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Vendemiatti E, Benedito VA. Optical and Scanning Electron Microscopy are Essential Approaches to Studying Trichome Development. Microsc Microanal 2023; 29:1092-1093. [PMID: 37613499 DOI: 10.1093/micmic/ozad067.562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Eloisa Vendemiatti
- Plant & Soil Sciences Division, School of Agriculture and Food, Davis College of Agriculture, Natural Resources, and Design, West Virginia University, WV, USA
| | - Vagner A Benedito
- Plant & Soil Sciences Division, School of Agriculture and Food, Davis College of Agriculture, Natural Resources, and Design, West Virginia University, WV, USA
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Warren D, Benedito VA, Skinner RC, Alawadi A, Vendemiatti E, Laub DJ, Showman C, Matak K, Tou JC. Low-Protein Diets Composed of Protein Recovered from Food Processing Supported Growth, but Induced Mild Hepatic Steatosis Compared with a No-Protein Diet in Young Female Rats. J Nutr 2023; 153:1668-1679. [PMID: 36990182 PMCID: PMC10447611 DOI: 10.1016/j.tjnut.2023.03.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 03/08/2023] [Accepted: 03/20/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND Living in low-income countries often restricts the consumption of adequate protein and animal protein. OBJECTIVES This study aimed to investigate the effects of feeding low-protein diets on growth and liver health using proteins recovered from animal processing. METHODS Female Sprague-Dawley rats (aged 28 d) were randomly assigned (n = 8 rats/group) to be fed standard purified diets with 0% or 10% kcal protein that was comprised of either carp, whey, or casein. RESULTS Rats that were fed low-protein diets showed higher growth but developed mild hepatic steatosis compared to rats that were fed a no-protein diet, regardless of the protein source. Real-time quantitative polymerase chain reactions targeting the expression of genes involved in liver lipid homeostasis were not significantly different among groups. Global RNA-sequencing technology identified 9 differentially expressed genes linked to folate-mediated 1-carbon metabolism, endoplasmic reticulum (ER) stress, and metabolic diseases. Canonical pathway analysis revealed that mechanisms differed depending on the protein source. ER stress and dysregulated energy metabolism were implicated in hepatic steatosis in carp- and whey-fed rats. In contrast, impaired liver one-carbon methylations, lipoprotein assembly, and lipid export were implicated in casein-fed rats. CONCLUSIONS Carp sarcoplasmic protein showed comparable results to commercially available casein and whey protein. A better understanding of the molecular mechanisms in hepatic steatosis development can assist formulation of proteins recovered from food processing into a sustainable source of high-quality protein.
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Affiliation(s)
- Derek Warren
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, United States; Department of Biology, University of the Ozarks, Clarksville, AR, United States
| | - Vagner A Benedito
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, United States
| | - R Chris Skinner
- Food Systems Research Center, College of Agriculture and Life Sciences, University of Vermont Burlington, VT, United States
| | - Ayad Alawadi
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, United States
| | - Eloisa Vendemiatti
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, United States
| | - David J Laub
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Casey Showman
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, United States
| | - Kristen Matak
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, United States
| | - Janet C Tou
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, United States.
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Alawadi AA, Benedito VA, Skinner RC, Warren DC, Showman C, Tou JC. RNA-sequencing revealed apple pomace ameliorates expression of genes in the hypothalamus associated with neurodegeneration in female rats fed a Western diet during adolescence to adulthood. Nutr Neurosci 2023; 26:332-344. [PMID: 35296223 DOI: 10.1080/1028415x.2022.2050008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
OBJECTIVES Apple pomace, a waste byproduct of apple processing, is rich in nutrients (e.g. polyphenols and soluble fiber) with the potential to be neuroprotective. The aim of this study was to employ RNA-sequencing (RNASeq) technology to investigate diet-gene interactions in the hypothalamus of rats after feeding a Western diet calorically substituted with apple pomace. METHODS Adolescent (age 21-29 days) female Sprague-Dawley rats were randomly assigned (n = 8 rats/group) to consume either a purified standard diet, Western (WE) diet, or Western diet calorically substituted with 10% apple pomace (WE/AP) for 8 weeks. RNA-seq was performed (n = 5 rats/group) to determine global differentially expressed genes in the hypothalamus. RESULTS RNA-seq results comparing rats fed WE to WE/AP revealed 15 differentially expressed genes in the hypothalamus. Caloric substitution of WE diet with 10% apple pomace downregulated (q < 0.06) five genes implicated in brain aging and neurodegenerative disorders: synuclein alpha, phospholipase D family member 5, NADH dehydrogenase Fe-S protein 6, choline O-acetyltransferase, and frizzled class receptor 6. DISCUSSION Altered gene expression of these five genes suggests that apple pomace ameliorated synthesis of the neurotransmitter, acetylcholine, in rats fed a WE diet. Apple pomace, a rich source of antioxidant polyphenols and soluble fiber, has been shown to reverse nonalcoholic fatty liver disease (NAFLD). Diet-induced NAFLD decreases hepatic de novo synthesis of choline, a precursor to acetylcholine. Based on preclinical evidence, apple pomace has the potential to be a sustainable functional food for maintaining brain function and for reducing the risk of neurodegeneration.
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Affiliation(s)
- Ayad A Alawadi
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, USA
| | - Vagner A Benedito
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - R Chris Skinner
- Food Systems Research Center, College of Agriculture and Life Sciences, University of Vermont Burlington, VT, USA
| | - Derek C Warren
- Division of Natural Sciences and Mathematics, University of Ozarks, Clarksville, AR, USA
| | - Casey Showman
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, USA
| | - Janet C Tou
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, USA
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Zhang Z, Song C, Zhao J, Xia E, Wen W, Zeng L, Benedito VA. Editorial: Secondary metabolites and metabolism in tea plants. Front Plant Sci 2023; 14:1143022. [PMID: 36866382 PMCID: PMC9972074 DOI: 10.3389/fpls.2023.1143022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 01/30/2023] [Indexed: 01/04/2024]
Affiliation(s)
- Zhaoliang Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science and Technology, Anhui Agriculture University, Anhui, China
| | - Chuankui Song
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science and Technology, Anhui Agriculture University, Anhui, China
| | - Jian Zhao
- Key Laboratory of Tea Science of Ministry of Education, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea and Food Science and Technology, Anhui Agriculture University, Anhui, China
| | - Weiwei Wen
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Lanting Zeng
- South China Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Vagner A. Benedito
- School of Agriculture and Food, Davis College of Agriculture, Natural Resources and Design, West Virginia University, Morgantown, WV, United States
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Ali M, Miao L, Soudy FA, Darwish DBE, Alrdahe SS, Alshehri D, Benedito VA, Tadege M, Wang X, Zhao J. Overexpression of Terpenoid Biosynthesis Genes Modifies Root Growth and Nodulation in Soybean (Glycine max). Cells 2022; 11:cells11172622. [PMID: 36078031 PMCID: PMC9454526 DOI: 10.3390/cells11172622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 12/03/2022] Open
Abstract
Root nodule formation in many leguminous plants is known to be affected by endogen ous and exogenous factors that affect formation, development, and longevity of nodules in roots. Therefore, it is important to understand the role of the genes which are involved in the regulation of the nodulation signaling pathway. This study aimed to investigate the effect of terpenoids and terpene biosynthesis genes on root nodule formation in Glycine max. The study aimed to clarify not only the impact of over-expressing five terpene synthesis genes isolated from G. max and Salvia guaranitica on soybean nodulation signaling pathway, but also on the strigolactones pathway. The obtained results revealed that the over expression of GmFDPS, GmGGPPS, SgGPS, SgFPPS, and SgLINS genes enhanced the root nodule numbers, fresh weight of nodules, root, and root length. Moreover, the terpene content in the transgenic G. max hairy roots was estimated. The results explored that the monoterpenes, sesquiterpenes and diterpenes were significantly increased in transgenic soybean hairy roots in comparison with the control. Our results indicate the potential effects of terpenoids and terpene synthesis genes on soybean root growth and nodulation. The study provides novel insights for understanding the epistatic relationship between terpenoids, root development, and nodulation in soybean.
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Affiliation(s)
- Mohammed Ali
- Egyptian Deserts Gene Bank, North Sinai Research Station, Desert Research Center, Department of Genetic Resources, Cairo 11753, Egypt
| | - Long Miao
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Fathia A. Soudy
- Department of Genetics and Genetic Engineering, Faculty of Agriculture, Benha University, Moshtohor, Toukh 13736, Egypt
| | - Doaa Bahaa Eldin Darwish
- Botany Department, Faculty of Science, Mansoura University, Mansoura 35511, Egypt
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Salma Saleh Alrdahe
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Dikhnah Alshehri
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Vagner A. Benedito
- Plant and Soil Sciences Division, Davis College of Agriculture, Natural Resources and Design, West Virginia University, Morgantown, WV 26506, USA
| | - Million Tadege
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK 73401, USA
| | - Xiaobo Wang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Correspondence: (X.W.); (J.Z.); Tel.: +86-186-7404-7685 (J.Z.)
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Correspondence: (X.W.); (J.Z.); Tel.: +86-186-7404-7685 (J.Z.)
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Pinto RT, Cardoso TB, Paiva LV, Benedito VA. Genomic and transcriptomic inventory of membrane transporters in coffee: Exploring molecular mechanisms of metabolite accumulation. Plant Sci 2021; 312:111018. [PMID: 34620453 DOI: 10.1016/j.plantsci.2021.111018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/07/2021] [Accepted: 08/07/2021] [Indexed: 06/13/2023]
Abstract
The genus Coffea (Rubiaceae) encompasses a group of perennial plant species, including a commodity crop from which seeds are roasted, ground, and infused to make one of the most appreciated beverages in the world. As an important tropical crop restricted to specific regions of the world, coffee production is highly susceptible to the effects of environmental instabilities (i.e., local year-to-year weather fluctuations and global climate change) and threatening pest pressures, not to mention an increasing quality rigor by consumers in industrialized countries. Specialized metabolites are substances that largely affect plant-environment interactions as well as how consumers experience agricultural products. Membrane transporters are key targets, albeit understudied, for understanding and tailoring the spatiotemporal distribution of specialized metabolites as they mediate and control molecular trafficking and substance accumulation. Therefore, we analyzed the transportome of C. canephora encoded within the 25,574 protein-coding genes annotated in the genome of this species and identified 1847 putative membrane transporters. Following, we mined 152 transcriptional profiles of C. canephora and C. arabica and performed a comprehensive co-expression analysis to identify transporters potentially involved in the accumulation of specialized metabolites associated with beverage quality and bioactivity attributes. In toto, this report points to an avenue of possibilities on Coffea genomic and transcriptomic data mining for genetic breeding strategies, which can lead to the development of new, resilient varieties for more sustainable coffee production systems.
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Affiliation(s)
- Renan T Pinto
- Division of Plant and Soil Sciences, West Virginia University, 3425 Agricultural Sciences Building, Morgantown, WV 26506-6108, USA; Molecular Biology Laboratory, Federal University of Lavras, Lavras, MG 37200-000, Brazil
| | - Thiago B Cardoso
- Molecular Biology Laboratory, Federal University of Lavras, Lavras, MG 37200-000, Brazil
| | - Luciano V Paiva
- Molecular Biology Laboratory, Federal University of Lavras, Lavras, MG 37200-000, Brazil
| | - Vagner A Benedito
- Division of Plant and Soil Sciences, West Virginia University, 3425 Agricultural Sciences Building, Morgantown, WV 26506-6108, USA.
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Ahmad MZ, Zhang Y, Zeng X, Li P, Wang X, Benedito VA, Zhao J. Isoflavone malonyl-CoA acyltransferase GmMaT2 is involved in nodulation of soybean by modifying synthesis and secretion of isoflavones. J Exp Bot 2021; 72:1349-1369. [PMID: 33130852 DOI: 10.1093/jxb/eraa511] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/26/2020] [Indexed: 05/20/2023]
Abstract
Malonyl-CoA:flavonoid acyltransferases (MaTs) modify isoflavones, but only a few have been characterized for activity and assigned to specific physiological processes. Legume roots exude isoflavone malonates into the rhizosphere, where they are hydrolyzed into isoflavone aglycones. Soybean GmMaT2 was highly expressed in seeds, root hairs, and nodules. GmMaT2 and GmMaT4 recombinant enzymes used isoflavone 7-O-glucosides as acceptors and malonyl-CoA as an acyl donor to generate isoflavone glucoside malonates. GmMaT2 had higher activity towards isoflavone glucosides than GmMaT4. Overexpression in hairy roots of GmMaT2 and GmMaT4 produced more malonyldaidzin, malonylgenistin, and malonylglycitin, and resulted in more nodules than control. However, only GmMaT2 knockdown (KD) hairy roots showed reduced levels of malonyldaidzin, malonylgenistin, and malonylglycitin, and, likewise, reduced nodule numbers. These were consistent with the up-regulation of only GmMaT2 by rhizobial infection, and higher expression levels of early nodulation genes in GmMaT2- and GmMaT4-overexpressing roots, but lower only in GmMaT2-KD roots compared with control roots. Higher malonyl isoflavonoid levels in transgenic hairy roots were associated with higher levels of isoflavones in root exudates and more nodules, and vice versa. We suggest that GmMaT2 participates in soybean nodulation by catalyzing isoflavone malonylation and affecting malonyl isoflavone secretion for activation of Nod factor and nodulation.
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Affiliation(s)
- Muhammad Zulfiqar Ahmad
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Yanrui Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Xiangsheng Zeng
- College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Penghui Li
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Xiaobo Wang
- College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Vagner A Benedito
- Division of Plant & Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
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Ali M, Miao L, Hou Q, Darwish DB, Alrdahe SS, Ali A, Benedito VA, Tadege M, Wang X, Zhao J. Overexpression of Terpenoid Biosynthesis Genes From Garden Sage ( Salvia officinalis) Modulates Rhizobia Interaction and Nodulation in Soybean. Front Plant Sci 2021; 12:783269. [PMID: 35003167 PMCID: PMC8733304 DOI: 10.3389/fpls.2021.783269] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 11/24/2021] [Indexed: 05/17/2023]
Abstract
In legumes, many endogenous and environmental factors affect root nodule formation through several key genes, and the regulation details of the nodulation signaling pathway are yet to be fully understood. This study investigated the potential roles of terpenoids and terpene biosynthesis genes on root nodule formation in Glycine max. We characterized six terpenoid synthesis genes from Salvia officinalis by overexpressing SoTPS6, SoNEOD, SoLINS, SoSABS, SoGPS, and SoCINS in soybean hairy roots and evaluating root growth and nodulation, and the expression of strigolactone (SL) biosynthesis and early nodulation genes. Interestingly, overexpression of some of the terpenoid and terpene genes increased nodule numbers, nodule and root fresh weight, and root length, while others inhibited these phenotypes. These results suggest the potential effects of terpenoids and terpene synthesis genes on soybean root growth and nodulation. This study provides novel insights into epistatic interactions between terpenoids, root development, and nodulation in soybean root biology and open new avenues for soybean research.
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Affiliation(s)
- Mohammed Ali
- Egyptian Deserts Gene Bank, North Sinai Research Station, Department of Genetic Resources, Desert Research Center, Cairo, Egypt
| | - Long Miao
- College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Qiuqiang Hou
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Doaa B. Darwish
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Salma Saleh Alrdahe
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Ahmed Ali
- Department of Plant Agricultural, Faculty of Agriculture Science, Al-Azhar University, Assiut, Egypt
| | - Vagner A. Benedito
- Plant and Soil Sciences Division, Davis College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, WV, United States
| | - Million Tadege
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, United States
| | - Xiaobo Wang
- College of Agronomy, Anhui Agricultural University, Hefei, China
- *Correspondence: Xiaobo Wang,
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
- Jian Zhao, ; orcid.org/0000-0002-4416-7334
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Warren D, Soule L, Taylor K, Skinner RC, Ku KM, Matak K, Benedito VA, Tou JC. Protein quality and safety evaluation of sarcoplasmic protein derived from silver carp (Hypophthalmichthys molitrix) using a rat model. J Food Sci 2020; 85:2544-2553. [PMID: 32632919 DOI: 10.1111/1750-3841.15321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 04/17/2020] [Accepted: 05/18/2020] [Indexed: 11/30/2022]
Abstract
Consisting of 25 to 30% of protein in carp, water-soluble sarcoplasmic proteins lost in wash water, have been recovered and freeze-dried into a protein-rich powder. Study objectives were to evaluate protein quality and safety of a silver carp sarcoplasm derived protein powder (CSP) compared to commercial protein supplements, casein, and whey. In vivo protein quality assessment of CSP showed a lower (P < 0.05) protein digestibility corrected amino acid score compared to the commercial protein sources. Despite greater (P < 0.05) fecal amino acid excretion in casein-fed rats, there were no significant differences in liver and muscle amino acid profiles. All low (10% kcal) protein diets supported growth with the normal range. However, whey protein supplementation resulted in greater (P < 0.05) adiposity. CSP, casein, or whey-fed rats showed no differences in major organ weights, renal damage biomarkers, or bone indices. Collectively, results indicated CSP was safe with protein quality comparable to casein. PRACTICAL APPLICATION: As much as 40 percent of protein in fish can be lost due to sarcoplasmic protein solubilization in processing wash water. Silver carp sarcoplasm protein powder may have similar commercial potential as a sustainable and nutritious alternative to whey and casein proteins. This project aimed to verify the protein quality and safety of this economical protein source.
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Affiliation(s)
- Derek Warren
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, U.S.A
| | - Lynsey Soule
- Department of Biology, West Virginia University, Morgantown, WV, U.S.A
| | - Kathryn Taylor
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, U.S.A
| | - R Chris Skinner
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, U.S.A
| | - Kang Mo Ku
- Department of Horticulture, Chonnam National University, Gwangju, Republic of Korea
| | - Kristen Matak
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, U.S.A
| | - Vagner A Benedito
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, U.S.A
| | - Janet C Tou
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, U.S.A
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Ahmad MZ, Li P, She G, Xia E, Benedito VA, Wan XC, Zhao J. Genome-Wide Analysis of Serine Carboxypeptidase-Like Acyltransferase Gene Family for Evolution and Characterization of Enzymes Involved in the Biosynthesis of Galloylated Catechins in the Tea Plant ( Camellia sinensis). Front Plant Sci 2020; 11:848. [PMID: 32670320 PMCID: PMC7330524 DOI: 10.3389/fpls.2020.00848] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/26/2020] [Indexed: 05/14/2023]
Abstract
Tea (Camellia sinensis L.) leaves synthesize and concentrate a vast array of galloylated catechins (e.g., EGCG and ECG) and non-galloylated catechins (e.g., EGC, catechin, and epicatechin), together constituting 8%-24% of the dry leaf mass. Galloylated catechins account for a major portion of soluble catechins in tea leaves (up to 75%) and make a major contribution to the astringency and bitter taste of the green tea, and their pharmacological activity for human health. However, the catechin galloylation mechanism in tea plants is largely unknown at molecular levels. Previous studies indicated that glucosyltransferases and serine carboxypeptidase-like acyltransferases (SCPL) might be involved in the process. However, details about the roles of SCPLs in the biosynthesis of galloylated catechins remain to be elucidated. Here, we performed the genome-wide identification of SCPL genes in the tea plant genome. Several SCPLs were grouped into clade IA, which encompasses previously characterized SCPL-IA enzymes with an acylation function. Twenty-eight tea genes in this clade were differentially expressed in young leaves and vegetative buds. We characterized three SCPL-IA enzymes (CsSCPL11-IA, CsSCPL13-IA, CsSCPL14-IA) with galloylation activity toward epicatechins using recombinant enzymes. Not only the expression levels of these SCPLIA genes coincide with the accumulation of galloylated catechins in tea plants, but their recombinant enzymes also displayed β-glucogallin:catechin galloyl acyltransferase activity. These findings provide the first insights into the identities of genes encoding glucogallin:catechin galloyl acyltransferases with an active role in the biosynthesis of galloylated catechins in tea plants.
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Affiliation(s)
- Muhammad Zulfiqar Ahmad
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Penghui Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Guangbiao She
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Vagner A. Benedito
- Division of Plant & Soil Sciences, West Virginia University, Morgantown, WV, United States
| | - Xiao Chun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- *Correspondence: Jian Zhao,
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Skinner RC, Gigliotti JC, Taylor KH, Warren DC, Benedito VA, Tou JC. Caloric Substitution of Diets with Apple Pomace was Determined to be Safe for Renal and Bone Health Using a Growing Rat Model. ACTA ACUST UNITED AC 2019. [DOI: 10.9734/ejnfs/2019/v9i330063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Aims: To determine the safety of caloric substitution with 10% (g/kg) apple pomace to a healthy or Western diet.
Study Design: Growing (age 22-29 days) female Sprague-Dawley rats were randomly assigned (n=8 rats/group) to consume a purified standard rodent diet (AIN-93G), AIN-93G/10% g/kg apple pomace (AIN/AP), Western diet, or Western/10% g/kg apple pomace (Western/AP) diets for 8 weeks.
Results: Histological evaluation showed renal interstitial hypercellularity in rats fed AIN/AP, Western, and Western/AP diets. However, there were no effects on renal expression of oxidative stress and inflammatory genes or serum measures of kidney damage and function among diet groups. Apple pomace was also high in calcium which can affect calcium balance. Dietary calcium consumption was highest (P < .001) in rats consuming Western/AP. However, there were no significant differences in calcium absorption and retention among diet groups. Further, there was no evidence of renal calcification. There were also no impacts on femoral calcium, total mineral content, size or strength.
Conclusions: Based on the results, apple pomace consumption was safe for renal and bone health in a rodent model, regardless of diet quality. Future preclinical studies should be conducted to further determine the efficacy and safety of apple pomace.
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Skinner RC, Warren DC, Agarwal G, Naveed M, Benedito VA, Chantler PD, Tou JC. Apple pomace influences liver‐adipose tissue inflammatory crosstalk in young female rats consuming a Western diet. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.872.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Derek C Warren
- Animal and Nutritional SciencesWest Virginia UniversityFairmontWV
| | - Garima Agarwal
- Animal and Nutritional SciencesWest Virginia UniversityMorgantownWV
| | - Minahal Naveed
- Animal and Nutritional SciencesWest Virginia UniversityMorgantownWV
| | | | | | - Janet C Tou
- Animal and Nutritional SciencesWest Virginia UniversityMorgantownWV
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Skinner RC, Warren DC, Lateef SN, Benedito VA, Tou JC. Apple Pomace Consumption Favorably Alters Hepatic Lipid Metabolism in Young Female Sprague-Dawley Rats Fed a Western Diet. Nutrients 2018; 10:E1882. [PMID: 30513881 PMCID: PMC6316627 DOI: 10.3390/nu10121882] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/05/2018] [Accepted: 11/20/2018] [Indexed: 02/06/2023] Open
Abstract
Apple pomace, which is a waste byproduct of processing, is rich in several nutrients, particularly dietary fiber, indicating potential benefits for diseases that are attributed to poor diets, such as non-alcoholic fatty liver disease (NAFLD). NAFLD affects over 25% of United States population and is increasing in children. Increasing fruit consumption can influence NAFLD. The study objective was to replace calories in standard or Western diets with apple pomace to determine the effects on genes regulating hepatic lipid metabolism and on risk of NAFLD. Female Sprague-Dawley rats were randomly assigned (n = 8 rats/group) to isocaloric diets of AIN-93G and AIN-93G/10% w/w apple pomace (AIN/AP) or isocaloric diets of Western (45% fat, 33% sucrose) and Western/10% w/w apple pomace (Western/AP) diets for eight weeks. There were no significant effects on hepatic lipid metabolism in rats fed AIN/AP. Western/AP diet containing fiber-rich apple pomace attenuated fat vacuole infiltration, elevated monounsaturated fatty acid content, and triglyceride storage in the liver due to higher circulating bile and upregulated hepatic DGAT2 gene expression induced by feeding a Western diet. The study results showed the replacement of calories in Western diet with apple pomace attenuated NAFLD risk. Therefore, apple pomace has the potential to be developed into a sustainable functional food for human consumption.
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Affiliation(s)
- Roy Chris Skinner
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA.
| | - Derek C Warren
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA.
| | - Soofia N Lateef
- Department of Chemical Engineering, West Virginia University, Morgantown, WV 26506, USA.
| | - Vagner A Benedito
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506, USA.
| | - Janet C Tou
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA.
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Skinner RC, Warren DC, Lateef SN, Benedito VA, Bryner RW, Tou JC. Apple Pomace Supplementation Favorably Alters Hepatic Lipid Metabolism in Young Female Sprague‐Dawley Rats fed a Western Diet. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.608.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Derek C. Warren
- Animal and Nutritional SciencesWest Virginia UniversityMorgantownWV
| | | | | | | | - Janet C. Tou
- Animal and Nutritional SciencesWest Virginia UniversityMorgantownWV
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Kryvoruchko IS, Routray P, Sinharoy S, Torres-Jerez I, Tejada-Jiménez M, Finney LA, Nakashima J, Pislariu CI, Benedito VA, González-Guerrero M, Roberts DM, Udvardi MK. An Iron-Activated Citrate Transporter, MtMATE67, Is Required for Symbiotic Nitrogen Fixation. Plant Physiol 2018; 176:2315-2329. [PMID: 29284744 PMCID: PMC5841734 DOI: 10.1104/pp.17.01538] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/21/2017] [Indexed: 05/23/2023]
Abstract
Iron (Fe) is an essential micronutrient for symbiotic nitrogen fixation in legume nodules, where it is required for the activity of bacterial nitrogenase, plant leghemoglobin, respiratory oxidases, and other Fe proteins in both organisms. Fe solubility and transport within and between plant tissues is facilitated by organic chelators, such as nicotianamine and citrate. We have characterized a nodule-specific citrate transporter of the multidrug and toxic compound extrusion family, MtMATE67 of Medicago truncatula The MtMATE67 gene was induced early during nodule development and expressed primarily in the invasion zone of mature nodules. The MtMATE67 protein was localized to the plasma membrane of nodule cells and also the symbiosome membrane surrounding bacteroids in infected cells. In oocytes, MtMATE67 transported citrate out of cells in an Fe-activated manner. Loss of MtMATE67 gene function resulted in accumulation of Fe in the apoplasm of nodule cells and a substantial decrease in symbiotic nitrogen fixation and plant growth. Taken together, the results point to a primary role of MtMATE67 in citrate efflux from nodule cells in response to an Fe signal. This efflux is necessary to ensure Fe(III) solubility and mobility in the apoplasm and uptake into nodule cells. Likewise, MtMATE67-mediated citrate transport into the symbiosome space would increase the solubility and availability of Fe(III) for rhizobial bacteroids.
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Affiliation(s)
| | - Pratyush Routray
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996
| | | | | | - Manuel Tejada-Jiménez
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Madrid 28223, Spain
| | | | | | | | - Vagner A Benedito
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia 26506
| | - Manuel González-Guerrero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Madrid 28223, Spain
| | - Daniel M Roberts
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996
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Ferreira JFS, Benedito VA, Sandhu D, Marchese JA, Liu S. Seasonal and Differential Sesquiterpene Accumulation in Artemisia annua Suggest Selection Based on Both Artemisinin and Dihydroartemisinic Acid may Increase Artemisinin in planta. Front Plant Sci 2018; 9:1096. [PMID: 30154807 PMCID: PMC6102481 DOI: 10.3389/fpls.2018.01096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 07/06/2018] [Indexed: 05/21/2023]
Abstract
Commercial Artemisia annua crops are the sole source of artemisinin (ART) worldwide. Data on seasonal accumulation and peak of sesquiterpenes, especially ART in commercial A. annua, is lacking while current breeding programs focus only on ART and plant biomass, but ignores dihydroartemisinic acid (DHAA) and artemisinic acid (AA). Despite past breeding successes, plants richer in ART are needed to decrease prices of artemisinin-combination therapy (ACT). Our results show that sesquiterpene concentrations vary greatly along the growing season and that sesquiterpene profiles differ widely among chemotypes. Field studies with elite Brazilian, Chinese, and Swiss germplasms established that ART peaked in vegetative plants from late August to early September, suggesting that ART is related to the photoperiod, not flowering. DHAA peaks with ART in Chinese and Swiss plants, but decreases, as ART increases, in Brazilian plants, while AA remained stable through the season in these genotypes. Chinese plants peaked at 0.9% ART, 1.6% DHAA; Brazilian plants at 0.9% ART, with less than 0.4% DHAA; Swiss plants at 0.8% ART and 1% DHAA. At single-date harvests, seeded Swiss plants produced 0.55-1.2% ART, with plants being higher in DHAA than ART; Brazilian plants produced 0.33-1.5% ART, with most having higher ART than DHAA. Elite germplasms produced from 0.02-0.43% AA, except Sandeman-UK (0.4-1.1% AA). Our data suggest that different chemotypes, high in ART and DHAA, have complementary pathways, while competing with AA. Crossing plants high in ART and DHAA may generate hybrids with higher ART than currently available in commercial germplasms. Selecting for high ART and DHAA (and low AA) can be a valuable approach for future selection and breeding to produce plants more efficient in transforming DHAA into ART in planta and during post-harvest. This novel approach could change the breeding focus of A. annua and other pharmaceutical species that produce more than one desired metabolite in the same pathway. Obtaining natural variants with high ART content will empower countries and farmers who select, improve, and cultivate A. annua as a commercial pharmaceutical crop. This selection approach could enable ART to be produced locally where it is most needed to fight malaria and other parasitic neglected diseases.
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Affiliation(s)
- Jorge F. S. Ferreira
- US Salinity Laboratory, Riverside, CA, United States
- *Correspondence: Jorge F. S. Ferreira
| | - Vagner A. Benedito
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, United States
| | | | - José A. Marchese
- Biochemistry and Plant Molecular Physiology Laboratory, Agronomy Department, Federal University of Technology–Paraná, Pato Branco, Brazil
| | - Shuoqian Liu
- Department of Tea Science, College of Horticulture and Hardening, Hunan Agricultural University, Changsha, China
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17
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Wang J, Hou Q, Li P, Yang L, Sun X, Benedito VA, Wen J, Chen B, Mysore KS, Zhao J. Diverse functions of multidrug and toxin extrusion (MATE) transporters in citric acid efflux and metal homeostasis in Medicago truncatula. Plant J 2017; 90:79-95. [PMID: 28052433 DOI: 10.1111/tpj.13471] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 12/14/2016] [Accepted: 12/19/2016] [Indexed: 05/02/2023]
Abstract
The multidrug and toxin extrusion (MATE) transporter family comprises 70 members in the Medicago truncatula genome, and they play seemingly important, yet mostly uncharacterized, physiological functions. Here, we employed bioinformatics and molecular genetics to identify and characterize MATE transporters involved in citric acid export, Al3+ tolerance and Fe translocation. MtMATE69 is a citric acid transporter induced by Fe-deficiency. Overexpression of MtMATE69 in hairy roots altered Fe homeostasis and hormone levels under Fe-deficient or Fe-oversupplied conditions. MtMATE66 is a plasma membrane citric acid transporter primarily expressed in root epidermal cells. The mtmate66 mutant had less root growth than the wild type under Al3+ stress, and seedlings were chlorotic under Fe-deficient conditions. Overexpression of MtMATE66 rendered hairy roots more tolerant to Al3+ toxicity. MtMATE55 is involved in seedling development and iron homeostasis, as well as hormone signaling. The mtmate55 mutant had delayed development and chlorotic leaves in mature plants. Both knock-out and overexpression mutants of MtMATE55 showed altered Fe accumulation and abnormal hormone levels compared with the wild type. We demonstrate that the zinc-finger transcription factor MtSTOP is essentially required for MtMATE66 expression and plant resistance to H+ and Al3+ toxicity. The proper expression of two previously characterized MATE flavonoid transporters MtMATE1 and MtMATE2 also depends on several transcription factors. This study reveals not only functional diversity of MATE transporters and regulatory mechanisms in legumes against H+ and Al3+ stresses, but also casts light on their role in metal nutrition and hormone signaling under various stresses.
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Affiliation(s)
- Junjie Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430075, China
| | - Qiuqiang Hou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430075, China
| | - Penghui Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430075, China
| | - Lina Yang
- Division of Plant & Soil Sciences, West Virginia University, Morgantown, WV, 26506, USA
| | - Xuecheng Sun
- College of Resources & Environment, Huazhong Agricultural University, Wuhan, 430075, China
| | - Vagner A Benedito
- Division of Plant & Soil Sciences, West Virginia University, Morgantown, WV, 26506, USA
| | - Jiangqi Wen
- Plant Biology Division, the Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA
| | - Beibei Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430075, China
| | - Kirankumar S Mysore
- Plant Biology Division, the Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA
| | - Jian Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430075, China
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18
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Valentine AJ, Kleinert A, Benedito VA. Adaptive strategies for nitrogen metabolism in phosphate deficient legume nodules. Plant Sci 2017; 256:46-52. [PMID: 28167037 DOI: 10.1016/j.plantsci.2016.12.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 12/17/2016] [Accepted: 12/19/2016] [Indexed: 05/23/2023]
Abstract
Legumes play a significant role in natural and agricultural ecosystems. They can fix atmospheric N2 and contribute the fixed N to soils and plant N budgets. In legumes, the availability of P does not only affect nodule development, but also N acquisition and metabolism. For legumes as an important source of plant proteins, their capacity to metabolise N during P deficiency is critical for their benefits to agriculture and the natural environment. In particular for farming, rock P is a non-renewable source of which the world has about 60-80 years of sustainable extraction of this P left. The global production of legume crops would be devastated during a scarcity of P fertiliser. Legume nodules have a high requirement for mineral P, which makes them vulnerable to soil P deficiencies. In order to maintain N metabolism, the nodules have evolved several strategies to resist the immediate effects of P limitation and to respond to prolonged P deficiency. In legumes nodules, N metabolism is determined by several processes involving the acquisition, assimilation, export, and recycling of N in various forms. Although these processes are integrated, the current literature lacks a clear synthesis of how legumes respond to P stress regarding its impact on N metabolism. In this review, we synthesise the current state of knowledge on how legumes maintain N metabolism during P deficiency. Moreover, we discuss the potential importance of two additional alterations to N metabolism during P deficiency. Our goals are to place these newly proposed mechanisms in perspective with other known adaptations of N metabolism to P deficiency and to discuss their practical benefits during P deficiency in legumes.
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Affiliation(s)
- Alex J Valentine
- Botany and Zoology Department, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa.
| | - Aleysia Kleinert
- Botany and Zoology Department, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
| | - Vagner A Benedito
- Division of Plant & Soil Sciences, 3425 New Agricultural Sciences Building, West Virginia University, P.O. Box 6108, Morgantown, WV 26506-6108, USA
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19
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Mock K, Lateef S, Benedito VA, Tou JC. High-fructose corn syrup-55 consumption alters hepatic lipid metabolism and promotes triglyceride accumulation. J Nutr Biochem 2016; 39:32-39. [PMID: 27768909 DOI: 10.1016/j.jnutbio.2016.09.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 09/24/2016] [Accepted: 09/27/2016] [Indexed: 12/28/2022]
Abstract
High-fructose corn syrup-55 (HFCS-55) has been suggested to be more lipogenic than sucrose, which increases the risk for nonalcoholic fatty liver disease (NAFLD) and dyslipidemia. The study objectives were to determine the effects of drinking different sugar-sweetened solutions on hepatic gene expression in relation to liver fatty acid composition and risk of NAFLD. Female rats were randomly assigned (n=7 rats/group) to drink water or water sweetened with 13% (w/v) HFCS-55, sucrose or fructose for 8 weeks. Rats drinking HFCS-55 solution had the highest (P=.03) hepatic total lipid and triglyceride content and histological evidence of fat infiltration. Rats drinking HFCS-55 solution had the highest hepatic de novo lipogenesis indicated by the up-regulation of stearoyl-CoA desaturase-1 and the highest (P<.001) oleic acid (18:1n-9) content. This was accompanied by reduced β-oxidation indicated by down-regulation of hepatic peroxisome proliferator-activated receptor α. Disposal of excess lipids by export of triglyceride-rich lipoprotein from the liver was increased as shown by up-regulation of gene expression of microsomal triglyceride transfer protein in rats drinking sucrose, but not HFCS-55 solution. The observed lipogenic effects were attributed to the slightly higher fructose content of HFCS-55 solution in the absence of differences in macronutrient and total caloric intake between rats drinking HFCS-55 and sucrose solution. Results from gene expression and fatty acid composition analysis showed that, in a hypercaloric state, some types of sugars are more detrimental to the liver. Based on these preclinical study results, excess consumption of caloric sweetened beverage, particularly HFCS-sweetened beverages, should be limited.
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Affiliation(s)
- Kaitlin Mock
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Sundus Lateef
- Department of Chemistry, West Virginia University, Morgantown, WV 26506, USA
| | - Vagner A Benedito
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Janet C Tou
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA.
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20
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Kryvoruchko IS, Sinharoy S, Torres-Jerez I, Sosso D, Pislariu CI, Guan D, Murray J, Benedito VA, Frommer WB, Udvardi MK. MtSWEET11, a Nodule-Specific Sucrose Transporter of Medicago truncatula. Plant Physiol 2016; 171:554-65. [PMID: 27021190 PMCID: PMC4854692 DOI: 10.1104/pp.15.01910] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/21/2016] [Indexed: 05/18/2023]
Abstract
Optimization of nitrogen fixation by rhizobia in legumes is a key area of research for sustainable agriculture. Symbiotic nitrogen fixation (SNF) occurs in specialized organs called nodules and depends on a steady supply of carbon to both plant and bacterial cells. Here we report the functional characterization of a nodule-specific Suc transporter, MtSWEET11 from Medicago truncatula MtSWEET11 belongs to a clade of plant SWEET proteins that are capable of transporting Suc and play critical roles in pathogen susceptibility. When expressed in mammalian cells, MtSWEET11 transported sucrose (Suc) but not glucose (Glc). The MtSWEET11 gene was found to be expressed in infected root hair cells, and in the meristem, invasion zone, and vasculature of nodules. Expression of an MtSWEET11-GFP fusion protein in nodules resulted in green fluorescence associated with the plasma membrane of uninfected cells and infection thread and symbiosome membranes of infected cells. Two independent Tnt1-insertion sweet11 mutants were uncompromised in SNF Therefore, although MtSWEET11 appears to be involved in Suc distribution within nodules, it is not crucial for SNF, probably because other Suc transporters can fulfill its role(s).
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Affiliation(s)
- Igor S Kryvoruchko
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK (I.S.K., S.S., I.T.-J., C.I.P., M.K.U.); Department of Plant Biology, Carnegie Institution of Science, Stanford, CA 94305 (D.S., W.B.F.); Department of Cell and Developmental Biology, John Innes Centre, Norwich, NR4 7UH, United Kingdom (D.G., J.M.); and Division of Plant & Soil Sciences, West Virginia University, Morgantown, WV 26506 (V.A.B.)
| | - Senjuti Sinharoy
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK (I.S.K., S.S., I.T.-J., C.I.P., M.K.U.); Department of Plant Biology, Carnegie Institution of Science, Stanford, CA 94305 (D.S., W.B.F.); Department of Cell and Developmental Biology, John Innes Centre, Norwich, NR4 7UH, United Kingdom (D.G., J.M.); and Division of Plant & Soil Sciences, West Virginia University, Morgantown, WV 26506 (V.A.B.)
| | - Ivone Torres-Jerez
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK (I.S.K., S.S., I.T.-J., C.I.P., M.K.U.); Department of Plant Biology, Carnegie Institution of Science, Stanford, CA 94305 (D.S., W.B.F.); Department of Cell and Developmental Biology, John Innes Centre, Norwich, NR4 7UH, United Kingdom (D.G., J.M.); and Division of Plant & Soil Sciences, West Virginia University, Morgantown, WV 26506 (V.A.B.)
| | - Davide Sosso
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK (I.S.K., S.S., I.T.-J., C.I.P., M.K.U.); Department of Plant Biology, Carnegie Institution of Science, Stanford, CA 94305 (D.S., W.B.F.); Department of Cell and Developmental Biology, John Innes Centre, Norwich, NR4 7UH, United Kingdom (D.G., J.M.); and Division of Plant & Soil Sciences, West Virginia University, Morgantown, WV 26506 (V.A.B.)
| | - Catalina I Pislariu
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK (I.S.K., S.S., I.T.-J., C.I.P., M.K.U.); Department of Plant Biology, Carnegie Institution of Science, Stanford, CA 94305 (D.S., W.B.F.); Department of Cell and Developmental Biology, John Innes Centre, Norwich, NR4 7UH, United Kingdom (D.G., J.M.); and Division of Plant & Soil Sciences, West Virginia University, Morgantown, WV 26506 (V.A.B.)
| | - Dian Guan
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK (I.S.K., S.S., I.T.-J., C.I.P., M.K.U.); Department of Plant Biology, Carnegie Institution of Science, Stanford, CA 94305 (D.S., W.B.F.); Department of Cell and Developmental Biology, John Innes Centre, Norwich, NR4 7UH, United Kingdom (D.G., J.M.); and Division of Plant & Soil Sciences, West Virginia University, Morgantown, WV 26506 (V.A.B.)
| | - Jeremy Murray
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK (I.S.K., S.S., I.T.-J., C.I.P., M.K.U.); Department of Plant Biology, Carnegie Institution of Science, Stanford, CA 94305 (D.S., W.B.F.); Department of Cell and Developmental Biology, John Innes Centre, Norwich, NR4 7UH, United Kingdom (D.G., J.M.); and Division of Plant & Soil Sciences, West Virginia University, Morgantown, WV 26506 (V.A.B.)
| | - Vagner A Benedito
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK (I.S.K., S.S., I.T.-J., C.I.P., M.K.U.); Department of Plant Biology, Carnegie Institution of Science, Stanford, CA 94305 (D.S., W.B.F.); Department of Cell and Developmental Biology, John Innes Centre, Norwich, NR4 7UH, United Kingdom (D.G., J.M.); and Division of Plant & Soil Sciences, West Virginia University, Morgantown, WV 26506 (V.A.B.)
| | - Wolf B Frommer
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK (I.S.K., S.S., I.T.-J., C.I.P., M.K.U.); Department of Plant Biology, Carnegie Institution of Science, Stanford, CA 94305 (D.S., W.B.F.); Department of Cell and Developmental Biology, John Innes Centre, Norwich, NR4 7UH, United Kingdom (D.G., J.M.); and Division of Plant & Soil Sciences, West Virginia University, Morgantown, WV 26506 (V.A.B.)
| | - Michael K Udvardi
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK (I.S.K., S.S., I.T.-J., C.I.P., M.K.U.); Department of Plant Biology, Carnegie Institution of Science, Stanford, CA 94305 (D.S., W.B.F.); Department of Cell and Developmental Biology, John Innes Centre, Norwich, NR4 7UH, United Kingdom (D.G., J.M.); and Division of Plant & Soil Sciences, West Virginia University, Morgantown, WV 26506 (V.A.B.)
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Breuillin-Sessoms F, Floss DS, Gomez SK, Pumplin N, Ding Y, Levesque-Tremblay V, Noar RD, Daniels DA, Bravo A, Eaglesham JB, Benedito VA, Udvardi MK, Harrison MJ. Suppression of Arbuscule Degeneration in Medicago truncatula phosphate transporter4 Mutants is Dependent on the Ammonium Transporter 2 Family Protein AMT2;3. Plant Cell 2015; 27:1352-66. [PMID: 25841038 PMCID: PMC4558683 DOI: 10.1105/tpc.114.131144] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 02/22/2015] [Accepted: 03/06/2015] [Indexed: 05/18/2023]
Abstract
During arbuscular mycorrhizal (AM) symbiosis, the plant gains access to phosphate (Pi) and nitrogen delivered by its fungal symbiont. Transfer of mineral nutrients occurs at the interface between branched hyphae called arbuscules and root cortical cells. In Medicago truncatula, a Pi transporter, PT4, is required for symbiotic Pi transport, and in pt4, symbiotic Pi transport fails, arbuscules degenerate prematurely, and the symbiosis is not maintained. Premature arbuscule degeneration (PAD) is suppressed when pt4 mutants are nitrogen-deprived, possibly the result of compensation by PT8, a second AM-induced Pi transporter. However, PAD is also suppressed in nitrogen-starved pt4 pt8 double mutants, negating this hypothesis and furthermore indicating that in this condition, neither of these symbiotic Pi transporters is required for symbiosis. In M. truncatula, three AMT2 family ammonium transporters are induced during AM symbiosis. To test the hypothesis that suppression of PAD involves AMT2 transporters, we analyzed double and triple Pi and ammonium transporter mutants. ATM2;3 but not AMT2;4 was required for suppression of PAD in pt4, while AMT2;4, but not AMT2;3, complemented growth of a yeast ammonium transporter mutant. In summary, arbuscule life span is influenced by PT4 and ATM2;3, and their relative importance varies with the nitrogen status of the plant.
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Affiliation(s)
| | - Daniela S Floss
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, New York 14853
| | - S Karen Gomez
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, New York 14853
| | - Nathan Pumplin
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, New York 14853
| | - Yi Ding
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, New York 14853
| | | | - Roslyn D Noar
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, New York 14853
| | - Dierdra A Daniels
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, New York 14853
| | - Armando Bravo
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, New York 14853
| | - James B Eaglesham
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, New York 14853
| | | | | | - Maria J Harrison
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, New York 14853
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Morton JB, Benedito VA, Panaccione DG, Jenks MA. Potential for Industrial Application of Microbes in Symbioses that Influence Plant Productivity and Sustainability in Agricultural, Natural, or Restored Ecosystems. Ind Biotechnol (New Rochelle N Y) 2014. [DOI: 10.1089/ind.2014.0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Joseph B. Morton
- Division of Plant and Soil Sciences, Davis College of Agriculture, Natural Resources and Design, West Virginia University, Morgantown, WV
| | - Vagner A. Benedito
- Division of Plant and Soil Sciences, Davis College of Agriculture, Natural Resources and Design, West Virginia University, Morgantown, WV
| | - Daniel G. Panaccione
- Division of Plant and Soil Sciences, Davis College of Agriculture, Natural Resources and Design, West Virginia University, Morgantown, WV
| | - Matthew A. Jenks
- Division of Plant and Soil Sciences, Davis College of Agriculture, Natural Resources and Design, West Virginia University, Morgantown, WV
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Benedito VA, Modolo LV. Introduction to metabolic genetic engineering for the production of valuable secondary metabolites in in vivo and in vitro plant systems. Recent Pat Biotechnol 2014; 8:61-75. [PMID: 24354528 DOI: 10.2174/1872208307666131218125801] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Revised: 10/15/2012] [Accepted: 11/19/2012] [Indexed: 05/22/2023]
Abstract
Plants are capable of producing a myriad of chemical compounds. While these compounds serve specific functions in the plant, many have surprising effects on the human body, often with positive action against diseases. These compounds are often difficult to synthesize ex vivo and require the coordinated and compartmentalized action of enzymes in living organisms. However, the amounts produced in whole plants are often small and restricted to single tissues of the plant or even cellular organelles, making their extraction an expensive process. Since most natural products used in therapeutics are specialized, secondary plant metabolites, we provide here an overview of the classification of the main classes of these compounds, with its biochemical pathways and how this information can be used to create efficient in and ex planta production pipelines to generate highly valuable compounds. Metabolic genetic engineering is introduced in light of physiological and genetic methods to enhance production of high-value plant secondary metabolites.
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Affiliation(s)
| | - Luzia V Modolo
- Genetics and Developmental Biology Program, Plant and Soil Sciences Division, West Virginia University, Morgantown, WV, USA 26506-6108.
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Sinharoy S, Torres-Jerez I, Bandyopadhyay K, Kereszt A, Pislariu CI, Nakashima J, Benedito VA, Kondorosi E, Udvardi MK. The C2H2 transcription factor regulator of symbiosome differentiation represses transcription of the secretory pathway gene VAMP721a and promotes symbiosome development in Medicago truncatula. Plant Cell 2013; 25:3584-601. [PMID: 24082011 PMCID: PMC3809551 DOI: 10.1105/tpc.113.114017] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 08/26/2013] [Accepted: 09/11/2013] [Indexed: 05/07/2023]
Abstract
Transcription factors (TFs) are thought to regulate many aspects of nodule and symbiosis development in legumes, although few TFs have been characterized functionally. Here, we describe regulator of symbiosome differentiation (RSD) of Medicago truncatula, a member of the Cysteine-2/Histidine-2 (C2H2) family of plant TFs that is required for normal symbiosome differentiation during nodule development. RSD is expressed in a nodule-specific manner, with maximal transcript levels in the bacterial invasion zone. A tobacco (Nicotiana tabacum) retrotransposon (Tnt1) insertion rsd mutant produced nodules that were unable to fix nitrogen and that contained incompletely differentiated symbiosomes and bacteroids. RSD protein was localized to the nucleus, consistent with a role of the protein in transcriptional regulation. RSD acted as a transcriptional repressor in a heterologous yeast assay. Transcriptome analysis of an rsd mutant identified 11 genes as potential targets of RSD repression. RSD interacted physically with the promoter of one of these genes, VAMP721a, which encodes vesicle-associated membrane protein 721a. Thus, RSD may influence symbiosome development in part by repressing transcription of VAMP721a and modifying vesicle trafficking in nodule cells. This establishes RSD as a TF implicated directly in symbiosome and bacteroid differentiation and a transcriptional regulator of secretory pathway genes in plants.
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Affiliation(s)
| | | | | | - Attila Kereszt
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary
| | | | - Jin Nakashima
- The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | | | - Eva Kondorosi
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Avenue de la Terrasse 91198 Gif sur Yvette, France
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Wang M, Verdier J, Benedito VA, Tang Y, Murray JD, Ge Y, Becker JD, Carvalho H, Rogers C, Udvardi M, He J. LegumeGRN: a gene regulatory network prediction server for functional and comparative studies. PLoS One 2013; 8:e67434. [PMID: 23844010 PMCID: PMC3701055 DOI: 10.1371/journal.pone.0067434] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 05/17/2013] [Indexed: 12/03/2022] Open
Abstract
Building accurate gene regulatory networks (GRNs) from high-throughput gene expression data is a long-standing challenge. However, with the emergence of new algorithms combined with the increase of transcriptomic data availability, it is now reachable. To help biologists to investigate gene regulatory relationships, we developed a web-based computational service to build, analyze and visualize GRNs that govern various biological processes. The web server is preloaded with all available Affymetrix GeneChip-based transcriptomic and annotation data from the three model legume species, i.e., Medicago truncatula, Lotus japonicus and Glycine max. Users can also upload their own transcriptomic and transcription factor datasets from any other species/organisms to analyze their in-house experiments. Users are able to select which experiments, genes and algorithms they will consider to perform their GRN analysis. To achieve this flexibility and improve prediction performance, we have implemented multiple mainstream GRN prediction algorithms including co-expression, Graphical Gaussian Models (GGMs), Context Likelihood of Relatedness (CLR), and parallelized versions of TIGRESS and GENIE3. Besides these existing algorithms, we also proposed a parallel Bayesian network learning algorithm, which can infer causal relationships (i.e., directionality of interaction) and scale up to several thousands of genes. Moreover, this web server also provides tools to allow integrative and comparative analysis between predicted GRNs obtained from different algorithms or experiments, as well as comparisons between legume species. The web site is available at http://legumegrn.noble.org.
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Affiliation(s)
- Mingyi Wang
- Division of Plant Biology, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, United States of America.
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Gigliotti JC, Benedito VA, Livengood R, Oldaker C, Nanda N, Tou JC. Feeding Different Omega-3 Polyunsaturated Fatty Acid Sources Influences Renal Fatty Acid Composition, Inflammation, and Occurrence of Nephrocalcinosis in Female Sprague-Dawley Rats. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/fns.2013.49a1020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Pislariu CI, D. Murray J, Wen J, Cosson V, Muni RRD, Wang M, A. Benedito V, Andriankaja A, Cheng X, Jerez IT, Mondy S, Zhang S, Taylor ME, Tadege M, Ratet P, Mysore KS, Chen R, Udvardi MK. A Medicago truncatula tobacco retrotransposon insertion mutant collection with defects in nodule development and symbiotic nitrogen fixation. Plant Physiol 2012; 159:1686-99. [PMID: 22679222 PMCID: PMC3425206 DOI: 10.1104/pp.112.197061] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 06/01/2012] [Indexed: 05/20/2023]
Abstract
A Tnt1-insertion mutant population of Medicago truncatula ecotype R108 was screened for defects in nodulation and symbiotic nitrogen fixation. Primary screening of 9,300 mutant lines yielded 317 lines with putative defects in nodule development and/or nitrogen fixation. Of these, 230 lines were rescreened, and 156 lines were confirmed with defective symbiotic nitrogen fixation. Mutants were sorted into six distinct phenotypic categories: 72 nonnodulating mutants (Nod-), 51 mutants with totally ineffective nodules (Nod+ Fix-), 17 mutants with partially ineffective nodules (Nod+ Fix+/-), 27 mutants defective in nodule emergence, elongation, and nitrogen fixation (Nod+/- Fix-), one mutant with delayed and reduced nodulation but effective in nitrogen fixation (dNod+/- Fix+), and 11 supernodulating mutants (Nod++Fix+/-). A total of 2,801 flanking sequence tags were generated from the 156 symbiotic mutant lines. Analysis of flanking sequence tags revealed 14 insertion alleles of the following known symbiotic genes: NODULE INCEPTION (NIN), DOESN'T MAKE INFECTIONS3 (DMI3/CCaMK), ERF REQUIRED FOR NODULATION, and SUPERNUMERARY NODULES (SUNN). In parallel, a polymerase chain reaction-based strategy was used to identify Tnt1 insertions in known symbiotic genes, which revealed 25 additional insertion alleles in the following genes: DMI1, DMI2, DMI3, NIN, NODULATION SIGNALING PATHWAY1 (NSP1), NSP2, SUNN, and SICKLE. Thirty-nine Nod- lines were also screened for arbuscular mycorrhizal symbiosis phenotypes, and 30 mutants exhibited defects in arbuscular mycorrhizal symbiosis. Morphological and developmental features of several new symbiotic mutants are reported. The collection of mutants described here is a source of novel alleles of known symbiotic genes and a resource for cloning novel symbiotic genes via Tnt1 tagging.
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Affiliation(s)
| | | | - JiangQi Wen
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Viviane Cosson
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - RajaSekhara Reddy Duvvuru Muni
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Mingyi Wang
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Vagner A. Benedito
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Andry Andriankaja
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Xiaofei Cheng
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Ivone Torres Jerez
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Samuel Mondy
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Shulan Zhang
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Mark E. Taylor
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Million Tadege
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Pascal Ratet
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Kirankumar S. Mysore
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Rujin Chen
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Michael K. Udvardi
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
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Young ND, Debellé F, Oldroyd GED, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KFX, Gouzy J, Schoof H, Van de Peer Y, Proost S, Cook DR, Meyers BC, Spannagl M, Cheung F, De Mita S, Krishnakumar V, Gundlach H, Zhou S, Mudge J, Bharti AK, Murray JD, Naoumkina MA, Rosen B, Silverstein KAT, Tang H, Rombauts S, Zhao PX, Zhou P, Barbe V, Bardou P, Bechner M, Bellec A, Berger A, Bergès H, Bidwell S, Bisseling T, Choisne N, Couloux A, Denny R, Deshpande S, Dai X, Doyle JJ, Dudez AM, Farmer AD, Fouteau S, Franken C, Gibelin C, Gish J, Goldstein S, González AJ, Green PJ, Hallab A, Hartog M, Hua A, Humphray SJ, Jeong DH, Jing Y, Jöcker A, Kenton SM, Kim DJ, Klee K, Lai H, Lang C, Lin S, Macmil SL, Magdelenat G, Matthews L, McCorrison J, Monaghan EL, Mun JH, Najar FZ, Nicholson C, Noirot C, O'Bleness M, Paule CR, Poulain J, Prion F, Qin B, Qu C, Retzel EF, Riddle C, Sallet E, Samain S, Samson N, Sanders I, Saurat O, Scarpelli C, Schiex T, Segurens B, Severin AJ, Sherrier DJ, Shi R, Sims S, Singer SR, Sinharoy S, Sterck L, Viollet A, Wang BB, Wang K, Wang M, Wang X, Warfsmann J, Weissenbach J, White DD, White JD, Wiley GB, Wincker P, Xing Y, Yang L, Yao Z, Ying F, Zhai J, Zhou L, Zuber A, Dénarié J, Dixon RA, May GD, Schwartz DC, Rogers J, Quétier F, Town CD, Roe BA. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 2011; 480:520-4. [PMID: 22089132 PMCID: PMC3272368 DOI: 10.1038/nature10625] [Citation(s) in RCA: 762] [Impact Index Per Article: 58.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 10/13/2011] [Indexed: 11/09/2022]
Abstract
Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species. Medicago truncatula is a long-established model for the study of legume biology. Here we describe the draft sequence of the M. truncatula euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing ∼94% of all M. truncatula genes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the M. truncatula genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max and Lotus japonicus. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa's genomic toolbox.
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Affiliation(s)
- Nevin D Young
- Department of Plant Pathology, University of Minnesota, St Paul, Minnesota 55108, USA.
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Tou JC, Altman SN, Gigliotti JC, Benedito VA, Cordonier EL. Different sources of omega-3 polyunsaturated fatty acids affects apparent digestibility, tissue deposition, and tissue oxidative stability in growing female rats. Lipids Health Dis 2011; 10:179. [PMID: 21999902 PMCID: PMC3216256 DOI: 10.1186/1476-511x-10-179] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 10/14/2011] [Indexed: 01/11/2023] Open
Abstract
Background Numerous health benefits associated with increased omega-3 polyunsaturated fatty acid (n-3 PUFA) consumption has lead to an increasing variety of available n-3 PUFA sources. However, sources differ in the type, amount, and structural form of the n-3 PUFAs. Therefore, the objective of this study was to determine the effect of different sources of ω-3 PUFAs on digestibility, tissue deposition, eicosanoid metabolism, and oxidative stability. Methods Female Sprague-Dawley rats (age 28 d) were randomly assigned (n = 10/group) to be fed a high fat 12% (wt) diet consisting of either corn oil (CO) or n-3 PUFA rich flaxseed (FO), krill (KO), menhaden (MO), salmon (SO) or tuna (TO) oil for 8 weeks. Rats were individually housed in metabolic cages to determine fatty acid digestibility. Diet and tissue fatty acid composition was analyzed by gas chromatography and lipid classes using thin layer chromatography. Eicosanoid metabolism was determined by measuring urinary metabolites of 2-series prostaglandins (PGs) and thromoboxanes (TXBs) using enzyme immunoassays. Oxidative stability was assessed by measuring thiobarbituric acid reactive substances (TBARS) and total antioxidant capacity (TAC) using colorimetric assays. Gene expression of antioxidant defense enzymes was determined by real time quantitative polymerase chain reaction (RT-qPCR). Results Rats fed KO had significantly lower DHA digestibility and brain DHA incorporation than SO and TO-fed rats. Of the n-3 PUFA sources, rats fed SO and TO had the highest n-3 PUFAs digestibility and in turn, tissue accretion. Higher tissue n-3 LC-PUFAs had no significant effect on 2-series PG and TXB metabolites. Despite higher tissue n-3 LC-PUFA deposition, there was no increase in oxidation susceptibility indicated by no significant increase in TBARS or decrease in TAC and gene expression of antioxidant defense enzymes, in SO or TO-fed rats. Conclusions On the basis that the optimal n-3 PUFA sources should provide high digestibility and efficient tissue incorporation with the least tissue lipid peroxidation, TO and SO appeared to be the most beneficial of the n-3 PUFAs sources evaluated in this study.
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Affiliation(s)
- Janet C Tou
- Division of Animal and Nutritional Sciences, West Virginia University, P.O. Box 6108, Morgantown, WV 26506, USA.
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Carvalho RF, Campos ML, Pino LE, Crestana SL, Zsögön A, Lima JE, Benedito VA, Peres LEP. Convergence of developmental mutants into a single tomato model system: 'Micro-Tom' as an effective toolkit for plant development research. Plant Methods 2011; 7:18. [PMID: 21714900 PMCID: PMC3146949 DOI: 10.1186/1746-4811-7-18] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 06/29/2011] [Indexed: 05/18/2023]
Abstract
BACKGROUND The tomato (Solanum lycopersicum L.) plant is both an economically important food crop and an ideal dicot model to investigate various physiological phenomena not possible in Arabidopsis thaliana. Due to the great diversity of tomato cultivars used by the research community, it is often difficult to reliably compare phenotypes. The lack of tomato developmental mutants in a single genetic background prevents the stacking of mutations to facilitate analysis of double and multiple mutants, often required for elucidating developmental pathways. RESULTS We took advantage of the small size and rapid life cycle of the tomato cultivar Micro-Tom (MT) to create near-isogenic lines (NILs) by introgressing a suite of hormonal and photomorphogenetic mutations (altered sensitivity or endogenous levels of auxin, ethylene, abscisic acid, gibberellin, brassinosteroid, and light response) into this genetic background. To demonstrate the usefulness of this collection, we compared developmental traits between the produced NILs. All expected mutant phenotypes were expressed in the NILs. We also created NILs harboring the wild type alleles for dwarf, self-pruning and uniform fruit, which are mutations characteristic of MT. This amplified both the applications of the mutant collection presented here and of MT as a genetic model system. CONCLUSIONS The community resource presented here is a useful toolkit for plant research, particularly for future studies in plant development, which will require the simultaneous observation of the effect of various hormones, signaling pathways and crosstalk.
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Affiliation(s)
- Rogério F Carvalho
- Laboratory of Hormonal Control of Plant Development, Department of Biological Sciences (LCB), Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo (USP) - Av. Pádua Dias, 11, CP 09, CEP 13418-900 Piracicaba - SP, Brazil
| | - Marcelo L Campos
- Laboratory of Hormonal Control of Plant Development, Department of Biological Sciences (LCB), Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo (USP) - Av. Pádua Dias, 11, CP 09, CEP 13418-900 Piracicaba - SP, Brazil
| | - Lilian E Pino
- Laboratory of Hormonal Control of Plant Development, Department of Biological Sciences (LCB), Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo (USP) - Av. Pádua Dias, 11, CP 09, CEP 13418-900 Piracicaba - SP, Brazil
- Center for Nuclear Energy in Agriculture (CENA), USP, Av. Centenário, 303, CEP 13400-970 Piracicaba, SP, Brazil
| | - Simone L Crestana
- Laboratory of Hormonal Control of Plant Development, Department of Biological Sciences (LCB), Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo (USP) - Av. Pádua Dias, 11, CP 09, CEP 13418-900 Piracicaba - SP, Brazil
| | - Agustin Zsögön
- Laboratory of Hormonal Control of Plant Development, Department of Biological Sciences (LCB), Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo (USP) - Av. Pádua Dias, 11, CP 09, CEP 13418-900 Piracicaba - SP, Brazil
| | - Joni E Lima
- Laboratory of Hormonal Control of Plant Development, Department of Biological Sciences (LCB), Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo (USP) - Av. Pádua Dias, 11, CP 09, CEP 13418-900 Piracicaba - SP, Brazil
- Center for Nuclear Energy in Agriculture (CENA), USP, Av. Centenário, 303, CEP 13400-970 Piracicaba, SP, Brazil
| | - Vagner A Benedito
- Genetics and Developmental Biology Program, Plant and Soil Sciences Division, West Virginia University, 2090 Agricultural Sciences Building, Morgantown, WV 26506, USA
| | - Lázaro EP Peres
- Laboratory of Hormonal Control of Plant Development, Department of Biological Sciences (LCB), Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo (USP) - Av. Pádua Dias, 11, CP 09, CEP 13418-900 Piracicaba - SP, Brazil
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Gigliotti J, Turk P, Benedito VA, Livengood R, Tou JC. Characterizing the influence of different sources of omega‐3 polyunsaturated fatty acids on renal function and health in female rats. FASEB J 2011. [DOI: 10.1096/fasebj.25.1_supplement.777.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | - Ryan Livengood
- Department of PathologyWest Virginia UniversityMorgantownWV
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Ward CL, Kleinert A, Scortecci KC, Benedito VA, Valentine AJ. Phosphorus-deficiency reduces aluminium toxicity by altering uptake and metabolism of root zone carbon dioxide. J Plant Physiol 2011; 168:459-465. [PMID: 20926158 DOI: 10.1016/j.jplph.2010.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Revised: 08/18/2010] [Accepted: 08/18/2010] [Indexed: 05/30/2023]
Abstract
The role of phosphorus (P) status in root-zone CO(2) utilisation for organic acid synthesis during Al(3+) toxicity was assessed. Root-zone CO(2) can be incorporated into organic acids via Phosphoenolpyruvate carboxylase (PEPC, EC 4.1.1.31). P-deficiency and Al(3+) toxicity can induce organic acid synthesis, but it is unknown how P status affects the utilisation of PEPC-derived organic acids during Al(3+) toxicity. Two-week-old Solanum lycopersicum seedlings were transferred to hydroponic culture for 3 weeks. The hydroponic culture consisted of a standard Long Ashton nutrient solution containing either 0.1μM or 1mM P. Short-term Al(3+) toxicity was induced by a 60-min exposure to a pH-buffered solution (pH 4.5) containing 2mM CaSO(4) and 50μM AlCl(3). Al(3+) toxicity induced a decline in root respiration, adenylate concentrations and an increase in root-zone CO(2) utilisation for both P sufficient and P-deficient plants. However during Al(3+) toxicity, P deficiency enhanced the incorporation and metabolism of root-zone CO(2) via PEPC. Moreover, P deficiency led to a greater proportion of the PEPC-derived organic acids to be exuded during Al(3+) toxicity. These results indicate that P-status can influence the response to Al(3+) by inducing a greater utilisation of PEPC-derived organic acids for Al(3+) detoxification.
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Affiliation(s)
- Caroline L Ward
- Botany and Zoology Department, Faculty of Science, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
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Ahmed F, Benedito VA, Zhao PX. Mining Functional Elements in Messenger RNAs: Overview, Challenges, and Perspectives. Front Plant Sci 2011; 2:84. [PMID: 22639614 PMCID: PMC3355573 DOI: 10.3389/fpls.2011.00084] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 11/03/2011] [Indexed: 05/03/2023]
Abstract
Eukaryotic messenger RNA (mRNA) contains not only protein-coding regions but also a plethora of functional cis-elements that influence or coordinate a number of regulatory aspects of gene expression, such as mRNA stability, splicing forms, and translation rates. Understanding the rules that apply to each of these element types (e.g., whether the element is defined by primary or higher-order structure) allows for the discovery of novel mechanisms of gene expression as well as the design of transcripts with controlled expression. Bioinformatics plays a major role in creating databases and finding non-evident patterns governing each type of eukaryotic functional element. Much of what we currently know about mRNA regulatory elements in eukaryotes is derived from microorganism and animal systems, with the particularities of plant systems lagging behind. In this review, we provide a general introduction to the most well-known eukaryotic mRNA regulatory motifs (splicing regulatory elements, internal ribosome entry sites, iron-responsive elements, AU-rich elements, zipcodes, and polyadenylation signals) and describe available bioinformatics resources (databases and analysis tools) to analyze eukaryotic transcripts in search of functional elements, focusing on recent trends in bioinformatics methods and tool development. We also discuss future directions in the development of better computational tools based upon current knowledge of these functional elements. Improved computational tools would advance our understanding of the processes underlying gene regulations. We encourage plant bioinformaticians to turn their attention to this subject to help identify novel mechanisms of gene expression regulation using RNA motifs that have potentially evolved or diverged in plant species.
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Affiliation(s)
- Firoz Ahmed
- Bioinformatics Laboratory, Plant Biology Division, Samuel Roberts Noble FoundationArdmore, OK, USA
| | - Vagner A. Benedito
- Genetics and Developmental Biology, Plant and Soil Sciences Division, West Virginia UniversityMorgantown, WV, USA
| | - Patrick Xuechun Zhao
- Bioinformatics Laboratory, Plant Biology Division, Samuel Roberts Noble FoundationArdmore, OK, USA
- *Correspondence: Patrick Xuechun Zhao, Bioinformatics Laboratory, Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA e-mail:
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Benedito VA, Li H, Dai X, Wandrey M, He J, Kaundal R, Torres-Jerez I, Gomez SK, Harrison MJ, Tang Y, Zhao PX, Udvardi MK. Genomic inventory and transcriptional analysis of Medicago truncatula transporters. Plant Physiol 2010; 152:1716-30. [PMID: 20023147 PMCID: PMC2832251 DOI: 10.1104/pp.109.148684] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Accepted: 12/15/2009] [Indexed: 05/20/2023]
Abstract
Transporters move hydrophilic substrates across hydrophobic biological membranes and play key roles in plant nutrition, metabolism, and signaling and, consequently, in plant growth, development, and responses to the environment. To initiate and support systematic characterization of transporters in the model legume Medicago truncatula, we identified 3,830 transporters and classified 2,673 of these into 113 families and 146 subfamilies. Analysis of gene expression data for 2,611 of these transporters identified 129 that are expressed in an organ-specific manner, including 50 that are nodule specific and 36 specific to mycorrhizal roots. Further analysis uncovered 196 transporters that are induced at least 5-fold during nodule development and 44 in roots during arbuscular mycorrhizal symbiosis. Among the nodule- and mycorrhiza-induced transporter genes are many candidates for known transport activities in these beneficial symbioses. The data presented here are a unique resource for the selection and functional characterization of legume transporters.
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He J, Benedito VA, Wang M, Murray JD, Zhao PX, Tang Y, Udvardi MK. The Medicago truncatula gene expression atlas web server. BMC Bioinformatics 2009. [PMID: 20028527 DOI: 10.1186/1471‐2105‐10‐441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Legumes (Leguminosae or Fabaceae) play a major role in agriculture. Transcriptomics studies in the model legume species, Medicago truncatula, are instrumental in helping to formulate hypotheses about the role of legume genes. With the rapid growth of publically available Affymetrix GeneChip Medicago Genome Array GeneChip data from a great range of tissues, cell types, growth conditions, and stress treatments, the legume research community desires an effective bioinformatics system to aid efforts to interpret the Medicago genome through functional genomics. We developed the Medicago truncatula Gene Expression Atlas (MtGEA) web server for this purpose. DESCRIPTION The Medicago truncatula Gene Expression Atlas (MtGEA) web server is a centralized platform for analyzing the Medicago transcriptome. Currently, the web server hosts gene expression data from 156 Affymetrix GeneChip(R) Medicago genome arrays in 64 different experiments, covering a broad range of developmental and environmental conditions. The server enables flexible, multifaceted analyses of transcript data and provides a range of additional information about genes, including different types of annotation and links to the genome sequence, which help users formulate hypotheses about gene function. Transcript data can be accessed using Affymetrix probe identification number, DNA sequence, gene name, functional description in natural language, GO and KEGG annotation terms, and InterPro domain number. Transcripts can also be discovered through co-expression or differential expression analysis. Flexible tools to select a subset of experiments and to visualize and compare expression profiles of multiple genes have been implemented. Data can be downloaded, in part or full, in a tabular form compatible with common analytical and visualization software. The web server will be updated on a regular basis to incorporate new gene expression data and genome annotation, and is accessible at: http://bioinfo.noble.org/gene-atlas/. CONCLUSIONS The MtGEA web server has a well managed rich data set, and offers data retrieval and analysis tools provided in the web platform. It's proven to be a powerful resource for plant biologists to effectively and efficiently identify Medicago transcripts of interest from a multitude of aspects, formulate hypothesis about gene function, and overall interpret the Medicago genome from a systematic point of view.
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Affiliation(s)
- Ji He
- Plant Biology Division, the Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA.
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He J, Benedito VA, Wang M, Murray JD, Zhao PX, Tang Y, Udvardi MK. The Medicago truncatula gene expression atlas web server. BMC Bioinformatics 2009; 10:441. [PMID: 20028527 PMCID: PMC2804685 DOI: 10.1186/1471-2105-10-441] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Accepted: 12/22/2009] [Indexed: 01/19/2023] Open
Abstract
Background Legumes (Leguminosae or Fabaceae) play a major role in agriculture. Transcriptomics studies in the model legume species, Medicago truncatula, are instrumental in helping to formulate hypotheses about the role of legume genes. With the rapid growth of publically available Affymetrix GeneChip Medicago Genome Array GeneChip data from a great range of tissues, cell types, growth conditions, and stress treatments, the legume research community desires an effective bioinformatics system to aid efforts to interpret the Medicago genome through functional genomics. We developed the Medicago truncatula Gene Expression Atlas (MtGEA) web server for this purpose. Description The Medicago truncatula Gene Expression Atlas (MtGEA) web server is a centralized platform for analyzing the Medicago transcriptome. Currently, the web server hosts gene expression data from 156 Affymetrix GeneChip® Medicago genome arrays in 64 different experiments, covering a broad range of developmental and environmental conditions. The server enables flexible, multifaceted analyses of transcript data and provides a range of additional information about genes, including different types of annotation and links to the genome sequence, which help users formulate hypotheses about gene function. Transcript data can be accessed using Affymetrix probe identification number, DNA sequence, gene name, functional description in natural language, GO and KEGG annotation terms, and InterPro domain number. Transcripts can also be discovered through co-expression or differential expression analysis. Flexible tools to select a subset of experiments and to visualize and compare expression profiles of multiple genes have been implemented. Data can be downloaded, in part or full, in a tabular form compatible with common analytical and visualization software. The web server will be updated on a regular basis to incorporate new gene expression data and genome annotation, and is accessible at: http://bioinfo.noble.org/gene-atlas/. Conclusions The MtGEA web server has a well managed rich data set, and offers data retrieval and analysis tools provided in the web platform. It's proven to be a powerful resource for plant biologists to effectively and efficiently identify Medicago transcripts of interest from a multitude of aspects, formulate hypothesis about gene function, and overall interpret the Medicago genome from a systematic point of view.
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Affiliation(s)
- Ji He
- Plant Biology Division, the Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA.
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Li H, Benedito VA, Udvardi MK, Zhao PX. TransportTP: a two-phase classification approach for membrane transporter prediction and characterization. BMC Bioinformatics 2009; 10:418. [PMID: 20003433 PMCID: PMC3087344 DOI: 10.1186/1471-2105-10-418] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Accepted: 12/14/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Membrane transporters play crucial roles in living cells. Experimental characterization of transporters is costly and time-consuming. Current computational methods for transporter characterization still require extensive curation efforts, especially for eukaryotic organisms. We developed a novel genome-scale transporter prediction and characterization system called TransportTP that combined homology-based and machine learning methods in a two-phase classification approach. First, traditional homology methods were employed to predict novel transporters based on sequence similarity to known classified proteins in the Transporter Classification Database (TCDB). Second, machine learning methods were used to integrate a variety of features to refine the initial predictions. A set of rules based on transporter features was developed by machine learning using well-curated proteomes as guides. RESULTS In a cross-validation using the yeast proteome for training and the proteomes of ten other organisms for testing, TransportTP achieved an equivalent recall and precision of 81.8%, based on TransportDB, a manually annotated transporter database. In an independent test using the Arabidopsis proteome for training and four recently sequenced plant proteomes for testing, it achieved a recall of 74.6% and a precision of 73.4%, according to our manual curation. CONCLUSIONS TransportTP is the most effective tool for eukaryotic transporter characterization up to date.
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Affiliation(s)
- Haiquan Li
- Plant Biology Division, The Samuel Roberts Noble Foundation, Inc, Ardmore, OK 73401, USA.
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Libault M, Joshi T, Benedito VA, Xu D, Udvardi MK, Stacey G. Legume transcription factor genes: what makes legumes so special? Plant Physiol 2009; 151:991-1001. [PMID: 19726573 PMCID: PMC2773095 DOI: 10.1104/pp.109.144105] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 08/26/2009] [Indexed: 05/18/2023]
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Benedito VA, Torres-Jerez I, Murray JD, Andriankaja A, Allen S, Kakar K, Wandrey M, Verdier J, Zuber H, Ott T, Moreau S, Niebel A, Frickey T, Weiller G, He J, Dai X, Zhao PX, Tang Y, Udvardi MK. A gene expression atlas of the model legume Medicago truncatula. Plant J 2008; 55:504-13. [PMID: 18410479 DOI: 10.1111/j.1365-313x.2008.03519.x] [Citation(s) in RCA: 462] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Legumes played central roles in the development of agriculture and civilization, and today account for approximately one-third of the world's primary crop production. Unfortunately, most cultivated legumes are poor model systems for genomic research. Therefore, Medicago truncatula, which has a relatively small diploid genome, has been adopted as a model species for legume genomics. To enhance its value as a model, we have generated a gene expression atlas that provides a global view of gene expression in all major organ systems of this species, with special emphasis on nodule and seed development. The atlas reveals massive differences in gene expression between organs that are accompanied by changes in the expression of key regulatory genes, such as transcription factor genes, which presumably orchestrate genetic reprogramming during development and differentiation. Interestingly, many legume-specific genes are preferentially expressed in nitrogen-fixing nodules, indicating that evolution endowed them with special roles in this unique and important organ. Comparative transcriptome analysis of Medicago versus Arabidopsis revealed significant divergence in developmental expression profiles of orthologous genes, which indicates that phylogenetic analysis alone is insufficient to predict the function of orthologs in different species. The data presented here represent an unparalleled resource for legume functional genomics, which will accelerate discoveries in legume biology.
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Affiliation(s)
- Vagner A Benedito
- Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
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Benedito VA, Dai X, He J, Zhao PX, Udvardi MK. Functional genomics of plant transporters in legume nodules. Funct Plant Biol 2006; 33:731-736. [PMID: 32689283 DOI: 10.1071/fp06085] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2006] [Accepted: 05/25/2006] [Indexed: 06/11/2023]
Abstract
Over the past few decades, a combination of physiology, biochemistry, molecular and cell biology, and genetics has given us a basic understanding of some of the key transport processes at work in nitrogen-fixing legume nodules, especially those involved in nutrient exchange between infected plant cells and their endosymbiotic rhizobia. However, our knowledge in this area remains patchy and dispersed over numerous legume species. Recent progress in the areas of genomics and functional genomics of the two model legumes, Medicago truncatula and Lotus japonicus is rapidly filling the gap in knowledge about which plant transporter genes are expressed constitutively in nodules and other organs, and which are induced or expressed specifically in nodules. The latter class in particular is the focus of current efforts to understand specialised, nodule-specific roles of transporters. This article briefly reviews past work on the biochemistry and molecular biology of plant transporters in nodules, before describing recent work in the areas of transcriptomics and bioinformatics. Finally, we consider where functional genomics together with more classical approaches are likely to lead us in this area of research in the future.
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Affiliation(s)
- Vagner A Benedito
- Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Xinbin Dai
- Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Ji He
- Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Patrick X Zhao
- Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Michael K Udvardi
- Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
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Benedito VA, Visser PB, Angenent GC, Krens FA. The potential of virus-induced gene silencing for speeding up functional characterization of plant genes. Genet Mol Res 2004; 3:323-41. [PMID: 15614725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Virus-induced gene silencing (VIGS) has been shown to be of great potential in plant reverse genetics. Advantages of VIGS over other approaches, such as T-DNA or transposon tagging, include the circumvention of plant transformation, methodological simplicity and robustness, and speedy results. These features make VIGS an attractive alternative instrument in functional genomics, even in a high throughput fashion. The system is already well established in Nicotiana benthamiana; however, efforts are being made to improve VIGS in other species, including monocots. Current research is focussed on unravelling the mechanisms of post-transcriptional gene silencing and VIGS, as well as on finding novel viral vectors in order to broaden the host species spectrum. We examined how VIGS has been used to assess gene functions in plants, including molecular mechanisms involved in the process, available methodological elements, such as vectors and inoculation procedures, and we looked for examples in which the system has been applied successfully to characterize gene function in plants.
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Affiliation(s)
- Vagner A Benedito
- Plant Research International, Wageningen University and Research Centre, P.O. Box 16, 6700 AA, Wageningen, the Netherlands
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Benedito VA, Visser PB, van Tuyl JM, Angenent GC, de Vries SC, Krens FA. Ectopic expression of LLAG1, an AGAMOUS homologue from lily (Lilium longiflorum Thunb.) causes floral homeotic modifications in Arabidopsis. J Exp Bot 2004; 55:1391-9. [PMID: 15155783 DOI: 10.1093/jxb/erh156] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The ABC model for floral development was proposed more than 10 years ago and since then many studies have been performed on model species, such as Arabidopsis thaliana, Antirrhinum majus, and many other species in order to confirm this hypothesis. This led to additional information on flower development and to more complex molecular models. AGAMOUS (AG) is the only C type gene in Arabidopsis and it is responsible for stamen and carpel development as well as floral determinacy. LLAG1, an AG homologue from lily (Lilium longiflorum Thunb.) was isolated by screening a cDNA library derived from developing floral buds. The deduced amino acid sequence revealed the MIKC structure and a high homology in the MADS-box among AG and other orthologues. Phylogenetic analysis indicated a close relationship between LLAG1 and AG orthologues from monocot species. Spatial expression data showed LLAG1 transcripts exclusively in stamens and carpels, constituting the C domain of the ABC model. Functional analysis was carried out in Arabidopsis by overexpression of LLAG1 driven by the CaMV35S promoter. Transformed plants showed homeotic changes in the two outer floral whorls with some plants presenting the second whorl completely converted into stamens. Altogether, these data strongly indicated the functional homology between LLAG1 and AG.
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MESH Headings
- AGAMOUS Protein, Arabidopsis/genetics
- AGAMOUS Protein, Arabidopsis/metabolism
- Amino Acid Sequence
- Arabidopsis/genetics
- Arabidopsis/growth & development
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- Flowers/genetics
- Flowers/growth & development
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Plant
- Genes, Homeobox/genetics
- Genes, Homeobox/physiology
- Lilium/genetics
- MADS Domain Proteins/genetics
- MADS Domain Proteins/metabolism
- Molecular Sequence Data
- Phylogeny
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Plants, Genetically Modified
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
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