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Masura SS, Shaharuddin NA, Masani MYA, Chan KL, Low ETL, Chan PL, Rahmah ARS, Amiruddin N, Abdullah MP, Azzeme AM, Parveez GKA, Rasid OA. Functional analysis of root-preferential oil palm metallothionein promoter in tobacco. Transgenic Res 2024:10.1007/s11248-024-00396-8. [PMID: 39120800 DOI: 10.1007/s11248-024-00396-8] [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: 04/15/2024] [Accepted: 07/04/2024] [Indexed: 08/10/2024]
Abstract
Root-specific or preferential promoters are essential to genetically modify plants with beneficial root traits. We have characterised the promoter from an oil palm metallothionein gene (EgMT) and performed a serial 5' deletion analysis to identify the region(s) essential for transgenes expression in roots. Stable functional characterisation of tobacco transgenic lines using the T1 generation showed that a deletion construct, designated as RSP-2D (1107 bp), directed strong GUS expression at all stages of root development, particularly in mature roots. Other constructs, RSP-2A (2481 bp) and RSP-2C (1639 bp), drove GUS expression in roots with an intensity lower than RSP-2D. The promoter activity was also detectable in seed pods and immature seeds, albeit at lower levels than CaMV35S. The promoter activity may also be induced by wounding as intact GUS staining was observed at the flower- and leaf-cutting sites of T1 samples carrying either RSP-2C or RSP-2D constructs. The promoter sequence contains cis-acting elements that may act as negative regulators and be responsible for root specificity. The results further indicated that the 5' UTR and ATATT sequences are essential for strong promoter activity. This study highlights the potential of RSP-2D promoter as a tool for modifying root traits through genetic engineering.
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Affiliation(s)
- Subhi Siti Masura
- Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Bandar Baru Bangi, Kajang, Selangor, Malaysia.
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia.
| | - Noor Azmi Shaharuddin
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia.
- Centre for Foundation Studies in Science of Universiti Putra Malaysia (ASPutra), Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia.
| | - Mat Yunus Abdul Masani
- Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Kuang-Lim Chan
- Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Eng-Ti Leslie Low
- Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Pek-Lan Chan
- Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Abdul Rahman Siti Rahmah
- Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Nadzirah Amiruddin
- Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Mohd Puad Abdullah
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Azzreena Mohamad Azzeme
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | | | - Omar Abd Rasid
- Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Bandar Baru Bangi, Kajang, Selangor, Malaysia.
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Hernández-Soriano L, Gálvez-Sandre L, Ávila de Dios E, Simpson J. How to awaken a sleeping giant: antagonistic expression of Flowering locus T homologs and elements of the age-related pathway are associated with the flowering transition in Agave tequilana. PLANT REPRODUCTION 2024; 37:111-132. [PMID: 38082036 PMCID: PMC11180032 DOI: 10.1007/s00497-023-00489-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 11/08/2023] [Indexed: 06/16/2024]
Abstract
KEY MESSAGE Antagonistic expression of Flowering locus T proteins and the ageing pathway via miRNAs and sugar metabolism regulate the initiation of flowering in A. tequilana. Flowering in commercial plantations of Agave tequilana signals that plants are ready to harvest for tequila production. However, time of flowering is often unpredictable and a detailed understanding of the process would be beneficial in the field, for breeding and for the development of future research. This report describes the functional analysis of A. tequilana FLOWERING LOCUS T (FT) genes by heterologous expression in A. thaliana and in situ hybridization in agave plants. The gene structures of the Agave tequilana FT family are also described and putative regulatory promoter elements were identified. Most Agave species have monocarpic, perennial life cycles that can last over 25 years during which plants do not respond to the normal environmental signals which induce flowering, suggesting that the ageing pathway as described in Arabidopsis may play an important role in determining flowering time in these species. Elements of this pathway were analyzed and in silico data is presented that supports the regulation of SQUAMOSA PROMOTER BINDING LIKE proteins (SPL), APETALA2 (AP2) proteins and members of Plant Glycoside Hydrolase Family 32 (PGHF32) by interactions with miRNAs 156, 172 and 164 during the initiation of flowering in A. tequilana.
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Affiliation(s)
| | - Laura Gálvez-Sandre
- Department of Genetic Engineering, Cinvestav Unidad Irapuato, Guanajuato, Mexico
| | - Emmanuel Ávila de Dios
- Department of Genetic Engineering, Cinvestav Unidad Irapuato, Guanajuato, Mexico
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - June Simpson
- Department of Genetic Engineering, Cinvestav Unidad Irapuato, Guanajuato, Mexico.
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Zhang X, Chen JX, Lian WT, Zhou HW, He Y, Li XX, Liao H. Molecular module GmPTF1a/b-GmNPLa regulates rhizobia infection and nodule formation in soybean. THE NEW PHYTOLOGIST 2024; 241:1813-1828. [PMID: 38062896 DOI: 10.1111/nph.19462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/08/2023] [Indexed: 01/26/2024]
Abstract
Nodulation begins with the initiation of infection threads (ITs) in root hairs. Though mutual recognition and early symbiotic signaling cascades in legumes are well understood, molecular mechanisms underlying bacterial infection processes and successive nodule organogenesis remain largely unexplored. We functionally investigated a novel pectate lyase enzyme, GmNPLa, and its transcriptional regulator GmPTF1a/b in soybean (Glycine max), where their regulatory roles in IT development and nodule formation were elucidated through investigation of gene expression patterns, bioinformatics analysis, biochemical verification of genetic interactions, and observation of phenotypic impacts in transgenic soybean plants. GmNPLa was specifically induced by rhizobium inoculation in root hairs. Manipulation of GmNPLa produced remarkable effects on IT and nodule formation. GmPTF1a/b displayed similar expression patterns as GmNPLa, and manipulation of GmPTF1a/b also severely influenced nodulation traits. LI soybeans with low nodulation phenotypes were nearly restored to HI nodulation level by complementation of GmNPLa and/or GmPTF1a. Further genetic and biochemical analysis demonstrated that GmPTF1a can bind to the E-box motif to activate transcription of GmNPLa, and thereby facilitate nodulation. Taken together, our findings potentially reveal novel mediation of cell wall gene expression involving the basic helix-loop-helix transcription factor GmPTF1a/b acts as a key early regulator of nodulation in soybean.
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Affiliation(s)
- Xiao Zhang
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jia-Xin Chen
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wen-Ting Lian
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hui-Wen Zhou
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ying He
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xin-Xin Li
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hong Liao
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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4
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Zhang Y, Fu Y, Xian W, Li X, Feng Y, Bu F, Shi Y, Chen S, van Velzen R, Battenberg K, Berry AM, Salgado MG, Liu H, Yi T, Fournier P, Alloisio N, Pujic P, Boubakri H, Schranz ME, Delaux PM, Wong GKS, Hocher V, Svistoonoff S, Gherbi H, Wang E, Kohlen W, Wall LG, Parniske M, Pawlowski K, Normand P, Doyle JJ, Cheng S. Comparative phylogenomics and phylotranscriptomics provide insights into the genetic complexity of nitrogen-fixing root-nodule symbiosis. PLANT COMMUNICATIONS 2024; 5:100671. [PMID: 37553834 PMCID: PMC10811378 DOI: 10.1016/j.xplc.2023.100671] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/10/2023] [Accepted: 08/03/2023] [Indexed: 08/10/2023]
Abstract
Plant root-nodule symbiosis (RNS) with mutualistic nitrogen-fixing bacteria is restricted to a single clade of angiosperms, the Nitrogen-Fixing Nodulation Clade (NFNC), and is best understood in the legume family. Nodulating species share many commonalities, explained either by divergence from a common ancestor over 100 million years ago or by convergence following independent origins over that same time period. Regardless, comparative analyses of diverse nodulation syndromes can provide insights into constraints on nodulation-what must be acquired or cannot be lost for a functional symbiosis-and the latitude for variation in the symbiosis. However, much remains to be learned about nodulation, especially outside of legumes. Here, we employed a large-scale phylogenomic analysis across 88 species, complemented by 151 RNA-seq libraries, to elucidate the evolution of RNS. Our phylogenomic analyses further emphasize the uniqueness of the transcription factor NIN as a master regulator of nodulation and identify key mutations that affect its function across the NFNC. Comparative transcriptomic assessment revealed nodule-specific upregulated genes across diverse nodulating plants, while also identifying nodule-specific and nitrogen-response genes. Approximately 70% of symbiosis-related genes are highly conserved in the four representative species, whereas defense-related and host-range restriction genes tend to be lineage specific. Our study also identified over 900 000 conserved non-coding elements (CNEs), over 300 000 of which are unique to sampled NFNC species. NFNC-specific CNEs are enriched with the active H3K9ac mark and are correlated with accessible chromatin regions, thus representing a pool of candidate regulatory elements for genes involved in RNS. Collectively, our results provide novel insights into the evolution of nodulation and lay a foundation for engineering of RNS traits in agriculturally important crops.
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Affiliation(s)
- Yu Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yuan Fu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenfei Xian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xiuli Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yong Feng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Fengjiao Bu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yan Shi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Shiyu Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Robin van Velzen
- Biosystematics Group, Department of Plant Sciences, Wageningen University, 6708PB Wageningen, the Netherlands
| | - Kai Battenberg
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Alison M Berry
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Marco G Salgado
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Hui Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road, Kunming 650201, China
| | - Tingshuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road, Kunming 650201, China
| | - Pascale Fournier
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Nicole Alloisio
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Petar Pujic
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Hasna Boubakri
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - M Eric Schranz
- Biosystematics Group, Department of Plant Sciences, Wageningen University, 6708PB Wageningen, the Netherlands
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326 Castanet Tolosan, France
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Valerie Hocher
- French National Research Institute for Sustainable Development (IRD), UMR LSTM (IRD/CIRAD/INRAe/Montpellier University/Supagro)- Campus International Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Sergio Svistoonoff
- French National Research Institute for Sustainable Development (IRD), UMR LSTM (IRD/CIRAD/INRAe/Montpellier University/Supagro)- Campus International Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Hassen Gherbi
- French National Research Institute for Sustainable Development (IRD), UMR LSTM (IRD/CIRAD/INRAe/Montpellier University/Supagro)- Campus International Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai, China
| | - Wouter Kohlen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, 6708PB Wageningen, the Netherlands
| | - Luis G Wall
- Laboratory of Biochemistry, Microbiology and Soil Biological Interactions, Department of Science and Technology, National University of Quilmes, CONICET, Bernal, Argentina
| | - Martin Parniske
- Faculty of Biology, Genetics, LMU Munich, Großhaderner Strasse 2-4, 82152 Martinsried, Germany
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Philippe Normand
- Université de Lyon, Université Lyon 1, CNRS, UMR5557, Ecologie Microbienne, INRA, UMR 1418, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Jeffrey J Doyle
- School of Integrative Plant Science, Sections of Plant Biology and Plant Breeding & Genetics, Cornell University, Ithaca, NY 14853, USA.
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
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Srivastava A, Pusuluri M, Balakrishnan D, Vattikuti JL, Neelamraju S, Sundaram RM, Mangrauthia SK, Ram T. Identification and Functional Characterization of Two Major Loci Associated with Resistance against Brown Planthoppers ( Nilaparvata lugens (Stål)) Derived from Oryza nivara. Genes (Basel) 2023; 14:2066. [PMID: 38003009 PMCID: PMC10671472 DOI: 10.3390/genes14112066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/28/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
The brown planthopper (BPH) is a highly destructive pest of rice, causing significant economic losses in various regions of South and Southeast Asia. Researchers have made promising strides in developing resistance against BPH in rice. Introgression line RPBio4918-230S, derived from Oryza nivara, has shown consistent resistance to BPH at both the seedling and adult stages of rice plants. Segregation analysis has revealed that this resistance is governed by two recessive loci, known as bph39(t) and bph40(t), contributing to 21% and 22% of the phenotypic variance, respectively. We later mapped the genes using a backcross population derived from a cross between Swarna and RPBio4918-230S. We identified specific marker loci, namely RM8213, RM5953, and R4M17, on chromosome 4, flanking the bph39(t) and bph40(t) loci. Furthermore, quantitative expression analysis of candidate genes situated between the RM8213 and R4M17 markers was conducted. It was observed that eight genes exhibited up-regulation in RPBio4918-230S and down-regulation in Swarna after BPH infestation. One gene of particular interest, a serine/threonine-protein kinase receptor (STPKR), showed significant up-regulation in RPBio4918-230S. In-depth sequencing of the susceptible and resistant alleles of STPKR from Swarna and RPBio4918-230S, respectively, revealed numerous single nucleotide polymorphisms (SNPs) and insertion-deletion (InDel) mutations, both in the coding and regulatory regions of the gene. Notably, six of these mutations resulted in amino acid substitutions in the coding region of STPKR (R5K, I38L, S120N, T319A, T320S, and F348S) when compared to Swarna and the reference sequence of Nipponbare. Further validation of these mutations in a set of highly resistant and susceptible backcross inbred lines confirmed the candidacy of the STPKR gene with respect to BPH resistance controlled by bph39(t) and bph40(t). Functional markers specific for STPKR have been developed and validated and can be used for accelerated transfer of the resistant locus to elite rice cultivars.
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Affiliation(s)
- Akanksha Srivastava
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (A.S.); (M.P.); (D.B.); (R.M.S.)
| | - Madhu Pusuluri
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (A.S.); (M.P.); (D.B.); (R.M.S.)
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Divya Balakrishnan
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (A.S.); (M.P.); (D.B.); (R.M.S.)
| | - Jhansi Lakshmi Vattikuti
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (A.S.); (M.P.); (D.B.); (R.M.S.)
| | - Sarla Neelamraju
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (A.S.); (M.P.); (D.B.); (R.M.S.)
| | - Raman Meenakshi Sundaram
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (A.S.); (M.P.); (D.B.); (R.M.S.)
| | | | - Tilathoo Ram
- ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (A.S.); (M.P.); (D.B.); (R.M.S.)
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6
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Yao K, Wang Y, Li X, Ji H. Genome-Wide Identification of the Soybean LysM-RLK Family Genes and Its Nitrogen Response. Int J Mol Sci 2023; 24:13621. [PMID: 37686427 PMCID: PMC10487828 DOI: 10.3390/ijms241713621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/27/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
Lysin-Motif receptor-like kinase (LysM-RLK) proteins are widely distributed in plants and serve a critical role in defending against pathogens and establishing symbiotic relationships. However, there is a lack of comprehensive identification and analysis of LysM-RLK family members in the soybean genome. In this study, we discovered and named 27 LysM-RLK genes in soybean. The majority of LysM-RLKs were highly conserved in Arabidopsis and soybean, while certain members of subclades III, VI, and VII are unique to soybean. The promoters of these LysM-RLKs contain specific cis-elements associated with plant development and responses to environmental factors. Notably, all LysM-RLK gene promoters feature nodule specificity elements, while 51.86% of them also possess NBS sites (NIN/NLP binding site). The expression profiles revealed that genes from subclade V in soybean roots were regulated by both rhizobia and nitrogen treatment. The expression levels of subclade V genes were then validated by real-time quantitative PCR, and it was observed that the level of GmLYK4a and GmLYK4c in roots was inhibited by rhizobia but induced via varying concentrations of nitrate. Consequently, our findings provide a comprehensive understanding of the soybean LysM-RLK gene family and emphasize the role of subclade V in coupling soybean symbiotic nitrogen fixation and nitrogen response.
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Affiliation(s)
- Kaijie Yao
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (K.Y.); (Y.W.); (X.L.)
| | - Yongliang Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (K.Y.); (Y.W.); (X.L.)
| | - Xia Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (K.Y.); (Y.W.); (X.L.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongtao Ji
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (K.Y.); (Y.W.); (X.L.)
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7
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Yu L, Zhang H, Guan R, Li Y, Guo Y, Qiu L. Genome-Wide Tissue-Specific Genes Identification for Novel Tissue-Specific Promoters Discovery in Soybean. Genes (Basel) 2023; 14:1150. [PMID: 37372330 DOI: 10.3390/genes14061150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Promoters play a crucial role in controlling the spatial and temporal expression of genes at transcriptional levels in the process of higher plant growth and development. The spatial, efficient, and correct regulation of exogenous genes expression, as desired, is the key point in plant genetic engineering research. Constitutive promoters widely used in plant genetic transformation are limited because, sometimes, they may cause potential negative effects. This issue can be solved, to a certain extent, by using tissue-specific promoters. Compared with constitutive promoters, a few tissue-specific promoters have been isolated and applied. In this study, based on the transcriptome data, a total of 288 tissue-specific genes were collected, expressed in seven tissues, including the leaves, stems, flowers, pods, seeds, roots, and nodules of soybean (Glycine max). KEGG pathway enrichment analysis was carried out, and 52 metabolites were annotated. A total of 12 tissue-specific genes were selected via the transcription expression level and validated through real-time quantitative PCR, of which 10 genes showed tissue-specific expression. The 3-kb 5' upstream regions of ten genes were obtained as putative promoters. Further analysis showed that all the 10 promoters contained many tissue-specific cis-elements. These results demonstrate that high-throughput transcriptional data can be used as effective tools, providing a guide for high-throughput novel tissue-specific promoter discovery.
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Affiliation(s)
- Lili Yu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hao Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rongxia Guan
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yinghui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yong Guo
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lijuan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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8
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Yang W, Dong X, Yuan Z, Zhang Y, Li X, Wang Y. Genome-Wide Identification and Expression Analysis of the Ammonium Transporter Family Genes in Soybean. Int J Mol Sci 2023; 24:ijms24043991. [PMID: 36835403 PMCID: PMC9960152 DOI: 10.3390/ijms24043991] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/04/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
Ammonium transporters (AMTs) are responsible for ammonium absorption and utilization in plants. As a high-nitrogen-demand crop and a legume, soybean can also obtain ammonium from symbiotic root nodules in which nitrogen-fixing rhizobia convert atmospheric nitrogen (N2) into ammonium. Although increasing evidence implicates vital roles of ammonium transport in soybean, no systematic analyses of AMTs in soybean (named GmAMTs) or functional analyses of GmAMTs are available. In this study, we aimed to identify all GmAMT family genes and gain a better understanding of the characteristics of GmAMT genes in soybean. Here, due to the improved genome assembly and annotation of soybean, we tried to generate a phylogenetic tree of 16 GmAMTs based on new information. Consistent with reported data, GmAMT family members can be divided into two subfamilies of GmAMT1 (6 genes) and GmAMT2 (10 genes). Interestingly, unlike Arabidopsis, which has only one AMT2, soybean has substantially increased the number of GmAMT2s, suggesting enhanced demand for ammonium transport. These genes were distributed on nine chromosomes, of which GmAMT1.3, GmAMT1.4, and GmAMT1.5 were three tandem repeat genes. The gene structures and conserved protein motifs of the GmAMT1 and GmAMT2 subfamilies were different. All the GmAMTs were membrane proteins with varying numbers of transmembrane domains ranging from 4 to 11. Promoter analysis found that these GmAMT genes have phytohormone-, circadian control-, and organ expression-related cis-elements in their promoters, and notably, there were nodulation-specific and nitrogen-responsive elements in the promoters of the GmAMT1 and GmAMT2 genes. Further expression data showed that these GmAMT family genes exhibited different spatiotemporal expression patterns across tissues and organs. In addition, GmAMT1.1, GmAMT1.2, GmAMT2.2, and GmAMT2.3 were responsive to nitrogen treatment, while GmAMT1.2, GmAMT1.3, GmAMT1.4, GmAMT1.5, GmAMT1.6, GmAMT2.1, GmAMT2.2, GmAMT2.3, GmAMT3.1, and GmAMT4.6 showed circadian rhythms in transcription. RT-qPCR validated the expression patterns of GmAMTs in response to different forms of nitrogen and exogenous ABA treatments. Gene expression analysis also confirmed that GmAMTs are regulated by key nodulation gene GmNINa, indicating a role of GmAMTs in symbiosis. Together, these data indicate that GmAMTs may differentially and/or redundantly regulate ammonium transport during plant development and in response to environmental factors. These findings provide a basis for future research on the functions of GmAMTs and the mechanisms through which GmAMTs regulate ammonium metabolism and nodulation in soybean.
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Affiliation(s)
- Wei Yang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoxu Dong
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhanxin Yuan
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xia Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: (X.L.); (Y.W.)
| | - Youning Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: (X.L.); (Y.W.)
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9
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Wang X, Chen K, Zhou M, Gao Y, Huang H, Liu C, Fan Y, Fan Z, Wang Y, Li X. GmNAC181 promotes symbiotic nodulation and salt tolerance of nodulation by directly regulating GmNINa expression in soybean. THE NEW PHYTOLOGIST 2022; 236:656-670. [PMID: 35751548 DOI: 10.1111/nph.18343] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
Soybean (Glycine max) is one of the most important crops world-wide. Under low nitrogen (N) condition, soybean can form a symbiotic relationship with rhizobia to acquire sufficient N for their growth and production. Nodulation signaling controls soybean symbiosis with rhizobia. The soybean Nodule Inception (GmNINa) gene is a central regulator of soybean nodulation. However, the transcriptional regulation of GmNINa remains largely unknown. Nodulation is sensitive to salt stress, but the underlying mechanisms are unclear. Here, we identified an NAC transcription factor designated GmNAC181 (also known as GmNAC11) as the interacting protein of GmNSP1a. GmNAC181 overexpression or knockdown in soybean resulted in increased or decreased numbers of nodules, respectively. Accordingly, the expression of GmNINa was greatly up- and downregulated, respectively. Furthermore, we showed that GmNAC181 can directly bind to the GmNINa promoter to activate its gene expression. Intriguingly, GmNAC181 was highly induced by salt stress during nodulation and promoted symbiotic nodulation under salt stress. We identified a new transcriptional activator of GmNINa in the nodulation pathway and revealed a mechanism by which GmNAC181 acts as a network node orchestrating the expression of GmNINa and symbiotic nodulation under salt stress conditions.
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Affiliation(s)
- Xiaodi Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Wushan Road, Guangzhou, Guangdong, 510642, China
| | - Kuan Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Miaomiao Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yongkang Gao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Huimei Huang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Chao Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yuanyuan Fan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zihui Fan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Youning Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xia Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Wushan Road, Guangzhou, Guangdong, 510642, China
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10
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Zhao Y, Zhang Y, Zhang W, Shi Y, Jiang C, Song X, Tuskan GA, Zeng W, Zhang J, Lu M. The PagKNAT2/6b-PagBOP1/2a Regulatory Module Controls Leaf Morphogenesis in Populus. Int J Mol Sci 2022; 23:ijms23105581. [PMID: 35628391 PMCID: PMC9145908 DOI: 10.3390/ijms23105581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/12/2022] [Accepted: 05/15/2022] [Indexed: 12/04/2022] Open
Abstract
Leaf morphogenesis requires precise regulation of gene expression to achieve organ separation and flat-leaf form. The poplar KNOTTED-like homeobox gene PagKNAT2/6b could change plant architecture, especially leaf shape, in response to drought stress. However, its regulatory mechanism in leaf development remains unclear. In this work, gene expression analyses of PagKNAT2/6b suggested that PagKNAT2/6b was highly expressed during leaf development. Moreover, the leaf shape changes along the adaxial-abaxial, medial-lateral, and proximal-distal axes caused by the mis-expression of PagKNAT2/6b demonstrated that its overexpression (PagKNAT2/6b OE) and SRDX dominant repression (PagKNAT2/6b SRDX) poplars had an impact on the leaf axial development. The crinkle leaf of PagKNAT2/6b OE was consistent with the differential expression gene PagBOP1/2a (BLADE-ON-PETIOLE), which was the critical gene for regulating leaf development. Further study showed that PagBOP1/2a was directly activated by PagKNAT2/6b through a novel cis-acting element "CTCTT". Together, the PagKNAT2/6b-PagBOP1/2a module regulates poplar leaf morphology by affecting axial development, which provides insights aimed at leaf shape modification for further improving the drought tolerance of woody plants.
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Affiliation(s)
- Yanqiu Zhao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Z.); (Y.Z.); (W.Z.); (Y.S.); (C.J.); (W.Z.)
| | - Yifan Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Z.); (Y.Z.); (W.Z.); (Y.S.); (C.J.); (W.Z.)
| | - Weilin Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Z.); (Y.Z.); (W.Z.); (Y.S.); (C.J.); (W.Z.)
| | - Yangxin Shi
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Z.); (Y.Z.); (W.Z.); (Y.S.); (C.J.); (W.Z.)
| | - Cheng Jiang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Z.); (Y.Z.); (W.Z.); (Y.S.); (C.J.); (W.Z.)
| | - Xueqin Song
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China;
| | - Gerald A. Tuskan
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA;
| | - Wei Zeng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Z.); (Y.Z.); (W.Z.); (Y.S.); (C.J.); (W.Z.)
| | - Jin Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Z.); (Y.Z.); (W.Z.); (Y.S.); (C.J.); (W.Z.)
- Correspondence: (J.Z.); (M.L.)
| | - Mengzhu Lu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; (Y.Z.); (Y.Z.); (W.Z.); (Y.S.); (C.J.); (W.Z.)
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China;
- Correspondence: (J.Z.); (M.L.)
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11
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Yang Z, Gao Z, Zhou H, He Y, Liu Y, Lai Y, Zheng J, Li X, Liao H. GmPTF1 modifies root architecture responses to phosphate starvation primarily through regulating GmEXPB2 expression in soybean. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:525-543. [PMID: 33960526 DOI: 10.1111/tpj.15307] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
Though root architecture modifications may be critically important for improving phosphorus (P) efficiency in crops, the regulatory mechanisms triggering these changes remain unclear. In this study, we demonstrate that genotypic variation in GmEXPB2 expression is strongly correlated with root elongation and P acquisition efficiency, and enhancing its transcription significantly improves soybean yield in the field. Promoter deletion analysis was performed using 5' truncation fragments (P1-P6) of GmEXPB2 fused with the GUS gene in soybean transgenic hairy roots, which revealed that the P1 segment containing three E-box elements significantly enhances induction of gene expression in response to phosphate (Pi) starvation. Further experimentation demonstrated that GmPTF1, a basic-helix-loop-helix transcription factor, is the regulatory factor responsible for the induction of GmEXPB2 expression in response to Pi starvation. In short, Pi starvation induced expression of GmPTF1, with the GmPTF1 product directly binding to the E-box motif in the P1 region of the GmEXPB2 promoter. Plus, both GmPTF1 and GmEXPB2 highly expressed in lateral roots, and were significantly enhanced by P deficiency. Further work with soybean stable transgenic plants through RNA sequencing analysis showed that altering GmPTF1 expression significantly impacted the transcription of a series of cell wall genes, including GmEXPB2, and thereby affected root growth, biomass and P uptake. Taken together, this work identifies a novel regulatory factor, GmPTF1, involved in changing soybean root architecture partially through regulation of the expression of GmEXPB2 by binding the E-box motif in its promoter region.
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Affiliation(s)
- Zhaojun Yang
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhi Gao
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huiwen Zhou
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ying He
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yanxing Liu
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yelin Lai
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jiakun Zheng
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xinxin Li
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hong Liao
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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12
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Jiménez-Guillen D, Pérez-Pascual D, Souza-Perera R, Godoy-Hernández G, Zúñiga-Aguilar JJ. Cloning of the Coffea canephora SERK1 promoter and its molecular analysis during the cell-to-embryo transition. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2018.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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13
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Prihatna C, Larkan NJ, Barbetti MJ, Barker SJ. Tomato CYCLOPS/IPD3 is required for mycorrhizal symbiosis but not tolerance to Fusarium wilt in mycorrhiza-deficient tomato mutant rmc. MYCORRHIZA 2018; 28:495-507. [PMID: 29948410 DOI: 10.1007/s00572-018-0842-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 05/31/2018] [Indexed: 06/08/2023]
Abstract
Mycorrhizal symbiosis requires several common symbiosis genes including CYCLOPS/IPD3. The reduced mycorrhizal colonisation (rmc) tomato mutant has a deletion of five genes including CYCLOPS/IPD3, and rmc is more susceptible to Fusarium wilt than its wild-type parental line. This study investigated the genetic defects leading to both fungal interaction phenotypes and whether these were separable. Complementation was performed in rmc to test the requirement for CYCLOPS/IPD3 in mycorrhiza formation and Fusarium wilt tolerance. Promoter analysis via GFP expression in roots was conducted to determine the role of native regulatory elements in the proper functioning of CYCLOPS/IPD3. CYCLOPS/IPD3 regulated by its native promoter, but not a 2×35S promoter, restores mycorrhizal association in rmc. GFP regulated by the 2×35S promoter is not expressed in epidermal cells of roots, indicating that expression of CYCLOPS/IPD3 in these cells is required for colonisation by the fungi utilised in this research. CYCLOPS/IPD3 did not restore Fusarium wilt tolerance, however, showing that the genetic requirements for mycorrhizal association and Fusarium wilt tolerance are different. Our results confirm the expected role of CYCLOPS/IPD3 in mycorrhizal symbiosis and suggest that Fusarium tolerance is conferred by one of the other four genes affected by the deletion.
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Affiliation(s)
- Cahya Prihatna
- School of Agriculture and Environment, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia.
- PT Wilmar Benih Indonesia, Jalan Jababeka X Blok F No. 9, Bekasi, Jawa Barat, 17530, Indonesia.
| | | | - Martin John Barbetti
- School of Agriculture and Environment, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
- The UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Susan Jane Barker
- School of Agriculture and Environment, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
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Moon S, Chandran AKN, Gho YS, Park SA, Kim SR, Yoo YH, Jung KH. Integrated omics analysis of root-preferred genes across diverse rice varieties including Japonica and indica cultivars. JOURNAL OF PLANT PHYSIOLOGY 2018; 220:11-23. [PMID: 29132026 DOI: 10.1016/j.jplph.2017.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 10/02/2017] [Accepted: 10/16/2017] [Indexed: 06/07/2023]
Abstract
Plant root systems play essential roles in developmental processes, such as the absorption of water and inorganic nutrients, and structural support. Gene expression is affected by growth conditions and the genetic background of plants. To identify highly conserved root-preferred genes in rice across diverse growth conditions and varieties, we used two independent meta-anatomical expression profiles based on a large collection of Affymetrix and Agilent 44K microarray data sets available for public use. We then identified 684 loci with root-preferred expression, which were validated with in silico analysis using both meta-expression profiles. The expression patterns of four candidate genes were confirmed in vivo by monitoring expression of β-glucuronidase under control of the candidate-gene promoters, providing new tools to manipulate agronomic traits associated with roots. We also utilized real-time PCR to examine the root-preferential expression of 14 genes across four rice varieties, including japonica and indica cultivars. Using a database of rice genes with known functions, we identified the reported functions of 39 out of the 684 candidate genes. Sixteen genes are directly involved in root development, while the remaining are involved in processes indirectly related to root development (i.e., soil-stress tolerance or growth retardation). This indicates the importance of our candidate genes for studies on root development and function. Gene ontology enrichment analysis in the 'biological processes' category revealed that root-preferred genes in rice are closely associated with nutrient transport-related genes, indicating that the primary role of roots is the uptake of nutrients from soil. In addition, predicted protein-protein interaction analysis suggested a molecular network for root development composed of 215 interactions associated with 44 root-preferred or root development-related genes. Taken together, our data provide an important foundation for future research on root development in rice.
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Affiliation(s)
- Sunok Moon
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | | | - Yun-Shil Gho
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Sun-A Park
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Sung-Ryul Kim
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Yo-Han Yoo
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea.
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15
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Gho YS, Park SA, Kim SR, Chandran AKN, An G, Jung KH. Comparative Expression Analysis of Rice and Arabidopsis Peroxiredoxin Genes Suggests Conserved or Diversified Roles Between the Two Species and Leads to the Identification of Tandemly Duplicated Rice Peroxiredoxin Genes Differentially Expressed in Seeds. RICE (NEW YORK, N.Y.) 2017. [PMID: 28647924 PMCID: PMC5483221 DOI: 10.1186/s12284-017-0170-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
BACKGROUND Peroxiredoxins (PRXs) have recently been identified as plant antioxidants. Completion of various genome sequencing projects has provided genome-wide information about PRX genes in major plant species. Two of these -- Oryza sativa (rice) and Arabidopsis -- each have 10 PRX members. Although significant progress has been made in understanding their biological roles in Arabidopsis, those functions in rice, a model crop plant, have not been well studied. RESULTS We performed a comparative expression analysis of rice and Arabidopsis PRXs. Our phylogenetic analysis revealed that one subgroup contains three rice and three Arabidopsis Type-II PRXs that are expressed ubiquitously. This suggests that they are involved in housekeeping functions to process reactive oxygen species (ROS). Within the second subgroup, expression of Os1-CysPrxA (LOC_Os7g44430) and AtOs1-CysPrx is conserved in seeds while Os1-CysPrxB (LOC_Os7g44440) shows a root-preferential pattern of expression. We used transgenic plants expressing the GUS reporter gene under the control of the promoters of these two tandem duplicates to confirm their meta-expression patterns. Our GUS expression data from developing seeds and those that were germinating indicated that Os1-CysPrxB is involved in root development, as initiated from the embryo, while Os1-CysPrxA has roles in regulating endosperm development near the aleurone layer. For the third and fourth subgroups, the rice PRXs are more likely to show leaf/shoot-preferential expression, while those from Arabidopsis are significantly expressed in the flowers and seeds in addition to the leaf/shoot. To determine the biological meaning of those expression patterns that were dominantly identified in rice PRXs, we analyzed three rice genes showing leaf/shoot-preferential expression in a mutant of the light-responsive 1-deoxy-D-xylulose 5-phosphate reductoisomerase (dxr) gene and found that two of them were significantly down-regulated in the mutant. CONCLUSION A global expression analysis of the PRX family in rice identified tandem duplicates, Os1-CysPrxA and Os1-CysPrxB, in the 1-CysPrx subgroup that are differentially expressed in developing seeds and germinating seeds. Analysis of the cis-acting regulatory elements (CREs) revealed unique CREs responsible for embryo and root or endosperm-preferential expression. In addition, the presence of leaf/shoot-preferential PRXs in rice suggests that they are required in that crop because those plants must tolerate a higher light intensity in their normal growth environment when compared with that of Arabidopsis. Downregulation of two PRXs in the dxr mutant causing an albino phenotype, implying that those genes have roles in processing ROS produced during photosynthesis. Network analysis of four PRXs allowed us to model regulatory pathways that explain the underlying protein interaction network. This will be a useful hypothetical model for further study.
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Affiliation(s)
- Yun-Shil Gho
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Sun-A Park
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Sung-Ruyl Kim
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Metro Manila, Philippines
| | - Anil Kumar Nalini Chandran
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Gynheung An
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea.
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16
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Zhang C, Pan S, Chen H, Cai T, Zhuang C, Deng Y, Zhuang Y, Zeng Y, Chen S, Zhuang W. Characterization of NtREL1, a novel root-specific gene from tobacco, and upstream promoter activity analysis in homologous and heterologous hosts. PLANT CELL REPORTS 2016; 35:757-69. [PMID: 26849672 DOI: 10.1007/s00299-015-1918-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 11/30/2015] [Accepted: 12/08/2015] [Indexed: 06/05/2023]
Abstract
KEY MESSAGE A novel root-specific gene and its upstream promoter were cloned and characterized for potential application in root-specific expression of transgenes. The root is an important plant organ subjected to many biotic and abiotic stresses, such as infection by Ralstonia solanacearum. To isolate tobacco root-specific promoters for genetic applications, microarray screening was performed to identify genes highly and specifically expressed in the root. One root-specific gene encoding an extensin-like protein (NtREL1) was isolated, and its expression pattern was further characterized by both microarray analysis and reverse transcription-polymerase chain reaction. NtREL1 was highly expressed only in roots but not in any other organ. NtREL1 expression was affected by hormone treatment (salicylic acid, abscisic acid, and ethephon) as well as low temperature, drought, and R. solanacearum infection. A full-length 849 bp cDNA containing a 657-nucleotide open reading frame was cloned by Rapid Amplification of cDNA Ends. Subsequently, a fragment of 1,574 bp upstream of NtREL1 was isolated by flanking PCR and named pNtREL1. This promoter fragment contains TATA, GATA, and CAAT-boxes, the basic elements of a promoter, and six root-specific expression elements, namely OSE1, OSE2, ROOTMOTIFTAPOX1, SURECOREATSULTR11, P1BS, and WUSATAg. A construct containing the bacterial uidA reporter gene (β-glucuronidase, GUS) driven by the pNtREL1 promoter was transformed into tobacco plants. GUS staining was only detected in the root, but not in leaves and stems. Additionally, transgenic tobacco plants containing peanut resveratrol synthase gene (AhRS) driven by the pNtREL1 promoter produced resveratrol only in the root. Thus, the pNtREL1 promoter can be used to direct root-specific expression of target genes to protect the root from stress or for biological studies.
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Affiliation(s)
- Chong Zhang
- Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fuzhou, 350002, Fujian, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Shufang Pan
- Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fuzhou, 350002, Fujian, China
| | - Hua Chen
- Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fuzhou, 350002, Fujian, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Tiecheng Cai
- Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fuzhou, 350002, Fujian, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Chunhong Zhuang
- Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fuzhou, 350002, Fujian, China
| | - Ye Deng
- Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fuzhou, 350002, Fujian, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yuhui Zhuang
- Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fuzhou, 350002, Fujian, China
| | - Yuanhuan Zeng
- Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fuzhou, 350002, Fujian, China
| | - Shunhui Chen
- Institute of Tobacco Agricultural Science and Technology, Fujian Bureau of Tobacco, Fuzhou, 350000, Fujian, China.
| | - Weijian Zhuang
- Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Fuzhou, 350002, Fujian, China.
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, 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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18
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Indrasumunar A, Wilde J, Hayashi S, Li D, Gresshoff PM. Functional analysis of duplicated Symbiosis Receptor Kinase (SymRK) genes during nodulation and mycorrhizal infection in soybean (Glycine max). JOURNAL OF PLANT PHYSIOLOGY 2015; 176:157-68. [PMID: 25617765 DOI: 10.1016/j.jplph.2015.01.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 12/23/2014] [Accepted: 01/02/2015] [Indexed: 06/04/2023]
Abstract
Association between legumes and rhizobia results in the formation of root nodules, where symbiotic nitrogen fixation occurs. The early stages of this association involve a complex of signalling events between the host and microsymbiont. Several genes dealing with early signal transduction have been cloned, and one of them encodes the leucine-rich repeat (LRR) receptor kinase (SymRK; also termed NORK). The Symbiosis Receptor Kinase gene is required by legumes to establish a root endosymbiosis with Rhizobium bacteria as well as mycorrhizal fungi. Using degenerate primer and BAC sequencing, we cloned duplicated SymRK homeologues in soybean called GmSymRKα and GmSymRKβ. These duplicated genes have high similarity of nucleotide (96%) and amino acid sequence (95%). Sequence analysis predicted a malectin-like domain within the extracellular domain of both genes. Several putative cis-acting elements were found in promoter regions of GmSymRKα and GmSymRKβ, suggesting a participation in lateral root development, cell division and peribacteroid membrane formation. The mutant of SymRK genes is not available in soybean; therefore, to know the functions of these genes, RNA interference (RNAi) of these duplicated genes was performed. For this purpose, RNAi construct of each gene was generated and introduced into the soybean genome by Agrobacterium rhizogenes-mediated hairy root transformation. RNAi of GmSymRKβ gene resulted in an increased reduction of nodulation and mycorrhizal infection than RNAi of GmSymRKα, suggesting it has the major activity of the duplicated gene pair. The results from the important crop legume soybean confirm the joint phenotypic action of GmSymRK genes in both mycorrhizal and rhizobial infection seen in model legumes.
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Affiliation(s)
- Arief Indrasumunar
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane 4072, QLD, Australia
| | - Julia Wilde
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane 4072, QLD, Australia
| | - Satomi Hayashi
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane 4072, QLD, Australia
| | - Dongxue Li
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane 4072, QLD, Australia
| | - Peter M Gresshoff
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane 4072, QLD, Australia.
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19
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Wang Y, Wang L, Zou Y, Chen L, Cai Z, Zhang S, Zhao F, Tian Y, Jiang Q, Ferguson BJ, Gresshoff PM, Li X. Soybean miR172c targets the repressive AP2 transcription factor NNC1 to activate ENOD40 expression and regulate nodule initiation. THE PLANT CELL 2014; 26:4782-801. [PMID: 25549672 PMCID: PMC4311200 DOI: 10.1105/tpc.114.131607] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 11/19/2014] [Accepted: 12/08/2014] [Indexed: 05/18/2023]
Abstract
MicroRNAs are noncoding RNAs that act as master regulators to modulate various biological processes by posttranscriptionally repressing their target genes. Repression of their target mRNA(s) can modulate signaling cascades and subsequent cellular events. Recently, a role for miR172 in soybean (Glycine max) nodulation has been described; however, the molecular mechanism through which miR172 acts to regulate nodulation has yet to be explored. Here, we demonstrate that soybean miR172c modulates both rhizobium infection and nodule organogenesis. miR172c was induced in soybean roots inoculated with either compatible Bradyrhizobium japonicum or lipooligosaccharide Nod factor and was highly upregulated during nodule development. Reduced activity and overexpression of miR172c caused dramatic changes in nodule initiation and nodule number. We show that soybean miR172c regulates nodule formation by repressing its target gene, Nodule Number Control1, which encodes a protein that directly targets the promoter of the early nodulin gene, ENOD40. Interestingly, transcriptional levels of miR172c were regulated by both Nod Factor Receptor1α/5α-mediated activation and by autoregulation of nodulation-mediated inhibition. Thus, we established a direct link between miR172c and the Nod factor signaling pathway in addition to adding a new layer to the precise nodulation regulation mechanism of soybean.
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Affiliation(s)
- Youning Wang
- Key State Laboratory of Plant Cell and Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China
| | - Lixiang Wang
- Key State Laboratory of Plant Cell and Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yanmin Zou
- Key State Laboratory of Plant Cell and Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China
| | - Liang Chen
- Key State Laboratory of Plant Cell and Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China
| | - Zhaoming Cai
- Key State Laboratory of Plant Cell and Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Senlei Zhang
- Key State Laboratory of Plant Cell and Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Zhao
- Key State Laboratory of Plant Cell and Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China
| | - Yinping Tian
- Key State Laboratory of Plant Cell and Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China
| | - Qiong Jiang
- Key State Laboratory of Plant Cell and Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Brett J Ferguson
- Centre for Integrative Legume Research, University of Queensland, Brisbane St. Lucia, Queensland 4072, Australia
| | - Peter M Gresshoff
- Centre for Integrative Legume Research, University of Queensland, Brisbane St. Lucia, Queensland 4072, Australia
| | - Xia Li
- Key State Laboratory of Plant Cell and Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China
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20
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Mizuno H, Yazawa T, Kasuga S, Sawada Y, Ogata J, Ando T, Kanamori H, Yonemaru JI, Wu J, Hirai MY, Matsumoto T, Kawahigashi H. Expression level of a flavonoid 3'-hydroxylase gene determines pathogen-induced color variation in sorghum. BMC Res Notes 2014; 7:761. [PMID: 25346182 PMCID: PMC4219097 DOI: 10.1186/1756-0500-7-761] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 10/13/2014] [Indexed: 12/22/2022] Open
Abstract
Background Sorghum (Sorghum bicolor L. Moench) accumulates 3-deoxyanthocyanidins and exhibits orange to purple coloration on parts of the leaf in response to infection with the fungus Bipolaris sorghicola. We aimed to identify the key genes determining this color variation. Results Sorghum populations derived from Nakei-MS3B and M36001 accumulated apigeninidin, or both apigeninidin and luteolinidin, in different proportions in lesions caused by B. sorghicola infection, suggesting that the relative proportions of the two 3-deoxyanthocyanidins determine color variation. QTL analysis and genomic sequencing indicated that two closely linked loci on chromosome 4, containing the flavonoid 3′-hydroxylase (F3′H) and Tannin1 (Tan1) genes, were responsible for the lesion color variation. The F3′H locus in Nakei-MS3B had a genomic deletion resulting in the fusion of two tandemly arrayed F3′H genes. The recessive allele at the Tan1 locus derived from M36001 had a genomic insertion and encoded a non-functional WD40 repeat transcription factor. Whole-mRNA sequencing revealed that expression of the fused F3′H gene was conspicuously induced in purple sorghum lines. The levels of expression of F3′H matched the relative proportions of apigeninidin and luteolinidin. Conclusions Expression of F3′H is responsible for the synthesis of luteolinidin; the expression level of this gene is therefore critical in determining color variation in sorghum leaves infected with B. sorghicola. Electronic supplementary material The online version of this article (doi:10.1186/1756-0500-7-761) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hiroshi Mizuno
- National Institute of Agrobiological Sciences, Agrogenomics Research Center, 1-2, Kannondai 2-chome, Tsukuba, Ibaraki 305-8602, Japan.
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21
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The CarERF genes in chickpea (Cicer arietinum L.) and the identification of CarERF116 as abiotic stress responsive transcription factor. Funct Integr Genomics 2014; 15:27-46. [PMID: 25274312 DOI: 10.1007/s10142-014-0399-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 08/21/2014] [Accepted: 08/31/2014] [Indexed: 10/24/2022]
Abstract
The AP2/ERF family is one of the largest transcription factor gene families that are involved in various plant processes, especially in response to biotic and abiotic stresses. Complete genome sequences of one of the world's most important pulse crops chickpea (Cicer arietinum L.), has provided an important opportunity to identify and characterize genome-wide ERF genes. In this study, we identified 120 putative ERF genes from chickpea. The genomic organization of the chickpea ERF genes suggested that the gene family might have been expanded through the segmental duplications. The 120 member ERF family was classified into eleven distinct groups (I-X and VI-L). Transcriptional factor CarERF116, which is differentially expressed between drought tolerant and susceptible chickpea cultivar under terminal drought stress has been identified and functionally characterized. The CarERF116 encodes a putative protein of 241 amino acids and classified into group IX of ERF family. An in vitro CarERF116 protein-DNA binding assay demonstrated that CarERF116 protein specifically interacts with GCC box. We demonstrate that CarERF116 is capable of transactivation activity of and show that the functional transcriptional domain lies at the C-terminal region of the CarERF116. In transgenic Arabidopsis plants overexpressing CarERF116, significant up-regulation of several stress related genes were observed. These plants also exhibit resistance to osmotic stress and reduced sensitivity to ABA during seed germination. Based on these findings, we conclude that CarERF116 is an abiotic stress responsive gene, which plays an important role in stress tolerance. In addition, the present study leads to genome-wide identification and evolutionary analyses of chickpea ERF gene family, which will facilitate further research on this important group of genes and provides valuable resources for comparative genomics among the grain legumes.
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22
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Ashraf MA, Shahid AA, Rao AQ, Bajwa KS, Husnain T. Functional characterization of a bidirectional plant promoter from cotton leaf curl Burewala virus using an Agrobacterium-mediated transient assay. Viruses 2014; 6:223-42. [PMID: 24424501 PMCID: PMC3917440 DOI: 10.3390/v6010223] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/14/2013] [Accepted: 12/24/2013] [Indexed: 11/16/2022] Open
Abstract
The C1 promoter expressing the AC1 gene, and V1 promoter expressing the AV1 gene are located in opposite orientations in the large intergenic region of the Cotton leaf curl Burewala virus (CLCuBuV) genome. Agro-infiltration was used to transiently express putative promoter constructs in Nicotiana tabacum and Gossypium hirsutum leaves, which was monitored by a GUS reporter gene, and revealed that the bidirectional promoter of CLCuBuV transcriptionally regulates both the AC1 and AV1 genes. The CLCuBuV C1 gene promoter showed a strong, consistent transient expression of the reporter gene (GUS) in N. tabacum and G. hirsutum leaves and exhibited GUS activity two- to three-fold higher than the CaMV 35S promoter. The CLCuBuV bidirectional gene promoter is a nearly constitutive promoter that contains basic conserved elements. Many cis-regulatory elements (CREs) were also analyzed within the bidirectional plant promoters of CLCuBuV and closely related geminiviruses, which may be helpful in understanding the transcriptional regulation of both the virus and host plant.
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Affiliation(s)
- Muhammad Aleem Ashraf
- Plant Biotechnology Laboratory, Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore 53700, Pakistan.
| | - Ahmad Ali Shahid
- Plant Biotechnology Laboratory, Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore 53700, Pakistan.
| | - Abdul Qayyum Rao
- Plant Biotechnology Laboratory, Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore 53700, Pakistan.
| | - Kamran Shehzad Bajwa
- Plant Biotechnology Laboratory, Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore 53700, Pakistan.
| | - Tayyab Husnain
- Plant Biotechnology Laboratory, Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore 53700, Pakistan.
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23
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van der Knaap E, Chakrabarti M, Chu YH, Clevenger JP, Illa-Berenguer E, Huang Z, Keyhaninejad N, Mu Q, Sun L, Wang Y, Wu S. What lies beyond the eye: the molecular mechanisms regulating tomato fruit weight and shape. FRONTIERS IN PLANT SCIENCE 2014; 5:227. [PMID: 24904622 PMCID: PMC4034497 DOI: 10.3389/fpls.2014.00227] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 05/06/2014] [Indexed: 05/19/2023]
Abstract
Domestication of fruit and vegetables resulted in a huge diversity of shapes and sizes of the produce. Selections that took place over thousands of years of alleles that increased fruit weight and altered shape for specific culinary uses provide a wealth of resources to study the molecular bases of this diversity. Tomato (Solanum lycopersicum) evolved from a wild ancestor (S. pimpinellifolium) bearing small and round edible fruit. Molecular genetic studies led to the identification of two genes selected for fruit weight: FW2.2 encoding a member of the Cell Number Regulator family; and FW3.2 encoding a P450 enzyme and the ortholog of KLUH. Four genes were identified that were selected for fruit shape: SUN encoding a member of the IQD family of calmodulin-binding proteins leading to fruit elongation; OVATE encoding a member of the OVATE family proteins involved in transcriptional repression leading to fruit elongation; LC encoding most likely the ortholog of WUSCHEL controlling meristem size and locule number; FAS encoding a member in the YABBY family controlling locule number leading to flat or oxheart shape. For this article, we will provide an overview of the putative function of the known genes, when during floral and fruit development they are hypothesized to act and their potential importance in regulating morphological diversity in other fruit and vegetable crops.
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Affiliation(s)
- Esther van der Knaap
- Department of Horticulture and Crop Science, The Ohio State UniversityWooster, OH, USA
- *Correspondence: Esther van der Knaap, Department of Horticulture and Crop Science, The Ohio State University, 1680 Madison Ave., Wooster, OH, 44691, USA e-mail:
| | - Manohar Chakrabarti
- Department of Horticulture and Crop Science, The Ohio State UniversityWooster, OH, USA
| | - Yi Hsuan Chu
- Department of Horticulture and Crop Science, The Ohio State UniversityWooster, OH, USA
| | - Josh P. Clevenger
- Department of Horticulture and Crop Science, The Ohio State UniversityWooster, OH, USA
| | - Eudald Illa-Berenguer
- Department of Horticulture and Crop Science, The Ohio State UniversityWooster, OH, USA
| | - Zejun Huang
- Department of Horticulture and Crop Science, The Ohio State UniversityWooster, OH, USA
| | - Neda Keyhaninejad
- Department of Horticulture and Crop Science, The Ohio State UniversityWooster, OH, USA
| | - Qi Mu
- Department of Horticulture and Crop Science, The Ohio State UniversityWooster, OH, USA
| | - Liang Sun
- Department of Horticulture and Crop Science, The Ohio State UniversityWooster, OH, USA
| | - Yanping Wang
- Department of Horticulture and Crop Science, The Ohio State UniversityWooster, OH, USA
- Department of Pomology, College of Agriculture and Biotechnology, China Agricultural UniversityBeijing, China
| | - Shan Wu
- Department of Horticulture and Crop Science, The Ohio State UniversityWooster, OH, USA
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24
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A cytochrome P450 regulates a domestication trait in cultivated tomato. Proc Natl Acad Sci U S A 2013; 110:17125-30. [PMID: 24082112 DOI: 10.1073/pnas.1307313110] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Domestication of crop plants had effects on human lifestyle and agriculture. However, little is known about the underlying molecular mechanisms accompanying the changes in fruit appearance as a consequence of selection by early farmers. We report the fine mapping and cloning of a tomato (Solanum lycopersicum) fruit mass gene encoding the ortholog of KLUH, SlKLUH, a P450 enzyme of the CYP78A subfamily. The increase in fruit mass is predominantly the result of enlarged pericarp and septum tissues caused by increased cell number in the large fruited lines. SlKLUH also modulates plant architecture by regulating number and length of the side shoots, and ripening time, and these effects are particularly strong in plants that transgenically down-regulate SlKLUH expression carrying fruits of a dramatically reduced mass. Association mapping followed by segregation analyses revealed that a single nucleotide polymorphism in the promoter of the gene is highly associated with fruit mass. This single polymorphism may potentially underlie a regulatory mutation resulting in increased SlKLUH expression concomitant with increased fruit mass. Our findings suggest that the allele giving rise to large fruit arose in the early domesticates of tomato and becoming progressively more abundant upon further selections. We also detected association of fruit weight with CaKLUH in chile pepper (Capsicum annuum) suggesting that selection of the orthologous gene may have occurred independently in a separate domestication event. Altogether, our findings shed light on the molecular basis of fruit mass, a key domestication trait in tomato and other fruit and vegetable crops.
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25
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Balestrini R, Ott T, Güther M, Bonfante P, Udvardi MK, De Tullio MC. Ascorbate oxidase: the unexpected involvement of a 'wasteful enzyme' in the symbioses with nitrogen-fixing bacteria and arbuscular mycorrhizal fungi. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2012; 59:71-9. [PMID: 22863656 DOI: 10.1016/j.plaphy.2012.07.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 07/03/2012] [Indexed: 05/20/2023]
Abstract
Ascorbate oxidase (AO, EC 1.10.3.3) catalyzes the oxidation of ascorbate (AsA) to yield water. AO over-expressing plants are prone to ozone and salt stresses, whereas lower expression apparently confers resistance to unfavorable environmental conditions. Previous studies have suggested a role for AO as a regulator of oxygen content in photosynthetic tissues. For the first time we show here that the expression of a Lotus japonicus AO gene is induced in the symbiotic interaction with both nitrogen-fixing bacteria and arbuscular mycorrhizal (AM) fungi. In this framework, high AO expression is viewed as a possible strategy to down-regulate oxygen diffusion in root nodules, and a component of AM symbiosis. A general model of AO function in plants is discussed.
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26
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Severino FE, Brandalise M, Costa CS, Wilcken SRS, Maluf MP, Gonçalves W, Maia IG. CaPrx, a Coffea arabica gene encoding a putative class III peroxidase induced by root-knot nematode infection. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 191-192:35-42. [PMID: 22682563 DOI: 10.1016/j.plantsci.2012.04.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 04/18/2012] [Accepted: 04/21/2012] [Indexed: 06/01/2023]
Abstract
Class III peroxidases (Prxs) are enzymes involved in a multitude of physiological and stress-related processes in plants. Here, we report on the characterization of a putative peroxidase-encoding gene from Coffea arabica (CaPrx) that is expressed in early stages of root-knot nematode (RKN) infection. CaPrx showed enhanced expression in coffee roots inoculated with RKN (at 12 h post-inoculation), but no significant difference in expression was observed between susceptible and resistant plants. Assays using transgenic tobacco plants harboring a promoter-β-glucuronidase (GUS) fusion revealed that the CaPrx promoter was exclusively active in the galls induced by RKN. In cross sections of galls, GUS staining was predominantly localized in giant cells. Up-regulation of GUS expression in roots of transgenic plants following RKN inoculation was observed within 16 h. Moreover, no increase in GUS expression after treatment with jasmonic acid was detected. Altogether, these results point to a putative role of this peroxidase in the general coffee response to RKN infection.
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Affiliation(s)
- Fábio E Severino
- UNESP, Instituto de Biociências, Departamento de Genética, Botucatu, SP, Brazil
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27
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Li J, Farmer AD, Lindquist IE, Dukowic-Schulze S, Mudge J, Li T, Retzel EF, Chen C. Characterization of a set of novel meiotically-active promoters in Arabidopsis. BMC PLANT BIOLOGY 2012; 12:104. [PMID: 22776406 PMCID: PMC3462685 DOI: 10.1186/1471-2229-12-104] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 06/13/2012] [Indexed: 05/19/2023]
Abstract
BACKGROUND Homologous recombination, together with selection, laid the foundation for traditional plant breeding. The recombination process that takes place during meiotic cell division is crucial for the creation of novel variations of highly desired traits by breeders. Gaining control over this process is important for molecular breeding to achieve more precise, large-scale and quicker plant improvement. As conventional ubiquitous promoters are neither tissue-specific nor efficient in driving gene expression in meiocytes, promoters with high meiotic activities are potential candidates for manipulating the recombination process. So far, only a few meiotically-active promoters have been reported. Recently developed techniques to profile the transcriptome landscape of isolated meiocytes provided the means to discover promoters from genes that are actively expressed in meiosis. RESULTS In a screen for meiotically-active promoters, we examined ten promoter sequences that are associated with novel meiotic candidate genes. Each promoter was tested by expressing a GFP reporter gene in Arabidopsis. Characterization of regulatory regions revealed that these meiotically-active promoters possessed conserved motifs and motif arrangement. Some of the promoters unite optimal properties which are invaluable for meiosis-directed studies such as delivering specific gene expression in early meiosis I and/or meiosis II. Furthermore, the examination of homologs of the corresponding genes within green plants points to a great potential of applying the information from Arabidopsis to other species, especially crop plants. CONCLUSIONS We identified ten novel meiotically-active promoters; which, along with their homologs, are prime candidates to specifically drive gene expression during meiosis in plants and can thus provide important tools for meiosis study and crop breeding.
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Affiliation(s)
- Junhua Li
- Department of Horticultural Science, University of Minnesota, 1970 Folwell Avenue, St. Paul, MN, 55108, USA
- College of Life Sciences, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Andrew D Farmer
- National Center for Genome Resources, 2935 Rodeo Park Drive E, Santa Fe, NM, 87505, USA
| | - Ingrid E Lindquist
- National Center for Genome Resources, 2935 Rodeo Park Drive E, Santa Fe, NM, 87505, USA
| | - Stefanie Dukowic-Schulze
- Department of Horticultural Science, University of Minnesota, 1970 Folwell Avenue, St. Paul, MN, 55108, USA
| | - Joann Mudge
- National Center for Genome Resources, 2935 Rodeo Park Drive E, Santa Fe, NM, 87505, USA
| | - Tao Li
- Department of Horticultural Science, University of Minnesota, 1970 Folwell Avenue, St. Paul, MN, 55108, USA
| | - Ernest F Retzel
- National Center for Genome Resources, 2935 Rodeo Park Drive E, Santa Fe, NM, 87505, USA
| | - Changbin Chen
- Department of Horticultural Science, University of Minnesota, 1970 Folwell Avenue, St. Paul, MN, 55108, USA
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28
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Ye R, Zhou F, Lin Y. Two novel positive cis-regulatory elements involved in green tissue-specific promoter activity in rice (Oryza sativa L ssp.). PLANT CELL REPORTS 2012; 31:1159-72. [PMID: 22388917 DOI: 10.1007/s00299-012-1238-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 02/05/2012] [Accepted: 02/06/2012] [Indexed: 05/23/2023]
Abstract
UNLABELLED In plant genetic engineering, using tissue-specific promoters to control the expression of target gene is an effective way to avoid potential negative effects of using constitutive promoter, such as metabolic burden and so on. However, until now, there are few tissue-specific promoters with strong and reliable expression that could be used in crop biotechnology application. In this study, based on microarray and RT-PCR data, we identified a rice green tissue-specific expression gene DX1 (LOC_Os12g33120). The expression pattern of DX1 gene promoter was examined by using the β-glucuronidase (GUS) reporter gene and analyzed in transgenic rice plants in different tissues. Histochemical assays and quantitative analyses of GUS activity confirmed that P (DX1):GUS was highly expressed in green tissues. To identify the regulatory elements controlling the expression of the DX1 gene, a series of 5' and 3' deletions of DX1 promoter were fused to GUS gene and stably introduced into rice plants. In addition, gel mobility shift assays and site-directed mutagenesis studies were used, allowing for the identification of two novel tissue-specific cis-acting elements (GSE1 and GSE2) within P(DX1). GSE1 acted as a positive regulator in all green tissues (leaf, sheath, stem and panicle). Compared with GSE1, GSE2 acted as a positive regulator only in sheath and stem tissue, and had a weaker effect on gene expression. In addition, P(DX1):GUS was not expressed in anther and seed, this characteristic reduced the potential ecological risk and potential food safety issues. Taken together, our results strongly suggest that the identified promoter, P(DX1), and its cis regulatory elements, GSE1 and GSE2, are potentially useful in the field of rice transgenic breeding. KEY MESSAGE We have isolated and characterized the rice green tissue-specific promoter P(DX1), and identified two novel positive cis-acting elements in P(DX1).
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Affiliation(s)
- Rongjian Ye
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
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29
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Chen A, Gu M, Sun S, Zhu L, Hong S, Xu G. Identification of two conserved cis-acting elements, MYCS and P1BS, involved in the regulation of mycorrhiza-activated phosphate transporters in eudicot species. THE NEW PHYTOLOGIST 2011; 189:1157-1169. [PMID: 21106037 DOI: 10.1111/j.1469-8137.2010.03556.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
• In this study, six putative promoter regions of phosphate transporter Pht1;3, Pht1;4 and Pht1;5 genes were isolated from eggplant and tobacco using the inverse polymerase chain reaction (iPCR). The isolated sequences show evolutionary conservation and divergence within/between the two groups of Pht1;3 and Pht1;4/Pht1;5. • Histochemical analyses showed that all six promoter fragments were sufficient to drive β-glucuronidase (GUS) expression specifically in arbuscular mycorrhizal (AM) tobacco roots and were confined to distinct cells containing AM fungal structures (arbuscules or intracellular hyphae). • A series of promoter truncation and mutation analyses combined with phylogenetic footprinting of these promoters revealed that at least two cis-regulatory elements--the mycorrhiza transcription factor binding sequence (MYCS) first identified in this study and P1BS--mediated the transcriptional activation of the AM-mediated inorganic phosphate (Pi) transporter genes. Deletion or partial mutation of either of the two motifs in the promoters could cause a remarkable decrease, or even complete absence, of the promoter activity. • Our results propose that uptake of inorganic phosphate (Pi) by AM fungi is regulated, at least partially, in an MYCS- and P1BS-dependent manner in eudicot species. Our finding offers new insights into the molecular mechanisms underlying the coordination between the AM and the Pi signalling pathways.
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Affiliation(s)
| | | | - Shubin Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lingling Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuai Hong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
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30
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Hohnjec N, Lenz F, Fehlberg V, Vieweg MF, Baier MC, Hause B, Küster H. The signal peptide of the Medicago truncatula modular nodulin MtNOD25 operates as an address label for the specific targeting of proteins to nitrogen-fixing symbiosomes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2009; 22:63-72. [PMID: 19061403 DOI: 10.1094/mpmi-22-1-0063] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The nodule-specific MtNOD25 gene of the model legume Medicago truncatula encodes a modular nodulin composed of different repetitive modules flanked by distinct N- and C-termini. Although similarities are low with respect to all repetitive modules, both the N-terminal signal peptide (SP) and the C-terminus are highly conserved in modular nodulins from different legumes. On the cellular level, MtNOD25 is only transcribed in the infected cells of root nodules, and this activation is mediated by a 299-bp minimal promoter containing an organ-specific element. By expressing mGFP6 translational fusions in transgenic nodules, we show that MtNOD25 proteins are exclusively translocated to the symbiosomes of infected cells. This specific targeting only requires an N-terminal MtNOD25 SP that is highly conserved across a family of legume-specific symbiosome proteins. Our finding sheds light on one possible mechanism for the delivery of host proteins to the symbiosomes of infected root nodule cells and, in addition, defines a short molecular address label of only 24 amino acids whose N-terminal presence is sufficient to translocate proteins across the peribacteroid membrane.
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Affiliation(s)
- Natalija Hohnjec
- Institute for Genome Research and Systems Biology (IGS), Bielefeld University, Bielefeld, Germany
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31
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George S, Usha B, Parida A. Isolation and characterization of an atypical LEA protein coding cDNA and its promoter from drought-tolerant plant Prosopis juliflora. Appl Biochem Biotechnol 2008; 157:244-53. [PMID: 19002660 DOI: 10.1007/s12010-008-8398-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2008] [Accepted: 10/09/2008] [Indexed: 10/21/2022]
Abstract
Plant growth and productivity are adversely affected by various abiotic and biotic stress factors. Despite the wealth of information on abiotic stress and stress tolerance in plants, many aspects still remain unclear. Prosopis juliflora is a hardy plant reported to be tolerant to drought, salinity, extremes of soil pH, and heavy metal stress. In this paper, we report the isolation and characterization of the complementary DNA clone for an atypical late embryogenesis abundant (LEA) protein (Pj LEA3) and its putative promoter sequence from P. juliflora. Unlike typical LEA proteins, rich in glycine, Pj LEA3 has alanine as the most abundant amino acid followed by serine and shows an average negative hydropathy. Pj LEA3 is significantly different from other LEA proteins in the NCBI database and shows high similarity to indole-3 acetic-acid-induced protein ARG2 from Vigna radiata. Northern analysis for Pj LEA3 in P. juliflora leaves under 90 mM H2O2 stress revealed up-regulation of transcript at 24 and 48 h. A 1.5-kb fragment upstream the 5' UTR of this gene (putative promoter) was isolated and analyzed in silico. The possible reasons for changes in gene expression during stress in relation to the host plant's stress tolerance mechanisms are discussed.
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Affiliation(s)
- Suja George
- M.S. Swaminathan Research Foundation, Taramani, Chennai 600113, India
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32
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Garrocho-Villegas V, Bustos-Rivera G, Gough J, Vinogradov SN, Arredondo-Peter R. Expression and in silico structural analysis of a rice (Oryza sativa) hemoglobin 5. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2008; 46:855-9. [PMID: 18586507 DOI: 10.1016/j.plaphy.2008.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Indexed: 04/30/2023]
Abstract
This work reports the analysis of an additional hemoglobin (hb) gene copy, hb5, in the genome of rice. The amino acid sequence of Hb5 differs from the previously determined rice Hbs 1-4 in missing 11 residues in helix E. Transcripts of hb5 were found to be ubiquitous in rice organs, and hormone- and stress-response promoters exist upstream of the rice hb5 gene. Furthermore, the modeled structure of Hb5 based on the known crystal structure of rice Hb1 is unusual in that the putative distal His is distant from the heme Fe. This observation suggests that Hb5 binds and releases O(2) easily and thus that it functions as an O(2)-carrier or in some aspects of the O(2) metabolism.
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Affiliation(s)
- Verónica Garrocho-Villegas
- Laboratorio de Biofísica y Biología Molecular, Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Colonia Chamilpa, 62210 Cuernavaca, Morelos, México
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33
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Silvente S, Reddy PM, Khandual S, Blanco L, Alvarado-Affantranger X, Sanchez F, Lara-Flores M. Evidence for sugar signalling in the regulation of asparagine synthetase gene expressed in Phaseolus vulgaris roots and nodules. JOURNAL OF EXPERIMENTAL BOTANY 2008; 59:1279-1294. [PMID: 18407964 DOI: 10.1093/jxb/ern034] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A cDNA clone, designated as PvNAS2, encoding asparagine amidotransferase (asparagine synthetase) was isolated from nodule tissue of common bean (Phaseolus vulgaris cv. Negro Jamapa). Southern blot analysis indicated that asparagine synthetase in bean is encoded by a small gene family. Northern analysis of RNAs from various plant organs demonstrated that PvNAS2 is highly expressed in roots, followed by nodules in which it is mainly induced during the early days of nitrogen fixation. Investigations with the PvNAS2 promoter gusA fusion revealed that the expression of PvNAS2 in roots is confined to vascular bundles and meristematic tissues, while in root nodules its expression is solely localized to vascular traces and outer cortical cells encompassing the central nitrogen-fixing zone, but never detected in either infected or non-infected cells located in the central region of the nodule. PvNAS2 is down-regulated when carbon availability is reduced in nodules, and the addition of sugars to the plants, mainly glucose, boosted its induction, leading to the increased asparagine production. In contrast to PvNAS2 expression and the concomitant asparagine synthesis, glucose supplement resulted in the reduction of ureide content in nodules. Studies with glucose analogues as well as hexokinase inhibitors suggested a role for hexokinase in the sugar-sensing mechanism that regulates PvNAS2 expression in roots. In light of the above results, it is proposed that, in bean, low carbon availability in nodules prompts the down-regulation of the asparagine synthetase enzyme and concomitantly asparagine production. Thereby a favourable environment is created for the efficient transfer of the amido group of glutamine for the synthesis of purines, and then ureide generation.
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MESH Headings
- 3' Untranslated Regions/metabolism
- Amino Acid Sequence
- Asparagine/metabolism
- Aspartate-Ammonia Ligase/chemistry
- Aspartate-Ammonia Ligase/genetics
- Base Sequence
- Carbohydrate Metabolism
- Cloning, Molecular
- Gene Expression Regulation, Enzymologic
- Gene Expression Regulation, Plant
- Glucose/metabolism
- Hexokinase/metabolism
- Molecular Sequence Data
- Nitrogen Fixation
- Phaseolus/enzymology
- Phaseolus/genetics
- Phaseolus/physiology
- Plant Roots/enzymology
- Plant Roots/genetics
- Plant Roots/physiology
- Plant Structures/enzymology
- Plant Structures/genetics
- Plant Structures/physiology
- Promoter Regions, Genetic
- RNA Processing, Post-Transcriptional
- RNA, Plant/chemistry
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Root Nodules, Plant/enzymology
- Root Nodules, Plant/genetics
- Root Nodules, Plant/physiology
- Sequence Alignment
- Signal Transduction
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Affiliation(s)
- Sonia Silvente
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Colonia Chamilpa, Cuernavaca, CP 62210, Morelos, México
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34
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Blanco L, Reddy PM, Silvente S, Bucciarelli B, Khandual S, Alvarado-Affantranger X, Sánchez F, Miller S, Vance C, Lara-Flores M. Molecular cloning, characterization and regulation of two different NADH-glutamate synthase cDNAs in bean nodules. PLANT, CELL & ENVIRONMENT 2008; 31:454-72. [PMID: 18182018 DOI: 10.1111/j.1365-3040.2008.01774.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
NADH-dependent glutamate synthase (NADH-GOGAT) is a key enzyme in primary ammonia assimilation in Phaseolus vulgaris nodules. Two different types of cDNA clones of PvNADH-GOGAT were isolated from the nodule cDNA libraries. The full-length cDNA clones of PvNADH-GOGAT-I (7.4 kb) and PvNADH-GOGAT-II (7.0 kb), which displayed an 83% homology between them, were isolated using cDNA library screening, 'cDNA library walking' and RT-PCR amplification. Southern analysis employing specific 5' cDNA probes derived from PvNADH-GOGAT-I and PvNADH-GOGAT-II indicated the existence of a single copy of each gene in the bean genome. Both these proteins contain approximately 100 amino acid sequences theoretically addressing each isoenzyme to different subcellular compartments. RT-PCR analysis indicated that PvNADH-GOGAT-II expression is higher than PvNADH-GOGAT-I during nodule development. Expression analysis by RT-PCR also revealed that both of these genes are differentially regulated by sucrose. On the other hand, the expression of PvNADH-GOGAT-I, but not PvNADH-GOGAT-II, was inhibited with nitrogen compounds. In situ hybridization and promoter expression analyses demonstrated that the NADH-GOGAT-I and -II genes are differentially expressed in bean root and nodule tissues. In silico analyses of the NADH-GOGAT promoters revealed the presence of potential cis elements in them that could mediate differential tissue-specific, and sugar and amino acid responsive expression of these genes.
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Affiliation(s)
- Lourdes Blanco
- Centro de Ciencias Genómicas, Univrsidad Nacional Autónoma de México, Av Universidad, C.P. 62210, Cuernavaca, Morelos, México
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35
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Suprunova T, Krugman T, Distelfeld A, Fahima T, Nevo E, Korol A. Identification of a novel gene (Hsdr4) involved in water-stress tolerance in wild barley. PLANT MOLECULAR BIOLOGY 2007; 64:17-34. [PMID: 17238046 DOI: 10.1007/s11103-006-9131-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Accepted: 12/18/2006] [Indexed: 05/13/2023]
Abstract
Drought is one of the most severe stresses limiting plant growth and yield. Genes involved in water stress tolerance of wild barley (Hordeum spontaneoum), the progenitor of cultivated barley, were investigated using genotypes contrasting in their response to water stress. Gene expression profiles of water-stress tolerant vs. water-stress sensitive wild barley genotypes, under severe dehydration stress applied at the seedling stage, were compared using cDNA-AFLP analysis. Of the 1100 transcript-derived fragments (TDFs) amplified about 70 displayed differential expression between control and stress conditions. Eleven of them showed clear difference (up- or down-regulation) between tolerant and susceptible genotypes. These TDFs were isolated, sequenced and tested by RT-PCR. The differential expression of seven TDFs was confirmed by RT-PCR, and TDF-4 was selected as a promising candidate gene for water-stress tolerance. The corresponding gene, designated Hsdr4 (Hordeum spontaneum dehydration-responsive), was sequenced and the transcribed and flanking regions were determined. The deduced amino acid sequence has similarity to the rice Rho-GTPase-activating protein-like with a Sec14 p-like lipid-binding domain. Analysis of Hsdr4 promoter region that was isolated by screening a barley BAC library, revealed a new putative miniature inverted-repeat transposable element (MITE), and several potential stress-related binding sites for transcription factors (MYC, MYB, LTRE, and GT-1), suggesting a role of the Hsdr4 gene in plant tolerance to dehydration stress. Furthermore, the Hsdr4 gene was mapped using wild barley mapping population to the long arm of chromosome 3H between markers EBmac541 and EBmag705, within a region that previously was shown to affect osmotic adaptation in barley.
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Affiliation(s)
- Tatiana Suprunova
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel
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36
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Xu W, Sato SJ, Clemente TE, Chollet R. The PEP-carboxylase kinase gene family in Glycine max (GmPpcK1-4): an in-depth molecular analysis with nodulated, non-transgenic and transgenic plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 49:910-23. [PMID: 17257170 DOI: 10.1111/j.1365-313x.2006.03006.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Phosphoenolpyruvate carboxylase (PEPC) is a widely distributed metabolic enzyme among plant and prokaryotic species. In vascular plants, the typical PEPC is regulated post-translationally by a complex interplay between opposing metabolite effectors and reversible protein phosphorylation. This phosphorylation event is controlled primarily by the up-/down-regulation of PEPC-kinase (PpcK), an approximately 31-kDa Ser/Thr-kinase. As a sequel to earlier investigations related to PEPC phosphorylation in N(2)-fixing nodules of Glycine max, we now present a detailed molecular analysis of the PpcK multigene family in nodulated soybeans. Although the GmPpcK1-4 transcripts are all expressed throughout nodule development, only the nearly identical GmPpcK2/3 homologs are nodule-enhanced and up-/down-regulated in vivo by photosynthate supply from the shoots. In contrast, GmPpcK1 is a 'housekeeping' gene, and GmPpcK4 is a highly divergent member, distantly removed from the legume PpcK subfamily. Real-time qRT-PCR analysis indicates that GmPpcK2/3 are overwhelmingly the dominant PpcKs expressed and up-/down-regulated throughout nodule development, mirroring the expression properties of nodule-enhanced PEPC (GmPpc7). In situ RT-PCR investigation of the spatial localization of the GmPpcK1-4 and GmPpc7 transcripts in mature nodules is entirely consistent with this view. Complementary histochemical and related RNA gel-blot findings with nodulated, GmPpcK1/3 promoter::GUS-expressing T(2) plants provide direct experimental evidence that (i) PpcK gene expression is controlled primarily at the transcriptional level; and (ii) the contrasting expression properties of GmPpcK1/3 are conferred largely by regulatory element(s) within the approximately 1.4-kb 5'-upstream region. As a result of our multifaceted analyses of GmPpcK1-4, GmPpc7 and PEPC-phosphorylation in the soybean nodule, it is proposed that the GmPpcK2/3 homologs and GmPpc7 together comprise the key molecular 'downstream players' in this regulatory phosphorylation system within the mature nodule's central zone.
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Affiliation(s)
- Wenxin Xu
- Department of Biochemistry, University of Nebraska-Lincoln, George W. Beadle Center, Lincoln, NE 68588-0664, USA
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37
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Frenzel A, Tiller N, Hause B, Krajinski F. The conserved arbuscular mycorrhiza-specific transcription of the secretory lectin MtLec5 is mediated by a short upstream sequence containing specific protein binding sites. PLANTA 2006; 224:792-800. [PMID: 16596411 DOI: 10.1007/s00425-006-0262-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Accepted: 03/06/2006] [Indexed: 05/08/2023]
Abstract
In Medicago truncatula a family of mycorrhiza-specific expressed lectins has been identified recently, but the function and regulation of these lectins during the arbuscular mycorrhiza symbiosis are still unknown. In order to characterize a first member of this protein family, MtLec5 was analyzed concerning its localization and regulation. Confocal laser scanning microscopy showed that MtLec5 is a secretory protein indicating a role as a vegetative storage protein, which is specifically expressed in mycorrhizal root systems. To study the molecular mechanisms leading to the mycorrhiza-specific transcription, deletion studies of pMtLec5 were done using reporter gene fusions. Potential cis-acting elements could be narrowed down to a 150 bp fragment that was located approximately at -300/-150 according to the transcription start, suggesting the binding of positive regulators to this area. Similar expression pattern of the reporter gene was found after transforming roots of the non-legume Nicotiana tabacum with the heterologous promoter-reporter fusions. This indicated that the observed mycorrhiza-specific transcriptional induction is not legume-specific. Electrophoretic mobility shift assays showed that several factors which were exclusively present in mycorrhizal roots bind within the 150 bp promoter area. This strengthens the hypothesis of positive regulators mediating the AM-specific gene expression.
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Affiliation(s)
- André Frenzel
- Lehrgebiet Molekulargenetik, Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
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38
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Sullivan S, Jenkins GI, Nimmo HG. Roots, cycles and leaves. Expression of the phosphoenolpyruvate carboxylase kinase gene family in soybean. PLANT PHYSIOLOGY 2004; 135:2078-87. [PMID: 15299132 PMCID: PMC520779 DOI: 10.1104/pp.104.042762] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2004] [Revised: 05/21/2004] [Accepted: 05/25/2004] [Indexed: 05/18/2023]
Abstract
Phosphorylation of phosphoenolpyruvate carboxylase (PEPc; EC 4.1.1.31) plays an important role in the control of central metabolism of higher plants. This phosphorylation is controlled largely at the level of expression of PEPc kinase (PPCK) genes. We have analyzed the expression of both PPCK genes and the PEPC genes that encode PEPc in soybean (Glycine max). Soybean contains at least four PPCK genes. We report the genomic and cDNA sequences of these genes and demonstrate the function of the gene products by in vitro expression and enzyme assays. For two of these genes, GmPPCK2 and GmPPCK3, transcript abundance is highest in nodules and is markedly influenced by supply of photosynthate from the shoots. One gene, GmPPCK4, is under robust circadian control in leaves but not in roots. Its transcript abundance peaks in the latter stages of subjective day, and its promoter contains a sequence very similar to the evening element found in Arabidopsis genes expressed at this time. We report the expression patterns of five PEPC genes, including one encoding a bacterial-type PEPc lacking the phosphorylation site of the plant-type PEPcs. The PEPc expression patterns do not match those of any of the PPCK genes, arguing against the existence of specific PEPc-PPCK expression partners. The PEPC and PPCK gene families in soybean are significantly more complex than previously understood.
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Affiliation(s)
- Stuart Sullivan
- Plant Molecular Science Group, Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
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39
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Nakagawa T, Takane K, Sugimoto T, Izui K, Kouchi H, Hata S. Regulatory regions and nuclear factors involved in nodule-enhanced expression of a soybean phosphoenolpyruvate carboxylase gene: implications for molecular evolution. Mol Genet Genomics 2003; 269:163-72. [PMID: 12684874 DOI: 10.1007/s00438-002-0794-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2002] [Accepted: 12/04/2002] [Indexed: 10/25/2022]
Abstract
We have determined the genomic organization of two closely related phosphoenolpyruvate carboxylase genes in soybean, GmPEPC7, which is expressed at high levels in root nodules, and the housekeeping gene GmPEPC15. Their nucleotide sequences, including most introns and 5;-flanking regions within 600 bp upstream from the transcription start sites, are well conserved, suggesting that they were duplicated quite recently. To gain insights into the process of evolution of the tissue-specifically expressed GmPEPC7gene, we produced chimeric constructs carrying either the GmPEPC7or GmPEPC15promoter fused to the beta-glucuronidase gene. The expression patterns of the reporter observed in nodules that developed on transgenic hairy roots reflected the levels of mRNA levels produced by the genes in wild-type soybean plants, indicating that the GmPEPC7promoter directs nodule-specific expression. Loss-of-function experiments showed that the segment of GmPEPC7between -466 and -400, designated as the "switch region" (SR), was necessary for expression in nodules, although proteins that bind to SR were not detectable in a gel-retardation assay. Another gel-retardation assay indicated that putative nodule nuclear proteins bind specifically to the region of GmPEPC7between -400 and -318, designated as the "amplifier region" (AR). Both SR and AR have characteristic sequences that are not found in the GmPEPC15promoter. Furthermore, experiments using hybrid promoters derived from GmPEPC15demonstrated that AR confers high-level expression in nodules only in combination with SR. When wild-type soybean plants were subjected to prolonged darkness and subsequently illuminated, the level of GmPEPC7mRNA in nodules decreased and then recovered. This study suggests that the acquisition of two interdependent cis-acting elements resulted in molecular evolution of the nodule-enhanced GmPEPC7gene.
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Affiliation(s)
- T Nakagawa
- Laboratory of Plant Physiology, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Japan
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40
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Suzuki A, Kobayashi F, Abe M, Uchiumi T, Higashi S. Cloning and expression of a down-regulated gene (TrEnodDR1) of white clover responded by the nod genes derived from Rhizobium leguminosarum bv. trifolii strain 4S. Gene 2001; 266:77-84. [PMID: 11290421 DOI: 10.1016/s0378-1119(01)00377-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The nodulation genes of Rhizobium leguminosarum bv. trifolii 4S (strain 4S) were cloned into cosmid vector pLAFR1 named pC4S8 which was contained nodNMLFEDABCIJ and a part of nodT as an insert. The pC4S8 was transferred to strain H1, Sym plasmid (pRt4Sa) cured strain of strain 4S, and isolated as Tc resistant and nodulation restored mutant, strain H1(pC4S8). During infection process of this strain, visible symbiotic features, such as root hair curling (Hac), root hair deformation (Had) and infection thread formation (Inf) were also restored. The nodule forming ability of strain H1(pC4S8) was increased 3-4 times in nodule number than that of strain 4S. Then, to investigate the effect of Rhizobium nod genes on the host plant (Trifolium repens L.) gene expression, cDNAs which were responded to the inoculation of rhizobia were differentially screened based on the presence or absence of nod genes treated with strains H1(pC4S8) or H1, respectively. The cDNA, TrEnodDR1 (Trifolium repens early nodulin down regulation 1) gene was isolated from cDNA library prepared from white clover seedlings treated with nod- strain H1, but didn't exhibit in nod+ treated cDNA library, as a down-regulated gene. Expression analysis of TrEnodDR1 was performed in various tissues of white clover, it is suppressed in root nodule and also strongly suppressed by the inoculation of rhizobia in the seedlings. It is discussed that TrEnodDR1 gene is suppressed when the white clover comes into symbiosis with rhizobia.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Cloning, Molecular
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- Down-Regulation
- Fabaceae/genetics
- Gene Expression Regulation, Plant
- Genes, Bacterial/genetics
- Genes, Plant/genetics
- Molecular Sequence Data
- Nitrogen Fixation/genetics
- Plant Roots/microbiology
- Plants, Medicinal
- Plasmids/genetics
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Rhizobium leguminosarum/genetics
- Rhizobium leguminosarum/isolation & purification
- Sequence Analysis, DNA
- Symbiosis/genetics
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Affiliation(s)
- A Suzuki
- Department of Chemistry and BioScience, Faculty of Science, Kagoshima, University, 890-0065, Kagoshima, Japan.
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41
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Stougaard J. Regulators and regulation of legume root nodule development. PLANT PHYSIOLOGY 2000; 124:531-40. [PMID: 11027704 PMCID: PMC1539285 DOI: 10.1104/pp.124.2.531] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Affiliation(s)
- J Stougaard
- Laboratory of Gene Expression, Department of Molecular and Structural Biology, University of Aarhus, Gustav Wieds Vej 10, 8000 C Aarhus, Denmark.
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42
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Fang Y, Hirsch AM. Studying early nodulin gene ENOD40 expression and induction by nodulation factor and cytokinin in transgenic alfalfa. PLANT PHYSIOLOGY 1998; 116:53-68. [PMID: 9449836 PMCID: PMC35188 DOI: 10.1104/pp.116.1.53] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/1997] [Accepted: 09/17/1997] [Indexed: 05/18/2023]
Abstract
ENOD40, an early nodulin gene, is expressed following inoculation with Rhizobium meliloti or by adding R. meliloti-produced nodulation (Nod) factors or the plant hormone cytokinin to uninoculated roots. We isolated two MsENOD40 clones, designated MsENOD40-1 and MsENOD40-2, with distinct promoters from an alfalfa (Medicago sativa cv Chief) genomic library. The promoters were fused to the reporter gene uidA (gus), and the constructs were introduced into alfalfa. We observed that the MsENOD40-1 construct was expressed almost exclusively under symbiotic conditions. The MsENOD40-2 construct was transcribed under both symbiotic and nonsymbiotic conditions and in nonnodular and nodular tissues. Both MsENOD40 promoter-gus constructs were similarly expressed as nodules developed, and both were expressed in roots treated with 6-benzylaminopurine or purified Nod factor. However, no blue color was detected in nodule-like structures induced by the auxin transport inhibitor N-1-(naphthyl)phthalamic acid on roots of plants containing the MsENOD40-1 promoter construct, whereas pseudonodules from plants containing the MsENOD40-2 promoter construct stained blue. A 616-bp region at the distal 5' end of the promoter is important for proper spatial expression of MsENOD40 in nodules and also for Nod-factor and cytokinin-induced expression.
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Affiliation(s)
- Y Fang
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles 90095-1606, USA
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43
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Christiansen H, Hansen AC, Vijn I, Pallisgaard N, Larsen K, Yang WC, Bisseling T, Marcker KA, Jensen EO. A novel type of DNA-binding protein interacts with a conserved sequence in an early nodulin ENOD12 promoter. PLANT MOLECULAR BIOLOGY 1996; 32:809-821. [PMID: 8980533 DOI: 10.1007/bf00020479] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The pea genes PsENOD12A and PsENOD12B are expressed in the root hairs shortly after infection with the nitrogen-fixing bacterium Rhizobium leguminosarum bv. viciae or after application of purified Nod factors. A 199 bp promoter fragment of the PsENOD12B gene contains sufficient information for Nod factor-induced tissue-specific expression. We have isolated a Vicia sativa cDNA encoding a 1641 amino acid protein, ENBP1, that interacts with the 199 bp ENOD12 promoter. Two different DNA-binding domains were identified in ENBP1. A domain containing six AT-hooks interacts specifically with an AT-rich sequence located between positions -95 and -77 in the PsENOD12B promoter. A second domain in ENBP1 is a cysteine-rich region that binds to the ENOD12 promoter in a sequence non-specific but metal-dependent way. ENBP1 is expressed in the same cell types as ENOD12. However, additional expression is observed in the nodule parenchyma and meristem. The presence of three small overlapping ORFs in the 5'-untranslated region of the ENBP1 cDNA indicates that ENBP1 expression might be regulated at the translational level. The interaction of ENBP1 with a conserved AT-rich element within the ENOD12 promoter and the presence of the ENBP1 transcript in cells expressing ENOD12 strongly suggest that ENBP1 is a transcription factor involved in the regulation of ENOD12. Finally, the C-terminal region of ENBP1 shows strong homology to a protein from rat that is specifically expressed in testis tissue.
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Affiliation(s)
- H Christiansen
- Department of Molecular Biology, University of Aarhus, Denmark
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44
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Abstract
Rhizobium, Bradyrhizobium and Azorhizobium can elicit the formation of N2-fixing nodules on the roots or stems of their leguminous host plants. The nodule formation involves several developmental steps determined by different sets of genes from both partners, the gene expression being temporally and spatially coordinated. The plant proteins that are specifically synthesised during the formation and function of the nodule are called nodulins. The nodulins that are expressed before the onset of N2 fixation are termed early nodulins. These proteins are probably involved in the infection process as well as in nodule morphogenesis rather than in nodule function. The nodulins expressed just before or during N2 fixation are termed late nodulins and they participate in the function of the nodule by creating the physiological conditions required for nitrogen fixation, ammonium assimilation and transport. In this review we will describe nodulins, nodulin genes and the relationship between nodulin gene expression and nodule development. The study of nodulin gene expression may provide insight into root-nodule development and the mechanism of communication between bacteria and host plant.
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45
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Macknight RC, Reynolds PH, Farnden KJ. Analysis of the lupin Nodulin-45 promoter: conserved regulatory sequences are important for promoter activity. PLANT MOLECULAR BIOLOGY 1995; 27:457-466. [PMID: 7894011 DOI: 10.1007/bf00019313] [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 promoter from the Lupinus angustifolius late nodulin gene, Nodulin-45, has been analysed to identify cis-elements and trans-acting factors. Various regions of the Nodulin-45 promoter, fused to the luciferase reporter gene, were introduced into Lotus roots using an Agrobacterium rhizogenes, transformation procedure. The transgenic roots were then nodulated. The promoter region A (-172 to +13, relative to the transcription start site) was capable of directing low-level expression of the reporter gene and in a nodule-enhanced manner when compared to roots. The addition of region C (-676 to -345) resulted in a significant increase in the expression within the nodule, whilst a low level of root expression was maintained. The C region, which confers this high-level nodule expression, contains the nodule consensus motifs AAAGAT and CTCTT. When region C was ligated to a minimal promoter element from the unrelated asparaginase gene rather than the Nodulin-45 A region, nodule-enhanced expression was still apparent, but at a much lower level. Mutation of the AAAGAT element in this construct resulted in a further significant decrease of expression. Gel retardation assays revealed that a factor from lupin nodule nuclear extracts interacted with two sequences of the C region. The binding of the factor to both of these regions could be removed by the addition of an oligonucleotide containing the AT-rich binding site for the soybean factor NAT2. This suggests that the lupin factor identified here is a NAT2 homologue. No factor binding was observed to the AAAGAT or CTCTT elements present in the C region.
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Affiliation(s)
- R C Macknight
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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46
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Marsolier MC, Debrosses G, Hirel B. Identification of several soybean cytosolic glutamine synthetase transcripts highly or specifically expressed in nodules: expression studies using one of the corresponding genes in transgenic Lotus corniculatus. PLANT MOLECULAR BIOLOGY 1995; 27:1-15. [PMID: 7865779 DOI: 10.1007/bf00019174] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A DNA fragment containing sequences hybridizing to the 5' region of GS15, a gene encoding soybean cytosolic glutamine synthetase, was isolated from a soybean genomic library. Mapping and partial sequence analysis of the genomic clone revealed that it encodes a cytosolic GS gene, GS21, which is different from GS15. In parallel, a number of cDNA clones encoding cytosolic GS were isolated using the coding region of pGS20 as a probe (pGS20 is a cDNA clone which corresponds to a transcript of the GS15 gene). Two new full-length cDNAs designated pGS34 and pGS38 were isolated and sequenced. In the 5' non-coding region a strong homology was found between the two clones and the GS21 gene. However, none of these sequences were identical, which suggests that there are at least three members in this group of genes. In order to determine their relative levels of transcription, specific sequences from pGS34, pGS38 and GS21 were used in an RNAse protection assay. This experiment clearly showed that GS21 and the gene encoding pGS38 are specifically expressed in young or mature nodules, whereas the gene encoding pGS34 is highly transcribed in nodules and constitutively expressed at a lower level in other soybean organs. In order to further analyse the molecular mechanisms controlling GS21 transcription, different fragments of the promoter region were fused to the Escherichia coli reporter gene encoding beta-glucuronidase (GUS) and the constructs were introduced into Lotus corniculatus via Agrobacterium rhizogenes-mediated transformation. Analysis of GUS activity showed that the GS21 promoter-GUS constructs were expressed in the vasculature of all vegetative organs. This result is discussed in relation to species-specific metabolic and developmental characteristics of soybean and Lotus.
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Affiliation(s)
- M C Marsolier
- Laboratoire du Métabolisme et de la Nutrition des Plantes, INRA, Centre de Versailles, France
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47
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Carsolio C, Campos F, Sánchez F, Rocha-Sosa M. The expression of a chimeric Phaseolus vulgaris nodulin 30-GUS gene is restricted to the rhizobially infected cells in transgenic Lotus corniculatus nodules. PLANT MOLECULAR BIOLOGY 1994; 26:1995-2001. [PMID: 7858234 DOI: 10.1007/bf00019510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In Phaseolus vulgaris there is a nodulin family, Npv30, of ca. 30 kDa, as detected in an in vitro translation assay [2]. We isolated a gene (npv30-1) for one of the members of this family. The nucleotide sequence of the promoter of npv30-1 contains nodule-specific motifs common to other late nodulin genes. The promoter was fused to the GUS reporter gene; this chimeric fusion was introduced into Lotus corniculatus via Agrobacterium rhizogenes transformation. GUS activity was only detected in the infected cells of the nodules of transgenic plants. By contrast, the expression of a 35S-GUS construct was restricted to the uninfected cells and the vascular tissue.
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Affiliation(s)
- C Carsolio
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mor
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48
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Vincze E, Reeves JM, Lamping E, Farnden KJ, Reynolds PH. Repression of the L-asparaginase gene during nodule development in Lupinus angustifolius. PLANT MOLECULAR BIOLOGY 1994; 26:303-311. [PMID: 7948878 DOI: 10.1007/bf00039541] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Upon the establishment of an effective nitrogen-fixing symbiosis in amide-transporting plants the enzymatic activity and transcript levels of L-asparaginase are dramatically decreased. This decrease in L-asparaginase activity is essential for the correct functioning of the Rhizobium-legume symbiosis in lupin in which asparagine, synthesized from recently fixed nitrogen, is exported to aerial parts of the plant for use in growth and development. Concomitant with this decrease in L-asparaginase transcript a DNA-binding protein was detected in the nodules. This binding protein was not detectable in ineffective nodules, in nodules treated with nitrate, or in root tips, mature roots, developing flowers or developing seeds. The DNA-binding activity was shown to interact with a 59 bp sequence proximal to the transcription start site. Within this sequence a CTAAAAT direct repeat and a ACTGT/TGTCA incomplete inverted repeat were implicated in the binding of protein to the DNA by DNase I protection experiments. Competitive binding studies with synthesized binding sites were consistent with the CTAAAAT/TGTCA sequence pair proximal to the transcription start site having the highest affinity for the DNA-binding protein. We postulate that this DNA-binding protein is associated with repression of L-asparaginase gene expression in mature lupin root nodules.
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Affiliation(s)
- E Vincze
- Plant Improvement Division, Horticulture and Food Research Institute of New Zealand, Palmerston North
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49
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Forde BG. AT-rich elements (ATREs) in the promoter regions of nodulin and other higher plant genes: a novel class of cis-acting regulatory element? Results Probl Cell Differ 1994; 20:87-103. [PMID: 8036322 DOI: 10.1007/978-3-540-48037-2_4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- B G Forde
- Biochemistry and Physiology Department, Rothamsted Experimental Station, Institute of Arable Crops Research, Harpenden, Herts, UK
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50
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Boroń LJ, Legocki AB. Cloning and characterization of a nodule-enhanced glutamine synthetase-encoding gene from Lupinus luteus. Gene X 1993; 136:95-102. [PMID: 7904975 DOI: 10.1016/0378-1119(93)90452-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Glutamine synthetase (GS)-encoding genes in Lupinus luteus constitute a small family of genes showing different expression patterns [Boroń et al., Acta Biochim. Polon. 36 (1989) 295-301]. One member of this family, the LlNGS1 gene, is strongly induced in root nodules close to the onset of nitrogen fixation and is referred to as a nodule-enhanced GS gene. We present here the structure of the nodule-enhanced LlNGS1 gene, the first gene of this class which has been sequenced. LlNGS1 is composed of twelve exons and shows structural similarity to the GS gene from Medicago sativa, indicating structure conservation of GS genes in legumes. Comparison of protein coding regions, as well as 5'-untranslated regions derived from LlNGS1 and a Lupinus angustifolius pGS5 GS cDNA clone [Grant et al., Plant Mol. Biol. 13 (1989) 481-490], revealed a high degree of shared identity between both genes, indicating that they are orthologous. The sequence of the LlNGS1 5'-flanking region (2.3 kb) contains several elements implicated in regulation of nodulin genes, as well as other characteristic DNA motifs. RNA blot hybridization analysis carried out using a probe corresponding to the LlNGS1 3'-untranslated region revealed that this gene is also transcribed in leaves, but at a barely detectable level.
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Affiliation(s)
- L J Boroń
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań
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