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Saini DK, Chopra Y, Pal N, Chahal A, Srivastava P, Gupta PK. Meta-QTLs, ortho-MQTLs and candidate genes for nitrogen use efficiency and root system architecture in bread wheat ( Triticum aestivum L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2245-2267. [PMID: 34744364 PMCID: PMC8526679 DOI: 10.1007/s12298-021-01085-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 05/04/2023]
Abstract
In wheat, meta-QTLs (MQTLs), ortho-MQTLs, and candidate genes (CGs) were identified for nitrogen use efficiency and root system architecture. For this purpose, 1788 QTLs were available from 24 studies published during 2006-2020. Of these, 1098 QTLs were projected onto the consensus map resulting in 118 MQTLs. The average confidence interval (CI) of MQTLs was reduced up to 8.56 folds in comparison to the average CI of QTLs. Of the 118 MQTLs, 112 were anchored to the physical map of the wheat reference genome. The physical interval of MQTLs ranged from 0.02 to 666.18 Mb with a mean of 94.36 Mb. Eighty-eight of these 112 MQTLs were verified by marker-trait associations (MTAs) identified in published genome-wide association studies (GWAS); the MQTLs that were verified using GWAS also included 9 most robust MQTLs, which are particularly useful for breeders; we call them 'Breeder's QTLs'. Some selected wheat MQTLs were further utilized for the identification of ortho-MQTLs for wheat and maize; 9 such ortho-MQTLs were available. As many as 1991 candidate genes (CGs) were also detected, which included 930 CGs with an expression level of > 2 transcripts per million in relevant organs/tissues. Among the CGs, 97 CGs with functions previously reported as important for the traits under study were selected. Based on homology analysis and expression patterns, 49 orthologues of 35 rice genes were also identified in MQTL regions. The results of the present study may prove useful for the improvement of selection strategy for yield potential, stability, and performance under N-limiting conditions. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01085-0.
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Affiliation(s)
- Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| | - Yuvraj Chopra
- College of Agriculture, Punjab Agricultural University, Ludhiana, 141004 India
- Present Address: Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583 USA
| | - Neeraj Pal
- Department of Molecular Biology and Genetic Engineering, G. B. Pant, University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Amneek Chahal
- College of Agriculture, Punjab Agricultural University, Ludhiana, 141004 India
| | - Puja Srivastava
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004 India
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Yoneyama T, Suzuki A. Exploration of nitrate-to-glutamate assimilation in non-photosynthetic roots of higher plants by studies of 15N-tracing, enzymes involved, reductant supply, and nitrate signaling: A review and synthesis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 136:245-254. [PMID: 30710774 DOI: 10.1016/j.plaphy.2018.12.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 12/16/2018] [Indexed: 05/03/2023]
Abstract
Roots of the higher plants can assimilate inorganic nitrogen by an enzymatic reduction of the most oxidized form (+6) nitrate to the reduced form (-2) glutamate. For such reactions, the substrates (originated from photosynthates) must be imported to supply energy through the reductant-generating systems within the root cells. Intensive studies over last 70 years (reviewed here) revealed the precise mechanisms of nitrate-to-glutamate transformation in roots with elaborate searches of 15N-tracing, enzymes involved, the reductant-supplying system, and nitrate signaling. In the 1970s, the tracing of 15N-labeled nitrate and ammonia in the roots demonstrated the sequential reduction and assimilation of nitrate to nitrite, ammonia, glutamine amide, and then glutamate. These reactions involve nitrate reductase (NADH-NR, EC 1.7.1.1) in the cytosol, nitrite reductase (ferredoxin [Fd]-NiR, EC 1.7.7.1), glutamine synthetase (GS2, EC 6.3.1.2), and glutamate synthase (Fd-GOGAT, EC 1.4.7.1) in the plastids. NADH for NR is generated by glycolysis in the cytosol, and NADPH for Fd-NIR and Fd-GOGAT are produced by the oxidative pentose phosphate pathway (OPPP). Electrons from NADPH are conveyed to reduce NIR and Fd-GOGAT through Fd-NADP+ reductase (FNR, EC 1.6.7.1) specifically in the roots. Physiological and molecular analyses showed the parallel inductions of NR, NIR, GS2, Fd-GOGAT, OPPP enzymes, FNR, and Fd in response to a short-term nitrate supply. Recent studies proposed a molecular mechanism of nitrate-induction of these genes and proteins. Roots can also assimilate the reduced form of inorganic ammonia by the combination of cytosolic GS1 and plastidic NADH-GOGAT.
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Affiliation(s)
- Tadakatsu Yoneyama
- Department of Applied Biological Chemistry, The University of Tokyo, Tokyo, Japan.
| | - Akira Suzuki
- INRA, IJPB, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, Versailles, F-78026, France.
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Ma S, Ding Z, Li P. Maize network analysis revealed gene modules involved in development, nutrients utilization, metabolism, and stress response. BMC PLANT BIOLOGY 2017; 17:131. [PMID: 28764653 PMCID: PMC5540570 DOI: 10.1186/s12870-017-1077-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 07/19/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The advent of big data in biology offers opportunities while poses challenges to derive biological insights. For maize, a large amount of publicly available transcriptome datasets have been generated but a comprehensive analysis is lacking. RESULTS We constructed a maize gene co-expression network based on the graphical Gaussian model, using massive RNA-seq data. The network, containing 20,269 genes, assembles into 964 gene modules that function in a variety of plant processes, such as cell organization, the development of inflorescences, ligules and kernels, the uptake and utilization of nutrients (e.g. nitrogen and phosphate), the metabolism of benzoxazionids, oxylipins, flavonoids, and wax, and the response to stresses. Among them, the inflorescences development module is enriched with domestication genes (like ra1, ba1, gt1, tb1, tga1) that control plant architecture and kernel structure, while multiple other modules relate to diverse agronomic traits. Contained within these modules are transcription factors acting as known or potential expression regulators for the genes within the same modules, suggesting them as candidate regulators for related biological processes. A comparison with an established Arabidopsis network revealed conserved gene association patterns for specific modules involved in cell organization, nutrients uptake & utilization, and metabolism. The analysis also identified significant divergences between the two species for modules that orchestrate developmental pathways. CONCLUSIONS This network sheds light on how gene modules are organized between different species in the context of evolutionary divergence and highlights modules whose structure and gene content can provide important resources for maize gene functional studies with application potential.
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Affiliation(s)
- Shisong Ma
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui China
| | - Zehong Ding
- The Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan China
| | - Pinghua Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong China
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Liu X, Feng H, Huang D, Song M, Fan X, Xu G. Two short sequences in OsNAR2.1 promoter are necessary for fully activating the nitrate induced gene expression in rice roots. Sci Rep 2015; 5:11950. [PMID: 26150107 PMCID: PMC4493634 DOI: 10.1038/srep11950] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 06/09/2015] [Indexed: 11/09/2022] Open
Abstract
Nitrate is an essential nitrogen source and serves as a signal to control growth and gene expression in plants. In rice, OsNAR2.1 is an essential partner of multiple OsNRT2 nitrate transporters for nitrate uptake over low and high concentration range. Previously, we have reported that -311 bp upstream fragment from the translational start site in the promoter of OsNAR2.1 gene is the nitrate responsive region. To identify the cis-acting DNA elements necessary for nitrate induced gene expression, we detected the expression of beta-glucuronidase (GUS) reporter in the transgenic rice driven by the OsNAR2.1 promoter with different lengths and site mutations of the 311 bp region. We found that -129 to -1 bp region is necessary for the nitrate-induced full activation of OsNAR2.1. Besides, the site mutations showed that the 20 bp fragment between -191 and -172 bp contains an enhancer binding site necessary to fully drive the OsNAR2.1 expression. Part of the 20 bp fragment is commonly presented in the sequences of different promoters of both the nitrate induced NAR2 genes and nitrite reductase NIR1 genes from various higher plants. These findings thus reveal the presence of conserved cis-acting element for mediating nitrate responses in plants.
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Affiliation(s)
- Xiaoqin Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
| | - Huimin Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
| | - Daimin Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
| | - Miaoquan Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaorong Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
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Mohr H, Neininger A, Seith B. Control of Nitrate Reductase and Nitrite Reductase Gene Expression by Light, Nitrate and a Plastidic Factor. ACTA ACUST UNITED AC 2014. [DOI: 10.1111/j.1438-8677.1992.tb00270.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Liseron-Monfils C, Bi YM, Downs GS, Wu W, Signorelli T, Lu G, Chen X, Bondo E, Zhu T, Lukens LN, Colasanti J, Rothstein SJ, Raizada MN. Nitrogen transporter and assimilation genes exhibit developmental stage-selective expression in maize (Zea mays L.) associated with distinct cis-acting promoter motifs. PLANT SIGNALING & BEHAVIOR 2013; 8:26056. [PMID: 24270626 PMCID: PMC4091066 DOI: 10.4161/psb.26056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Nitrogen is considered the most limiting nutrient for maize (Zea mays L.), but there is limited understanding of the regulation of nitrogen-related genes during maize development. An Affymetrix 82K maize array was used to analyze the expression of ≤ 46 unique nitrogen uptake and assimilation probes in 50 maize tissues from seedling emergence to 31 d after pollination. Four nitrogen-related expression clusters were identified in roots and shoots corresponding to, or overlapping, juvenile, adult, and reproductive phases of development. Quantitative real time PCR data was consistent with the existence of these distinct expression clusters. Promoters corresponding to each cluster were screened for over-represented cis-acting elements. The 8-bp distal motif of the Arabidopsis 43-bp nitrogen response element (NRE) was over-represented in nitrogen-related maize gene promoters. This conserved motif, referred to here as NRE43-d8, was previously shown to be critical for nitrate-activated transcription of nitrate reductase (NIA1) and nitrite reductase (NIR1) by the NIN-LIKE PROTEIN 6 (NLP6) in Arabidopsis. Here, NRE43-d8 was over-represented in the promoters of maize nitrate and ammonium transporter genes, specifically those that showed peak expression during early-stage vegetative development. This result predicts an expansion of the NRE-NLP6 regulon and suggests that it may have a developmental component in maize. We also report leaf expression of putative orthologs of nitrite transporters (NiTR1), a transporter not previously reported in maize. We conclude by discussing how each of the four transcriptional modules may be responsible for the different nitrogen uptake and assimilation requirements of leaves and roots at different stages of maize development.
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Affiliation(s)
| | - Yong-Mei Bi
- Department of Molecular and Cellular Biology; University of Guelph; Guelph, ON Canada
| | - Gregory S Downs
- Department of Plant Agriculture; University of Guelph; Guelph, ON Canada
| | - Wenqing Wu
- Department of Molecular and Cellular Biology; University of Guelph; Guelph, ON Canada
| | - Tara Signorelli
- Department of Molecular and Cellular Biology; University of Guelph; Guelph, ON Canada
| | - Guangwen Lu
- Department of Molecular and Cellular Biology; University of Guelph; Guelph, ON Canada
| | - Xi Chen
- Syngenta Biotechnology Inc.; Research Triangle Park; Greensboro, NC USA
| | - Eddie Bondo
- Syngenta Biotechnology Inc.; Research Triangle Park; Greensboro, NC USA
| | - Tong Zhu
- Syngenta Biotechnology Inc.; Research Triangle Park; Greensboro, NC USA
| | - Lewis N Lukens
- Department of Plant Agriculture; University of Guelph; Guelph, ON Canada
| | - Joseph Colasanti
- Department of Molecular and Cellular Biology; University of Guelph; Guelph, ON Canada
| | - Steven J Rothstein
- Department of Molecular and Cellular Biology; University of Guelph; Guelph, ON Canada
| | - Manish N Raizada
- Department of Plant Agriculture; University of Guelph; Guelph, ON Canada
- Correspondence to: Manish N Raizada,
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7
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Roles of the transcriptional regulation mediated by the nitrate-responsive cis-element in higher plants. Biochem Biophys Res Commun 2011; 411:708-13. [DOI: 10.1016/j.bbrc.2011.07.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 07/02/2011] [Indexed: 11/24/2022]
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Konishi M, Yanagisawa S. Identification of a nitrate-responsive cis-element in the Arabidopsis NIR1 promoter defines the presence of multiple cis-regulatory elements for nitrogen response. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 63:269-282. [PMID: 20444232 DOI: 10.1111/j.1365-313x.2010.04239.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Nitrate is a major nitrogen source for land plants and also acts as a signaling molecule that induces changes in growth and gene expression. To identify the cis-acting DNA element involved in nitrate-responsive gene expression, we analyzed the promoter of the Arabidopsis gene encoding nitrite reductase (NIR1). A region from positions -188 to -1, relative to the translation start site, was found to contain at least one cis-element necessary for the nitrate-dependent activation of the promoter, in which the activity of nitrate transporter NRT2.1 and/or NRT2.2 plays a critical role. To define this nitrate-responsive cis-element (NRE), we compared the sequences of several nitrite reductase gene promoters from various higher plants and identified a conserved sequence motif as the putative NRE. A synthetic promoter in which the four copies of a 43-bp sequence containing the motif were fused to the 35S minimal promoter was found to direct nitrate-responsive transcription. Furthermore, mutations within this conserved motif in the native NIR1 promoter markedly reduced the nitrate-responsive activity of the promoter, indicating that the 43-bp sequence is an NRE that is both necessary and sufficient for nitrate-responsive transcription. We also show that both the native NIR1 promoter and the synthetic promoter display a similar level of sensitivity to nitrate, but respond differentially to exogenously supplied glutamine, indicating independent modulation of NIR1 expression by NRE-mediated nitrate induction and feedback repression mediated by other cis-element(s). These findings thus define the presence of multiple cis-elements involved in the nitrogen response in Arabidopsis.
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Affiliation(s)
- Mineko Konishi
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
- Research Fellow of the Japan Society for the Promotion of Science, Tiyoda-ku, Tokyo 102-8471, Japan
| | - Shuichi Yanagisawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
- The Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi 332-0012, Japan
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9
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Wei F, Stein JC, Liang C, Zhang J, Fulton RS, Baucom RS, De Paoli E, Zhou S, Yang L, Han Y, Pasternak S, Narechania A, Zhang L, Yeh CT, Ying K, Nagel DH, Collura K, Kudrna D, Currie J, Lin J, Kim H, Angelova A, Scara G, Wissotski M, Golser W, Courtney L, Kruchowski S, Graves TA, Rock SM, Adams S, Fulton LA, Fronick C, Courtney W, Kramer M, Spiegel L, Nascimento L, Kalyanaraman A, Chaparro C, Deragon JM, Miguel PS, Jiang N, Wessler SR, Green PJ, Yu Y, Schwartz DC, Meyers BC, Bennetzen JL, Martienssen RA, McCombie WR, Aluru S, Clifton SW, Schnable PS, Ware D, Wilson RK, Wing RA. Detailed analysis of a contiguous 22-Mb region of the maize genome. PLoS Genet 2009; 5:e1000728. [PMID: 19936048 PMCID: PMC2773423 DOI: 10.1371/journal.pgen.1000728] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Accepted: 10/16/2009] [Indexed: 12/20/2022] Open
Abstract
Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on approximately 1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses.
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Affiliation(s)
- Fusheng Wei
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Joshua C. Stein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Chengzhi Liang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Robert S. Fulton
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Regina S. Baucom
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Emanuele De Paoli
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
| | - Shiguo Zhou
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Lixing Yang
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Yujun Han
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - Shiran Pasternak
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Apurva Narechania
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Lifang Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Cheng-Ting Yeh
- Department of Agronomy and Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Kai Ying
- Department of Agronomy and Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Dawn H. Nagel
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - Kristi Collura
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - David Kudrna
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Jennifer Currie
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Jinke Lin
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - HyeRan Kim
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Angelina Angelova
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Gabriel Scara
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Marina Wissotski
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Wolfgang Golser
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - Laura Courtney
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Scott Kruchowski
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Tina A. Graves
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Susan M. Rock
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Stephanie Adams
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Lucinda A. Fulton
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Catrina Fronick
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - William Courtney
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Melissa Kramer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Lori Spiegel
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Lydia Nascimento
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Ananth Kalyanaraman
- School of Electrical Engineering and Computer Science, Washington State University, Pullman, Washington, United States of America
| | - Cristian Chaparro
- Université de Perpignan Via Domitia, CNRS UMR 5096, Perpignan, France
| | - Jean-Marc Deragon
- Université de Perpignan Via Domitia, CNRS UMR 5096, Perpignan, France
| | - Phillip San Miguel
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of America
| | - Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | - Susan R. Wessler
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - Pamela J. Green
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
| | - Yeisoo Yu
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
| | - David C. Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Blake C. Meyers
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
| | - Jeffrey L. Bennetzen
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Robert A. Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - W. Richard McCombie
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Srinivas Aluru
- Department of Electrical and Computer Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Sandra W. Clifton
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Patrick S. Schnable
- Department of Agronomy and Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Richard K. Wilson
- The Genome Center and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Rod A. Wing
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
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10
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Boisson M, Mondon K, Torney V, Nicot N, Laine AL, Bahrman N, Gouy A, Daniel-Vedele F, Hirel B, Sourdille P, Dardevet M, Ravel C, Le Gouis J. Partial sequences of nitrogen metabolism genes in hexaploid wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 110:932-40. [PMID: 15714330 DOI: 10.1007/s00122-004-1913-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2004] [Accepted: 12/15/2004] [Indexed: 05/21/2023]
Abstract
Our objective was to partially sequence genes controlling nitrogen metabolism in wheat species in order to find sequence polymorphism that would enable their mapping. Primers were designed for nitrate reductase, nitrite reductase, glutamate dehydrogenase and glutamate synthase (GOGAT), and gene fragments were amplified on Triticum aestivum, T. durum, T. monococcum, T. speltoides and T. tauschii. We obtained more than 8 kb of gene sequences, mainly as coding regions (60%). Polymorphism was quantified by comparing two-by-two the three genomes of the hexaploid cultivar Arche and genomes of diploid wheat species. On average, the polymorphism rate was higher for non-coding regions, where it ranged from 1/60 to 1/23, than for coding regions (range: 1/110-1/40) except when the hexaploid D genome was compared to that of T. tauschii (1/800 and 1/816, respectively). Genome-specific primers were devised for the ferredoxin-dependent (Fd)-GOGAT gene, and they enabled the mapping of this gene on homoeologous chromosomes of group 2 using Chinese Spring deletion lines. A single nucleotide polymorphism (SNP) detected between the two hexaploid wheat cultivars Arche and Recital was used to genetically map Fd-GOGAT on chromosome 2D using a population of dihaploid lines. Fd-GOGAT-specific primers were used to estimate the SNP rate on a set of 11 hexaploid and nine Durum wheat genotypes leading to the estimate of 1 SNP/515 bp. We demonstrate that polymorphism detection enables heterologous, homeologous and even paralogous copies to be assigned, even if the elaboration of specific primer pairs is time-consuming and expensive because of the sequencing.
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Affiliation(s)
- M Boisson
- INRA URGAP, Domaine de Brunehaut, Péronne, BP 136, 80200, Estrées-Mons, France
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11
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Debnam PM, Fernie AR, Leisse A, Golding A, Bowsher CG, Grimshaw C, Knight JS, Emes MJ. Altered activity of the P2 isoform of plastidic glucose 6-phosphate dehydrogenase in tobacco (Nicotiana tabacum cv. Samsun) causes changes in carbohydrate metabolism and response to oxidative stress in leaves. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2004; 38:49-59. [PMID: 15053759 DOI: 10.1111/j.1365-313x.2004.02017.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Expression of one specific isoform of plastidic glucose 6-phosphate dehydrogenase (G6PDH) was manipulated in transgenic tobacco. Antisense and sense constructs of the endogenous P2 form of G6PDH were used to transform plants under the control of the cauliflower mosaic virus (CaMV) 35S promotor. Recombinant plants with altered expression were taken through to homozygosity by selective screening. Northern analyses revealed substantial changes in the expression of the P2 form of G6PDH, with no apparent impact on the activity of the cytosolic isoenzyme. Analysis of G6PDH activity in chloroplasts showed that despite the large changes in expression of P2-G6PDH, the range of enzyme activity varied only from approximately 50 to 200% of the wild type, reflecting the presence of a second G6PDH chloroplastic isoform (P1). Although none of the transgenic plants showed any visible phenotype, there were marked differences in metabolism of both sense and antisense lines when compared with wild-type/control lines. Sucrose, glucose and fructose contents of leaves were higher in antisense lines, whereas in overexpressing lines, the soluble sugar content was reduced below that of control plants. Even more striking was the observation that contents of glucose 6-phosphate (Glc6P) and 6-phosphogluconate (6PG) changed, such that the ratio of Glc6P:6PG was some 2.5-fold greater in the most severe antisense lines, compared with those with the highest levels of overexpression. Because of the distinctive biochemical properties of P2-G6PDH, we investigated the impact of altered expression on the contents of antioxidants and the response of plants to oxidative stress induced by methyl viologen (MV). Plants with decreased expression of P2-G6PDH showed increased content of reduced glutathione (GSH) compared to other lines. They also possessed elevated contents of ascorbate and exhibited a much higher ratio of reduced:oxidised ascorbate. When exposed to MV, leaf discs of wild-type and overexpressing lines demonstrated increased oxidative damage as measured by lipid peroxidation. Remarkably, leaf discs from plants with decreased P2-G6PDH did not show any change in lipid peroxidation in response to increasing concentrations of up to 15 micro m MV. The results are discussed from the perspective of the role of G6PDH in carbohydrate metabolism and oxidative stress. It is suggested that the activity of P2-G6PDH may be crucial in balancing the redox poise in chloroplasts.
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Affiliation(s)
- Phillip M Debnam
- College of Biological Science, University of Guelph, Gordon Street, Guelph, Ont., Canada N1G 2W1
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12
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Gallais A, Hirel B. An approach to the genetics of nitrogen use efficiency in maize. JOURNAL OF EXPERIMENTAL BOTANY 2004; 55:295-306. [PMID: 14739258 DOI: 10.1093/jxb/erh006] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
To study the genetic variability and the genetic basis of nitrogen (N) use efficiency in maize, a set of recombinant inbred lines crossed with a tester was studied at low input (N-) and high input (N+) for grain yield and its components, grain protein content, and post-anthesis nitrogen uptake and remobilization. Other physiological traits, such as nitrate content, nitrate reductase, glutamine synthetase (GS), and glutamate dehydrogenase activities were studied at the level of the lines. Genotypexnitrogen (GxN) interaction was significant for yield and explained by variation in kernel number. In N-, N-uptake, the nitrogen nutrition index, and GS activity in the vegetative stage were positively correlated with grain yield, whereas leaf senescence was negatively correlated. Whatever N-input, post-anthesis N-uptake was highly negatively related to N-remobilization. As a whole, genetic variability was expressed differently in N+ and N-. This was confirmed by the detection of QTLs. More QTLs were detected in N+ than in N- for traits of vegetative development, N-uptake, and grain yield and its components, whereas it was the reverse for grain protein content and N-utilization efficiency. Several coincidences between genes encoding for enzymes of N metabolism and QTLs for the traits studied were observed. In particular, coincidences in three chromosome regions of QTLs for yield and N-remobilization, QTLs for GS activity and a gene encoding cytosolic GS were observed. This may have a physiological meaning. The GS locus on chromosome 5 appears to be a good candidate gene which can, at least partially, explain the variation in nitrogen use efficiency.
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Affiliation(s)
- A Gallais
- Station de Génétique Végétale, INRA-UPS-INAPG, Ferme du Moulon, 91190 Gif/Yvette, France.
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13
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Orea A, Pajuelo P, Pajuelo E, Márquez AJ, Romero JM. Characterisation and expression studies of a root cDNA encoding for ferredoxin-nitrite reductase from Lotus japonicus. PHYSIOLOGIA PLANTARUM 2001; 113:193-202. [PMID: 12060296 DOI: 10.1034/j.1399-3054.2001.1130206.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A full-length cDNA encoding for ferredoxin-nitrite reductase (NiR, EC 1.7.7.1), has been isolated from a root cDNA library from the legume Lotus japonicus and characterised. The NiR gene (Nii) is present as a single copy in this plant, and encodes a protein of 582 amino acids. The Lotus NiR protein is synthesised as a precursor with an amino-terminal transit peptide consisting of 25 amino acid residues. Sequence comparisons with leaf NiRs from different plant species and with other related redox proteins identified in the root NiR the same highly conserved residues involved in the cofactor binding than previously reported for leaves. Besides, a putative binding site for ferredoxin was also found in the N-terminal region of the protein. The NiR gene is expressed in roots and leaves, although the level of expression is much higher in roots, in accordance with the fact that L. japonicus assimilates nitrate mainly in roots. NiR mRNA, protein and activity are induced by nitrate in roots and leaves, while ammonium-grown plants only showed basal levels. No oscillations of NiR mRNA, protein and activity were observed during the day/night cycle, neither in roots nor leaves, making an interesting difference with rhythms observed in other plant species.
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Affiliation(s)
- Alicia Orea
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química. Universidad de Sevilla, Apdo. 553, E-41080-Sevilla, Spain Instituto de Bioquímica Vegetal y Fotosíntesis. Centro de Investigaciones Científicas Isla de la Cartuja, c/ Americo Vespucio s/n, E-41092-Sevilla, Spain
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14
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Takahashi M, Sasaki Y, Ida S, Morikawa H. Nitrite reductase gene enrichment improves assimilation of NO(2) in Arabidopsis. PLANT PHYSIOLOGY 2001; 126:731-41. [PMID: 11402201 PMCID: PMC111163 DOI: 10.1104/pp.126.2.731] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2001] [Accepted: 01/19/2001] [Indexed: 05/18/2023]
Abstract
Transgenic plants of Arabidopsis bearing the spinach (Spinacia oleracea) nitrite reductase (NiR, EC 1.7.7.1) gene that catalyzes the six-electron reduction of nitrite to ammonium in the second step of the nitrate assimilation pathway were produced by use of the cauliflower mosaic virus 35S promoter and nopaline synthase terminator. Integration of the gene was confirmed by a genomic polymerase chain reaction (PCR) and Southern-blot analysis; its expression by a reverse transcriptase-PCR and two-dimensional polyacrylamide gel electrophoresis western-blot analysis; total (spinach + Arabidopsis) NiR mRNA content by a competitive reverse transcriptase-PCR; localization of NiR activity (NiRA) in the chloroplast by fractionation analysis; and NO(2) assimilation by analysis of the reduced nitrogen derived from NO(2) (NO(2)-RN). Twelve independent transgenic plant lines were characterized in depth. Three positive correlations were found for NiR gene expression; between the total NiR mRNA and total NiR protein contents (r = 0.74), between the total NiR protein and NiRA (r = 0.71), and between NiRA and NO(2)-RN (r = 0.65). Of these twelve lines, four had significantly higher NiRA than the wild-type control (P < 0.01), and three had significantly higher NO(2)-RN (P < 0.01). Each of the latter three had one to two copies of spinach NiR cDNA per haploid genome. The NiR flux control coefficient for NO(2) assimilation was estimated to be about 0.4. A similar value was obtained for an NiR antisense tobacco (Nicotiana tabacum cv Xanthi XHFD8). The flux control coefficients of nitrate reductase and glutamine synthetase were much smaller than this value. Together, these findings indicate that NiR is a controlling enzyme in NO(2) assimilation by plants.
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Affiliation(s)
- M Takahashi
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8526 Japan
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15
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Hirel B, Bertin P, Quilleré I, Bourdoncle W, Attagnant C, Dellay C, Gouy A, Cadiou S, Retailliau C, Falque M, Gallais A. Towards a better understanding of the genetic and physiological basis for nitrogen use efficiency in maize. PLANT PHYSIOLOGY 2001; 125:1258-70. [PMID: 11244107 PMCID: PMC65606 DOI: 10.1104/pp.125.3.1258] [Citation(s) in RCA: 192] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2000] [Accepted: 12/20/2000] [Indexed: 05/18/2023]
Abstract
To enhance our understanding of the genetic basis of nitrogen use efficiency in maize (Zea mays), we have developed a quantitative genetic approach by associating metabolic functions and agronomic traits to DNA markers. In this study, leaves of vegetative recombinant inbred lines of maize, already assessed for their agronomic performance, were analyzed for physiological traits such as nitrate content, nitrate reductase (NR), and glutamine synthetase (GS) activities. A significant genotypic variation was found for these traits and a positive correlation was observed between nitrate content, GS activity and yield, and its components. NR activity, on the other hand, was negatively correlated. These results suggest that increased productivity in maize genotypes was due to their ability to accumulate nitrate in their leaves during vegetative growth and to efficiently remobilize this stored nitrogen during grain filling. Quantitative trait loci (QTL) for various agronomic and physiological traits were searched for and located on the genetic map of maize. Coincidences of QTL for yield and its components with genes encoding cytosolic GS and the corresponding enzyme activity were detected. In particular, it appears that the GS locus on chromosome 5 is a good candidate gene that can, at least partially, explain variations in yield or kernel weight. Because at this locus coincidences of QTLs for grain yield, GS, NR activity, and nitrate content were also observed, we hypothesize that leaf nitrate accumulation and the reactions catalyzed by NR and GS are coregulated and represent key elements controlling nitrogen use efficiency in maize.
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Affiliation(s)
- B Hirel
- Unité de Nutrition Azotée des Plantes, Institut National de la Recherche Agronomique, Route de St-Cyr 78026, Versailles cedex, France.
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16
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Wang R, Guegler K, LaBrie ST, Crawford NM. Genomic analysis of a nutrient response in Arabidopsis reveals diverse expression patterns and novel metabolic and potential regulatory genes induced by nitrate. THE PLANT CELL 2000; 12:1491-509. [PMID: 10948265 PMCID: PMC149118 DOI: 10.1105/tpc.12.8.1491] [Citation(s) in RCA: 337] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2000] [Accepted: 05/26/2000] [Indexed: 05/17/2023]
Abstract
Microarray and RNA gel blot analyses were performed to identify Arabidopsis genes that responded to nitrate at both low (250 microM) and high (5 to 10 mM) nitrate concentrations. Genes involved directly or indirectly with nitrite reduction were the most highly induced by nitrate. Most of the known nitrate-regulated genes (including those encoding nitrate reductase, the nitrate transporter NRT1, and glutamate synthase) appeared in the 40 most strongly nitrate-induced genes/clones on at least one of the microarrays of the 5524 genes/clones investigated. Novel nitrate-induced genes were also found, including those encoding (1) possible regulatory proteins, including an MYB transcription factor, a calcium antiporter, and putative protein kinases; (2) metabolic enzymes, including transaldolase and transketolase of the nonoxidative pentose pathway, malate dehydrogenase, asparagine synthetase, and histidine decarboxylase; and (3) proteins with unknown functions, including nonsymbiotic hemoglobin, a senescence-associated protein, and two methyltransferases. The primary pattern of induction observed for many of these genes was a transient increase in mRNA at low nitrate concentrations and a sustained increase when treated with high nitrate concentrations. Other patterns of induction observed included transient inductions after both low and high nitrate treatments and sustained or increasing amounts of mRNA after either treatment. Two genes, AMT1;1 encoding an ammonium transporter and ANR1 encoding a MADS-box factor, were repressed by nitrate. These findings indicate that nitrate induces not just one but many diverse responses at the mRNA level in Arabidopsis.
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Affiliation(s)
- R Wang
- Division of Biology, University of California at San Diego, La Jolla, California 92093-0016, USA
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17
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Wang R, Guegler K, LaBrie ST, Crawford NM. Genomic analysis of a nutrient response in Arabidopsis reveals diverse expression patterns and novel metabolic and potential regulatory genes induced by nitrate. THE PLANT CELL 2000. [PMID: 10948265 DOI: 10.2307/3871145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Microarray and RNA gel blot analyses were performed to identify Arabidopsis genes that responded to nitrate at both low (250 microM) and high (5 to 10 mM) nitrate concentrations. Genes involved directly or indirectly with nitrite reduction were the most highly induced by nitrate. Most of the known nitrate-regulated genes (including those encoding nitrate reductase, the nitrate transporter NRT1, and glutamate synthase) appeared in the 40 most strongly nitrate-induced genes/clones on at least one of the microarrays of the 5524 genes/clones investigated. Novel nitrate-induced genes were also found, including those encoding (1) possible regulatory proteins, including an MYB transcription factor, a calcium antiporter, and putative protein kinases; (2) metabolic enzymes, including transaldolase and transketolase of the nonoxidative pentose pathway, malate dehydrogenase, asparagine synthetase, and histidine decarboxylase; and (3) proteins with unknown functions, including nonsymbiotic hemoglobin, a senescence-associated protein, and two methyltransferases. The primary pattern of induction observed for many of these genes was a transient increase in mRNA at low nitrate concentrations and a sustained increase when treated with high nitrate concentrations. Other patterns of induction observed included transient inductions after both low and high nitrate treatments and sustained or increasing amounts of mRNA after either treatment. Two genes, AMT1;1 encoding an ammonium transporter and ANR1 encoding a MADS-box factor, were repressed by nitrate. These findings indicate that nitrate induces not just one but many diverse responses at the mRNA level in Arabidopsis.
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Affiliation(s)
- R Wang
- Division of Biology, University of California at San Diego, La Jolla, California 92093-0016, USA
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18
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Hirasawa M, Dose MM, Kleis-SanFrancisco S, Hurley JK, Tollin G, Knaff DB. A conserved tryptophan at the ferredoxin-binding site of ferredoxin:nitrite oxidoreductase. Arch Biochem Biophys 1998; 354:95-101. [PMID: 9633602 DOI: 10.1006/abbi.1998.0630] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Treatment of spinach leaf ferredoxin-dependent nitrite reductase with N-bromosuccinimide (NBS), under conditions where slightly less than 1 mol of tryptophan is modified per mole of nitrite reductase, inhibits the catalytic activity of the enzyme by ca. 80% without any effect on substrate binding or other enzyme properties. Complex formation between nitrite reductase and ferredoxin completely protects the enzyme against this inhibition. Transient kinetic measurements show that the second-order rate constant for reduction of NBS-modified nitrite reductase by reduced ferredoxin is approximately four-fold larger than that observed for the native, unmodified enzyme. Also, reduction of NBS-modified nitrite reductase by the 5-deazariboflavin radical shows a different kinetic pattern than that observed with the native enzyme, suggesting that tryptophan modification increases access of the radical to the low-potential [4Fe-4S] cluster of the enzyme, decreases the accessibility to the siroheme group of the enzyme, or both. The tryptophan that is modified has been identified as the absolutely conserved W92. A methionine, M73, that is also modified by NBS, has been identified. The ferredoxin-binding site on spinach nitrite reductase thus appears to include W92 and perhaps M73, in addition to the previously identified R375, R556, and K436.
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Affiliation(s)
- M Hirasawa
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock 79409-1061, USA
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19
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Dose MM, Hirasawa M, Kleis-SanFrancisco S, Lew EL, Knaff DB. The ferredoxin-binding site of ferredoxin: Nitrite oxidoreductase. Differential chemical modification of the free enzyme and its complex with ferredoxin. PLANT PHYSIOLOGY 1997; 114:1047-53. [PMID: 9232882 PMCID: PMC158393 DOI: 10.1104/pp.114.3.1047] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Spinach (Spinacea oleracea) leaf ferredoxin (Fd)-dependent nitrite reductase was treated with either the arginine-modifying reagent phenyl-glyoxal or the lysine-modifying reagent pyridoxal-5'-phosphate under conditions where only the Fd-binding affinity of the enzyme was affected and where complex formation between Fd and the enzyme prevented the inhibition by either reagent. Modification with [14C]phenylglyoxal allowed the identification of two nitrite reductase arginines, R375 and R556, that are protected by Fd against labeling. Modification of nitrite reductase with pyridoxal-5'-phosphate, followed by reduction with NaBH4, allowed the identification of a lysine, K436, that is protected by Fd against labeling. Positive charges are present at these positions in all of the Fd-dependent nitrite reductase for which sequences are available, suggesting that these amino acids are directly involved in electrostatic binding of Fd to the enzyme.
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Affiliation(s)
- M M Dose
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock 79409-1061, USA
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20
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Sivasankar S, Rothstein S, Oaks A. Regulation of the Accumulation and Reduction of Nitrate by Nitrogen and Carbon Metabolites in Maize Seedlings. PLANT PHYSIOLOGY 1997; 114:583-589. [PMID: 12223730 PMCID: PMC158340 DOI: 10.1104/pp.114.2.583] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The accumulation and reduction of nitrate in the presence of the nitrogen metabolites asparagine (Asn) and glutamine (Gln) and the carbon metabolite sucrose (Suc) were examined in maize (Zea mays L.) seedlings in an attempt to separate their effects on the nitrate uptake system and the nitrate reduction system. After 8 h of exposure to nitrate in the presence of 1 mM Asn, tissue nitrate accumulation was reduced at 250 [mu]M external nitrate, but not at 5 mM Asn. The induction of nitrate reductase (NR) activity was reduced at both external nitrate concentrations. In the presence of 1 mM Gln or 1% Suc, tissue nitrate concentration was not significantly altered, but the induction of root NR activity was reduced or enhanced, respectively. The induction of root nitrite reductase (NiR) activity was also reduced in the presence of Asn or Gln and enhanced in the presence of Suc. Transcript levels of NR and NiR in roots were reduced in the presence of the amides and enhanced in the presence of Suc. When Suc was present in combination with either amide, there was complete relief from the inhibition of NiR transcription observed in the presence of amide alone. In the case of NR, however, this relief from inhibition was negligible. The inhibition of the induction of NR and NiR activities in the presence of Gln and Asn is a direct effect and is not the result of altered nitrate uptake in the presence of these metabolites.
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Affiliation(s)
- S. Sivasankar
- Departments of Botany (A.O.), and Molecular Biology and Genetics (S.S., S.R.), University of Guelph, Guelph, Ontario, Canada N1G 2W1
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21
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Matsumura T, Sakakibara H, Nakano R, Kimata Y, Sugiyama T, Hase T. A nitrate-inducible ferredoxin in maize roots. Genomic organization and differential expression of two nonphotosynthetic ferredoxin isoproteins. PLANT PHYSIOLOGY 1997; 114:653-60. [PMID: 9193097 PMCID: PMC158349 DOI: 10.1104/pp.114.2.653] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We have identified and characterized a nitrate-inducible ferredoxin (Fd) in maize (Zea mays L.) roots by structural analysis of the purified protein and by cloning of its cDNA and gene. In maize Fd isoproteins are encoded by a small multigene family, and the nitrate-inducible Fd was identified as a novel isoprotein, designated Fd VI, which differed from an Fd I to Fd V identified to date. In the roots of seedlings cultured without nitrate, Fd VI was undetectable. However, during the induction of the capacity for nitrate assimilation, the amount of Fd VI increased markedly within 24 h. Concurrently, the level of transcript for Fd VI increased, but more quickly, reaching a maximal level within 2 h with kinetics similar to those of nitrite reductase and Fd-NADP+ reductase. Fd III was constitutively expressed in roots, and no such changes at the protein and mRNA levels were observed during the nitrate induction. In the 5' flanking region of the gene for Fd VI only, we identified NIT-2 motifs, which are widely found in genes for enzymes related to nitrogen metabolism. These data indicate that Fd VI is co-induced with the previously characterized enzymes involved in nitrate assimilation, and they suggest that the novel Fd isoprotein, distinct from the constitutively expressed Fd, might play an important role as an electron carrier from NADPH to nitrite reductase and other Fd-dependent enzymes in root plastids.
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Affiliation(s)
- T Matsumura
- Division of Enzymology, Osaksa University, Japan. matumura/
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22
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Colandene JD, Garrett RH. Functional dissection and site-directed mutagenesis of the structural gene for NAD(P)H-nitrite reductase in Neurospora crassa. J Biol Chem 1996; 271:24096-104. [PMID: 8798648 DOI: 10.1074/jbc.271.39.24096] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Neurospora crassa NAD(P)H-nitrite reductase, encoded by the nit-6 gene, is a soluble, alpha2-type homodimeric protein composed of 127-kDa polypeptide subunits. This multicenter oxidation-reduction enzyme utilizes either NADH or NADPH as electron donor and possesses as prosthetic groups two iron-sulfur (Fe4S4) clusters, two siroheme groups, and two FAD molecules. The native activity of the enzyme is the NAD(P)H-dependent reduction of nitrite to ammonia. In addition, N. crassa nitrite reductase displays several partial activities in vitro, including a siroheme-independent NAD(P)H-cytochrome c reductase activity and an FAD-independent dithionite-nitrite reductase activity. These partial activities are presumed to be manifestations of discrete functional domains within the protein. A full-length nit-6 cDNA was constructed and used in developing an expression system within E. coli capable of yielding high levels of NADPH-nitrite reductase activity. Maximal expression was obtained in nirB- E. coli cells grown anaerobically at 22 +/- 1 degrees C, in conjunction with co-expression of a plasmid-borne cysG gene (encoding the rate-limiting enzyme in siroheme synthesis) and co-transformation with plasmid pGroESL (encoding bacterial chaperonins GroES and GroEL). Dissection of gene segments encoding putative functional domains within the nit-6 gene was performed. Expression of a partial cDNA construct encoding the FAD-/NAD-binding domain yielded extracts with NADPH-cytochrome c reductase activity but no NADPH-nitrite reductase activity or dithionite-nitrite reductase activity. Expression of a cDNA construct encoding the (Fe4S4)-siroheme-binding domain resulted in extracts possessing dithionite-nitrite reductase activity but no NADPH-nitrite reductase or NADPH-cytochrome c reductase activity. Analysis of site-directed mutations altering amino acid residues Cys-331 within the FAD-/NAD-binding domain and Ser-755 within the (Fe4S4)-siroheme-binding domain of the nitrite reductase demonstrated that these residues were not essential for native or partial enzyme activity. Cys-757 within the (Fe4S4)-siroheme-binding domain was essential for native enzyme activity.
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Affiliation(s)
- J D Colandene
- Department of Biology, Gilmer Hall, University of Virginia, Charlottesville, Virginia 22903-2477, USA
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Sengupta S, Shaila MS, Rao GR. Purification and characterization of assimilatory nitrite reductase from Candida utilis. Biochem J 1996; 317 ( Pt 1):147-55. [PMID: 8694757 PMCID: PMC1217456 DOI: 10.1042/bj3170147] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Nitrate assimilation in many plants, algae, yeasts and bacteria is mediated by two enzymes, nitrate reductase (EC 1.6.6.2) and nitrite reductase (EC 1.7.7.1). They catalyse the stepwise reduction of nitrate to nitrite and nitrite to ammonia respectively. The nitrite reductase from an industrially important yeast, Candida utilis, has been purified to homogeneity. Purified nitrite reductase is a heterodimer and the molecular masses of the two subunits are 58 and 66 kDa. The native enzyme exhibits a molecular mass of 126 kDa as analysed by gel filtration. The identify of the two subunits of nitrite reductase was confirmed by immunoblotting using antibody for Cucurbita pepo leaf nitrite reductase. The presence of two different sized transcripts coding for the two subunits was confirmed by (a) in vitro translation of mRNA from nitrate-induced C. utilis followed by immunoprecipitation of the in vitro translated products with heterologous nitrite reductase antibody and (b) Northern-blot analysis. The 66 kDa subunit is acidic in nature which is probably due to its phosphorylated status. The enzyme is stable over a range of temperatures. Both subunits can catalyse nitrite reduction, and the reconstituted enzyme, at a higher protein concentration, shows an activity similar to that of the purified enzyme. Each of these subunits has been shown to contain a few unique peptides in addition to a large number of common peptides. Reduced Methyl Viologen has been found to be as effective an electron donor as NADPH in the catalytic process, a phenomenon not commonly seen for nitrite reductases from other systems.
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Affiliation(s)
- S Sengupta
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
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Suzuki I, Kikuchi H, Nakanishi S, Fujita Y, Sugiyama T, Omata T. A novel nitrite reductase gene from the cyanobacterium Plectonema boryanum. J Bacteriol 1995; 177:6137-43. [PMID: 7592378 PMCID: PMC177453 DOI: 10.1128/jb.177.21.6137-6143.1995] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The gene (nirA) for nitrite reductase was cloned from the nonheterocystous, filamentous cyanobacterium Plectonema boryanum. The predicted protein consists of 654 amino acids and has a calculated molecular weight of 72,135. The deduced amino acid sequence from positions 1 to 511 is strongly similar to the entire sequence of the ferredoxin-dependent nitrite reductases from other phototrophs, while the remainder of the protein is unique to the Plectonema nitrite reductase. The C-terminal portion of the protein (amino acids 584 to 654) is 30 to 35% identical to [2Fe-2S] ferredoxins from higher plants and cyanobacteria, with all of the four Cys residues involved in binding of the [2Fe-2S] cluster in the ferredoxins being conserved. Immunoblotting analysis of the extracts of P. boryanum cells showed that the NirA polypeptide has an apparent molecular mass of 75 kDa. An insertional mutant of nirA lacked the 75-kDa polypeptide, had no nitrite reductase activity, and failed to grow on nitrate and nitrite, indicating that the novel nirA is the sole nitrite reductase gene in P. boryanum and that the NirA polypeptide with the ferredoxin-like domain is the apoprotein of the functional nitrite reductase. As in Synechococcus sp. strain PCC7942, nirA is the first gene of a large transcription unit (> 7 kb in size) and is repressed by ammonium and derepressed simply by deprivation of ammonium from the medium. The development of nitrite reductase activity was, however, found to require the presence of nitrate in the medium.
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Affiliation(s)
- I Suzuki
- Department of Applied Biological Sciences, School of Agricultural Sciences, Nagoya University, Japan
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25
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Wu S, Lu Q, Kriz AL, Harper JE. Identification of cDNA clones corresponding to two inducible nitrate reductase genes in soybean: analysis in wild-type and nr1 mutant. PLANT MOLECULAR BIOLOGY 1995; 29:491-506. [PMID: 8534848 DOI: 10.1007/bf00020980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Among higher plants, soybean is unique in that biochemically it has been characterized as having two constitutive nitrate reductase (cNR) isoforms and one substrate-inducible nitrate reductase (iNR) isoform in leaves. All three NR isoforms are expressed in cv. Williams 82 while the nr1 mutant expresses only the iNR isoform. The genetic and molecular mechanisms for regulation of these isoforms have not been elucidated. We describe here the isolation, by reverse transcription-polymerase chain reaction (RT-PCR), of two cDNA clones encoding soybean NR. They were designated as iNR1 and iNR2, respectively, since both were inducible by nitrate. The iNR1 and iNR2 cDNAs cover total encoding regions of 2661 and 2673 nucleotides, respectively. The iNR1 clone shows a 12 bp deletion at the 5' end, relative to iNR2. They show overall similarity of 89% at the nucleotide level, and 87% at the amino acid level. Like all plant NRs cloned so far, deduced amino acid sequences between iNR1 and iNR2 show greatest variation at the N-terminal region while no difference was observed at the C-terminus. Soybean iNR mRNAs were found to be different from those of maize and tobacco in response to tungsten inhibitor treatment, since the inhibitor decreased the steady-state levels of mRNA for soybean iNR and for NiR. Using the same 5' regions of both cDNAs as the probes, Southern blot analysis of genomic DNA revealed differences in organization between iNR1 and iNR2. The genomic DNA from wild-type Williams 82 soybean was shown to have three Eco RI fragments while the nr1 mutant lacked an 8 kb fragment when probed with iNR1 cDNA. Likewise, the nr1 mutant lacked three Hae III restriction fragments when probed with iNR1 cDNA. When probed with iNR2, both wildtype and nr1 mutant showed one identical Eco RI band and two identical Hae III bands. In northern blots, the steady-state level of iNR1 mRNA was similar for the nr1 mutant and the wild-type parent after 20 to 48 h induction by nitrate. Based on the Eco RI and Hae III restriction enzyme digestion patterns observed in Southern blot analysis of soybean DNA, it is concluded that in soybean iNR1 is encoded by a small multiple gene family and iNR2 is a single gene.
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Affiliation(s)
- S Wu
- Department of Agronomy, University of Illinois, Urbana 61801, USA
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26
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Ward MP, Abberton MT, Forde BG, Sherman A, Thomas WT, Wray JL. The Nir1 locus in barley is tightly linked to the nitrite reductase apoprotein gene Nii. MOLECULAR & GENERAL GENETICS : MGG 1995; 247:579-82. [PMID: 7603437 DOI: 10.1007/bf00290349] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
pBNiR1, a cDNA clone encoding part of the barley nitrite reductase apoprotein, was isolated from a barley (cv. Maris Mink) leaf cDNA library using the 1.85 kb insert of the maize nitrite reductase cDNA clone pCIB808 as a heterologous probe. The cDNA insert of pBNiR1 is 503 bp in length. The nucleotide coding sequence could be aligned with the 3' end of other higher plant nitrite reductase apoprotein cDNA sequences but diverges in the 3' untranslated region. The whole-plant barley mutant STA3999, previously isolated from the cultivar Tweed, accumulates nitrite after nitrate treatment in the light, has very much lowered levels of nitrite reductase activity and lacks detectable nitrite reductase cross-reacting material due to a recessive mutation in a single nuclear gene which we have designated Nir1. STA3999 has the characteristics expected of a nitrite reductase apoprotein gene mutant. Here we have used pB-NiR1 in RFLP analysis to determine whether the mutation carried by STA3999 is linked to the nitrite reductase apoprotein gene locus Nii. An RFLP was identified between the wild-type barley cultivars Tweed (major hybridising band of 11.5 kb) and Golden Promise (major hybridising band of 7.5 kb) when DraI-digested DNA was probed with the insert from the partial barley nitrite reductase cDNA clone, pBNiR1. DraI-digested DNA from the mutant STA3999 also exhibited a major hybridising band of 11.5 kb after hybridisation with the insert from pBNiR1.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- M P Ward
- Plant Sciences Laboratory, School of Biological and Medical Sciences, University of St. Andrews, Fife, UK
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27
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Merchán F, Prieto R, Kindle KL, Llama MJ, Serra JL, Fernández E. Isolation, sequence and expression in Escherichia coli of the nitrite reductase gene from the filamentous, thermophilic cyanobacterium Phormidium laminosum. PLANT MOLECULAR BIOLOGY 1995; 27:1037-1042. [PMID: 7766873 DOI: 10.1007/bf00037030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The nitrite reductase (NiR) gene (nirA) has been isolated and sequenced from the filamentous, thermophilic non-N2-fixing cyanobacterium Phormidium laminosum. Putative promoter-like and Shine-Dalgarno sequences appear at the 5' end of the 1533 bp long nir-coding region. The deduced amino acid sequence of NiR from P. laminosum corresponds to a 56 kDa polypeptide, a size identical to the molecular mass previously determined for the pure enzyme, and shows a high identity with amino acid sequences from ferredoxin-dependent NiR. This cyanobacterial NiR gene has been efficiently expressed in Escherichia coli DH5 alpha from the E. coli lac promoter and probably from the P. laminosum NiR promoter.
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Affiliation(s)
- F Merchán
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Córdoba, Spain
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28
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Sander L, Jensen PE, Back LF, Stummann BM, Henningsen KW. Structure and expression of a nitrite reductase gene from bean (Phaseolus vulgaris) and promoter analysis in transgenic tobacco. PLANT MOLECULAR BIOLOGY 1995; 27:165-77. [PMID: 7865786 DOI: 10.1007/bf00019188] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A structural gene encoding nitrite reductase (NiR) in bean (Phaseolus vulgaris) has been cloned and sequenced. The NiR gene is present as a single copy encoding a protein of 582 amino acids. The bean NiR protein is synthesized as a precursor with an amino-terminal transit peptide (TP) consisting of 18 amino acid residues. The bean NiR transit peptide shows similarity to the TPs of other known plant NiRs. The NiR gene is expressed in trifoliate leaves and in roots of 20-day old bean plants where transcript accumulation is nitrate-inducible. Gene expression occurs in a circadian rhythm and induced by light in leaves of dark-adapted plants. A particular 100 bp sequence is present in the promoter and in the first intron of the NiR gene. Several copies of this 100 bp sequence are present in the bean genome. Comparisons between the promoter of the bean NiR gene and of two bean nitrate reductase genes (NR1 and NR2) show a limited number of conserved motifs, although the genes are presumed to be co-regulated. Comparisons are also made between the bean NiR promoter and the spinach NiR promoter. Transformation of tobacco plants with the bean NiR promoter fused to the GUS reporter gene (beta-glucuronidase) shows that the bean NiR promoter is nitrate-regulated and that the presence of the 100 bp sequence influences the level of GUS activity. NiR-coding sequences are not required for nitrate regulation but have a quantitative effect on the measured GUS activity.
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Affiliation(s)
- L Sander
- Genetics Section, Royal Veterinary and Agricultural University, Frederiksberg, Denmark
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29
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Ritchie SW, Redinbaugh MG, Shiraishi N, Vrba JM, Campbell WH. Identification of a maize root transcript expressed in the primary response to nitrate: characterization of a cDNA with homology to ferredoxin-NADP+ oxidoreductase. PLANT MOLECULAR BIOLOGY 1994; 26:679-690. [PMID: 7948922 DOI: 10.1007/bf00013753] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
To more fully understand the biochemical and molecular events which occur in plants exposed to nitrate, cDNAs whose accumulation was enhanced in nitrate- and cycloheximide-treated maize (Zea mays L. W64A x W182E) roots were isolated. The 340 bp Zmrprn1 (for Zea mays root primary response to nitrate) cDNA also hybridized with a probe enriched for nitrate-induced sequences, and was characterized further. Sequence analysis of a near full-length cDNA (Zmrprn1A) showed strong homology (> 90% amino acid identity) with a root ferredoxin-NADP+ oxidoreductase (FNR) of rice, and 45-50% amino acid identify with leaf FNR genes. When expressed in Escherichia coli, the Zmrprn1A cDNA produced a protein with NADPH: ferricyanide reductase activity, consistent with the enzymatic properties of an FNR. The Zmrprn1 cDNA hybridized with a 1.4 kb transcript which was expressed in the maize root primary response to nitrate. That is, mRNA levels in roots increased rapidly and transiently in response to external nitrate, and low levels of nitrate (10 microM) induced transcript accumulation. The accumulation of the Zmrprn1 transcript was not prevented by cycloheximide, indicating that the cellular factor(s) required for expression were constitutively present in maize roots. The Zmrprn1 mRNA accumulated specifically in response to nitrate, since neither K+ nor NH4+ treatment of roots caused transcript accumulation. Maize leaves had about 5% of the transcript level found in roots, indicating a strong preference for expression of Zmrprn1 in roots. Analysis of maize genomic DNA indicated the presence of only a single gene or very small gene family for the Zmrprn1. Together, the data indicate that Zmrprn1A encodes a nitrate regulated maize root FNR.
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Affiliation(s)
- S W Ritchie
- USDA-ARS Crops Research Laboratory, Oxford, NC
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30
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The role of tryptophan in the reaction catalyzed by spinach ferredoxin-dependent nitrite reductase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1994. [DOI: 10.1016/0005-2728(94)90169-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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31
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Moffatt BA, McWhinnie EA, Agarwal SK, Schaff DA. The adenine phosphoribosyltransferase-encoding gene of Arabidopsis thaliana. Gene X 1994; 143:211-6. [PMID: 8206375 DOI: 10.1016/0378-1119(94)90098-1] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The apt gene, coding for adenine phosphoribosyltransferase (APRT), has been isolated from the plant Arabidopsis thaliana. Data from both Southern analysis and characterization of apt clones isolated from a genomic library is consistent with the occurrence of one apt within the A. thaliana genome. Comparison of the nucleotide sequence of the apt gene with its corresponding cDNA indicates that the gene contains five introns, whereas all other apt isolated to date have fewer introns (four in mammals, two in Drosophila). The locations of the introns within the plant apt coding region are not consistent with the placement of introns in the previously isolated apt of murines, human and Drosophila species. In agreement with its expression pattern in vivo, the upstream region of this plant apt is able to express the beta-glucuronidase-encoding gene (gus) in an apparently constitutive manner in transgenic A. thaliana plants. The apt promoter region is notable for its lack of conventional promoter elements such as TATA, CCAAT or G+C-rich sequence elements.
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Affiliation(s)
- B A Moffatt
- Department of Biology, University of Waterloo, Canada
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32
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Neininger A, Seith B, Hoch B, Mohr H. Gene expression of nitrite reductase in Scots pine (Pinus sylvestris L.) as affected by light and nitrate. PLANT MOLECULAR BIOLOGY 1994; 25:449-457. [PMID: 8049370 DOI: 10.1007/bf00043873] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A partial cDNA clone (PSnir) encoding the C-terminal region of nitrite reductase was isolated from a lambda gt11 library of the gymnosperm Pimus sylvestris (L.). Nucleotide sequence analysis showed that PSnir contains a reading frame encoding 105 amino acid residues. The amino acid sequence revealed a homology to NiR of 63-68% to dicotyledoneous and of 57-59% to monocotyledoneous species. The protein region implicated to be involved in binding of the prosthetic group is highly conserved between the NiR of the gymnosperm and of angiosperms. In all organs (cotyledonary whorls, hypocotyls, roots) the pattern of NiR gene expression in response to nitrate and light is the same at the level of transcript accumulation and at the enzyme level. This suggests that regulation of NiR gene expression in the Scots pine seedling is predominantly at the level of transcript accumulation. The highest NiR appearance was observed in roots and hypocotyls. In the cotyledonary whorls only small amounts of NiR were found. In roots and hypocotyls the accumulation of NiR mRNA and the appearance of NiR protein is mainly controlled by nitrate, whereas the regulation of NiR gene expression in the whorls is strongly affected by light and the inducive effect of nitrate is only weak.
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Affiliation(s)
- A Neininger
- Institut für Biologie II, Universität Freiburg, Germany
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33
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Hirasawa M, Tollin G, Salamon Z, Knaff DB. Transient kinetic and oxidation-reduction studies of spinach ferredoxin:nitrite oxidoreductase. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1185:336-45. [PMID: 8180238 DOI: 10.1016/0005-2728(94)90249-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The oxidation-reduction midpoint potentials for the two prosthetic groups of the chloroplast-located, ferredoxin-dependent nitrite reductase of spinach leaves have been determined by spectroelectrochemical titrations and cyclic voltammetry. The average of the results obtained by the two techniques are Em = -290 mV for the siroheme group and Em = -365 mV for the [4Fe-4S] cluster. The value obtained for the [4Fe-4S] cluster is substantially more positive than values obtained previously in experiments which utilized electron paramagnetic resonance spectroscopy at cryogenic temperatures to monitor the reduction state of the cluster. Laser flash photolysis experiments have been used to monitor electron transfer from reduced ferredoxin to nitrite reductase and have provided the first evidence for electron transfer between the two prosthetic groups of the enzyme. The effect of ionic strength on the observed kinetics has provided support for the proposal that electrostatic interactions between ferredoxin and nitrite reductase play an important role in the reaction mechanism.
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Affiliation(s)
- M Hirasawa
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock 79409-1061
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34
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35
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Tanaka T, Ida S, Irifune K, Oeda K, Morikawa H. Nucleotide sequence of a gene for nitrite reductase from Arabidopsis thaliana. DNA SEQUENCE : THE JOURNAL OF DNA SEQUENCING AND MAPPING 1994; 5:57-61. [PMID: 7894060 DOI: 10.3109/10425179409039705] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A nitrite reductase (NiR) gene was recovered from Arabidopsis thaliana genomic library by the homology with a cDNA of spinach NiR and sequenced. Based on the comparison with the spinach cDNA, the Arabidopsis NiR gene was concluded to contain 4 exons [exon 1 of 376 bp (beginning with ATG start codon), exon 2 of 355 bp, exon 3 of 289 bp and exon 4 of 741 bp (ending at TGA stop codon)] and 3 introns (intron 1 of 196 bp, intron 2 of 81 bp and intron 3 of 77 bp). This conclusion was confirmed by the analysis using the RT-PCR method. The deduced amino acid sequence of the coding region of the Arabidopsis NiR gene had high similarities with those of NiR genes of other plants including spinach.
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Affiliation(s)
- T Tanaka
- Graduate Department of Gene Science, Faculty of Science, Hiroshima University, Japan
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36
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Quesada A, Fernández E. Expression of nitrate assimilation related genes in Chlamydomonas reinhardtii. PLANT MOLECULAR BIOLOGY 1994; 24:185-94. [PMID: 8111016 DOI: 10.1007/bf00040584] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The mRNA accumulation pattern of the Chlamydomonas reinhardtii nitrate assimilation-related gene cluster has been elucidated. In ammonium-grown wild-type cells, nit-1 (nitrate reductase, NR), nar-1, nar-2 and nar-3 (nitrate transporter) genes showed very similar kinetics of expression when transferred to nitrate medium. Transcripts of all these genes accumulated transiently in ammonium-grown wild-type cells after a one-hour incubation in nitrogen-free medium, and practically disappeared at about 2 hours. Mutant strains lacking functional nitrate reductase showed similar accumulation kinetics of these transcripts during both nitrate induction and derepression in nitrogen-free media. In contrast to the other nar transcripts, that nar-4, a gene sharing similar sequences with nar-3, accumulated in small amounts in wild-type cells, and only increased after a long nitrate induction period. Nitrate and light showed a strong positive effect on the accumulation of nit-1 gene transcripts. Acetate as a carbon source allowed accumulation of nit-1 mRNA in the dark, indicating the existence of interactions between light and carbon metabolism in nit-1 gene expression. Our data strongly suggest that NR negatively autoregulates its own expression and that of nar genes.
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Affiliation(s)
- A Quesada
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Córdoba, Spain
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37
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Wray JL. Molecular biology, genetics and regulation of nitrite reduction in higher plants. PHYSIOLOGIA PLANTARUM 1993; 89:607-612. [PMID: 0 DOI: 10.1111/j.1399-3054.1993.tb05222.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
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38
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Gisselmann G, Klausmeier P, Schwenn JD. The ferredoxin:sulphite reductase gene from Synechococcus PCC7942. BIOCHIMICA ET BIOPHYSICA ACTA 1993; 1144:102-6. [PMID: 8347657 DOI: 10.1016/0005-2728(93)90037-g] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The structural gene of the ferredoxin:sulphite reductase (EC 1.8.7.1) from the cyanobacterium Synechococcus PCC7942 (formerly 'Anacystis nidulans') was cloned and sequenced. The gene termed 'sir' was detected by heterologous Southern hybridisation with the structural gene cysI from Escherichia coli encoding the iron-sulphur haemoprotein of the NADPH:sulphite reductase. The open reading frame is comprised of 1875 bp encoding for a polypeptide of M(r) 70.028. The deduced amino acid sequence is 35.6% identical with the enterobacterial iron-sulphur haemoprotein. This putative fd-dependent sulphite reductase is only distantly related to the fd-dependent nitrite reductase (binary matching coefficient SAB: 0.23) or with the NADPH-sulphite reductase (SAB: 0.32). Highly conserved residues are found within the two Cys clusters forming the reactive Fe4S4-sirohaem centre of the enzyme. Expression of the sir gene using a fusion vector gave a single gene product which is immunologically related with the fd-sulphite reductase from the wild-type bacterium.
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Affiliation(s)
- G Gisselmann
- Biochemistry of Plants, Faculty of Biology, Ruhr University Bochum, Germany
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39
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Luque I, Flores E, Herrero A. Nitrite reductase gene from Synechococcus sp. PCC 7942: homology between cyanobacterial and higher-plant nitrite reductases. PLANT MOLECULAR BIOLOGY 1993; 21:1201-1205. [PMID: 8490140 DOI: 10.1007/bf00023618] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The gene encoding nitrite reductase (nir) from the cyanobacterium Synechococcus sp. PCC 7942 has been identified and sequenced. This gene comprises 1536 nucleotides and would encode a polypeptide of 56,506 Da that shows similarity to nitrite reductase from higher plants and to the sulfite reductase hemoprotein from enteric bacteria. Identities found at positions corresponding to those amino acids which in the above-mentioned proteins hold the Fe4S4-siroheme active center suggest that nitrite reductase from Synechococcus bears an active site much alike that present in those reductases. The fact that the Synechococcus and higher-plant nitrite reductases are homologous proteins gives support to the endosymbiont theory for the origin of chloroplasts.
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Affiliation(s)
- I Luque
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla, Spain
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40
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Kronenberger J, Lepingle A, Caboche M, Vaucheret H. Cloning and expression of distinct nitrite reductases in tobacco leaves and roots. MOLECULAR & GENERAL GENETICS : MGG 1993; 236:203-8. [PMID: 8437565 DOI: 10.1007/bf00277113] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Three tobacco nitrite reductase (NiR) cDNA clones were isolated using spinach NiR cDNA as a probe. Sequence analysis and Southern blot hybridization revealed four genes in tobacco. Two of these genes presumably derived from the ancestral species Nicotiana tomentosiformis, the other two from the ancestor N. sylvestris. Northern blot analysis showed that one gene from each ancestral genome was expressed predominantly in leaves, whilst RNA from the other was detected mostly in roots. The accumulation of both leaf and root NiR mRNAs was induced by nitrate and repressed by nitrate- or ammonium-derived metabolites. In addition, the expression of the root NiR gene was detectable in leaves of a tobacco nitrate reductase (NR)-deficient mutant. Thus, the regulation of expression of tobacco NiR genes is comparable to the regulation of expression of barley NR genes.
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Affiliation(s)
- J Kronenberger
- Laboratoire de Biologie Cellulaire, INRA, Versailles, France
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41
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Last RL. The genetics of nitrogen assimilation and amino acid biosynthesis in flowering plants: progress and prospects. INTERNATIONAL REVIEW OF CYTOLOGY 1993; 143:297-330. [PMID: 8449664 DOI: 10.1016/s0074-7696(08)61878-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- R L Last
- Plant Molecular Biology Program, Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853-1801
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42
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Duncanson E, Gilkes AF, Kirk DW, Sherman A, Wray JL. nir1, a conditional-lethal mutation in barley causing a defect in nitrite reduction. MOLECULAR & GENERAL GENETICS : MGG 1993; 236:275-82. [PMID: 8437574 DOI: 10.1007/bf00277123] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Eleven green individuals were isolated when 95000 M2 plants of barley (Hordeum vulgare L.), mutagenised with azide in the M1, were screened for nitrite accumulation in their leaves after nitrate treatment in the light. The selected plants were maintained in aerated liquid culture solution containing glutamine as sole nitrogen source. Not all plants survived to flowering and some others that did were not fertile. One of the selected plants, STA3999, from the cultivar Tweed could be crossed to the wild-type cultivar and analysis of the F2 progeny showed that leaf nitrite accumulation was due to a recessive mutation in a single nuclear gene, which has been designated Nir1. The homozygous nir1 mutant could be maintained to flowering in liquid culture with either glutamine or ammonium as sole nitrogen source, but died within 14 days after transfer to compost. The nitrite reductase cross-reacting material seen in nitrate-treated wild-type plants could not be detected in either the leaf or the root of the homozygous nir1 mutant. Nitrite reductase activity, measured with dithionite-reduced methyl viologen as electron donor, of the nitrate-treated homozygous nir1 mutant was much reduced but NADH-nitrate reductase activity was elevated compared to wild-type plants. We conclude that the Nir1 locus determines the formation of nitrite reductase apoprotein in both the leaf and root of barley and speculate that it represents either the nitrite reductase apoprotein gene locus or, less likely, a regulatory locus whose product is required for the synthesis of nitrite reductase, but not nitrate reductase.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- E Duncanson
- Division of Environmental and Evolutionary Biology, School of Biological and Medical Sciences, University of St. Andrews, Scotland, UK
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Control of Metabolism and Development in Higher Plant Plastids. INTERNATIONAL REVIEW OF CYTOLOGY VOLUME 145 1993. [DOI: 10.1016/s0074-7696(08)60427-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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44
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Friemann A, Brinkmann K, Hachtel W. Sequence of a cDNA encoding nitrite reductase from the tree Betula pendula and identification of conserved protein regions. ACTA ACUST UNITED AC 1992; 231:411-6. [PMID: 1347145 DOI: 10.1007/bf00292710] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The sequence of an mRNA encoding nitrite reductase (NiR, EC 1.7.7.1.) from the tree Betula pendula was determined. A cDNA library constructed from leaf poly(A)+ mRNA was screened with an oligonucleotide probe deduced from NiR sequences from spinach and maize. A 2.5 kb cDNA was isolated that hybridized to an mRNA, the steady-state level of which increased markedly upon induction with nitrate. The nucleotide sequence of the cDNA contains a reading frame encoding a protein of 583 amino acids that reveals 79% identity with NiR from spinach. The transit peptide of the NiR precursor from birch was determined to be 22 amino acids in size by sequence comparison with NiR from spinach and maize and is the shortest transit peptide reported so far. A graphical evaluation of identities found in the NiR sequence alignment revealed nine well conserved sections each exceeding ten amino acids in size. Sequence comparisons with related redox proteins identified essential residues involved in cofactor binding. A putative binding site for ferredoxin was found in the N-terminal half of the protein.
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Affiliation(s)
- A Friemann
- Botanisches Institut der Universität Bonn, FRG
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Abstract
A differentially expressed maize gene has been cloned and sequenced. Transcriptional and translational start sites have been mapped and 2.5 kb of 5' flanking DNA were sequenced. The 8 kDa protein encoded by this gene shows striking similarity to the metallothionein-like proteins recently described in Pisum sativum and Mimulus guttatus. The maize MT-L gene message is very abundant in roots without exposure to high levels of metals, present at lower concentration in leaves and pith, and at very low concentration in seed.
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Affiliation(s)
- A J de Framond
- Department of Plant Molecular Biology, CIBA-Geigy Agricultural Biotechnology Research Unit, Research Triangle Park, NC 27709-2257
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46
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Back E, Dunne W, Schneiderbauer A, de Framond A, Rastogi R, Rothstein SJ. Isolation of the spinach nitrite reductase gene promoter which confers nitrate inducibility on GUS gene expression in transgenic tobacco. PLANT MOLECULAR BIOLOGY 1991; 17:9-18. [PMID: 1868226 DOI: 10.1007/bf00036801] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Nitrite reductase is the second enzyme in the nitrate assimilatory pathway. The transcription of this gene is regulated by nitrate as well as a variety of other environmental and developmental factors. Genomic clones containing the entire nitrite reductase gene have been isolated from a spinach genomic library and sequenced. The sequence is identical in the transcribed region to a previously isolated spinach NiR cDNA clone (Back et al., 1988) except for the presence of three introns. The analysis of the genomic clones and DNA blot hybridization demonstrates that there is a single NiR gene per haploid genome in spinach. This is in contrast to what has been found for other plant species. The transcription initiation site has been determined by S1 mapping and the 5' upstream region has been used to regulate the GUS reporter gene in transgenic tobacco plants. This gene was found to be regulated by the addition of nitrate in the transgenic plants.
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Affiliation(s)
- E Back
- GSF-Institut für Biochemische Pflanzenpathologie, Neuerberg, Germany
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47
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Galván A, Córdoba F, Cárdenas J, Fernández E. Regulation of nitrite uptake and nitrite reductase expression in Chlamydomonas reinhardtii. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1074:6-11. [PMID: 2043680 DOI: 10.1016/0304-4165(91)90030-k] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Expression of nitrite uptake and nitrite reductase activities has been studied in Chlamydomonas reinhardtii under different nutritional conditions. Both activities were expressed at a low level in derepressed cells (with no nitrogen source) and at a high level in induced cells (with nitrate or nitrite). Nitrate was required for both activities to be maximally expressed. Ammonium-grown cells did not show nitrite uptake capability and had a basal nitrite reductase activity. Nitrite uptake but not nitrite reductase levels decreased very significantly in nitrate-induced cells subject to cycloheximide treatment, which suggests that protein(s) involved in the uptake are under a rapid turnover. Nitrite uptake expression was strongly inhibited by the presence of the glutamine synthetase inhibitor L-methionine-D,L-sulfoximine under either derepression or induction conditions, whereas that of nitrite reductase was not affected under the same conditions. Our results indicate that nitrite uptake expression is regulated primarily by ammonium, and that of nitrite reductase by both ammonium and ammonium derivative(s).
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Affiliation(s)
- A Galván
- Departamento de Bioquímica y Biología Molecular y Fisiología, Facultad de Ciencias, Universidad de Córdoba, Spain
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48
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Seith B, Schuster C, Mohr H. Coaction of light, nitrate and a plastidic factor in controlling nitrite-reductase gene expression in spinach. PLANTA 1991; 184:74-80. [PMID: 24193932 DOI: 10.1007/bf00208239] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/14/1990] [Indexed: 06/02/2023]
Abstract
It is well established that nitrite reductase (NIR; EC 1.7.7.1) a key enzyme of nitrate reduction - is "induced" by nitrate and light. In the present study with the spinach (Spinacia oleracea L.) seedling the dependency of NIR appearance on nitrate, light and a 'plastidic factor' was investigated to establish the nature of the coaction between these controlling factors. A cDNA clone coding for spinach NIR was available as a probe. The major results we have obtained are the following: (i) The light effect on the appearance of NIR activity occurs through phytochrome. No specific bluelight effect is involved, (ii) Immunotitration data indicate that light affects the appearance of NIR by inducing the de-novo synthesis of the NIR protein, (iii) A multiplicative relationship exists between the action of nitrate and light on NIR appearance. This indicates that the actions of light and nitrate are indeed independent of each other but that both factors operate on the same causal sequence, (iv) Anion-exchange chromatography revealed only a single form of NIR in spinach. Experiments involving plastid photooxidation indicate that this NIR is exclusively plastidic. (v) Northern blot analysis of NIR mRNA showed a strong increase of the steady-state level in the presence of nitrate whereas light had no effect; NIR mRNA was almost undetectable when the plastids were damaged by photooxidation. It is concluded that NIR gene expression in spinach requires positive control by a 'plastidic factor'. Moreover, nitrate exerts a coarse control at the mRNA level whereas fine tuning of NIR protein synthesis is post-transcriptional and is exerted by light, operating via phytochrome.
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Affiliation(s)
- B Seith
- Biologisches Institut II der Universität, Schänzlestrasse 1, W-7800, Freiburg, Germany
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49
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Sakakibara H, Watanabe M, Hase T, Sugiyama T. Molecular cloning and characterization of complementary DNA encoding for ferredoxin-dependent glutamate synthase in maize leaf. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)52204-3] [Citation(s) in RCA: 94] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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50
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Knaff DB, Hirasawa M. Ferredoxin-dependent chloroplast enzymes. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1056:93-125. [PMID: 1671559 DOI: 10.1016/s0005-2728(05)80277-4] [Citation(s) in RCA: 198] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- D B Knaff
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock 79409-1061
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