23, 25 and 26) in fruits were consistent with the changes of fruit lignin and stone cells contents. In addition, the subfamily of PbDIRs in fruits showed significant responses after treatment with ABA, SA, and MeJA. According to the protein tertiary structure, key amino acid residues and expression patterns analysis found that PbDIR4 might be involved in the metabolism of lignin and related to stone cells contents in pear fruits. In this study, we systematically analyzed the structure, evolution, function and expression of PbDIR family, which not only confirmed the characteristics of PbDIR family, but also laid the foundation for revealing the role of DIR in pear stone cell development and lignin polymerization.
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Affiliation(s)
- Xi Cheng
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Xueqiang Su
- School of Life Science, Anhui Agricultural University, Hefei, China
| | | | - Manli Li
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Jinyun Zhang
- School of Life Science, Anhui Agricultural University, Hefei, China.,Institute of Horticultural, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yanming Sun
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Guohui Li
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Qing Jin
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Yongping Cai
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Yi Lin
- School of Life Science, Anhui Agricultural University, Hefei, China
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13
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Genome-wide analysis of dirigent gene family in pepper (Capsicum annuum L.) and characterization of CaDIR7 in biotic and abiotic stresses. Sci Rep 2018; 8:5500. [PMID: 29615685 PMCID: PMC5883049 DOI: 10.1038/s41598-018-23761-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 03/19/2018] [Indexed: 11/22/2022] Open
Abstract
The dirigent (DIR and DIR-like) proteins involved in lignification, play a pivotal role against biotic and abiotic stresses in plants. However, no information is available about DIR gene family in pepper (Capsicum annuum L.). In this study, 24 putative dirigent genes (CaDIRs) were identified, their gene structure, genome location, gene duplication and phylogenetic relationship were elucidated. Tissue-specific expression analysis displayed the highest transcription levels in flower, stem and leaf. Some CaDIRs were up-regulated by virulent (CaDIR2, 3, 6, 7, 11, 14, 16, 22 and 23) and avirulent (CaDIR3, 5, 7, 16, 20, 22, 23 and 24) Phytophthora capsici strains, as well as by Methyl jasmonate, salicylic acid, NaCl and mannitol stresses. Acid-soluble lignin content increased (103.21%) after P. capsici inoculation (48-hour). Silencing of CaDIR7 weakened plant defense by reducing (~50%) root activity and made plants more susceptible (35.7%) to P. capsici and NaCl (300 mM). Leaf discs of the CaDIR7:silenced plants exposed to NaCl and mannitol (300 mM each), exhibited a significant decrease (56.25% and 48% respectively) in the chlorophyll content. These results suggested that CaDIR7 is involved in pepper defense response against pathogen and abiotic stresses and the study will provide basic insights for future research regarding CaDIRs.
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14
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Cheavegatti-Gianotto A, Gentile A, Oldemburgo DA, Merheb GDA, Sereno ML, Lirette RP, Ferreira THS, de Oliveira WS. Lack of Detection of Bt Sugarcane Cry1Ab and NptII DNA and Proteins in Sugarcane Processing Products Including Raw Sugar. Front Bioeng Biotechnol 2018; 6:24. [PMID: 29637070 PMCID: PMC5880997 DOI: 10.3389/fbioe.2018.00024] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 02/28/2018] [Indexed: 11/26/2022] Open
Abstract
Brazil is the largest sugarcane producer and the main sugar exporter in the world. The industrial processes applied by Brazilian mills are very efficient in producing highly purified sugar and ethanol. Literature presents evidence of lack of DNA/protein in these products, regardless of the nature of sugarcane used as raw material. Recently CTNBio, the Brazilian biosafety authority, has approved the first biotechnology-derived sugarcane variety for cultivation, event CTC175-A, which expresses the Cry1Ab protein to control the sugarcane borer (Diatraea saccharalis). The event also expresses neomycin-phosphotransferase type II (NptII) protein used as selectable marker during the transformation process. Because of the high purity of sugar and ethanol produced from genetically modified sugarcane, these end-products should potentially be classified as “pure substances, chemically defined,” by Brazilian Biosafety Law No. 11.105. If this classification is to be adopted, these substances are not considered as “GMO derivatives” and fall out of the scope of Law No. 11.105. In order to assess sugar composition and quality, we evaluate Cry1Ab and NptII expression in several sugarcane tissues and in several fractions from laboratory-scale processing of event CTC175-A for the presence of these heterologous proteins as well as for the presence of traces of recombinant DNA. The results of these studies show that CTC175-A presents high expression of Cry1Ab in leaves and barely detectable expression of heterologous proteins in stalks. We also evaluated the presence of ribulose-1,5-bisphosphate carboxylase/oxygenase protein and DNA in the fractions of the industrial processing of conventional Brazilian sugarcane cultivars. Results from both laboratory and industrial processing were concordant, demonstrating that DNA and protein are not detected in the clarified juice and downstream processed fractions, including ethanol and raw sugar, indicating that protein and DNA are removed and/or degraded during processing. In conclusion, the processing of conventional sugarcane and CTC175-A Bt event results in downstream products with no detectable concentrations of heterologous DNA or new protein. These results help in the classification of sugar and ethanol derived from CTC175-A event as pure, chemically defined substances in Brazil and may relieve regulatory burdens in countries that import Brazilian sugar.
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Affiliation(s)
| | - Agustina Gentile
- Biotechnology Department, Centro de Tecnologia Canavieira (CTC), Piracicaba, Brazil
| | | | | | - Maria Lorena Sereno
- Regulatory Department, Centro de Tecnologia Canavieira (CTC), Piracicaba, Brazil
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15
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Chiong KT, Damaj MB, Padilla CS, Avila CA, Pant SR, Mandadi KK, Ramos NR, Carvalho DV, Mirkov TE. Reproducible genomic DNA preparation from diverse crop species for molecular genetic applications. PLANT METHODS 2017; 13:106. [PMID: 29213298 PMCID: PMC5712126 DOI: 10.1186/s13007-017-0255-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 11/20/2017] [Indexed: 06/02/2023]
Abstract
BACKGROUND Several high-throughput molecular genetic analyses rely on high-quality genomic DNA. Copurification of other molecules can negatively impact the functionality of plant DNA preparations employed in these procedures. Isolating DNA from agronomically important crops, such as sugarcane, rice, citrus, potato and tomato is a challenge due to the presence of high fiber, polysaccharides, or secondary metabolites. We present a simplified, rapid and reproducible SDS-based method that provides high-quality and -quantity of DNA from small amounts of leaf tissue, as required by the emerging biotechnology and molecular genetic applications. RESULTS We developed the TENS-CO method as a simplified SDS-based isolation procedure with sequential steps of purification to remove polysaccharides and polyphenols using 2-mercaptoethanol and potassium acetate, chloroform partitioning, and sodium acetate/ethanol precipitation to yield high-quantity and -quality DNA consistently from small amounts of tissue (0.15 g) for different plant species. The method is simplified and rapid in terms of requiring minimal manipulation, smaller extraction volume, reduced homogenization time (20 s) and DNA precipitation (one precipitation for 1 h). The method has been demonstrated to accelerate screening of large amounts of plant tissues from species that are rich in polysaccharides and secondary metabolites for Southern blot analysis of reporter gene overexpressing lines, pathogen detection by quantitative PCR, and genotyping of disease-resistant plants using marker-assisted selection. CONCLUSION To facilitate molecular genetic studies in major agronomical crops, we have developed the TENS-CO method as a simple, rapid, reproducible and scalable protocol enabling efficient and robust isolation of high-quality and -quantity DNA from small amounts of tissue from sugarcane, rice, citrus, potato, and tomato, thereby reducing significantly the time and resources used for DNA isolation.
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Affiliation(s)
- Kelvin T. Chiong
- Texas A&M AgriLife Research and Extension Center, 2415 East US Highway 83, Weslaco, TX 78596 USA
- Present Address: Department of Plant Pathology and Microbiology, Texas A&M University, 2132 TAMU, College Station, TX 77843 USA
| | - Mona B. Damaj
- Texas A&M AgriLife Research and Extension Center, 2415 East US Highway 83, Weslaco, TX 78596 USA
| | - Carmen S. Padilla
- Texas A&M AgriLife Research and Extension Center, 2415 East US Highway 83, Weslaco, TX 78596 USA
| | - Carlos A. Avila
- Texas A&M AgriLife Research and Extension Center, 2415 East US Highway 83, Weslaco, TX 78596 USA
- Department of Horticultural Sciences, Texas A&M University, 2133 TAMU, College Station, TX 77843 USA
| | - Shankar R. Pant
- Texas A&M AgriLife Research and Extension Center, 2415 East US Highway 83, Weslaco, TX 78596 USA
| | - Kranthi K. Mandadi
- Texas A&M AgriLife Research and Extension Center, 2415 East US Highway 83, Weslaco, TX 78596 USA
- Department of Plant Pathology and Microbiology, Texas A&M University, 2132 TAMU, College Station, TX 77843 USA
| | - Ninfa R. Ramos
- Texas A&M AgriLife Research and Extension Center, 2415 East US Highway 83, Weslaco, TX 78596 USA
| | - Denise V. Carvalho
- Texas A&M AgriLife Research and Extension Center, 2415 East US Highway 83, Weslaco, TX 78596 USA
- Present Address: FuturaGene Ltd, Av. Dr. José Lembo, #1010 Bairro, Jardim Bela Vista, Itapetininga, São Paulo Brazil
| | - T. Erik Mirkov
- Texas A&M AgriLife Research and Extension Center, 2415 East US Highway 83, Weslaco, TX 78596 USA
- Department of Plant Pathology and Microbiology, Texas A&M University, 2132 TAMU, College Station, TX 77843 USA
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16
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Identification, classification and transcriptional profiles of dirigent domain-containing proteins in sugarcane. Mol Genet Genomics 2017; 292:1323-1340. [PMID: 28699001 DOI: 10.1007/s00438-017-1349-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/04/2017] [Indexed: 01/13/2023]
Abstract
Dirigent (DIR) proteins, encoded by DIR genes, are referred to as "dirigent" because they direct the outcome of the coupling of the monolignol coniferyl alcohol into (+) or (-) pinoresinol, the first intermediates in the enantiocomplementary pathways for lignan biosynthesis. DIR domain-containing or DIR-like proteins are, thus, termed for not having a clear characterization. A transcriptome- and genome-wide survey of DIR domain-containing proteins in sugarcane was carried out, in addition to phylogenetic, physicochemical and transcriptional analyses. A total of 120 non-redundant sequences containing the DIR domain were identified and classified into 64 groups according to phylogenetic and sequence alignment analyses. In silico analysis of transcript abundance showed that these sequences are expressed at low levels in leaves and genes in the same phylogenetic clade have similar expression patterns. Expression analysis of ShDIR1-like transcripts in the culm internodes of sugarcane demonstrates their abundance in mature internodes, their induction by nitrogen fertilization and their predominant expression in cells that have a lignified secondary cell wall, such as vascular bundles of young internodes and parenchymal cells of the pith of mature internodes. Due to the lack of information about the functional role of DIR in plants, a possible relationship is discussed between the ShDIR1-like transcriptional profile and cell wall development in parenchyma cells of sugarcane culm, which typically accumulates large amounts of sucrose. The number of genes encoding the DIR domain-containing proteins in sugarcane is intriguing and is an indication per se that these proteins may have an important metabolic role and thus deserve to be better studied.
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17
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Gao SJ, Damaj MB, Park JW, Wu XB, Sun SR, Chen RK, Mirkov TE. A novel Sugarcane bacilliform virus promoter confers gene expression preferentially in the vascular bundle and storage parenchyma of the sugarcane culm. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:172. [PMID: 28680479 PMCID: PMC5496340 DOI: 10.1186/s13068-017-0850-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 06/16/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Saccharum species such as sugarcane and energy cane are key players in the expanding bioeconomy for sugars, bioenergy, and production of high-value proteins. Genomic tools such as culm-regulated promoters would be of great value in terms of improving biomass characteristics through enhanced carbon metabolism for sugar accumulation and/or fiber content for biofuel feedstock. Unlike the situation in dicots, monocot promoters currently used are limited and mostly derived from highly expressed constitutive plant genes and viruses. In this study, a novel promoter region of Sugarcane bacilliform virus (SCBV; genus Badnavirus, family Caulimoviridae), SCBV21 was cloned and mapped by deletion analysis and functionally characterized transiently in monocot and dicot species and stably in sugarcane. RESULTS In silico analysis of SCBV21 [1816 base pair (bp)] identified two putative promoter regions (PPR1 and PPR2) with transcription start sites (TSS1 and TSS2) and two TATA-boxes (TATAAAT and ATATAA), and several vascular-specific and regulatory elements. Deletion analysis revealed that the 710 bp region spanning PPR2 (with TSS2 and ATATAA) at the 3' end of SCBV21 retained the full promoter activity in both dicots and monocots, as shown by transient expression of the enhanced yellow fluorescent protein (EYFP) gene. In sugarcane young leaf segments, SCBV21 directed a 1.8- and 2.4-fold higher transient EYFP expression than the common maize ubiquitin 1 (Ubi1) and Cauliflower mosaic virus 35S promoters, respectively. In transgenic sugarcane, SCBV21 conferred a preferential expression of the β-glucuronidase (GUS) gene in leaves and culms and specifically in the culm storage parenchyma surrounding the vascular bundle and in vascular phloem cells. Among the transgenic events and tissues characterized in this study, the SCBV21 promoter frequently produced higher GUS activity than the Ubi1 or 35S promoters in a manner that was not obviously correlated with the transgene copy number. CONCLUSIONS The newly developed plant viral SCBV21 promoter is distinct from the few existing SCBV promoters in its sequence and expression pattern. The potential of SCBV21 as a tissue-regulated promoter with a strong activity in the culm vascular bundle and its storage parenchyma makes it useful in sugarcane engineering for improved carbon metabolism, increased bioenergy production, and enhanced stress tolerance.
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Affiliation(s)
- San-Ji Gao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | | | | | - Xiao-Bin Wu
- Guangdong Key Lab of Sugarcane Improvement & Biorefinery, Guangzhou Sugarcane Industry Research Institute, Guangzhou, 510316 Guangdong China
| | - Sheng-Ren Sun
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Ru-Kai Chen
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
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18
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Li N, Zhao M, Liu T, Dong L, Cheng Q, Wu J, Wang L, Chen X, Zhang C, Lu W, Xu P, Zhang S. A Novel Soybean Dirigent Gene GmDIR22 Contributes to Promotion of Lignan Biosynthesis and Enhances Resistance to Phytophthora sojae. FRONTIERS IN PLANT SCIENCE 2017; 8:1185. [PMID: 28725237 PMCID: PMC5495835 DOI: 10.3389/fpls.2017.01185] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 06/21/2017] [Indexed: 05/20/2023]
Abstract
Phytophthora root and stem rot caused by the oomycete pathogen Phytophthora sojae is a destructive disease of soybean worldwide. Plant dirigent proteins (DIR) are proposed to have roles in biosynthesis of either lignan or lignin-like molecules, and are important for defense responses, secondary metabolism, and pathogen resistance. In the present work, a novel DIR gene expressed sequence tag is identified as up-regulated in the highly resistant soybean cultivar 'Suinong 10' inoculated with P. sojae. The full length cDNA is isolated using rapid amplification of cDNA ends, and designated GmDIR22 (GenBank accession no. HQ_993047). The full length GmDIR22 is 789 bp and contains a 567 bp open reading frame encoding a polypeptide of 188 amino acids. The sequence analysis indicated that GmDIR22 contains a conserved dirigent domain at amino acid residues 43-187. The quantitative real-time reverse transcription PCR demonstrated that soybean GmDIR22 mRNA is expressed most highly in stems, followed by roots and leaves. The treatments with stresses demonstrated that GmDIR22 is significantly induced by P. sojae and gibberellic acid (GA3), and also responds to salicylic acid, methyl jasmonic acid, and abscisic acid. The GmDIR22 is targeted to the cytomembrane when transiently expressed in Arabidopsis protoplasts. Moreover, The GmDIR22 recombinant protein purified from Escherichia coli could effectively direct E-coniferyl alcohol coupling into lignan (+)-pinoresinol. Accordingly, the overexpression of GmDIR22 in transgenic soybean increased total lignan accumulation. Moreover, the lignan extracts from GmDIR22 transgenic plants effectively inhibits P. sojae hyphal growth. Furthermore, the transgenic overexpression of GmDIR22 in the susceptible soybean cultivar 'Dongnong 50' enhances its resistance to P. sojae. Collectively, these data suggested that the primary role of GmDIR22 is probably involved in the regulation of lignan biosynthesis, and which contributes to resistance to P. sojae.
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Affiliation(s)
- Ninghui Li
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
- Jiamusi Branch of Heilongjiang Academy of Agricultural SciencesJiamusi, China
| | - Ming Zhao
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Tengfei Liu
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Lidong Dong
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Qun Cheng
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Junjiang Wu
- Key Laboratory of Soybean Cultivation of Ministry of Agriculture China, Soybean Research Institute, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Le Wang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Xi Chen
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Chuanzhong Zhang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Wencheng Lu
- Heihe Branch of Heilongjiang Academy of Agricultural SciencesHeihe, China
| | - Pengfei Xu
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
| | - Shuzhen Zhang
- Key Laboratory of Soybean Biology of Chinese Education Ministry, Soybean Research Institute, Northeast Agricultural UniversityHarbin, China
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19
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Casu RE, Rae AL, Nielsen JM, Perroux JM, Bonnett GD, Manners JM. Tissue-specific transcriptome analysis within the maturing sugarcane stalk reveals spatial regulation in the expression of cellulose synthase and sucrose transporter gene families. PLANT MOLECULAR BIOLOGY 2015; 89:607-28. [PMID: 26456093 DOI: 10.1007/s11103-015-0388-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 09/29/2015] [Indexed: 05/23/2023]
Abstract
Sugarcane (Saccharum spp. hybrids) accumulates high concentrations of sucrose in its mature stalk and a considerable portion of carbohydrate metabolism is also devoted to cell wall synthesis and fibre production. We examined tissue-specific expression patterns to explore the spatial deployment of pathways responsible for sucrose accumulation and fibre synthesis within the stalk. We performed expression profiling of storage parenchyma, vascular bundles and rind dissected from a maturing stalk internode of sugarcane, identifying ten cellulose synthase subunit genes and examining significant differences in the expression of their corresponding transcripts and those of several sugar transporters. These were correlated with differential expression patterns for transcripts of genes encoding COBRA-like proteins and other cell wall metabolism-related proteins. The sugar transporters genes ShPST2a, ShPST2b and ShSUT4 were significantly up-regulated in storage parenchyma while ShSUT1 was up-regulated in vascular bundles. Two co-ordinately expressed groups of cell wall related transcripts were also identified. One group, associated with primary cell wall synthesis (ShCesA1, ShCesA7, ShCesA9 and Shbk2l3), was up-regulated in parenchyma. The other group, associated with secondary cell wall synthesis (ShCesA10, ShCesA11, ShCesA12 and Shbk-2), was up-regulated in rind. In transformed sugarcane plants, the ShCesA7 promoter conferred stable expression of green fluorescent protein preferentially in the storage parenchyma of the maturing stalk internode. Our results indicate that there is spatial separation for elevated expression of these important targets in both sucrose accumulation and cell wall synthesis, allowing for increased clarity in our understanding of sucrose transport and fibre synthesis in sugarcane.
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Affiliation(s)
- Rosanne E Casu
- CSIRO Agriculture, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, QLD, 4067, Australia.
| | - Anne L Rae
- CSIRO Agriculture, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, QLD, 4067, Australia
| | - Janine M Nielsen
- CSIRO Agriculture, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, QLD, 4067, Australia
| | - Jai M Perroux
- CSIRO Agriculture, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, QLD, 4067, Australia
| | - Graham D Bonnett
- CSIRO Agriculture, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, QLD, 4067, Australia
| | - John M Manners
- CSIRO Agriculture, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, QLD, 4067, Australia
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Lambret-Frotté J, de Almeida LCS, de Moura SM, Souza FLF, Linhares FS, Alves-Ferreira M. Validating Internal Control Genes for the Accurate Normalization of qPCR Expression Analysis of the Novel Model Plant Setaria viridis. PLoS One 2015; 10:e0135006. [PMID: 26247784 PMCID: PMC4527663 DOI: 10.1371/journal.pone.0135006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 07/15/2015] [Indexed: 01/10/2023] Open
Abstract
Employing reference genes to normalize the data generated with quantitative PCR (qPCR) can increase the accuracy and reliability of this method. Previous results have shown that no single housekeeping gene can be universally applied to all experiments. Thus, the identification of a suitable reference gene represents a critical step of any qPCR analysis. Setaria viridis has recently been proposed as a model system for the study of Panicoid grasses, a crop family of major agronomic importance. Therefore, this paper aims to identify suitable S. viridis reference genes that can enhance the analysis of gene expression in this novel model plant. The first aim of this study was the identification of a suitable RNA extraction method that could retrieve a high quality and yield of RNA. After this, two distinct algorithms were used to assess the gene expression of fifteen different candidate genes in eighteen different samples, which were divided into two major datasets, the developmental and the leaf gradient. The best-ranked pair of reference genes from the developmental dataset included genes that encoded a phosphoglucomutase and a folylpolyglutamate synthase; genes that encoded a cullin and the same phosphoglucomutase as above were the most stable genes in the leaf gradient dataset. Additionally, the expression pattern of two target genes, a SvAP3/PI MADS-box transcription factor and the carbon-fixation enzyme PEPC, were assessed to illustrate the reliability of the chosen reference genes. This study has shown that novel reference genes may perform better than traditional housekeeping genes, a phenomenon which has been previously reported. These results illustrate the importance of carefully validating reference gene candidates for each experimental set before employing them as universal standards. Additionally, the robustness of the expression of the target genes may increase the utility of S. viridis as a model for Panicoid grasses.
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Affiliation(s)
- Julia Lambret-Frotté
- Department of Genetics, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, Brazil
| | | | - Stéfanie M. de Moura
- Department of Genetics, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, Brazil
| | - Flavio L. F. Souza
- Department of Genetics, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, Brazil
| | - Francisco S. Linhares
- Department of Genetics, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, Brazil
| | - Marcio Alves-Ferreira
- Department of Genetics, Universidade Federal do Rio de Janeiro, UFRJ, Rio de Janeiro, Brazil
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Abstract
With current advances in genomics, several technological processes have been generated, resulting in improvement in different segments of molecular research involving prokaryotic and eukaryotic systems. A widely used contribution is the identification of new genes and their functions, which has led to the elucidation of several issues concerning cell regulation and interactions. For this, increase in the knowledge generated from the identification of promoters becomes considerably relevant, especially considering that to generate new technological processes, such as genetically modified organisms, the availability of promoters that regulate the expression of new genes is still limited. Considering that this issue is essential for biotechnologists, this paper presents an updated review of promoters, from their structure to expression, and focuses on the knowledge already available in eukaryotic systems. Information on current promoters and methodologies available for studying their expression are also reported.
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Molecular Profiling of Systemic Acquired Resistance (SAR)-Responsive Transcripts in Sugarcane Challenged with Colletotrichum falcatum. Appl Biochem Biotechnol 2014; 174:2839-50. [DOI: 10.1007/s12010-014-1230-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 09/10/2014] [Indexed: 01/24/2023]
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23
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Chou TC, Moyle RL. Synthetic versions of firefly luciferase and Renilla luciferase reporter genes that resist transgene silencing in sugarcane. BMC PLANT BIOLOGY 2014; 14:92. [PMID: 24708613 PMCID: PMC4021088 DOI: 10.1186/1471-2229-14-92] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 03/31/2014] [Indexed: 05/10/2023]
Abstract
BACKGROUND Down-regulation or silencing of transgene expression can be a major hurdle to both molecular studies and biotechnology applications in many plant species. Sugarcane is particularly effective at silencing introduced transgenes, including reporter genes such as the firefly luciferase gene.Synthesizing transgene coding sequences optimized for usage in the host plant is one method of enhancing transgene expression and stability. Using specified design rules we have synthesised new coding sequences for both the firefly luciferase and Renilla luciferase reporter genes. We have tested these optimized versions for enhanced levels of luciferase activity and for increased steady state luciferase mRNA levels in sugarcane. RESULTS The synthetic firefly luciferase (luc*) and Renilla luciferase (Renluc*) coding sequences have elevated G + C contents in line with sugarcane codon usage, but maintain 75% identity to the native firefly or Renilla luciferase nucleotide sequences and 100% identity to the protein coding sequences.Under the control of the maize pUbi promoter, the synthetic luc* and Renluc* genes yielded 60x and 15x higher luciferase activity respectively, over the native firefly and Renilla luciferase genes in transient assays on sugarcane suspension cell cultures.Using a novel transient assay in sugarcane suspension cells combining co-bombardment and qRT-PCR, we showed that synthetic luc* and Renluc* genes generate increased transcript levels compared to the native firefly and Renilla luciferase genes.In stable transgenic lines, the luc* transgene generated significantly higher levels of expression than the native firefly luciferase transgene. The fold difference in expression was highest in the youngest tissues. CONCLUSIONS We developed synthetic versions of both the firefly and Renilla luciferase reporter genes that resist transgene silencing in sugarcane. These transgenes will be particularly useful for evaluating the expression patterns conferred by existing and newly isolated promoters in sugarcane tissues. The strategies used to design the synthetic luciferase transgenes could be applied to other transgenes that are aggressively silenced in sugarcane.
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MESH Headings
- Gene Expression Regulation, Plant
- Gene Silencing
- Genes, Plant
- Genes, Reporter
- Luciferases, Firefly/genetics
- Luciferases, Renilla/genetics
- Luminescent Measurements
- Open Reading Frames/genetics
- Plant Cells/metabolism
- Plant Stems/metabolism
- Plants, Genetically Modified
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Saccharum/genetics
- Sequence Alignment
- Sequence Analysis, DNA
- Suspensions
- Synthetic Biology
- Transformation, Genetic
- Transgenes/genetics
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Affiliation(s)
- Ting-Chun Chou
- School of Agriculture and Food Sciences, University of Queensland, Brisbane 4072, Australia
| | - Richard L Moyle
- School of Agriculture and Food Sciences, University of Queensland, Brisbane 4072, Australia
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Kinkema M, Geijskes J, Delucca P, Palupe A, Shand K, Coleman HD, Brinin A, Williams B, Sainz M, Dale JL. Improved molecular tools for sugar cane biotechnology. PLANT MOLECULAR BIOLOGY 2014; 84:497-508. [PMID: 24150836 DOI: 10.1007/s11103-013-0147-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 10/16/2013] [Indexed: 06/02/2023]
Abstract
Sugar cane is a major source of food and fuel worldwide. Biotechnology has the potential to improve economically-important traits in sugar cane as well as diversify sugar cane beyond traditional applications such as sucrose production. High levels of transgene expression are key to the success of improving crops through biotechnology. Here we describe new molecular tools that both expand and improve gene expression capabilities in sugar cane. We have identified promoters that can be used to drive high levels of gene expression in the leaf and stem of transgenic sugar cane. One of these promoters, derived from the Cestrum yellow leaf curling virus, drives levels of constitutive transgene expression that are significantly higher than those achieved by the historical benchmark maize polyubiquitin-1 (Zm-Ubi1) promoter. A second promoter, the maize phosphonenolpyruvate carboxylate promoter, was found to be a strong, leaf-preferred promoter that enables levels of expression comparable to Zm-Ubi1 in this organ. Transgene expression was increased approximately 50-fold by gene modification, which included optimising the codon usage of the coding sequence to better suit sugar cane. We also describe a novel dual transcriptional enhancer that increased gene expression from different promoters, boosting expression from Zm-Ubi1 over eightfold. These molecular tools will be extremely valuable for the improvement of sugar cane through biotechnology.
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Affiliation(s)
- Mark Kinkema
- Syngenta Centre for Sugar Cane Biofuels Development, Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, 4001, Australia,
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25
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Su YC, Xu LP, Xue BT, Wu QB, Guo JL, Wu LG, Que YX. Molecular cloning and characterization of two pathogenesis-related β-1,3-glucanase genes ScGluA1 and ScGluD1 from sugarcane infected by Sporisorium scitamineum. PLANT CELL REPORTS 2013; 32:1503-19. [PMID: 23842883 DOI: 10.1007/s00299-013-1463-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/23/2013] [Accepted: 05/22/2013] [Indexed: 05/02/2023]
Abstract
Two β-1,3-glucanase genes from sugarcane were cloned and characterized. They were all located in apoplast and involves in different expression patterns in biotic and abiotic stress. Smut caused by Sporisorium scitamineum is a serious disease in the sugarcane industry. β-1,3-Glucanase, a typical pathogenesis-related protein, has been shown to express during plant-pathogen interaction and involves in sugarcane defense response. In this study, β-1,3-glucanase enzyme activity in the resistant variety increased faster and lasted longer than that of the susceptible one when inoculated with S. scitamineum, along with a positive correlation between the activity of the β-1,3-glucanase and smut resistance. Furthermore, two β-1,3-glucanase genes from S. scitamineum infected sugarcane, ScGluA1 (GenBank Accession No. KC848050) and ScGluD1 (GenBank Accession No. KC848051) were cloned and characterized. Phylogenetic analysis suggested that ScGluA1 and ScGluD1 clustered within subfamily A and subfamily D, respectively. Subcellular localization analysis demonstrated that both gene products were targeted to apoplast. Escherichia coli Rosetta (DE3) cells expressing ScGluA1 and ScGluD1 showed varying degrees of tolerance to NaCl, CdCl2, PEG, CuCl2 and ZnSO4. Q-PCR analysis showed up-regulation of ScGluA1 and slight down-regulation of ScGluD1 in response to S. scitamineum infection. It suggested that ScGluA1 may be involved in the defense reaction of the sugarcane to the smut, while it is likely that ScGluD1 was inhibited. The gene expression patterns of ScGluA1 and ScGluD1, in response to abiotic stresses, were similar to sugarcane response against smut infection. Together, β-1,3-glucanase may function in sugarcane defense mechanism for S. scitamineum. The positive responses of ScGluA1 and the negative responses of ScGluD1 to biotic and abiotic stresses indicate they play different roles in interaction between sugarcane and biotic or abiotic stresses.
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Affiliation(s)
- Ya-chun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou, 350002, China
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26
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Moyle RL, Birch RG. Diversity of sequences and expression patterns among alleles of a sugarcane loading stem gene. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1775-82. [PMID: 23546592 DOI: 10.1007/s00122-013-2091-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 03/21/2013] [Indexed: 05/13/2023]
Abstract
Modern sugarcane cultivars are highly polyploid and aneuploid hybrids, which are propagated as clones. Their complex genome structure comprises 100-130 chromosomes and 10-13 hom(e)ologous copies of most loci. There is preliminary evidence of very high heterozygosity, with implications for genetic improvement approaches ranging from marker-assisted selection to transgenics. Here, we report that sugarcane cultivar Q200 has at least nine alleles at the Loading Stem Gene (ScLSG) locus. Exon-intron structure is identical and the predicted protein products show at least 92 % identity, across sugarcane alleles and the Sorghum homologue Sb07g027880. There is substantial variation in the 5' UTR and promoter regions including numerous allele-specific nucleotide polymorphisms, insertions and deletions. We developed an allele-specific qRT-PCR method to undertake the first compelling test of allele-specific expression in polyploid sugarcane. Seven alleles distinguished by this method all showed peak expression in the sucrose-loading zone of the stem, but there was apparent variability in expression patterns across other tissues. The ScLSG2 and ScLSG5 alleles appear promising for specificity of expression in stems, relative to leaf, meristem, emerging shoot and root tissues. Within the stem, there was activity in parenchyma, vascular and rind tissues. This expression pattern is of interest in basic research and biotechnology aimed at enhanced sucrose content, engineering value-added products, and manipulation of stem biomass composition.
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Affiliation(s)
- Richard L Moyle
- Hines Plant Science Building, University of Queensland, Brisbane 4072, Australia
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27
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Mudge SR, Basnayake SWV, Moyle RL, Osabe K, Graham MW, Morgan TE, Birch RG. Mature-stem expression of a silencing-resistant sucrose isomerase gene drives isomaltulose accumulation to high levels in sugarcane. PLANT BIOTECHNOLOGY JOURNAL 2013; 11:502-9. [PMID: 23297683 DOI: 10.1111/pbi.12038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 11/22/2012] [Accepted: 11/26/2012] [Indexed: 05/25/2023]
Abstract
Isomaltulose (IM) is a natural isomer of sucrose. It is widely approved as a food with properties including slower digestion, lower glycaemic index and low cariogenicity, which can benefit consumers. Availability is currently limited by the cost of fermentative conversion from sucrose. Transgenic sugarcane plants with developmentally-controlled expression of a silencing-resistant gene encoding a vacuole-targeted IM synthase were tested under field conditions typical of commercial sugarcane cultivation. High yields of IM were obtained, up to 483 mm or 81% of total sugars in whole-cane juice from plants aged 13 months. Using promoters from sugarcane to drive expression preferentially in the sugarcane stem, IM levels were consistent between stalks and stools within a transgenic line and across consecutive vegetative field generations of tested high-isomer lines. Germination and early growth of plants from setts were unaffected by IM accumulation, up to the tested level around 500 mm in flanking stem internodes. These are the highest yields ever achieved of value-added materials through plant metabolic engineering. The sugarcane stem promoters are promising for strategies to achieve even higher IM levels and for other applications in sugarcane molecular improvement. Silencing-resistant transgenes are critical to deliver the potential of these promoters in practical sugarcane improvement. At the IM levels now achieved in field-grown sugarcane, direct production of IM in plants is feasible at a cost approaching that of sucrose, which should make the benefits of IM affordable on a much wider scale.
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Affiliation(s)
- Stephen R Mudge
- Hines Plant Science Building, The University of Queensland, Brisbane, Qld, Australia
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28
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Moyle RL, Birch RG. Sugarcane Loading Stem Gene promoters drive transgene expression preferentially in the stem. PLANT MOLECULAR BIOLOGY 2013; 82:51-8. [PMID: 23479084 DOI: 10.1007/s11103-013-0034-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 02/21/2013] [Indexed: 05/10/2023]
Abstract
Promoter regions of six sugarcane Loading Stem Gene (ScLSG) alleles were analyzed using bioinformatic and transgenic approaches. Stable transgene expression analyses, on multiple independent lines per construct, revealed differences between ScLSG promoters in absolute levels and in tissue-selectivity of luciferase reporter activity. Four promoters drove peak expression in the sucrose-loading zone and maintained substantial expression throughout mature stems. One drove a pattern of gradual increase along the stem maturation profile. In general, stem: root expression ratio increased with plant age. The ScLSG5 promoter had the fewest light-enhanced and root-expression motifs in bioinformatic analysis, and drove the highest level and specificity of transgene expression in stems. This indicates the potential to further improve the stem specificity of ScLSG promoter sequences by eliminating enhancers of expression in other tissues. An intron in the 5'UTR was important for expression strength. The ScLSG promoters will be useful for research and biotechnology in sugarcane, where the tailored expression of transgenes in stems is important for enhanced accumulation of sugar or value-added products, and for development as a bioenergy feedstock.
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Affiliation(s)
- Richard L Moyle
- Hines Plant Science Building, The University of Queensland, Brisbane 4072, Australia
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29
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Jirschitzka J, Mattern DJ, Gershenzon J, D'Auria JC. Learning from nature: new approaches to the metabolic engineering of plant defense pathways. Curr Opin Biotechnol 2012; 24:320-8. [PMID: 23141769 DOI: 10.1016/j.copbio.2012.10.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 10/12/2012] [Accepted: 10/18/2012] [Indexed: 12/31/2022]
Abstract
Biotechnological manipulation of plant defense pathways can increase crop resistance to herbivores and pathogens while also increasing yields of medicinal, industrial, flavor and fragrance compounds. The most successful achievements in engineering defense pathways can be attributed to researchers striving to imitate natural plant regulatory mechanisms. For example, the introduction of transcription factors that control several genes in one pathway is often a valuable strategy to increase flux in that pathway. The use of multi-gene cassettes which mimic natural gene clusters can facilitate coordinated regulation of a pathway and speed transformation efforts. The targeting of defense pathway genes to organs and tissues in which the defensive products are typically made and stored can also increase yield as well as defensive potential.
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Affiliation(s)
- Jan Jirschitzka
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, D-07745 Jena, Germany
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30
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Jin-Long G, Li-Ping X, Jing-Ping F, Ya-Chun S, Hua-Ying F, You-Xiong Q, Jing-Sheng X. A novel dirigent protein gene with highly stem-specific expression from sugarcane, response to drought, salt and oxidative stresses. PLANT CELL REPORTS 2012; 31:1801-12. [PMID: 22696141 DOI: 10.1007/s00299-012-1293-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2012] [Revised: 05/18/2012] [Accepted: 05/25/2012] [Indexed: 05/02/2023]
Abstract
Dirigent and dirigent-like family proteins contain a number of proteins involved in lignification or in the response to pathogen infection and abiotic stress in plants. In the present study, a full-length cDNA sequence of a dirigent-like gene designated ScDir (GenBank Accession Number JQ622282) was obtained from sugarcane based on the stem full-length cDNA library. The ScDir gene was 819-bp long, including a 564-bp ORF encoding 187 amino acid residues. The protein N-terminus contained signal peptides at amino acid residues of 1-25 and transmembrane regions at 7-26 aa. A his-tagged ScDir protein with an estimated molecular mass of 27.4 kDa was expressed in Escherichia coli system. The expressed ScDir protein had increased the host cell's tolerance to PEG and NaCl. When an endogenous GAPDH gene was used as internal control, results from real-time qPCR demonstrated that the ScDir mRNA amount in sugarcane stems was significantly higher than that in the roots, leaves and buds by 18.64 ± 0.48, 25,635.16 ± 2,966.03 and 721.50 ± 8.17-fold, respectively. The ScDir transcript levels in sugarcane seedling increased under H(2)O(2), PEG or NaCl stress. The expression level of ScDir was significantly upregulated under PEG stress, and the highest level was observed at 12 h after stress. Thus, both the ScDir-hosted cell performance and the enhanced expressions in sugarcane imply that the ScDir gene is involved in the response to abiotic stresses of drought, salts and oxidation. The transcription of the ScDir gene is highly stem-specific, as revealed by real-time qPCR. Key message A novel sugarcane Sc-Dir gene, DIRd subfamily, which is highly stalk-specific expression and involved in the response to artificial stresses of drought, salts, and oxidatives.
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Affiliation(s)
- Guo Jin-Long
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou, 350002, China
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31
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Egelkrout E, Rajan V, Howard JA. Overproduction of recombinant proteins in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 184:83-101. [PMID: 22284713 DOI: 10.1016/j.plantsci.2011.12.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 12/06/2011] [Accepted: 12/09/2011] [Indexed: 05/21/2023]
Abstract
Recombinant protein production in microbial hosts and animal cell cultures has revolutionized the pharmaceutical and industrial enzyme industries. Plants as alternative hosts for the production of recombinant proteins are being actively pursued, taking advantage of their unique characteristics. The key to cost-efficient production in any system is the level of protein accumulation, which is inversely proportional to the cost. Levels of up to 5 g/kg biomass have been obtained in plants, making this production system competitive with microbial hosts. Increasing protein accumulation at the cellular level by varying host, germplasm, location of protein accumulation, and transformation procedure is reviewed. At the molecular level increased expression by improving transcription, translation and accumulation of the protein is critically evaluated. The greatest increases in protein accumulation will occur when various optimized parameters are more fully integrated with each other. Because of the complex nature of plants, this will take more time and effort to accomplish than has been the case for the simpler unicellular systems. However the potential for plants to become one of the major avenues for protein production appears very promising.
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Affiliation(s)
- Erin Egelkrout
- Applied Biotechnology Institute, Cal Poly Technology Park, Building 83, San Luis Obispo, CA 93407, USA
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32
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Damaj MB, Beremand PD, Buenrostro-Nava MT, Ivy J, Kumpatla SP, Jifon J, Beyene G, Yu Q, Thomas TL, Mirkov TE. Isolating promoters of multigene family members from the polyploid sugarcane genome by PCR-based walking in BAC DNA. Genome 2011; 53:840-7. [PMID: 20962891 DOI: 10.1139/g10-064] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The availability of a wider range of promoters for regulated expression in valuable transgenic crops would benefit functional genomics studies and current biotechnology programs aimed at improved productivity. Polymerase chain reaction (PCR)-based genome walking techniques are commonly used to isolate promoters or 5' flanking genomic regions adjacent to known cDNA sequences in genomes that are not yet completely sequenced. However, these techniques are problematic when applied directly to DNA isolated from crops with highly complex and large genomes. An adaptor ligation-mediated PCR-based BAC genome walking method is described here for the efficient isolation of promoters of multigene family members, such as the putative defense and fiber biosynthesis DIRIGENT genes that are abundant in the stem of sugarcane, a species with a highly polyploid genome. The advantage of this method is the efficient and specific amplification of the target promoter using BAC genomic DNA as template for the adaptor ligation-mediated PCR walking.
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Affiliation(s)
- Mona B Damaj
- Department of Plant Pathology and Microbiology, Texas AgriLife Research, Texas A&M System, Weslaco, TX 78596-8344, USA
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33
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Engineering Advantages, Challenges and Status of Sugarcane and other Sugar-Based Biomass Resources. ACTA ACUST UNITED AC 2010. [DOI: 10.1007/978-3-642-13440-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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