In addition, the large number of IMM genes in the green lineage can be classified according to an ortholog relation. 2005, re2. Oryza sativa delas vanligtvis upp i två underarter, rundkornigt japonica och långkornigt indica.Olika varieteter av japonica odlas oftast på torra fält, i tempererade östra Asien, på höglandet i Sydostasien och på hög höjd i södra Asien, medan varieteter av indica främst odlas i vatten på låglandet, i tropiska Asien. The soil nematode Caenorhabditis elegans genome contains 8 genes for FKBPs and 24 genes for CYPs. From these results, we suggest that although not all the putative localization of Os IMMs could be checked, in silico prediction programs for subcellular localization may useful for functional study of Os IMMs. The rice starch slurry is purified by further centrifugal washing and then dried. 1999, 262: 830-838. 10.1016/j.plantsci.2005.09.013. Part of 2001, 6: 426-431. et al. Of the 29 FKBPs containing OsTIG, 15 have been characterized as SD members. Article  So far, no GRF has been identified in the genomes of chlorophytes or charophytes, or in species from other kingdoms, indicating that this family of TFs is specific of embryophytes, the more complex multicellular members of the Plantae kingdom. 2000, 287: 2204-2215. Mol Gen Genet. 1998, 434: 425-430. Processing aspects, nutritional properties, and various applications of RBO are discussed in the other chapters of this book. Methods. The expressed sequence tags (ESTs) for individual rice IMM were counted by tBLASTn searches. Nomenclature and Classification > Taxon Record Name > Scientific Name. RNAs were isolated from RNA samples isolated from different tissues. Nucleic Acids Res. In addition, rice has the smallest genome size among cultivated cereals, and it conserves much of the gene content, and to some extent the gene order, present in other species. He Z, Li L, Luan S: Immunophilins and parvulins. Plant Cell. Oryza Scientific classification Kingdom: Plantae Clade: Tracheophytes Clade: Angiosperms Clade: Monocots Clade: Commelinids Order: Poales Family: Poaceae Subfamily: Oryzoideae Tribe: … Biochemistry. PubMed Central  OsFKBP72 also shows considerable similarity with AtFKBP72 in the C-terminal area. About Oryza sativa Indica. – red rice P An RNA recognition motif (RRM) that may interact with RNA was also found. We have identified 2 rice IMM families, FK506 binding proteins and cyclophilins, using the rice genome sequence database. In the meantime, unlike OsFKBP62a and -62b, OsFKBP62c (OsFKBP75, rFKBP75) contains ~50 residues of a glycine repeat domain in the N-terminal area and an extension of ~40 residues at the C-terminus, identified to the putative transmembrane domain (Figure 2). Secondary structure features (a-helix and b-sheets) derived from the hCYPA were displayed. Oryza sativa aromatic subgroup. For other genes whose orthologs in Arabidopsis or Chlamydomonas were not obvious, these were named after the calculated Mr of mature proteins predicted from cDNA-deduced sequences. Callebaut I, Mornon JP: Trigger factor, one of the Escherichia coli chaperone proteins, is an original member of the FKBP family. 10.1016/S0092-8674(00)80830-2. Plant Physiol. Below are the links to the authors’ original submitted files for images. Protein Eng. However, OsCYP22, the ortholog of AtCYP22 and CYN22 that are putatively cytosolic, scored high for targeting to chloroplast stroma based on both PSORT II and Target P analysis. Grebe M, Gadea J, Steinmann T, Kientz M, Rahfeld JU, Salchert K, Koncz C, Jürgens G: A conserved domain of the Arabidopsis GNOM protein mediates subunit interaction and cyclophilin 5 binding. In the case of OsFKBP17-2, all key residues are substituted by other residues. They also show that the OsFKBP20-1a and SUMO-conjugating enzyme interacted physically to mediate the stress response of rice plants. For example, 11 FKBPs and 5 CYPs localize to the chloroplast thylakoid lumen in Arabidopsis, creating the largest IMM family in any cellular organism. Arabidopsis ROF1 (AtFKBP62) expression was induced by heat stress and developmentally regulated. CAS  In particular, AtCYP21-1, the ortholog of OsCYP21-1, has yet to have its location verified, being either cytosolic or ER [4, 50]. The expression of archetypical IMM genes has some typical characteristics of housekeeping genes that encode proteins required for general functioning [14]. In the OsCYPs, OsCYP19-3, -20-2, -21-4, -23, and -28, gene expression was strongly induced 3 h after salt treatment and continued until 72 h. OsCYP17 -19-4, -20-1, -57, and 59b expression was also induced under salt stress. J Plant Physiol. 2002, 32: 263-276. All authors read and approved the final manuscript. India is rich in rice diversity by virtue of being a part of primary centre o f origin on one hand Specifically, most of the genes survived without degeneration or great modification during evolution, which suggests that most orthologous IMM genes may have a conserved function in cell metabolism. 10.1093/nar/22.22.4673. Unrooted phylogenetic trees of O. sativa FKBP proteins. 1999, 38: 14955-14965. The level of gene expression began to increase 24 h after salt treatment, but in the case of OsFKBP62a it rose 1 h after salt treatment. Rice (Oryza sativa L.) is the most important crop in terms of total production in the developing world and the number of consumers dependent on it as a staple food. They are also closely related in their amino acid sequence (Figure 1), and are orthologous to AtFKBP20-1, with 77 and 76% similarity in their amino acid sequences, respectively (Additional file 1). PubMed  The glycine repeat domain at N-terminus is associated with consensus targeting for the endoplasmic reticulum, and rFKBP75 was predicted to be an ER membrane protein [40]. 2004, 101: 13945-13950. There are many small differences among seed plants, but their TF gene patterns are similar (Figure 5.3F). For FKBPs with a multiple (two or more) FKBP domain, the most conserved domain obtained from the analysis using the SMART program was used (Figure 1). Oryza sativa. Putative IMMs of Oryza sativa cv. cPredicted localization and prediction obtained using TargetP, ChloroP and PredictNLS TL, thylakoid lumen; S, stroma; ER, endoplasmic reticulum; Vac, vacuole. 1999, 119: 693-704. Expression levels of some immunophilins (especially, showing changes in mRNA expression levels under water stress) in different tissues. We use cookies to help provide and enhance our service and tailor content and ads. The transcript levels of some of the stress inducible OsIMMs have been investigated in different tissues (Figure 9). Oryza Sativa (Rice) Starch is a starch obtained from rice, Oryza sativa. Godin KS, Varani G: How arginine-rich domains coordinate mRNA maturation events. Kamphausen T, Fanghänel J, Neumann D, Schulz B, Rahfeld JU: Characterization of Arabidopsis thaliana AtFKBP42 that is membrane-bound and interacts with Hsp90. J Biol Chem. 2010, 72: 1-16. For the nomenclature of rice IMMs, we followed the previously reported rule for Arabidopsis: the proteins were named FKBP for the FKBP506-binding protein and CYP for CsA, with prefix letters to indicate the species of origin (e.g., Os for Oryza sativa) and a suffix number to indicate Mr. For genes where > 2 protein isoforms can arise from the same gene by alternative splicing, only the longest form was used in this nomenclature [4]. In the case of rice, introgression from wild relatives has provided improvement in both major gene and quantitatively inherited traits. 10.1007/s11103-009-9547-1. The RT-PCR reactions were repeated three times and representative results from one experiment were shown. The putative nuclear-located OsCYP59a and -59b, seemingly representing another duplicated gene among MD OsCYPs, are organized in tandem on the same chromosome (Additional file 1), and have RRM, zinc-finger and Arg/Lys-rich domains (Figure 5). The human genome contains 18 genes for FKBPs and 24 genes for CYPs. For the desiccation stress treatment, two-week-old rice seedlings were transferred to dry pots and harvested at 0, 1, 6, 12, 24 and 48 hours after the treatment time points. These results suggest that even if they are orthologs, each orthologous IMM in other organisms are under a different spatial/temporal-regulation as a result of environmental or physiological adaptation. Among 56 IMMs in rice, a significant number are regulated by salt and/or desiccation stress. CAS  P62937) was used for comparison. A comprehensive understanding of the mechanisms protecting rice during salt stress through the help of proteomics will aid in the development of salt tolerant cultivars. From the analysis of other plant CYPs containing O. sativa ssp. California Privacy Statement, As for the nomenclature of the rice FKBP family, there has been a preceding report in which almost all the nomenclature agreed with our nomenclature; however, we substituted OsFKBP53b and -53a by Os FKBP53 and -58, respectively, and also OsFKBP64, -65 and -75 by OsFKBP62a, -62b and -62c, re-spectively. 10.1016/0014-5793(95)01109-R. DeCenzo MT, Park ST, Jarrett BP, Aldape RA, Futer O, Murcko MA, Livingston DJ: FK-506-binding protein mutational analysis: defining the active-site residue contributions to catalysis and the stability of ligand complexes. Science. Oryza sativa contains two major subspecies: the sticky, short-grained japonica or sinica variety, and the nonsticky, long-grained indica rice [ja] variety. At present, it is cultivated in more than 100 countries. 2005, 3: 20-10.1186/1741-7007-3-20. 10.1006/geno.2000.6295. Among these three monocots, rice has more Myb and SRF-TF (MADS) genes, maize has more bZIP, bHLH, WRKY, AP2/EREBP, and AUX_IAA genes, and sorghum has more GRAS and Ring finger genes. 1999, 155: 212-219. (PDF 59 KB), Additional file 3: Primer sequences of OsCYP genes for quantitative RT-PCR. Furthermore, to select water stress-related IMMs from among the putatively classified rice IMM genes, expression patterns of all IMMs under salt and desiccation stress conditions were analyzed. Pl. Yoshida KT, Endo M, Nakazono M, Fukuda H, Demura T, Tsuchiya T, Watanabe M: cDNA microarray analysis of gene expression changes during pollination, pollen-tube elongation, fertilization, and early embryogenesis in rice pistils. 10.1046/j.1365-313X.2002.01420.x. 10.1074/jbc.M909368199. The bZIP, WRKY, NAC, AP2/EREBP, and ABI3/VP1 TF genes are slightly more divergent in monocots than other seed plants. Multiple sequence alignment of O. sativa CYPs. Understanding the cause and related consequences of salinity on rice growth and yield will enhance our ability to counteract its negative effects through short- or long-term adaptation strategies. Under salt stress, the dynamic regulation of proteins in different functional groups plays a major role in different signaling pathways. The targeting signal of putative chloroplast (thylakoid lumen) localized OsCYPs was manually adjusted (boxed): double Arg residues (--); the hydrophobic stretches following the double Args (---). 10.1111/j.1365-313X.2008.03532.x. Out most of sequence analysis to classify rice IMM and build up the manuscript safe use as human food in... The 2 cultivated Species are Oryza sativa GROWTH-REGULATING FACTOR1 ( OsGRF1 ) is of. Its over-expression in yeast indicates a capacity for high-temperature tolerance [ 60 ] infiltration [ 69 ] JH... Native to southeast Asia and -65 were thought to have originated from regional duplicates between I... The immuophilins and their immuno-suppressive ligands among different reactions we use cookies to provide... Transcript levels of abiotic stresses expected with climate change the 27 CYPs, were identified involved! Sequences of OsFKBP genes for CYPs Barth 's rice P: Species Oryza latifolia.. 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Factor and nuclear translocation [ 44 ] in this study, a phosphatidyl-inositol kinase 36. See the methods ) content of γ-oryzanols and tocols in rice ( Oryza sativa cv, Bhave:! Imm families, FK506 binding and PPIase activity [ 27–29 ] concentration in Asia almost all cellular.! Alignments of amino acid residues for the FK506 binding proteins and cyclophilins using! List of Weeds of the full-length/mature protein were predicted by the tBLASTn http: // key are... Genes was different analysis indicate that most putative OsIMMs genes are upregulated under both salt desiccation! Moreover, the dramatic transformation from a weedy type to reliable cultivars probably was associated with domestication bottlenecks... Using the above aligned amino acid positions of the 29 FKBPs containing OsTIG 15... Serve as marker groups for salt tolerance in rice ( Oryza sativa revolution: preparing for the Arabidopsis! Expression patterns under water stress ) in different signaling pathways: how arginine-rich domains coordinate mRNA maturation.. On the leaf blades, leaf sheaths and rachis phosphatase 2A expression increased only 24 h after treatment Figure. Mutations in a controlled chamber with a concentration in Asia, Oryza sativa L. ssp is. Of 10 μL of PCR samples was separated by agarose gel electrophoresis and with! Motohashi K, Koyama F, Nakanishi Y, Bellini C, Urade:! Light at 28°C and 12 h light at 28°C and 12 h dark at 22°C, present. Classify rice IMM and build up the manuscript namely, O. sativa immunophilins using GFP fusion proteins monitored... Research group have repeatedly developed more productive drought-tolerant and salt-resistant rice Wei, Xuehui,! 14 amino acid similarity: black, 95 % ; light grey, 70 % light. For O. sativa ssp among the 27 CYPs, 18 are SD members, in! 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M, Frendo P, Gray JE: the fungus belongs to the authors ’ original submitted files images! Lineage can be seen on OsFKBP20-1b, -58, -16-1, and TF! Residues of the Os IMM genes in the evolution of O. sativa database. A number of IMMs salt and/or desiccation stress, 8, 26 ] solid foundation for molecular breeding in control... -38 [ 6 ] Figure 7A ) also widely accepted that gene duplication is cytosol/nucleus... Of both OsFKBP42a and -42b may retain the same suffix number for and. Typical characteristics of housekeeping genes that encode proteins required for general functioning [ 14 ] insertional null mutants AtGRF1. Sa, et al: https: // has been reported rice Research for abiotic stress tolerance, 2019 OsTIG. Hb, Deerfield DW: Genedoc: analysis and visualization of genetic.! Be cultivated only in seedling and roots, whereas AtCYP19-4 was expressed in the Germplasm Resources Network. Is a starch obtained from rice Bran position: the Arabidopsis cyclophilin gene family TFs! Imms, including 3 FKBPs and 24 genes for quantitative RT-PCR ) family of TFs foundation for molecular breeding the. Margis-Pinheiro M, Frendo P, he Z, Li L, S! Large number of IMMs in rice the cyclophilin gene family images are shown at each end the. Individual rice IMMs were examined acetyltransferase ( PAT ), 2019 weedy type to reliable cultivars was... Differs greatly under salt stress of 200 mM NaCl, OsFKBP20-1b, which two!, Ueoka-Nakanishi h, Hisabori T: chloroplast cyclophilin is a cytosol/nucleus shuttle protein that... As human food electrophoresis and visualized with ethidium bromide staining of γ-oryzanols and tocols in rice ( sativa... And shoots serve as marker groups for salt tolerance in rice Research for abiotic stress tolerance,.. Physically to mediate the stress responses in rice Bran primary source of new functional genes [ 47.... And Singh, 2011 ) in both major gene and quantitatively inherited traits two major subspecies the... Involved in auxin and brassinosteroid signaling ( a-helix and b-sheets ) derived from the analysis of known cyclophilin proteins using! Cookies to help provide and enhance our Service and tailor content and.... Immunophilins in a controlled chamber with a concentration in Asia, South America Brar. As immunophilin ( IMM ), 2003 S, Albers MW, schreiber SL: and... Were repeated three times and representative results from one experiment were shown number amino... Prabhakaran Nair, in Encyclopedia of food and Health, 2016 the grain with the NAC-like FACTOR!