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Prathap V, Kumar S, Tyagi A. Comparative proteome analysis of phosphorus-responsive genotypes reveals the proteins differentially expressed under phosphorous starvation stress in rice. Int J Biol Macromol 2023; 234:123760. [PMID: 36812961 DOI: 10.1016/j.ijbiomac.2023.123760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 02/23/2023]
Abstract
Phosphorus (P)-deficiency is one of the major nutrient constraints for global rice production. P-deficiency tolerance in rice involves complex regulatory mechanisms. To gain insights into the proteins involved in phosphorus acquisition and use efficiency in rice, proteome analysis of a high-yielding rice cultivar Pusa-44 and its near-isogenic line (NIL)-23 harboring a major phosphorous uptake (Pup1) QTL, grown under control and P-starvation stress, was performed. Comparative proteome profiling of shoot and root tissues from the plants grown hydroponically with P (16 ppm, +P) or without P (0 ppm, -P) resulted in the identification of 681 and 567 differentially expressed proteins (DEPs) in shoot of Pusa-44 and NIL-23, respectively. Similarly, 66 and 93 DEPs were identified in root of Pusa-44 and NIL-23, respectively. These P-starvation responsive DEPs were annotated to be involved in metabolic processes like photosynthesis, starch-, sucrose-, energy-metabolism, transcription factors (mainly ARF, ZFP, HD-ZIP, MYB), and phytohormone signaling. Comparative analysis of the expression patterns observed by proteome analysis with that reported at the transcriptome level indicated the Pup1 QTL-mediated post-transcriptional regulation plays an important role under -P stress. Thus, the present study describes the molecular aspect of the regulatory functions of Pup1 QTL under P-starvation stress in rice, which might help develop an efficient rice cultivar with enhanced P acquisition and assimilation for better performance in P-deficient soil.
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Affiliation(s)
- V Prathap
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India.
| | - Aruna Tyagi
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India.
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2
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El-Khishin DA, Ageez A, Saad ME, Ibrahim A, Shokrof M, Hassan LR, Abouelhoda MI. Sequencing and assembly of the Egyptian buffalo genome. PLoS One 2020; 15:e0237087. [PMID: 32813723 PMCID: PMC7437910 DOI: 10.1371/journal.pone.0237087] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 07/20/2020] [Indexed: 01/09/2023] Open
Abstract
Water buffalo (Bubalus bubalis) is an important source of meat and milk in countries with relatively warm weather. Compared to the cattle genome, a little has been done to reveal its genome structure and genomic traits. This is due to the complications stemming from the large genome size, the complexity of the genome, and the high repetitive content. In this paper, we introduce a high-quality draft assembly of the Egyptian water buffalo genome. The Egyptian breed is used as a dual purpose animal (milk/meat). It is distinguished by its adaptability to the local environment, quality of feed changes, as well as its high resistance to diseases. The genome assembly of the Egyptian water buffalo has been achieved using a reference-based assembly workflow. Our workflow significantly reduced the computational complexity of the assembly process, and improved the assembly quality by integrating different public resources. We also compared our assembly to the currently available draft assemblies of water buffalo breeds. A total of 21,128 genes were identified in the produced assembly. A list of milk virgin-related genes; milk pregnancy-related genes; milk lactation-related genes; milk involution-related genes; and milk mastitis-related genes were identified in the assembly. Our results will significantly contribute to a better understanding of the genetics of the Egyptian water buffalo which will eventually support the ongoing breeding efforts and facilitate the future discovery of genes responsible for complex processes of dairy, meat production and disease resistance among other significant traits.
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Affiliation(s)
- Dina A. El-Khishin
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
- * E-mail:
| | - Amr Ageez
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
- Faculty of Biotechnology, MSA University, October City, Egypt
| | - Mohamed E. Saad
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
- Department of Biology, Taibah University, Almadinah Almonawarah, KSA
| | - Amr Ibrahim
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Moustafa Shokrof
- Centre for Informatics Sciences, Nile University Giza, October city, Egypt
- Department of Computer Science, University of California at Davis, Davis, CA, United States of America
| | - Laila R. Hassan
- Animal Production Research Institute, Agricultural Research Center (ARC), Ministry of Agriculture and Land Reclamation, Giza, Egypt
| | - Mohamed I. Abouelhoda
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Giza, Egypt
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3
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Sega P, Kruszka K, Szewc Ł, Szweykowska-Kulińska Z, Pacak A. Identification of transcription factors that bind to the 5'-UTR of the barley PHO2 gene. PLANT MOLECULAR BIOLOGY 2020; 102:73-88. [PMID: 31745747 DOI: 10.1007/s11103-019-00932-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/09/2019] [Indexed: 06/10/2023]
Abstract
In barley and other higher plants, phosphate homeostasis is maintained by a regulatory network involving the PHO2 (PHOSPHATE2) encoding ubiquitin-conjugating (UBC) E2 enzyme, the PHR1 (PHOSPHATE STARVATION RESPONSE 1) transcription factor (TF), IPS1 (INDUCED BYPHOSPHATESTARVATION1) RNA, and miR399. During phosphate ion (Pi) deprivation, PHR1 positively regulates MIR399 expression, after transcription and processing mature miR399 guides the Ago protein to the 5'-UTR of PHO2 transcripts. Non-coding IPS1 RNA is highly expressed during Pi starvation, and the sequestration of miR399 molecules protects PHO2 mRNA from complete degradation. Here, we reveal new cis- and trans-regulatory elements that are crucial for efficient PHO2 gene expression in barley. We found that the 5'-UTR of PHO2 contains two PHR1 binding sites (P1BSs) and one Pi-responsive PHO element. Using a yeast one-hybrid (Y1H) assay, we identified two candidate proteins that might mediate this transcriptional regulation: a barley PHR1 ortholog and a TF containing an uncharacterized MYB domain. Additional results classified this new potential TF as belonging to the APL (ALTERED PHLOEM DEVELOPMENT) protein family, and we observed its nuclear localization in barley protoplasts. Pi starvation induced the accumulation of barley APL transcripts in both the shoots and roots. Interestingly, the deletion of the P1BS motif from the first intron of the barley 5'-UTR led to a significant increase in the transcription of a downstream β-glucuronidase (GUS) reporter gene in tobacco leaves. Our work extends the current knowledge about putative cis- and trans-regulatory elements that may affect the expression of the barley PHO2 gene.
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Affiliation(s)
- Paweł Sega
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Katarzyna Kruszka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Łukasz Szewc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Zofia Szweykowska-Kulińska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Andrzej Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
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Fan S, Dong L, Han D, Zhang F, Wu J, Jiang L, Cheng Q, Li R, Lu W, Meng F, Zhang S, Xu P. GmWRKY31 and GmHDL56 Enhances Resistance to Phytophthora sojae by Regulating Defense-Related Gene Expression in Soybean. FRONTIERS IN PLANT SCIENCE 2017; 8:781. [PMID: 28553307 PMCID: PMC5427154 DOI: 10.3389/fpls.2017.00781] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/25/2017] [Indexed: 05/23/2023]
Abstract
Phytophthora root and stem rot of soybean [Glycine max (L.) Merr.] caused by the oomycete Phytophthora sojae, is a destructive disease worldwide. The molecular mechanism of the soybean response to P. sojae is largely unclear. We report a novel WRKY transcription factor (TF) in soybean, GmWRKY31, in the host response to P. sojae. Overexpression and RNA interference analysis demonstrated that GmWRKY31 enhanced resistance to P. sojae in transgenic soybean plants. GmWRKY31 was targeted to the nucleus, where it bound to the W-box and acted as an activator of gene transcription. Moreover, we determined that GmWRKY31 physically interacted with GmHDL56, which improved resistance to P. sojae in transgenic soybean roots. GmWRKY31 and GmHDL56 shared a common target GmNPR1 which was induced by P. sojae. Overexpression and RNA interference analysis demonstrated that GmNPR1 enhanced resistance to P. sojae in transgenic soybean plants. Several pathogenesis-related (PR) genes were constitutively activated, including GmPR1a, GmPR2, GmPR3, GmPR4, GmPR5a, and GmPR10, in soybean plants overexpressing GmNPR1 transcripts. By contrast, the induction of PR genes was compromised in transgenic GmNPR1-RNAi lines. Taken together, these findings suggested that the interaction between GmWRKY31 and GmHDL56 enhances resistance to P. sojae by regulating defense-related gene expression in soybean.
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Affiliation(s)
- Sujie Fan
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural UniversityHarbin, China
- Center for Plant Biotechnology, College of Agronomy, Jilin Agricultural UniversityChangchun, China
| | - Lidong Dong
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural UniversityHarbin, China
| | - Dan Han
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural UniversityHarbin, China
| | - Feng Zhang
- First Affiliated Hospital of Harbin Medical UniversityHarbin, China
| | - Junjiang Wu
- Soybean Research Institute, Key Laboratory of Soybean Cultivation of Ministry of Agriculture, Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Liangyu Jiang
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural UniversityHarbin, China
- Center for Plant Biotechnology, College of Agronomy, Jilin Agricultural UniversityChangchun, China
| | - Qun Cheng
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural UniversityHarbin, China
| | - Rongpeng Li
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural UniversityHarbin, China
| | - Wencheng Lu
- Heihe Branch of Heilongjiang Academy of Agricultural SciencesHeihe, China
| | - Fanshan Meng
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural UniversityHarbin, China
| | - Shuzhen Zhang
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural UniversityHarbin, China
| | - Pengfei Xu
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural UniversityHarbin, China
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Intronic Sequence Regulates Sugar-Dependent Expression of Arabidopsis thaliana Production of Anthocyanin Pigment-1/MYB75. PLoS One 2016; 11:e0156673. [PMID: 27248141 PMCID: PMC4889055 DOI: 10.1371/journal.pone.0156673] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 05/18/2016] [Indexed: 01/12/2023] Open
Abstract
Sucrose-specific regulation of gene expression is recognized as an important signaling response, distinct from glucose, which serves to modulate plant growth, metabolism, and physiology. The Arabidopsis MYB transcription factor Production of Anthocyanin Pigment-1 (PAP1) plays a key role in anthocyanin biosynthesis and expression of PAP1 is known to be regulated by sucrose. Sucrose treatment of Arabidopsis seedlings led to a 20-fold induction of PAP1 transcript, which represented a 6-fold increase over levels in glucose-treated seedlings. The PAP1 promoter was not sufficient for conferring a sucrose response to a reporter gene and did not correctly report expression of PAP1 in plants. Although we identified 3 putative sucrose response elements in the PAP1 gene, none were found to be necessary for this response. Using deletion analysis, we identified a 90 bp sequence within intron 1 of PAP1 that is necessary for the sucrose response. This sequence was sufficient for conferring a sucrose response to a minimal promoter: luciferase reporter when present in multiple copies upstream of the promoter. This work lays the foundation for dissecting the sucrose signaling pathway of PAP1 and contributes to understanding the interplay between sucrose signaling, anthocyanin biosynthesis, and stress responses.
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Liu Y, Wang L, Deng M, Li Z, Lu Y, Wang J, Wei Y, Zheng Y. Genome-wide association study of phosphorus-deficiency-tolerance traits in Aegilops tauschii. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:2203-12. [PMID: 26187748 DOI: 10.1007/s00122-015-2578-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 07/01/2015] [Indexed: 05/19/2023]
Abstract
Using GWAS, 13 significant SNPs distributed on six of the seven Aegilops tauschii chromosomes (all but 5D) were identified, and several candidate P-deficiency-responsive genes were proposed from searches of public databases. Aegilops tauschii, the wheat (Triticum aestivum) D-genome progenitor, possesses numerous genes for stress resistance, including genes for tolerance of phosphorus (P) deficiency. Investigation of the genetic architecture of A. tauschii will help in developing P-deficiency-tolerant varieties of wheat. We evaluated nine traits in a population of 380 A. tauschii specimens under conditions with and without P application, and we performed genome-wide association studies for these traits using single nucleotide polymorphism (SNP) chips containing 7185 markers. Using a general linear model, we identified 119 SNPs that were significantly associated with all nine traits, and a mixed linear model revealed 18 SNPs associated with all traits. Both models detected 13 significant markers distributed on six of the seven A. tauschii chromosomes (all but 5D). Searches of public databases revealed several candidate/flanking genes related to P-deficiency tolerance. These genes were grouped in five categories by the types of proteins they encoded: defense response proteins, enzymes, promoters and transcription factors, storage proteins, or proteins triggered by P deficiency. The identified SNPs and genes contain essential information for cloning genes related to P-deficiency tolerance in A. tauschii and wheat, and they provide a foundation for breeding P-deficiency tolerant wheat cultivars.
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Affiliation(s)
- Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Lang Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Zhanyi Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
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Zahur M, Asif MA, Zeeshan N, Mehmood S, Malik MF, Asif AR. Homeobox leucine zipper proteins and cotton improvement. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/abb.2013.410a3003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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8
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Rouached H, Stefanovic A, Secco D, Bulak Arpat A, Gout E, Bligny R, Poirier Y. Uncoupling phosphate deficiency from its major effects on growth and transcriptome via PHO1 expression in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 65:557-70. [PMID: 21288266 DOI: 10.1111/j.1365-313x.2010.04442.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Inorganic phosphate (Pi) is one of the most limiting nutrients for plant growth in both natural and agricultural contexts. Pi-deficiency leads to a strong decrease in shoot growth, and triggers extensive changes at the developmental, biochemical and gene expression levels that are presumably aimed at improving the acquisition of this nutrient and sustaining growth. The Arabidopsis thaliana PHO1 gene has previously been shown to participate in the transport of Pi from roots to shoots, and the null pho1 mutant has all the hallmarks associated with shoot Pi deficiency. We show here that A. thaliana plants with a reduced expression of PHO1 in roots have shoot growth similar to Pi-sufficient plants, despite leaves being strongly Pi deficient. Furthermore, the gene expression profile normally triggered by Pi deficiency is suppressed in plants with low PHO1 expression. At comparable levels of shoot Pi supply, the wild type reduces shoot growth but maintains adequate shoot vacuolar Pi content, whereas the PHO1 underexpressor maintains maximal growth with strongly depleted Pi reserves. Expression of the Oryza sativa (rice) PHO1 ortholog in the pho1 null mutant also leads to plants that maintain normal growth and suppression of the Pi-deficiency response, despite the low shoot Pi. These data show that it is possible to unlink low shoot Pi content with the responses normally associated with Pi deficiency through the modulation of PHO1 expression or activity. These data also show that reduced shoot growth is not a direct consequence of Pi deficiency, but is more likely to be a result of extensive gene expression reprogramming triggered by Pi deficiency.
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Affiliation(s)
- Hatem Rouached
- Department of Plant Molecular Biology, Biophore, University of Lausanne, CH-1015 Lausanne, Switzerland
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Meitzel T, Radchuk R, Nunes-Nesi A, Fernie AR, Link W, Weschke W, Weber H. Hybrid embryos of Vicia faba develop enhanced sink strength, which is established during early development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 65:517-31. [PMID: 21235645 DOI: 10.1111/j.1365-313x.2010.04450.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Selfed and crossed seeds of two homozygous Vicia faba lines served as models for the analysis of the physiological and molecular mechanisms underlying embryo heterosis. Profiles of transcripts, metabolites and seed contents of developing embryos were analysed to compare the means of reciprocally crossed and selfed seeds growing on the same mother plants. The mean weight of mature hybrid seeds was demonstrably higher, revealing mid-parent heterosis. Hybrid embryos exhibited a prolonged early phase of development and delayed onset of storage activity. Accordingly, transcript profiling indicates stimulation of cell proliferation, an effect, which is potentially mediated by activation of auxin functions within a framework of growth-related transcription factors. At the transcript level, activated cell proliferation increased assimilate uptake activity and thereby seed sink strength. This situation might finally lead to the increased size of the hybrid seeds. We conclude that hybrid seeds are characterised by accelerated growth during early development, which increases storage capacity and leads to higher metabolic fluxes. These needs are, at least partially, met by increased assimilate uptake capacity. The stimulated growth of hybrid seeds shifted metabolite profiles and potentially depleted available pools. Such metabolic shifts are most likely secondary effects resulting from the higher storage capacity of hybrid seeds, a heterotic feature, which is itself established very early in seed development.
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Affiliation(s)
- Tobias Meitzel
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), D-06466 Gatersleben, Germany
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Nilsson L, Müller R, Nielsen TH. Dissecting the plant transcriptome and the regulatory responses to phosphate deprivation. PHYSIOLOGIA PLANTARUM 2010; 139:129-43. [PMID: 20113436 DOI: 10.1111/j.1399-3054.2010.01356.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Inorganic phosphate (Pi) is an essential nutrient for plants, and the low bioavailability of Pi in soils is often a limitation to growth and development. Consequently, plants have evolved a range of regulatory mechanisms to adapt to phosphorus-starvation in order to optimise uptake and assimilation of Pi. Recently, significant progress has been made in elucidating these mechanisms. The coordinated expression of a large number of genes is important for many of these adaptations. Several global expression studies using microarray analysis have been conducted in Arabidopsis thaliana. These studies provide a valuable basis for the identification of new regulatory genes and promoter elements to further the understanding of Pi-dependent gene regulation. With focus on the Arabidopsis transcriptome, we extract common findings that point to new groups of putative regulators, including the NAC, MYB, ethylene response factor/APETALA2, zinc-finger, WRKY and CCAAT-binding families. With a number of new discoveries of regulatory elements, a complex regulatory network is emerging. Some regulatory elements, e.g. the transcription factor PHR1 and the microRNA (miRNA) miR399 and associated factors are well documented, yet not fully understood, whereas other suggested components need further characterisation. Here, we evaluate the contribution of the regulatory elements to the P-responses and present a model comprising factors directly or indirectly involved in transcriptional regulation and the role of miRNAs as regulators and long-distance signals. A striking feature is a series of feedback loops and parallel mechanisms that can modify and attenuate responses. We suggest that these mechanisms are instrumental in providing an accurate response and in keeping P-homeostasis.
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Affiliation(s)
- Lena Nilsson
- Department of Plant Biology and Biotechnology, VKR Research Centre Pro-Active Plants, Faculty of Life Sciences, University of Copenhagen, Frederiksberg, Denmark
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Radchuk R, Emery RJN, Weier D, Vigeolas H, Geigenberger P, Lunn JE, Feil R, Weschke W, Weber H. Sucrose non-fermenting kinase 1 (SnRK1) coordinates metabolic and hormonal signals during pea cotyledon growth and differentiation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 61:324-38. [PMID: 19845880 DOI: 10.1111/j.1365-313x.2009.04057.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Seed development passes through developmental phases such as cell division, differentiation and maturation: each have specific metabolic demands. The ubiquitous sucrose non-fermenting-like kinase (SnRK1) coordinates and adjusts physiological and metabolic demands with growth. In protoplast assays sucrose deprivation and hormone supplementation, such as with auxin and abscisic acid (ABA), stimulate SnRK1-promoter activity. This indicates regulation by nutrients: hormonal crosstalk under conditions of nutrient demand and cell proliferation. SnRK1-repressed pea (Pisum sativum) embryos show lower cytokinin levels and deregulation of cotyledonary establishment and growth, together with downregulated gene expression related to cell proliferation, meristem maintenance and differentiation, leaf formation, and polarity. This suggests that at early stages of seed development SnRK1 regulates coordinated cotyledon emergence and growth via cytokinin-mediated auxin transport and/or distribution. Decreased ABA levels and reduced gene expression, involved in ABA-mediated seed maturation and response to sugars, indicate that SnRK1 is required for ABA synthesis and/or signal transduction at an early stage. Metabolic profiling of SnRK1-repressed embryos revealed lower levels of most organic and amino acids. In contrast, levels of sugars and glycolytic intermediates were higher or unchanged, indicating decreased carbon partitioning into subsequent pathways such as the tricarbonic acid cycle and amino acid biosynthesis. It is hypothesized that SnRK1 mediates the responses to sugar signals required for early cotyledon establishment and patterning. As a result, later maturation and storage activity are strongly impaired. Changes observed in SnRK1-repressed pea seeds provide a framework for how SnRK1 communicates nutrient and hormonal signals from auxins, cytokinins and ABA to control metabolism and development.
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Affiliation(s)
- Ruslana Radchuk
- Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany
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12
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Chen YF, Li LQ, Xu Q, Kong YH, Wang H, Wu WH. The WRKY6 transcription factor modulates PHOSPHATE1 expression in response to low Pi stress in Arabidopsis. THE PLANT CELL 2009; 21:3554-66. [PMID: 19934380 PMCID: PMC2798333 DOI: 10.1105/tpc.108.064980] [Citation(s) in RCA: 274] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Revised: 09/29/2009] [Accepted: 11/01/2009] [Indexed: 05/18/2023]
Abstract
Arabidopsis thaliana WRKY family comprises 74 members and some of them are involved in plant responses to biotic and abiotic stresses. This study demonstrated that WRKY6 is involved in Arabidopsis responses to low-Pi stress through regulating PHOSPHATE1 (PHO1) expression. WRKY6 overexpression lines, similar to the pho1 mutant, were more sensitive to low Pi stress and had lower Pi contents in shoots compared with wild-type seedlings and the wrky6-1 mutant. Immunoprecipitation assays demonstrated that WRKY6 can bind to two W-boxes of the PHO1 promoter. RNA gel blot and beta-glucuronidase activity assays showed that PHO1 expression was repressed in WRKY6-overexpressing lines and enhanced in the wrky6-1 mutant. Low Pi treatment reduced WRKY6 binding to the PHO1 promoter, which indicates that PHO1 regulation by WRKY6 is Pi dependent and that low Pi treatment may release inhibition of PHO1 expression. Protein gel blot analysis showed that the decrease in WRKY6 protein induced by low Pi treatment was inhibited by a 26S proteosome inhibitor, MG132, suggesting that low Pi-induced release of PHO1 repression may result from 26S proteosome-mediated proteolysis. In addition, WRKY42 also showed binding to W-boxes of the PHO1 promoter and repressed PHO1 expression. Our results demonstrate that WRKY6 and WRKY42 are involved in Arabidopsis responses to low Pi stress by regulation of PHO1 expression.
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13
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Gutjahr C, Paszkowski U. Weights in the balance: jasmonic acid and salicylic acid signaling in root-biotroph interactions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2009; 22:763-72. [PMID: 19522558 DOI: 10.1094/mpmi-22-7-0763] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Work on the interaction of aerial plant parts with pathogens has identified the signaling molecules jasmonic acid (JA) and salicylic acid (SA) as important players in induced defense of the plant against invading organisms. Much less is known about the role of JA and SA signaling in root infection. Recent progress has been made in research on plant interactions with biotrophic mutualists and parasites that exclusively associate with roots, namely arbuscular mycorrhizal and rhizobial symbioses on one hand and nematode and parasitic plant interactions on the other hand. Here, we review these recent advances relating JA and SA signaling to specific stages of root colonization and discuss how both signaling molecules contribute to a balance between compatibility and defense in mutualistic as well as parasitic biotroph-root interactions.
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Affiliation(s)
- Caroline Gutjahr
- Department of Plant Molecular Biology, University of Lausanne, Switzerland.
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14
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Creux NM, Ranik M, Berger DK, Myburg AA. Comparative analysis of orthologous cellulose synthase promoters from Arabidopsis, Populus and Eucalyptus: evidence of conserved regulatory elements in angiosperms. THE NEW PHYTOLOGIST 2008; 179:722-737. [PMID: 18547376 DOI: 10.1111/j.1469-8137.2008.02517.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
* The cellulose synthase (CesA) gene family encodes the catalytic subunits of a large protein complex responsible for the deposition of cellulose into plant cell walls. Early in vascular plant evolution, the gene family diverged into distinct members with conserved structures and functions (e.g. primary or secondary cell wall biosynthesis). Although the functions and expression domains of CesA genes have been extensively studied in plants, little is known about transcriptional regulation and promoter evolution in this gene family. * Here, comparative sequence analysis of orthologous CesA promoters from three angiosperm genera, Arabidopsis, Populus and Eucalyptus, was performed to identify putative cis-regulatory sequences. The promoter sequences of groups of Arabidopsis genes that are co-expressed with the primary or secondary cell wall-related CesA genes were also analyzed. * Reporter gene analysis of newly isolated promoter regions of six E. grandis CesA genes in Arabidopsis revealed the conserved functionality of the promoter sequences. Comparative sequence analysis identified 71 conserved sequence motifs, of which 66 were significantly over-represented in either primary or secondary wall-associated promoters. * The presence of conserved cis-regulatory elements in the evolutionary distant CesA promoters of Arabidopsis, Populus and Eucalyptus suggests an ancient transcriptional network regulating cellulose biosynthesis in vascular plants.
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Affiliation(s)
| | | | - David Kenneth Berger
- Department of Plant Science, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
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15
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Udvardi MK, Kakar K, Wandrey M, Montanari O, Murray J, Andriankaja A, Zhang JY, Benedito V, Hofer JMI, Chueng F, Town CD. Legume transcription factors: global regulators of plant development and response to the environment. PLANT PHYSIOLOGY 2007; 144:538-49. [PMID: 17556517 PMCID: PMC1914172 DOI: 10.1104/pp.107.098061] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2007] [Accepted: 03/24/2007] [Indexed: 05/15/2023]
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16
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Tesfaye M, Liu J, Allan DL, Vance CP. Genomic and genetic control of phosphate stress in legumes. PLANT PHYSIOLOGY 2007; 144:594-603. [PMID: 17556523 PMCID: PMC1914184 DOI: 10.1104/pp.107.097386] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2007] [Accepted: 04/10/2007] [Indexed: 05/15/2023]
Affiliation(s)
- Mesfin Tesfaye
- United States Department of Agriculture Agricultural Research Service , University of Minnesota, St. Paul, Minnesota 55108, USA
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17
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Müller R, Morant M, Jarmer H, Nilsson L, Nielsen TH. Genome-wide analysis of the Arabidopsis leaf transcriptome reveals interaction of phosphate and sugar metabolism. PLANT PHYSIOLOGY 2007; 143:156-71. [PMID: 17085508 PMCID: PMC1761981 DOI: 10.1104/pp.106.090167] [Citation(s) in RCA: 220] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2006] [Accepted: 10/17/2006] [Indexed: 05/12/2023]
Abstract
Global gene expression was analyzed in Arabidopsis (Arabidopsis thaliana) by microarrays comprising 21,500 genes. Leaf segments derived from phosphorus (P)-starved and P-replenished plants were incubated with or without sucrose (Suc) to obtain tissues with contrasting combinations of P and carbohydrate levels. Transcript profiling revealed the influence of the two factors individually and the interactions between P- and sugar-dependent gene regulation. A large number of gene transcripts changed more than 2-fold: In response to P starvation, 171 genes were induced and 16 repressed, whereas Suc incubation resulted in 337 induced and 307 repressed genes. A number of new candidate genes involved in P acquisition were discovered. In addition, several putative transcription factors and signaling proteins of P sensing were disclosed. Several genes previously identified to be sugar responsive were also regulated by P starvation and known P-responsive genes were sugar inducible. Nearly 150 genes were synergistically or antagonistically regulated by the two factors. These genes exhibit more prominent or contrasting regulation in response to Suc and P in combination than expected from the effect of the two factors individually. The genes exhibiting interactions form three main clusters with different response patterns and functionality of genes. One cluster (cluster 1) most likely represents a regulatory program to support increased growth and development when both P and carbohydrates are ample. Another cluster (cluster 3) represents genes induced to alleviate P starvation and these are further induced by carbohydrate accumulation. Thus, interactions between P and Suc reveal two different signaling programs and novel interactions in gene regulation in response to environmental factors. cis-Regulatory elements were analyzed for each factor and for interaction clusters. PHR1 binding sites were more frequent in promoters of P-regulated genes as compared to the entire Arabidopsis genome, and E2F and PHR1 binding sites were more frequent in interaction clusters 1 and 3, respectively.
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Affiliation(s)
- Renate Müller
- Plant Biochemistry Laboratory, Department of Plant Biology, Royal Veterinary and Agricultural University, DK-1871 Frederiksberg C, Denmark
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18
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Uhde-Stone C, Liu J, Zinn KE, Allan DL, Vance CP. Transgenic proteoid roots of white lupin: a vehicle for characterizing and silencing root genes involved in adaptation to P stress. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2005; 44:840-53. [PMID: 16297074 DOI: 10.1111/j.1365-313x.2005.02573.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
White lupin (Lupinus albus L.) has become an illuminating model for the study of plant adaptation to phosphorus (P) deficiency. It adapts to -P stress with a highly coordinated modification of root development and biochemistry resulting in short, densely clustered secondary roots called proteoid (or cluster) roots. In order to characterize genes involved in proteoid root formation and function in a homologous system, we have developed an Agrobacterium rhizogenes-based transformation system for white lupin roots that allows rapid analysis of reporter genes as well as RNA interference (RNA(i))-based gene silencing. We used this system to characterize a lupin multidrug and toxin efflux (Lupinus albus MULTIDRUG AND TOXIN EFFLUX, LaMATE) gene previously shown to have enhanced expression under -P stress. Here, we show that LaMATE had high expression in proteoid roots not only under -P, but also under -Fe, -N, -Mn and +Al stress. A portion containing the putative LaMATE promoter was fused to GUS and enhanced green fluorescence protein (EGFP) reporter genes, and a translational LaMATE::EGFP fusion was constructed under control of the LaMATE promoter. The LaMATE promoter directed P-dependent GUS and EGFP expression to proteoid roots. Confocal microscopy in white lupin and Arabidopsis point to the plasma membrane as the likely location of the LaMATE protein. LaMATE displayed homology to FRD3 in Arabidopsis, but did not complement an Arabidopsis ferric reductase defective 3 (FRD3) mutant. RNA(i)-based gene silencing was shown to effectively reduce LaMATE expression in transformed white lupin roots. LaMATE RNAi-silenced plants displayed an about 20% reduction in dry weight.
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Affiliation(s)
- Claudia Uhde-Stone
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, 55108, USA.
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19
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Liu Y, Ahn JE, Datta S, Salzman RA, Moon J, Huyghues-Despointes B, Pittendrigh B, Murdock LL, Koiwa H, Zhu-Salzman K. Arabidopsis vegetative storage protein is an anti-insect acid phosphatase. PLANT PHYSIOLOGY 2005; 139:1545-56. [PMID: 16258019 PMCID: PMC1283788 DOI: 10.1104/pp.105.066837] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Indirect evidence previously suggested that Arabidopsis (Arabidopsis thaliana) vegetative storage protein (VSP) could play a role in defense against herbivorous insects. To test this hypothesis, other AtVSP-like sequences in Arabidopsis were identified through a Basic Local Alignment Search Tool search, and their transcriptional profiles were investigated. In response to methyl jasmonate application or phosphate starvation, AtVSP and AtVSP-like genes exhibited differential expression patterns, suggesting distinct roles played by each member. Arabidopsis VSP2 (AtVSP2), a gene induced by wounding, methyl jasmonate, insect feeding, and phosphate deprivation, was selected for bacterial expression and functional characterization. The recombinant protein exhibited a divalent cation-dependent phosphatase activity in the acid pH range. When incorporated into the diets of three coleopteran and dipteran insects that have acidic gut lumen, recombinant AtVSP2 significantly delayed development of the insects and increased their mortality. To further determine the biochemical basis of the anti-insect activity of the protein, the nucleophilic aspartic acid-119 residue at the conserved DXDXT signature motif was substituted by glutamic acid via site-directed mutagenesis. This single-amino acid alteration did not compromise the protein's secondary or tertiary structure, but resulted in complete loss of its acid phosphatase activity as well as its anti-insect activity. Collectively, we conclude that AtVSP2 is an anti-insect protein and that its defense function is correlated with its acid phosphatase activity.
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Affiliation(s)
- Yilin Liu
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
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20
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Luo H, Song F, Zheng Z. Overexpression in transgenic tobacco reveals different roles for the rice homeodomain gene OsBIHD1 in biotic and abiotic stress responses. JOURNAL OF EXPERIMENTAL BOTANY 2005; 56:2673-82. [PMID: 16105854 DOI: 10.1093/jxb/eri260] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The rice OsBIHD1 gene encodes a transcriptional factor belonging to the homeodomain class. It had previously been shown to be activated by treatment with benzothiadiazole, a chemical inducer of disease resistance, and in an incompatible interaction between rice and the blast fungus. To allow a better understanding of the function of OsBIHD1 in plant disease resistance response, the OsBIHD1 gene in tobacco was overexpressed by Agrobacterium-mediated leaf disc transformation with a construct containing the OsBIHD1 ORF under control of the 35S promoter. Overexpression of the rice OsBIHD1 gene in some of the transgenic tobacco lines led to some morphological abnormalities in the top buds and roots. The transgenic tobacco plants showed an elevated level of defence-related PR-1 gene expression and enhanced disease resistance against infection by tomato mosaic virus, tobacco mosaic virus, and Phytophthora parasitica var. nicotianae. However, the transgenic tobacco plants overexpressing OsBIHD1 showed enhanced sensitivity to salt and oxidative stress as compared with the wild-type plants. The results suggested that the OsBIHD1 protein may be positively involved in activating expression of the defence-related genes in disease resistance responses, and is also important in rice development and abiotic stress tolerance.
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Affiliation(s)
- Hongli Luo
- Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310029, PR China
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Luo H, Song F, Goodman RM, Zheng Z. Up-regulation of OsBIHD1, a rice gene encoding BELL homeodomain transcriptional factor, in disease resistance responses. PLANT BIOLOGY (STUTTGART, GERMANY) 2005; 7:459-68. [PMID: 16163610 DOI: 10.1055/s-2005-865851] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
In the present study, we cloned and identified a full-length cDNA of a rice gene, OsBIHD1, encoding a homeodomain type transcriptional factor. OsBIHD1 is predicted to encode a 642 amino acid protein and the deduced protein sequence of OsBIHD1 contains all conserved domains, a homeodomain, a BELL domain, a SKY box, and a VSLTLGL box, which are characteristics of the BELL type homedomain proteins. The recombinant OsBIHD1 protein expressed in Escherichia coli bound to the TGTCA motif that is the characteristic cis-element DNA sequence of the homeodomain transcriptional factors. Subcellular localization analysis revealed that the OsBIHD1 protein localized in the nucleus of the plant cells. The OsBIHD1 gene was mapped to chromosome 3 of the rice genome and is a single-copy gene with four exons and three introns. Northern blot analysis showed that expression of OsBIHD1 was activated upon treatment with benzothiadiazole (BTH), which is capable of inducing disease resistance. Expression of OsBIHD1 was also up-regulated rapidly during the first 6 h after inoculation with Magnaporthe grisea in BTH-treated rice seedlings and during the incompatible interaction between M. grisea and a resistant genotype. These results suggest that OsBIHD1 is a BELL type of homeodomain transcription factor present in the nucleus, whose induction is associated with resistance response in rice.
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Affiliation(s)
- H Luo
- Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, PR China
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22
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Wang YJ, Li YD, Luo GZ, Tian AG, Wang HW, Zhang JS, Chen SY. Cloning and characterization of an HDZip I gene GmHZ1 from soybean. PLANTA 2005; 221:831-43. [PMID: 15754189 DOI: 10.1007/s00425-005-1496-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2005] [Accepted: 01/29/2005] [Indexed: 05/24/2023]
Abstract
By using cDNA-AFLP, we analyzed a recombinant inbred line population of soybean that was derived from a soybean mosaic virus (SMV) resistant cultivar Kefeng No.1 and a susceptible cultivar Nannong 1138-2. One hundred and eight fragments showing polymorphism between SMV resistant and susceptible pools were identified. One fragment w27 was 96 bp in length and showed homology to homeobox ggth with a coding region of 738 bp, encoding a protein of 245 amino acids. The genomic sequence analysis defined an intron of 521 bp in the coding region. GmHZ1 was characterized by the presence of a homeodomain (HD) with a closely linked leucine zipper motif (Zip). Southern blot analysis indicated that there was a single copy of GmHZ1 in the soybean genome. When inoculated with SMV strain N3, resistant and susceptible varieties showed reduced and increased expression of the GmHZ1, respectively. The fusion protein of GmHZ1 with GFP was targeted only in nucleus. Yeast two hybrid studies revealed that the GmHZ1 had transcriptional activation activity and can form homodimer. GmHZ1 can bind two 9-bp pseudopalindromic elements (CAAT(A/T)ATTG and CAAT(C/G)ATTG) with different affinity. Using GUS as a reporter gene, GmHZ1 was proved to be a transcriptional activator and enhanced GUS expression by binding with the two elements in plant cells. These results indicate that the GmHZ1 may have a transcriptional activator function in plant response to SMV infection.
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Affiliation(s)
- Yong-Jun Wang
- The National Plant Gene Reasearch Center (Beijing), National Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
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23
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Ageez A, Matsunaga S, Uchida W, Sugiyama R, Kazama Y, Kawano S. Isolation and characterization of two homeodomain leucine zipper genes from the dioecious plant Silene latifolia. Genes Genet Syst 2004; 78:353-61. [PMID: 14676426 DOI: 10.1266/ggs.78.353] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Homeodomain leucine zipper (HD-Zip) genes encode transcription factors that are characterized by both a homeodomain and a leucine zipper motif. Two HD-Zip genes were isolated from cDNA of the male flower bud of the dioecious plant Silene latifolia. The two isolated genes, SlHDL1 and SlHDL2, encode proteins with the characteristics of HD-Zip transcription factors belonging to HD-Zip classes I and II, respectively. The expression patterns of SlHDL1 and SlHDL2 throughout the floral developmental stages were studied using real-time PCR and in situ hybridization. SlHDL1 is specifically expressed in the outermost layer of the anthers and gynoeciums with a patchy pattern in the inner layers, suggesting that the product of SlHDL1 plays a role in the early developmental stage of the epidermal tissues of these floral organs. Its expression pattern in the anthers and gynoeciums suggests an involvement in differentiation of the reproductive organs. On the other hand, real-time PCR revealed accumulation of SlHDL2 transcripts in the anther and pollen grains of the male flower. These results suggest that SlHDL1 and SlHDL2 regulate specific targets in restricted regions leading to floral organ differentiation in S. latifolia.
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Affiliation(s)
- Amr Ageez
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan.
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24
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Hammond JP, Broadley MR, White PJ. Genetic responses to phosphorus deficiency. ANNALS OF BOTANY 2004; 94:323-32. [PMID: 15292042 PMCID: PMC4242181 DOI: 10.1093/aob/mch156] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2004] [Revised: 04/21/2004] [Accepted: 05/15/2004] [Indexed: 05/17/2023]
Abstract
BACKGROUND Phosphorus (P) is an essential macronutrient for plants. Plants take up P as phosphate (Pi) from the soil solution. Since little Pi is available in most soils, P fertilizers are applied to crops. However, the use of P fertilizers is unsustainable and may cause pollution. Consequently, there is a need to develop more P-use-efficient (PUE) crops and precise methods to monitor crop P-status. SCOPE Manipulating the expression of genes to improve the PUE of crops could reduce their P fertilizer requirement. This has stimulated research towards the identification of genes and signalling cascades involved in plant responses to P deficiency. Genes that respond to P deficiency can be grouped into 'early' genes that respond rapidly and often non-specifically to P deficiency, or 'late' genes that impact on the morphology, physiology or metabolism of plants upon prolonged P deficiency. SUMMARY The use of micro-array technology has allowed researchers to catalogue the genetic responses of plants to P deficiency. Genes whose expression is altered by P deficiency include various transcription factors, which are thought to coordinate plant responses to P deficiency, and other genes involved in P acquisition and tissue P economy. Several common cis-regulatory elements have been identified in the promoters of these genes, suggesting that their expression might be coordinated. It is suggested that knowledge of the genes whose expression changes in response to P deficiency might allow the development of crops with improved PUE, and could be used in diagnostic techniques to monitor P deficiency in crops either directly using 'smart' indicator plants or indirectly through transcript profiling. The development of crops with improved PUE and the adoption of diagnostic technology could reduce production costs, minimize the use of a non-renewable resource, reduce pollution and enhance biodiversity.
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Tian AG, Wang J, Cui P, Han YJ, Xu H, Cong LJ, Huang XG, Wang XL, Jiao YZ, Wang BJ, Wang YJ, Zhang JS, Chen SY. Characterization of soybean genomic features by analysis of its expressed sequence tags. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 108:903-13. [PMID: 14624337 DOI: 10.1007/s00122-003-1499-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2003] [Accepted: 10/09/2003] [Indexed: 05/23/2023]
Abstract
We analyzed 314,254 soybean expressed sequence tags (ESTs), including 29,540 from our laboratory and 284,714 from GenBank. These ESTs were assembled into 56,147 unigenes. About 76.92% of the unigenes were homologous to genes from Arabidopsis thaliana ( Arabidopsis). The putative products of these unigenes were annotated according to their homology with the categorized proteins of Arabidopsis. Genes corresponding to cell growth and/or maintenance, enzymes and cell communication belonged to the slow-evolving class, whereas genes related to transcription regulation, cell, binding and death appeared to be fast-evolving. Soybean unigenes with no match to genes within the Arabidopsis genome were identified as soybean-specific genes. These genes were mainly involved in nodule development and the synthesis of seed storage proteins. In addition, we also identified 61 genes regulated by salicylic acid, 1,322 transcription factor genes and 326 disease resistance-like genes from soybean unigenes. SSR analysis showed that the soybean genome was more complex than the Arabidopsis and the Medicago truncatula genomes. GC content in soybean unigene sequences is similar to that in Arabidopsis and M. truncatula. Furthermore, the combined analysis of the EST database and the BAC-contig sequences revealed that the total gene number in the soybean genome is about 63,501.
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Affiliation(s)
- Ai-Guo Tian
- Plant Biotechnology Laboratory, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, 100101, Beijing, China
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26
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Franco-Zorrilla JM, González E, Bustos R, Linhares F, Leyva A, Paz-Ares J. The transcriptional control of plant responses to phosphate limitation. JOURNAL OF EXPERIMENTAL BOTANY 2004; 55:285-93. [PMID: 14718495 DOI: 10.1093/jxb/erh009] [Citation(s) in RCA: 160] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plants have evolved an array of responses that adapt their growth to conditions of limited phosphate (Pi) supply. These involve biochemical and developmental changes that improve Pi acquisition and recycling, and protect against the stress of Pi starvation. The induction of these responses requires a sophisticated regulatory system that integrates information on external and internal plant Pi status and the details of this regulatory system are only just beginning to be elucidated. In this review, the current knowledge of this regulatory system is summarized, the hallmark of which is the central role of transcription factor PHR1 in the co-ordinated regulation of many phosphate-starvation-responsive genes. The role of hormonal signalling is also described, including auxins, ethylene and, particularly, cytokinins in the regulation of Pi-starvation responses.
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27
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Guerineau F, Benjdia M, Zhou DX. A jasmonate-responsive element within the A. thaliana vsp1 promoter. JOURNAL OF EXPERIMENTAL BOTANY 2003; 54:1153-62. [PMID: 12654866 DOI: 10.1093/jxb/erg123] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The vsp1 gene of Arabidopsis thaliana encodes a storage protein that accumulates in vegetative organs. Transgenic plants expressing a vsp1 promoter-gus (beta-glucuronidase) gene fusion were found to contain high GUS activity when challenged with jasmonate, a volatile plant hormone. The induction of vsp1-gus expression by jasmonate could be measured in tobacco mesophyll protoplasts, after transient expression. A number of deletions were operated in the vsp1 promoter in order to locate its jasmonate-responsive element. A 41 bp sequence taken approximately 150 bp upstream of the vsp1 TATA box could confer jasmonate responsiveness upon a short CaMV 35S promoter. Whereas the deletion of a CAAT box-like element within the 41 bp sequence did not affect promoter activity, mutation of a short palindromic motif completely abolished jasmonate responsiveness. This motif shows no homology with the jasmonate-responsive elements of other promoters.
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Affiliation(s)
- F Guerineau
- Université de Picardie Jules Verne, 33 rue St Leu, F-80039 Amiens, France.
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28
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Toyota K, Koizumi N, Sato F. Transcriptional activation of phosphoenolpyruvate carboxylase by phosphorus deficiency in tobacco. JOURNAL OF EXPERIMENTAL BOTANY 2003; 54:961-9. [PMID: 12598567 DOI: 10.1093/jxb/erg095] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Phosphoenolpyruvate carboxylase (PEPC), which catalyses the carboxylation of phosphoenolpyruvate using HCO(3)(-) to generate oxaloacetic acid, is an important enzyme in the primary metabolism of plants. Although the PEPC genes (ppc) comprise only a small gene family, the function of each gene is not clear, except for roles in C(4) photosynthesis and CAM. Three PEPC genes (Nsppc1-3) from the C(3) plant Nicotiana sylvestris were used to investigate their roles and regulation in a C(3) plant, and their regulation by phosphorus depletion in particular. First, the induction of PEPC by phosphorus depletion was confirmed. Next, Nsppc1 was determined to be mainly responsive to phosphorus deficiency at the transcriptional level. Further studies using transgenic tobacco harbouring a chimeric gene consisting of the 2.0 kb promoter region of Nsppc1 and the beta-glucuronidase (GUS) reporter showed that PEPC is transcriptionally induced. It was also found that sucrose had a synergistic effect on the induction of PEPC by phosphorus deficiency. A series of transgenic tobacco containing 5'-deletion mutants of Nsppc1 promoter::GUS fusion revealed that the -539 to -442 bp Nsppc1 promoter region, relative to the translation start site, was necessary for the response to phosphorus deficiency. Gain-of-function analysis using a construct containing three tandem repeats of the -539 to -442 bp region confirmed that this region was sufficient to induce the phosphorus-deficiency response in tobacco.
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Affiliation(s)
- Kentaro Toyota
- Laboratory of Molecular and Cellular Biology, Department of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto, 606-8502 Japan
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29
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Vance CP, Uhde-Stone C, Allan DL. Phosphorus acquisition and use: critical adaptations by plants for securing a nonrenewable resource. THE NEW PHYTOLOGIST 2003; 157:423-447. [PMID: 33873400 DOI: 10.1046/j.1469-8137.2003.00695.x] [Citation(s) in RCA: 962] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Phosphorus (P) is limiting for crop yield on > 30% of the world's arable land and, by some estimates, world resources of inexpensive P may be depleted by 2050. Improvement of P acquisition and use by plants is critical for economic, humanitarian and environmental reasons. Plants have evolved a diverse array of strategies to obtain adequate P under limiting conditions, including modifications to root architecture, carbon metabolism and membrane structure, exudation of low molecular weight organic acids, protons and enzymes, and enhanced expression of the numerous genes involved in low-P adaptation. These adaptations may be less pronounced in mycorrhizal-associated plants. The formation of cluster roots under P-stress by the nonmycorrhizal species white lupin (Lupinus albus), and the accompanying biochemical changes exemplify many of the plant adaptations that enhance P acquisition and use. Physiological, biochemical, and molecular studies of white lupin and other species response to P-deficiency have identified targets that may be useful for plant improvement. Genomic approaches involving identification of expressed sequence tags (ESTs) found under low-P stress may also yield target sites for plant improvement. Interdisciplinary studies uniting plant breeding, biochemistry, soil science, and genetics under the large umbrella of genomics are prerequisite for rapid progress in improving nutrient acquisition and use in plants. Contents I. Introduction 424 II. The phosphorus conundrum 424 III. Adaptations to low P 424 IV. Uptake of P 424 V. P deficiency alters root development and function 426 VI. P deficiency modifies carbon metabolism 431 VII. Acid phosphatase 436 VIII. Genetic regulation of P responsive genes 437 IX. Improving P acquisition 439 X. Synopsis 440.
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Affiliation(s)
- Carroll P Vance
- USDA, Agricultural Research Service, Plant Science Research Unit, University of Minnesota 1991 Upper Buford Circle, St Paul, MN 55108, USA
- Departments of Agronomy and Plant Genetics, University of Minnesota 1991 Upper Buford Circle, St Paul, MN 55108, USA
| | - Claudia Uhde-Stone
- Departments of Agronomy and Plant Genetics, University of Minnesota 1991 Upper Buford Circle, St Paul, MN 55108, USA
- Soil, Water and Climate, University of Minnesota 1991 Upper Buford Circle, St Paul, MN 55108, USA
| | - Deborah L Allan
- Soil, Water and Climate, University of Minnesota 1991 Upper Buford Circle, St Paul, MN 55108, USA
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Desvoyes B, Faure-Rabasse S, Chen MH, Park JW, Scholthof HB. A novel plant homeodomain protein interacts in a functionally relevant manner with a virus movement protein. PLANT PHYSIOLOGY 2002; 129:1521-32. [PMID: 12177465 PMCID: PMC166740 DOI: 10.1104/pp.004754] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2002] [Accepted: 03/27/2002] [Indexed: 05/20/2023]
Abstract
Tomato bushy stunt virus and its cell-to-cell movement protein (MP; P22) provide valuable tools to study trafficking of macromolecules through plants. This study shows that wild-type P22 and selected movement-defective P22 amino acid substitution mutants were equivalent for biochemical features commonly associated with MPs (i.e. RNA binding, phosphorylation, and membrane partitioning). This generated the hypothesis that their movement defect was caused by improper interaction between the P22 mutants and one or more host factors. To test this, P22 was used as bait in a yeast (Saccharomyces cerevisiae) two-hybrid screen with a tobacco (Nicotiana tabacum) cDNA library, which identified a new plant homeodomain leucine-zipper protein that reproducibly interacted with P22 but not with various control proteins. These results were confirmed with an independent in vitro binding test. An mRNA for the host protein was detected in plants, and its accumulation was enhanced upon Tomato bushy stunt virus infection of two plant species. The significance of this interaction was further demonstrated by the failure of the homeodomain protein to interact efficiently with two of the well-defined movement-deficient P22 mutants in yeast and in vitro. This is the first report, to our knowledge, that a new plant homeodomain leucine-zipper protein interacts specifically and in a functionally relevant manner with a plant virus MP.
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Affiliation(s)
- Bénédicte Desvoyes
- Department of Plant Pathology and Microbiology, Texas A&M University, 2132 TAMU, College Station, Texas 77843, USA
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31
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Swarup R, Parry G, Graham N, Allen T, Bennett M. Auxin cross-talk: integration of signalling pathways to control plant development. PLANT MOLECULAR BIOLOGY 2002; 49:411-26. [PMID: 12036264 DOI: 10.1007/978-94-010-0377-3_12] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Plants sense and respond to endogenous signals and environmental cues to ensure optimal growth and development. Plant cells must integrate the myriad transduction events into a comprehensive network of signalling pathways and responses. The phytohormone auxin occupies a central place within this transduction network, frequently acting in conjunction with other signals, to co-ordinately regulate cellular processes such as division, elongation and differentiation. As a non-cell autonomous signal, auxin also interacts with other signalling pathways to regulate inter-cellular developmental processes. As part of this especially themed edition of Plant Molecular Biology, we will review examples of 'cross-talk' between auxin and other signalling pathways. Given the current state of knowledge, we have deliberately focused our efforts reviewing auxin interactions with other phytohormone and light signalling pathways. We conclude by discussing how new genomic approaches and the Arabidopsis genome sequence are likely to impact this area of research in the future.
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Affiliation(s)
- Ranjan Swarup
- School of Biosciences, Sutton Bonington, University of Nottingham, Leicestershire, UK
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32
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Zourelidou M, de Torres-Zabala M, Smith C, Bevan MW. Storekeeper defines a new class of plant-specific DNA-binding proteins and is a putative regulator of patatin expression. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2002; 30:489-97. [PMID: 12028578 DOI: 10.1046/j.1365-313x.2002.01302.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The expression of class I patatin genes is restricted to potato tubers but can be induced in other tissues by exogenous sucrose. Here we show that tuber-specific and sucrose-inducible gene expression is reduced in transgenic potato plants by mutations in a conserved 10 base pair motif within the B-box of the patatin promoter. In a southwestern screen, we have isolated a novel DNA-binding protein designated Storekeeper (STK) that specifically recognises the B-box motif in vitro. Gel shift experiments with an STK-specific antibody suggest that STK is the B-box binding protein found in tuber nuclei. We propose that STK, the defining member of a new class of DNA binding proteins, regulates patatin expression in potato tubers via the B-box motif.
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Affiliation(s)
- Melina Zourelidou
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
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