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Prasad G, Mittal S, Kumar A, Chauhan D, Sahu TK, Kumar S, Singh R, Yadav MC, Singh AK. Transcriptome Analysis of Bread Wheat Genotype KRL3-4 Provides a New Insight Into Regulatory Mechanisms Associated With Sodicity (High pH) Tolerance. Front Genet 2022; 12:782366. [PMID: 35222517 PMCID: PMC8864244 DOI: 10.3389/fgene.2021.782366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/14/2021] [Indexed: 11/24/2022] Open
Abstract
Globally, sodicity is one of the major abiotic stresses limiting the wheat productivity in arid and semi-arid regions. With due consideration, an investigation of the complex gene network associated with sodicity stress tolerance is required to identify transcriptional changes in plants during abiotic stress conditions. For this purpose, we sequenced the flag leaf transcriptome of a highly tolerant bread wheat germplasm (KRL 3-4) in order to extend our knowledge and better understanding of the molecular basis of sodicity tolerance. A total of 1,980 genes were differentially expressed in the flag leaf due to sodicity stress. Among these genes, 872 DEGs were upregulated and 1,108 were downregulated. Furthermore, annotation of DEGs revealed that a total of 1,384 genes were assigned to 2,267 GO terms corresponding to 502 (biological process), 638 (cellular component), and 1,127 (molecular function). GO annotation also revealed the involvement of genes related to several transcription factors; the important ones are expansins, peroxidase, glutathione-S-transferase, and metal ion transporters in response to sodicity. Additionally, from 127 KEGG pathways, only 40 were confidently enriched at a p-value <0.05 covering the five main KEGG categories of metabolism, i.e., environmental information processing, genetic information processing, organismal systems, and cellular processes. Most enriched pathways were prioritized using MapMan software and revealed that lipid metabolism, nutrient uptake, and protein homeostasis were paramount. We have also found 39 SNPs that mapped to the important sodicity stress-responsive genes associated with various pathways such as ROS scavenging, serine/threonine protein kinase, calcium signaling, and metal ion transporters. In a nutshell, only 19 important candidate genes contributing to sodicity tolerance in bread wheat were identified, and these genes might be helpful for better understanding and further improvement of sodicity tolerance in bread wheat.
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Affiliation(s)
- Geeta Prasad
- Division of Genomic Resources, ICAR-NBPGR, New Delhi, India
| | - Shikha Mittal
- Division of Genomic Resources, ICAR-NBPGR, New Delhi, India
| | - Arvind Kumar
- ICAR-Central Soil Salinity Research Institute, Karnal, India
| | - Divya Chauhan
- Division of Genomic Resources, ICAR-NBPGR, New Delhi, India
| | | | - Sundeep Kumar
- Division of Genomic Resources, ICAR-NBPGR, New Delhi, India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-NBPGR, New Delhi, India
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Islam MS, Hasan MS, Hasan MN, Prodhan SH, Islam T, Ghosh A. Genome-wide identification, evolution, and transcript profiling of Aldehyde dehydrogenase superfamily in potato during development stages and stress conditions. Sci Rep 2021; 11:18284. [PMID: 34521910 PMCID: PMC8440639 DOI: 10.1038/s41598-021-97691-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 08/09/2021] [Indexed: 02/08/2023] Open
Abstract
The Aldehyde dehydrogenase (ALDH) superfamily comprises a group of enzymes involved in the scavenging of toxic aldehyde molecules by converting them into their corresponding non-toxic carboxylic acids. A genome-wide study in potato identified a total of 22 ALDH genes grouped into ten families that are presented unevenly throughout all the 12 chromosomes. Based on the evolutionary analysis of ALDH proteins from different plant species, ALDH2 and ALDH3 were found to be the most abundant families in the plant, while ALDH18 was found to be the most distantly related one. Gene expression analysis revealed that the expression of StALDH genes is highly tissue-specific and divergent in various abiotic, biotic, and hormonal treatments. Structural modelling and functional analysis of selected StALDH members revealed conservancy in their secondary structures and cofactor binding sites. Taken together, our findings provide comprehensive information on the ALDH gene family in potato that will help in developing a framework for further functional studies.
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Affiliation(s)
- Md Sifatul Islam
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Md Soyib Hasan
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Md Nazmul Hasan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Shamsul H Prodhan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh
| | - Tahmina Islam
- Department of Botany, University of Dhaka, Dhaka, 3114, Bangladesh
| | - Ajit Ghosh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh.
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Lu Y, Wu J, Wang R, Yan Y. Identification of stress defensive proteins in common wheat- Thinopyron intermedium translocation line YW642 developing grains via comparative proteome analysis. BREEDING SCIENCE 2020; 70:517-529. [PMID: 33603547 PMCID: PMC7878943 DOI: 10.1270/jsbbs.19133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 06/08/2020] [Indexed: 06/12/2023]
Abstract
Thinopyrum intermedium (2n = 6x = 42, E1E1E2E2XX) serves as an important gene source of desirable traits for genetic improvement of wheat cultivars resistant to stresses. This study used the comparative proteomic approach to identify stress defense related proteins in the developing grains of common wheat (Zhongmai 8601)-Thinopyron intermedium 7XL/7DS translocation line YW642 and to explore their potential values for improving wheat stress resistance. Two-dimensional electrophoresis identified 124 differentially accumulated protein spots representing 100 unique proteins, which mainly participated in stress defense, energy metabolism, protein metabolism and folding and storage protein synthesis. Among these, 16 were unique and 35 were upregulated in YW642. The upregulated DAPs were mainly involved in biotic and abiotic stress defense. Further cis-elements analysis of these stress-related DAP genes revealed that phytohormone responsive elements such as ABREs, G-box, CGTCA-motif and TGACG-motif, and environment responsive element As-1 were particularly abundant, which could play important roles in response to various stressors. Transcription expression analysis by RNA-seq and qRT-PCR demonstrated a large part of the stress-related DAP genes showed an upregulated expression in the early-to-middle stages of grain development. Our results proved that Thinopyron intermedium contains abundant stress responsive proteins that have potential values for the genetic improvement of wheat stress resistance.
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Affiliation(s)
- Yuxia Lu
- College of Life Science, Capital Normal University, Beijing, XisanhuanBeilu 105, 100048 Beijing, P.R. China
| | - Jisu Wu
- College of Life Science, Capital Normal University, Beijing, XisanhuanBeilu 105, 100048 Beijing, P.R. China
| | - Ruomei Wang
- College of Life Science, Capital Normal University, Beijing, XisanhuanBeilu 105, 100048 Beijing, P.R. China
| | - Yueming Yan
- College of Life Science, Capital Normal University, Beijing, XisanhuanBeilu 105, 100048 Beijing, P.R. China
- Hubei Collaborative Innovation Center for Grain Industry (HCICGI), Yangtze University, 434023 Jingzhou, P.R. China
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Cherenkov P, Novikova D, Omelyanchuk N, Levitsky V, Grosse I, Weijers D, Mironova V. Diversity of cis-regulatory elements associated with auxin response in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:329-339. [PMID: 28992117 PMCID: PMC5853796 DOI: 10.1093/jxb/erx254] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 07/06/2017] [Indexed: 05/20/2023]
Abstract
The phytohormone auxin regulates virtually every developmental process in land plants. This regulation is mediated via de-repression of DNA-binding auxin response factors (ARFs). ARFs bind TGTC-containing auxin response cis-elements (AuxREs), but there is growing evidence that additional cis-elements occur in auxin-responsive regulatory regions. The repertoire of auxin-related cis-elements and their involvement in different modes of auxin response are not yet known. Here we analyze the enrichment of nucleotide hexamers in upstream regions of auxin-responsive genes associated with auxin up- or down-regulation, with early or late response, ARF-binding domains, and with different chromatin states. Intriguingly, hexamers potentially bound by basic helix-loop-helix (bHLH) and basic leucine zipper (bZIP) factors as well as a family of A/T-rich hexamers are more highly enriched in auxin-responsive regions than canonical TGTC-containing AuxREs. We classify and annotate the whole spectrum of enriched hexamers and discuss their patterns of enrichment related to different modes of auxin response.
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Affiliation(s)
| | - Daria Novikova
- Novosibirsk State University, Russian Federation
- Institute of Cytology and Genetics, Russian Federation
- Department of Agrotechnology and Food Sciences, Subdivision Biochemistry, Wageningen University and Research Center, The Netherlands
| | - Nadya Omelyanchuk
- Novosibirsk State University, Russian Federation
- Institute of Cytology and Genetics, Russian Federation
| | - Victor Levitsky
- Novosibirsk State University, Russian Federation
- Institute of Cytology and Genetics, Russian Federation
| | - Ivo Grosse
- Novosibirsk State University, Russian Federation
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Germany
| | - Dolf Weijers
- Department of Agrotechnology and Food Sciences, Subdivision Biochemistry, Wageningen University and Research Center, The Netherlands
- Correspondence: or
| | - Victoria Mironova
- Novosibirsk State University, Russian Federation
- Institute of Cytology and Genetics, Russian Federation
- Correspondence: or
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Xu Y, Wang Y, Mattson N, Yang L, Jin Q. Genome-wide analysis of the Solanum tuberosum (potato) trehalose-6-phosphate synthase (TPS) gene family: evolution and differential expression during development and stress. BMC Genomics 2017; 18:926. [PMID: 29191157 PMCID: PMC5710090 DOI: 10.1186/s12864-017-4298-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 11/13/2017] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Trehalose-6-phosphate synthase (TPS) serves important functions in plant desiccation tolerance and response to environmental stimuli. At present, a comprehensive analysis, i.e. functional classification, molecular evolution, and expression patterns of this gene family are still lacking in Solanum tuberosum (potato). RESULTS In this study, a comprehensive analysis of the TPS gene family was conducted in potato. A total of eight putative potato TPS genes (StTPSs) were identified by searching the latest potato genome sequence. The amino acid identity among eight StTPSs varied from 59.91 to 89.54%. Analysis of dN/dS ratios suggested that regions in the TPP (trehalose-6-phosphate phosphatase) domains evolved faster than the TPS domains. Although the sequence of the eight StTPSs showed high similarity (2571-2796 bp), their gene length is highly differentiated (3189-8406 bp). Many of the regulatory elements possibly related to phytohormones, abiotic stress and development were identified in different TPS genes. Based on the phylogenetic tree constructed using TPS genes of potato, and four other Solanaceae plants, TPS genes could be categorized into 6 distinct groups. Analysis revealed that purifying selection most likely played a major role during the evolution of this family. Amino acid changes detected in specific branches of the phylogenetic tree suggests relaxed constraints might have contributed to functional divergence among groups. Moreover, StTPSs were found to exhibit tissue and treatment specific expression patterns upon analysis of transcriptome data, and performing qRT-PCR. CONCLUSIONS This study provides a reference for genome-wide identification of the potato TPS gene family and sets a framework for further functional studies of this important gene family in development and stress response.
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Affiliation(s)
- Yingchun Xu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanjie Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Neil Mattson
- Horticulture Section, School of Integrative Plant Science, Cornell University, 134A Plant Science Bldg, Ithaca, NY, 14853, USA
| | - Liu Yang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210095, China
| | - Qijiang Jin
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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Banerjee A, Roychoudhury A. Abscisic-acid-dependent basic leucine zipper (bZIP) transcription factors in plant abiotic stress. PROTOPLASMA 2017; 254:3-16. [PMID: 26669319 DOI: 10.1007/s00709-015-0920-4] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 12/01/2015] [Indexed: 05/21/2023]
Abstract
One of the major causes of significant crop loss throughout the world is the myriad of environmental stresses including drought, salinity, cold, heavy metal toxicity, and ultraviolet-B (UV-B) rays. Plants as sessile organisms have evolved various effective mechanism which enable them to withstand this plethora of stresses. Most of such regulatory mechanisms usually follow the abscisic-acid (ABA)-dependent pathway. In this review, we have primarily focussed on the basic leucine zipper (bZIP) transcription factors (TFs) activated by the ABA-mediated signalosome. Upon perception of ABA by specialized receptors, the signal is transduced via various groups of Ser/Thr kinases, which phosphorylate the bZIP TFs. Following such post-translational modification of TFs, they are activated so that they bind to specific cis-acting sequences called abscisic-acid-responsive elements (ABREs) or GC-rich coupling elements (CE), thereby influencing the expression of their target downstream genes. Several in silico techniques have been adopted so far to predict the structural features, recognize the regulatory modification sites, undergo phylogenetic analyses, and facilitate genome-wide survey of TF under multiple stresses. Current investigations on the epigenetic regulation that controls greater accessibility of the inducible regions of DNA of the target gene to the bZIP TFs exclusively under stress situations, along with the evolved stress memory responses via genomic imprinting mechanism, have been highlighted. The potentiality of overexpression of bZIP TFs, either in a homologous or in a heterologous background, in generating transgenic plants tolerant to various abiotic stressors have also been addressed by various groups. The present review will provide a coherent documentation on the functional characterization and regulation of bZIP TFs under multiple environmental stresses, with the major goal of generating multiple-stress-tolerant plant cultivars in near future.
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Affiliation(s)
- Aditya Banerjee
- Post Graduate Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata, 700016, West Bengal, India
| | - Aryadeep Roychoudhury
- Post Graduate Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata, 700016, West Bengal, India.
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Moumeni A, Satoh K, Venuprasad R, Serraj R, Kumar A, Leung H, Kikuchi S. Transcriptional profiling of the leaves of near-isogenic rice lines with contrasting drought tolerance at the reproductive stage in response to water deficit. BMC Genomics 2015; 16:1110. [PMID: 26715311 PMCID: PMC4696290 DOI: 10.1186/s12864-015-2335-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 12/19/2015] [Indexed: 02/05/2023] Open
Abstract
Background Drought tolerance is a complex quantitative trait that involves the coordination of a vast array of genes belonging to different pathways. To identify genes related to the drought-tolerance pathway in rice, we carried out gene-expression profiling of the leaves of near-isogenic lines (NILs) with similar genetic backgrounds and different set of QTLs but contrasting drought tolerance levels in response to long-term drought-stress treatments. This work will help differentiate mechanisms of tolerance in contrasting NILs and accelerate molecular breeding programs to improve drought tolerance in this crop. Results The two pairs of rice NILs, developed at the International Rice Research Institute, along with the drought-susceptible parent, IR64, showed distinct gene-expression profiles in leaves under different water-deficit (WD) treatments. Drought tolerance in the highly drought-tolerant NIL (DTN), IR77298-14-1-2-B-10, could be attributed to the up-regulation of genes with calcium ion binding, transferase, hydrolase and transcription factor activities, whereas in the moderate DTN, IR77298-5-6-B-18, genes with transporter, catalytic and structural molecule activities were up-regulated under WD. In IR77298-14-1-2-B-10, the induced genes were characterized by the presence of regulatory motifs in their promoters, including TGGTTAGTACC and ([CT]AAC[GT]G){2}, which are specific to the TFIIIA and Myb transcription factors, respectively. In IR77298-5-6-B-18, promoters containing a GCAC[AG][ACGT][AT]TCCC[AG]A[ACGT]G[CT] motif, common to MADS(AP1), HD-ZIP, AP2 and YABBY, were induced, suggesting that these factors may play key roles in the regulation of drought tolerance in these two DTNs under severe WD. Conclusions We report here that the two pairs of NILs with different levels of drought tolerance may elucidate potential mechanisms and pathways through transcriptome data from leaf tissue. The present study serves as a resource for marker discovery and provides detailed insight into the gene-expression profiles of rice leaves, including the main functional categories of drought-responsive genes and the genes that are involved in drought-tolerance mechanisms, to help breeders identify candidate genes (both up- and down-regulated) associated with drought tolerance and suitable targets for manipulating the drought-tolerance trait in rice. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2335-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ali Moumeni
- Rice Research Institute of Iran, Mazandaran Branch, Agricultural Research, Education and Extension Organization (AREEO), PO Box 145, Postal Code 46191-91951, Km8 Babol Rd., Amol, Mazandaran, Iran.
| | - Kouji Satoh
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Kan'non dai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan.
| | - Ramiah Venuprasad
- International Rice Research Institute, DAPO Box 7777, Metro Manila, 1301, Philippines. .,Africa Rice Centre (AfricaRice), Ibadan station, c/o IITA, PMB 5320 Oyo road, Ibadan, Nigeria.
| | - Rachid Serraj
- International Rice Research Institute, DAPO Box 7777, Metro Manila, 1301, Philippines. .,Agricultural Research (CGIAR ISPC), FAO, Rome, Italy.
| | - Arvind Kumar
- International Rice Research Institute, DAPO Box 7777, Metro Manila, 1301, Philippines.
| | - Hei Leung
- International Rice Research Institute, DAPO Box 7777, Metro Manila, 1301, Philippines.
| | - Shoshi Kikuchi
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Kan'non dai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan.
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Nuruzzaman M, Sharoni AM, Satoh K, Karim MR, Harikrishna JA, Shimizu T, Sasaya T, Omura T, Haque MA, Hasan SMZ, Ahmad A, Kikuchi S. NAC transcription factor family genes are differentially expressed in rice during infections with Rice dwarf virus, Rice black-streaked dwarf virus, Rice grassy stunt virus, Rice ragged stunt virus, and Rice transitory yellowing virus. FRONTIERS IN PLANT SCIENCE 2015; 6:676. [PMID: 26442000 PMCID: PMC4563162 DOI: 10.3389/fpls.2015.00676] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 08/15/2015] [Indexed: 05/17/2023]
Abstract
Expression levels of the NAC gene family were studied in rice infected with Rice dwarf virus (RDV), Rice black-streaked dwarf virus (RBSDV), Rice grassy stunt virus (RGSV), Rice ragged stunt virus (RRSV), and Rice transitory yellowing virus (RTYV). Microarray analysis showed that 75 (68%) OsNAC genes were differentially regulated during infection with RDV, RBSDV, RGSV, and RRSV compared with the control. The number of OsNAC genes up-regulated was highest during RGSV infection, while the lowest number was found during RTYV infection. These phenomena correlate with the severity of the syndromes induced by the virus infections. Most of the genes in the NAC subgroups NAC22, SND, ONAC2, ANAC34, and ONAC3 were down-regulated for all virus infections. These OsNAC genes might be related to the health stage maintenance of the host plants. Interestingly, most of the genes in the subgroups TIP and SNAC were more highly expressed during RBSDV and RGSV infections. These results suggested that OsNAC genes might be related to the responses induced by the virus infection. All of the genes assigned to the TIP subgroups were highly expressed during RGSV infection when compared with the control. For RDV infection, the number of activated genes was greatest during infection with the S-strain, followed by the D84-strain and the O-strain, with seven OsNAC genes up-regulated during infection by all three strains. The Os12g03050 and Os11g05614 genes showed higher expression during infection with four of the five viruses, and Os11g03310, Os11g03370, and Os07g37920 genes showed high expression during at least three viral infections. We identified some duplicate genes that are classified as neofunctional and subfunctional according to their expression levels in different viral infections. A number of putative cis-elements were identified, which may help to clarify the function of these key genes in network pathways.
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Affiliation(s)
- Mohammed Nuruzzaman
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological SciencesTsukuba, Japan
- Faculty of Science, Centre for Research for Biotechnology for Agriculture, Institute of Biological Sciences, University of MalayaKuala Lumpur, Malaysia
- Post Harvest Technology, School of Food Science and Technology, University Malaysia TerengganuKuala Terengganu, Malaysia
- Department of Agronomy and Agricultural Extension, Faculty of Agriculture, University of RajshahiRajshahi, Bangladesh
| | - Akhter M. Sharoni
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological SciencesTsukuba, Japan
| | - Kouji Satoh
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological SciencesTsukuba, Japan
- Research Team for Vector-Borne Plant Pathogens, National Agricultural Research CenterTsukuba, Japan
| | - Mohammad Rezaul Karim
- Faculty of Science, Centre for Research for Biotechnology for Agriculture, Institute of Biological Sciences, University of MalayaKuala Lumpur, Malaysia
| | - Jennifer A. Harikrishna
- Faculty of Science, Centre for Research for Biotechnology for Agriculture, Institute of Biological Sciences, University of MalayaKuala Lumpur, Malaysia
| | - Takumi Shimizu
- Research Team for Vector-Borne Plant Pathogens, National Agricultural Research CenterTsukuba, Japan
| | - Takahide Sasaya
- Research Team for Vector-Borne Plant Pathogens, National Agricultural Research CenterTsukuba, Japan
| | - Toshihiro Omura
- Research Team for Vector-Borne Plant Pathogens, National Agricultural Research CenterTsukuba, Japan
| | - Mohammad A. Haque
- Department of Agronomy and Agricultural Extension, Faculty of Agriculture, University of RajshahiRajshahi, Bangladesh
| | - Sayed M. Z. Hasan
- Post Harvest Technology, School of Food Science and Technology, University Malaysia TerengganuKuala Terengganu, Malaysia
| | - Aziz Ahmad
- Centre for Fundamental and Liberal Education, School of Science and Food Technology, Universiti Malaysia TerengganuKuala Terengganu, Malaysia
| | - Shoshi Kikuchi
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological SciencesTsukuba, Japan
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Singh M, Bag SK, Bhardwaj A, Ranjan A, Mantri S, Nigam D, Sharma YK, Sawant SV. Global nucleosome positioning regulates salicylic acid mediated transcription in Arabidopsis thaliana. BMC PLANT BIOLOGY 2015; 15:13. [PMID: 25604550 PMCID: PMC4318435 DOI: 10.1186/s12870-014-0404-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 12/22/2014] [Indexed: 05/09/2023]
Abstract
BACKGROUND The nucleosome positioning regulates the gene expression and many other DNA-related processes in eukaryotes. Genome-wide mapping of nucleosome positions and correlation of genome-wide nucleosomal remodeling with the changes in the gene expression can help us understanding gene regulation on genome level. RESULTS In the present study, we correlate the gene expression and the genomic nucleosomal remodeling in response to salicylic acid (SA) treatment in A. thaliana. We have mapped genome-wide nucleosomes by performing tiling microarray using 146 bp mononucleosomal template DNA. The average nucleosomal coverage is approximately 346 bp per nucleosome both under the control and the SA-treated conditions. The nucleosomal coverage is more in the coding region than in the 5' regulatory regions. We observe approximately 50% nucleosomal remodeling on SA treatment where significant nucleosomal depletion and nucleosomal enrichment around the transcription start site (TSS) occur in SA induced genes and SA repressed genes respectively in response to SA treatment. Especially in the case of the SA-induced group, the nucleosomal remodeling over the minimal promoter in response to SA is especially significant in the Non-expresser of PR1 (NPR1)-dependent genes. A detailed investigation of npr1-1 mutant confirms a distinct role of NPR1 in the nucleosome remodeling over the core promoter. We have also identified several motifs for various hormonal responses; including ABRE elements in the remodeled nucleosomal regions around the promoter region in the SA regulated genes. We have further identified that the W-box and TGACG/C motif, reported to play an important role in SA-mediated induction, are enriched in nucleosome free regions (NFRs) of the promoter region of the SA induced genes. CONCLUSIONS This is the first study reporting genome-wide effects of SA treatment on the chromatin architecture of A. thaliana. It also reports significant role of NPR1 in genome-wide nucleosomal remodeling in response to SA.
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Affiliation(s)
- Mala Singh
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India.
| | - Sumit Kumar Bag
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India.
- Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, 110 001, India.
| | - Archana Bhardwaj
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India.
- Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, 110 001, India.
| | - Amol Ranjan
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India.
| | - Shrikant Mantri
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India.
| | - Deepti Nigam
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India.
| | | | - Samir Vishwanath Sawant
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India.
- Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, 110 001, India.
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Yu X, Gao H, Zheng X, Li C, Wang J. A computational method of predicting regulatory interactions in Arabidopsis based on gene expression data and sequence information. Comput Biol Chem 2014; 51:36-41. [DOI: 10.1016/j.compbiolchem.2014.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 04/16/2014] [Accepted: 04/27/2014] [Indexed: 10/25/2022]
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Comprehensive gene expression analysis of the NAC gene family under normal growth conditions, hormone treatment, and drought stress conditions in rice using near-isogenic lines (NILs) generated from crossing Aday Selection (drought tolerant) and IR64. Mol Genet Genomics 2012; 287:389-410. [PMID: 22526427 PMCID: PMC3336058 DOI: 10.1007/s00438-012-0686-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 03/26/2012] [Indexed: 12/27/2022]
Abstract
The NAC (NAM, ATAF1/2 and CUC2) genes are plant-specific transcriptional factors known to play diverse roles in various plant developmental processes. We describe the rice (Oryza sativa) OsNAC genes expression profiles (GEPs) under normal and water-deficit treatments (WDTs). The GEPs of the OsNAC genes were analyzed in 25 tissues covering the entire life cycle of Minghui 63. High expression levels of 17 genes were demonstrated in certain tissues under normal conditions suggesting that these genes may play important roles in specific organs. We determined that 16 genes were differentially expressed under at least 1 phytohormone (NAA, GA3, KT, SA, ABA, and JA) treatment. To investigate the GEPs in the root, leaf, and panicle of three rice genotypes [e.g., 2 near-isogenic lines (NILs) and IR64], we used two NILs from a common genetic combination backcross developed by Aday Selection and IR64. WDTs were applied using the fraction of transpirable soil water at severe, mild, and control conditions. Transcriptomic analysis using a 44K oligoarray from Agilent was performed on all the tissue samples. We identified common and specific genes in all tissues from the two NILs under both WDTs, and the majority of the OsNAC genes that were activated were in the drought-tolerant IR77298-14-1-2-B-10 line compared with the drought-susceptible IR77298-14-1-2-B-13 or IR64. In IR77298-14-1-2-B-10, seventeen genes were very specific in their expression levels. Approximately 70 % of the genes from subgroups SNAC and NAM/CUC3 were activated in the leaf, but 37 % genes from subgroup SND were inactivated in the root compared with the control under severe stress conditions. These results provide a useful reference for the cloning of candidate genes from the specific subgroup for further functional analysis.
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Egelkrout E, Rajan V, Howard JA. Overproduction of recombinant proteins in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 184:83-101. [PMID: 22284713 DOI: 10.1016/j.plantsci.2011.12.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 12/06/2011] [Accepted: 12/09/2011] [Indexed: 05/21/2023]
Abstract
Recombinant protein production in microbial hosts and animal cell cultures has revolutionized the pharmaceutical and industrial enzyme industries. Plants as alternative hosts for the production of recombinant proteins are being actively pursued, taking advantage of their unique characteristics. The key to cost-efficient production in any system is the level of protein accumulation, which is inversely proportional to the cost. Levels of up to 5 g/kg biomass have been obtained in plants, making this production system competitive with microbial hosts. Increasing protein accumulation at the cellular level by varying host, germplasm, location of protein accumulation, and transformation procedure is reviewed. At the molecular level increased expression by improving transcription, translation and accumulation of the protein is critically evaluated. The greatest increases in protein accumulation will occur when various optimized parameters are more fully integrated with each other. Because of the complex nature of plants, this will take more time and effort to accomplish than has been the case for the simpler unicellular systems. However the potential for plants to become one of the major avenues for protein production appears very promising.
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Affiliation(s)
- Erin Egelkrout
- Applied Biotechnology Institute, Cal Poly Technology Park, Building 83, San Luis Obispo, CA 93407, USA
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Sharoni AM, Nuruzzaman M, Satoh K, Moumeni A, Attia K, Venuprasad R, Serraj R, Kumar A, Leung H, Islam AKMR, Kikuchi S. Comparative transcriptome analysis of AP2/EREBP gene family under normal and hormone treatments, and under two drought stresses in NILs setup by Aday Selection and IR64. Mol Genet Genomics 2011; 287:1-19. [PMID: 22102215 PMCID: PMC3249189 DOI: 10.1007/s00438-011-0659-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Accepted: 11/07/2011] [Indexed: 11/26/2022]
Abstract
The AP2/EREBP genes play various roles in developmental processes and in stress-related responses in plants. Genome-wide microarrays based on the gene expression profiles of the AP2/EREBP family were analyzed under conditions of normal growth and drought stress. The preferential expression of fifteen genes was observed in specific tissues, suggesting that these genes may play important roles in vegetative and reproductive stages of growth. A large number of redundant genes were differentially expressed following phytohormone treatments (NAA, GA3, KT, SA, JA, and ABA). To investigate the gene expression responses in the root, leaf, and panicle of three rice genotypes, two drought stress conditions were applied using the fraction of transpirable soil water (FTSW) under severe (0.2 FTSW), mild (0.5 FTSW), and control (1.0 FTSW) conditions. Following treatment, transcriptomic analysis using a 44-K oligoarray from Agilent was performed on all the tissue samples. We identified common and specific genes in all tissues from two near-isogenic lines, IR77298-14-1-2-B-10 (drought tolerant) and IR77298-14-1-2-B-13 (drought susceptible), under drought stress conditions. The majority of the genes that were activated in the IR77298-14-1-2-B-10 line were members of the AP2/EREBP gene family. Non-redundant genes (sixteen) were found in the drought-tolerant line, and four genes were selected as candidate novel reference genes because of their higher expression levels in IR77298-14-1-2-B-10. Most of the genes in the AP2, B3, and B5 subgroups were involved in the panicle under severe stress conditions, but genes from the B1 and B2 subgroups were down-regulated in the root. Of the four subfamilies, RAV exhibited the highest number of up-regulated genes (80%) in the panicle under severe stress conditions in the drought-tolerant line compared to Minghui 63 under normal conditions, and the gene structures of the RAV subfamily may be involved in the response to drought stress in the flowering stage. These results provide a useful reference for the cloning of candidate genes from the specific subgroup for further functional analysis.
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Affiliation(s)
- Akhter Most Sharoni
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602 Japan
- Department of Botany, University of Rajshahi, Rajshahi, 6205 Bangladesh
| | - Mohammed Nuruzzaman
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602 Japan
| | - Kouji Satoh
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602 Japan
| | - Ali Moumeni
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602 Japan
| | - Kotb Attia
- Graduate School of Science and Technology, Niigata University, Ikarashi-2, Niigata, 950-2181 Japan
- Centre of Excellence in Biotechnology Research, King Saud University, Riyadh, 11451 Kingdom of Saudi Arabia
| | - Ramiah Venuprasad
- Africa Rice Center (AfricaRice), Ibadan Station, c/o IITA, PMB 5320, Oyo Road, Ibadan, Nigeria
| | - Rachid Serraj
- Diversification and Sustainable Intensification of Production Systems Program (DSIPSP), International Center for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5466, Aleppo, Syria
| | - Arvind Kumar
- Plant Breeding, Genetics and Biotechnology Division (PBGB), International Rice Research Institute, DAPO Box 7777, 1301 Metro Manila, Philippines
| | - Hei Leung
- Plant Breeding, Genetics and Biotechnology Division (PBGB), International Rice Research Institute, DAPO Box 7777, 1301 Metro Manila, Philippines
| | | | - Shoshi Kikuchi
- Plant Genome Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602 Japan
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Reineke AR, Bornberg-Bauer E, Gu J. Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes. Nucleic Acids Res 2011; 39:6029-43. [PMID: 21470961 PMCID: PMC3152334 DOI: 10.1093/nar/gkr179] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 02/22/2011] [Accepted: 03/15/2011] [Indexed: 12/17/2022] Open
Abstract
The discovery of regulatory motifs embedded in upstream regions of plants is a particularly challenging bioinformatics task. Previous studies have shown that motifs in plants are short compared with those found in vertebrates. Furthermore, plant genomes have undergone several diversification mechanisms such as genome duplication events which impact the evolution of regulatory motifs. In this article, a systematic phylogenomic comparison of upstream regions is conducted to further identify features of the plant regulatory genomes, the component of genomes regulating gene expression, to enable future de novo discoveries. The findings highlight differences in upstream region properties between major plant groups and the effects of divergence times and duplication events. First, clear differences in upstream region evolution can be detected between monocots and dicots, thus suggesting that a separation of these groups should be made when searching for novel regulatory motifs, particularly since universal motifs such as the TATA box are rare. Second, investigating the decay rate of significantly aligned regions suggests that a divergence time of ~100 mya sets a limit for reliable conserved non-coding sequence (CNS) detection. Insights presented here will set a framework to help identify embedded motifs of functional relevance by understanding the limits of bioinformatics detection for CNSs.
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Affiliation(s)
| | | | - Jenny Gu
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, 48149, Münster, Germany
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Yu X, Liu T, Zheng X, Yang Z, Wang J. Prediction of regulatory interactions in Arabidopsis using gene-expression data and support vector machines. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2011; 49:280-283. [PMID: 21282061 DOI: 10.1016/j.plaphy.2011.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Revised: 12/15/2010] [Accepted: 01/02/2011] [Indexed: 05/30/2023]
Abstract
Identification of regulatory relationships between transcription factors (TFs) and their targets is a central problem in post-genomic biology. In this paper, we apply an approach based on the support vector machine (SVM) and gene-expression data to predict the regulatory interactions in Arabidopsis. A set of 125 experimentally validated TF-target interactions and 750 negative regulatory gene pairs are collected as the training data. Their expression profiles data at 79 experimental conditions are fed to the SVM to perform the prediction. Through the jackknife cross-validation test, we find that the overall prediction accuracy of our approach achieves 88.68%. Our approach could help to widen the understanding of Arabidopsis gene regulatory scheme and may offer a cost-effective alternative to construct the gene regulatory network.
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Affiliation(s)
- Xiaoqing Yu
- Department of Mathematics, Shanghai Normal University, Shanghai, China
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Dubey S, Misra P, Dwivedi S, Chatterjee S, Bag SK, Mantri S, Asif MH, Rai A, Kumar S, Shri M, Tripathi P, Tripathi RD, Trivedi PK, Chakrabarty D, Tuli R. Transcriptomic and metabolomic shifts in rice roots in response to Cr (VI) stress. BMC Genomics 2010; 11:648. [PMID: 21092124 PMCID: PMC3224690 DOI: 10.1186/1471-2164-11-648] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Accepted: 11/20/2010] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Widespread use of chromium (Cr) contaminated fields due to careless and inappropriate management practices of effluent discharge, mostly from industries related to metallurgy, electroplating, production of paints and pigments, tanning, and wood preservation elevates its concentration in surface soil and eventually into rice plants and grains. In spite of many previous studies having been conducted on the effects of chromium stress, the precise molecular mechanisms related to both the effects of chromium phytotoxicity, the defense reactions of plants against chromium exposure as well as translocation and accumulation in rice remain poorly understood. RESULTS Detailed analysis of genome-wide transcriptome profiling in rice root is reported here, following Cr-plant interaction. Such studies are important for the identification of genes responsible for tolerance, accumulation and defense response in plants with respect to Cr stress. Rice root metabolome analysis was also carried out to relate differential transcriptome data to biological processes affected by Cr (VI) stress in rice. To check whether the Cr-specific motifs were indeed significantly over represented in the promoter regions of Cr-responsive genes, occurrence of these motifs in whole genome sequence was carried out. In the background of whole genome, the lift value for these 14 and 13 motifs was significantly high in the test dataset. Though no functional role has been assigned to any of the motifs, but all of these are present as promoter motifs in the Database of orthologus promoters. CONCLUSION These findings clearly suggest that a complex network of regulatory pathways modulates Cr-response of rice. The integrated matrix of both transcriptome and metabolome data after suitable normalization and initial calculations provided us a visual picture of the correlations between components. Predominance of different motifs in the subsets of genes suggests the involvement of motif-specific transcription modulating proteins in Cr stress response of rice.
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Affiliation(s)
- Sonali Dubey
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226 001, India
| | - Prashant Misra
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226 001, India
| | - Sanjay Dwivedi
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226 001, India
| | - Sandipan Chatterjee
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226 001, India
| | - Sumit K Bag
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226 001, India
| | - Shrikant Mantri
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226 001, India
- National Agri-Food Biotechnology Institute (Department of Biotechnology, New Delhi), Mohali, Punjab, India
| | - Mehar H Asif
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226 001, India
| | - Arti Rai
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226 001, India
| | - Smita Kumar
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226 001, India
| | - Manju Shri
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226 001, India
| | - Preeti Tripathi
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226 001, India
| | - Rudra D Tripathi
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226 001, India
| | - Prabodh K Trivedi
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226 001, India
| | - Debasis Chakrabarty
- National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226 001, India
| | - Rakesh Tuli
- National Agri-Food Biotechnology Institute (Department of Biotechnology, New Delhi), Mohali, Punjab, India
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Nuruzzaman M, Manimekalai R, Sharoni AM, Satoh K, Kondoh H, Ooka H, Kikuchi S. Genome-wide analysis of NAC transcription factor family in rice. Gene 2010; 465:30-44. [PMID: 20600702 DOI: 10.1016/j.gene.2010.06.008] [Citation(s) in RCA: 432] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Revised: 06/09/2010] [Accepted: 06/16/2010] [Indexed: 12/19/2022]
Abstract
We investigated 151 non-redundant NAC genes in rice and 117 in Arabidopsis. A complete overview of this gene family in rice is presented, including gene structures, phylogenies, genome localizations, and expression profiles. We also performed a comparative analysis of these genes in rice and Arabidopsis. Conserved amino acid residues and phylogeny construction using the NAC conserved domain sequence suggest that OsNAC gene family was classified broadly into two major groups (A and B) and sixteen subgroups in rice. We presented more specific phylogenetic analysis of OsNAC proteins based on the DNA-binding domain and known gene function, respectively. Loss of introns was observed in the segmental duplication. Homologous, paralogous, and orthologous searches of rice and Arabidopsis revealed that the major functional diversification within the NAC gene family predated the divergence of monocots and dicots. The chromosomal localizations of OsNAC genes indicated nine segmental duplication events involving 18 genes; 32 non-redundant OsNAC genes were involved in tandem duplications. Expression levels of this gene family were checked under various abiotic stresses (cold, drought, submergence, laid-down submergence, osmotic, salinity and hormone) and biotic stresses [infection with rice viruses such as RSV (rice stripe virus) and RTSV (rice tungro spherical virus)]. Biotic stresses are novel work and increase the possibilities for finding the best candidate genes. A preliminary search based on our microarray (22K and 44K) data suggested that more than 45 and 26 non-redundant genes in this family were upregulated in response to abiotic and biotic stresses, respectively. All of the genes were further investigated for their stress responsiveness by RT-PCR analysis. Six genes showed preferential expression under both biotic RSV and RTSV stress. Eleven genes were upregulated by at least three abiotic treatments. Our study provides a very useful reference for cloning and functional analysis of members of this gene family in rice.
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Affiliation(s)
- Mohammed Nuruzzaman
- Plant Genome Research Unit, Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602, Japan
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Howell KA, Narsai R, Carroll A, Ivanova A, Lohse M, Usadel B, Millar AH, Whelan J. Mapping metabolic and transcript temporal switches during germination in rice highlights specific transcription factors and the role of RNA instability in the germination process. PLANT PHYSIOLOGY 2009; 149:961-80. [PMID: 19074628 PMCID: PMC2633829 DOI: 10.1104/pp.108.129874] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Accepted: 12/03/2008] [Indexed: 05/20/2023]
Abstract
Transcriptome and metabolite profiling of rice (Oryza sativa) embryo tissue during a detailed time course formed a foundation for examining transcriptional and posttranscriptional processes during germination. One hour after imbibition (HAI), independent of changes in transcript levels, rapid changes in metabolism occurred, including increases in hexose phosphates, tricarboxylic acid cycle intermediates, and gamma-aminobutyric acid. Later changes in the metabolome, including those involved in carbohydrate, amino acid, and cell wall metabolism, appeared to be driven by increases in transcript levels, given that the large group (over 6,000 transcripts) observed to increase from 12 HAI were enriched in metabolic functional categories. Analysis of transcripts encoding proteins located in the organelles of primary metabolism revealed that for the mitochondrial gene set, a greater proportion of transcripts peaked early, at 1 or 3 HAI, compared with the plastid set, and notably, many of these transcripts encoded proteins involved in transport functions. One group of over 2,000 transcripts displayed a unique expression pattern beginning with low levels in dry seeds, followed by a peak in expression levels at 1 or 3 HAI, before markedly declining at later time points. This group was enriched in transcription factors and signal transduction components. A subset of these transiently expressed transcription factors were further interrogated across publicly available rice array data, indicating that some were only expressed during the germination process. Analysis of the 1-kb upstream regions of transcripts displaying similar changes in abundance identified a variety of common sequence motifs, potential binding sites for transcription factors. Additionally, newly synthesized transcripts peaking at 3 HAI displayed a significant enrichment of sequence elements in the 3' untranslated region that have been previously associated with RNA instability. Overall, these analyses reveal that during rice germination, an immediate change in some metabolite levels is followed by a two-step, large-scale rearrangement of the transcriptome that is mediated by RNA synthesis and degradation and is accompanied by later changes in metabolite levels.
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Affiliation(s)
- Katharine A Howell
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia 6009, Australia
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Morris RT, O'Connor TR, Wyrick JJ. Osiris: an integrated promoter database for Oryza sativa L. ACTA ACUST UNITED AC 2008; 24:2915-7. [PMID: 18922805 DOI: 10.1093/bioinformatics/btn537] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
SUMMARY Rice (Oryza sativa L.) is an important model monocot and cereal crop. While the rice genome sequence has been published and annotated, relatively little is known about the transcriptional networks that regulate rice gene expression. For this reason, we have developed Osiris, a database containing promoter sequences, predicted transcription factor (TF) binding sites, gene ontology annotation and microarray expression data for 24 209 genes in the rice genome. These tools are seamlessly integrated in the Osiris web site, allowing the user to visualize TF binding sites in multiple promoters; analyze the statistical significance of enriched TF binding sites; query for genes containing similar promoter regulatory logic or gene function and visualize the microarray expression patterns of queried or selected gene sets. AVAILABILITY http://www.bioinformatics2.wsu.edu/Osiris
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Affiliation(s)
- Robert T Morris
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, USA
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