Oryza formosana Masam. Finally, the full length of the amino acid sequences of all FKBPs was used to generate a phylogenetic tree in order to assay the evolutionary relationships among the OsFKBPs (Figure 3). 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. We have identified 2 rice IMM families, FK506 binding proteins and cyclophilins, using the rice genome sequence database. Rice is the world's largest crop and serves as a staple food for a large part of the world's human population. CAS  10.1016/S1360-1385(96)80041-0. 1998, 17: 1577-1587. Rice (Oryza sativa L.) is one of the most important staple crops, feeding almost half of the world population. Plant Physiol. OsCYP20-2 GFP protein, which contains double arginine residues and hydrophobic regions as a putative chloroplast lumenal protein, was clearly localized in chloroplasts. These results suggest that OsCYP17 occurred most recently in the evolution of O. sativa. Manage cookies/Do not sell my data we use in the preference centre. Plant Physiol. OsFKBP58 has 36% similarity to AtFKBP53 (Additional file 1) and retains 8 - 20 mer of amino acid insertion in 3 areas besides the FKBP domain, and thus the CCD domain was predicted to be between amino acids 353 and 381 (Figure 2). Vernacular names More to the point, Escherichia coli possesses 6 IMMs, including 3 FKBPs and 2 cyclophilins. 2006, 47: 720-734. Data source Beijing Genomics Institute OsFKBP44 and OsCYP17 did not show ESTs, but their expression was confirmed by RT-PCR analysis (Additional file 1). Nicholas E. Korres, ... Taghi Bararpour, in Advances in Rice Research for Abiotic Stress Tolerance, 2019. 10.1126/science.1702904. Notably, monocots and dicots are highly similar in their TF gene patterns. Otherwise, as in the case of PAS1, we infer that it is a cytosol/nucleus shuttle protein. However, the phenotype and protein composition of the thylakoid lumen in AtCYP20-2 mutants seems indistinguishable from that of the wild type plants, and it is concluded therefore that AtCYP20-2 is unrelated to its PPIase capacity [52, 53]. However, many IMMs in plants may serve a more diverse array of functions, especially in relation to photosynthesis, but may also involve a significant amount of redundancy [4]. The sequence alignment of Figure 4 (OsCYPs) was used and the phylogenetic analysis was based on the sequence alignments by ClustalX http://align.genome.jp. 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. From the analysis of other plant CYPs containing O. sativa ssp. The 29 OsFKBPs identified could be classified into single-domain (SD) members with a FKBP catalytic domain, and multiple-domain (MD) members with other functional domains in addition to a single or multiple FKBP domains (Figure 2). Most strikingly, of all genes encoding FKBPs and CYPs, a total of 12 can be deleted without seriously affecting the viability of Saccharomyces cerevisiae [11]. Plant Cell. Science. Two μg of RNA were transcribed reversely in a 20 μl reaction volume using oligo dT 14 to 18 primer (Invitrogen Life Technologies) and reverse transcriptase (SuperScript III, Invitrogen Life Technologies). The soil nematode Caenorhabditis elegans genome contains 8 genes for FKBPs and 24 genes for CYPs. 2007, 46: 9432-9442. Pl. Moreover, the diversity of IMM proteins was somewhat different for the monocot rice than for the dicot Arabidopsis. 10.1073/pnas.91.3.984. By continuing you agree to the use of cookies. (B) The Arabidopsis triple mutant grf1–grf2–grf3 has small leaves. In the case of rice, introgression from wild relatives has provided improvement in both major gene and quantitatively inherited traits. RNAs were isolated from two-week-old seedlings were exposed to drought stress and tissues were harvested at the indicated time points. In addition, a comprehensive analysis of rice IMM FKBPs and CYPs, including putative domain architecture, amino acid alignment, the conservation ratio of key amino residues for binding of immunosuppressive drugs, and phylogenetic relationships between family members, was also conducted. B.O. 10.1104/pp.118.4.1395. Semi-quantitative RT-PCR was performed with gene specific primers using cDNAs from RNA samples. 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. The GFP fusion proteins of OsFKBP20-1a and -b, predicted to be nuclear due to the C-terminal NLS sequences, were distinctly localized within the nucleus. PubMed  For the salt stress treatment, two-week-old rice seedlings were subjected to 200 mM NaCl and harvested at time courses of 0, 1, 3, 6, 12, 24, 48 and 72 hours after treatment. Japonica and ssp. 2005, 3: 20-10.1186/1741-7007-3-20. It is noteworthy that except for O. sativa ssp. Plant Physiol. This number compares well with the 29 AtCYPs for Arabidopsis and the 26 genes for Chlamydomonas, indicating that the diversity of CYPs has been maintained or even slightly increased since they were established in the photosynthetic green ancestor. 2004, 134: 1268-1282. Copyright © 2020 Elsevier B.V. or its licensors or contributors. The conservation patterns of OsFKBPs with the 14 amino acid residues of hFKBP12 were very similar to those of the Arabidopsis (Table 1) and Chlamydomonas orthologs [6]. Ultimately, the classification of putative FKBPs and CYPs in rice provides information about the evolutionary/functional significance of each FKBP and CYP based on a comparison with the relatively well studied Arabidopsis and Chlamydomonas IMMs. He Z, Li L, Luan S: Immunophilins and parvulins. Among 27 OsCYPs, 26 members could have matching orthology with a protein among Arabidopsis CYPs, whereas for only OsCYP17, we could find no obvious orthology with Arabidopsis CYPs. Rhoads AR, Friedberg F: Sequence motifs for calmodulin recognition. FEBS Lett. Also by investigating the expression of all OsFKBPs and OsCYPs under salt and desiccation stress conditions, we found that a significant number of genes were up-regulated in response to water stress. BMC Plant Biol 10, 253 (2010). Plant Physiol. Differentially expressed proteins in rice roots and shoots serve as marker groups for salt tolerance in rice. 10.1073/pnas.0405240101. Scholze C, Peterson A, Diettrich B, Luckner M: Cyclophilin isoforms from Digitalis lanata: sequences and expression during embryogenesis and stress. OsFKBP62a is expressed in leaves, stems and flowers, but not in seedlings and is extremely low in roots, whereas AtFKBP62 is expressed in all tissues. Symptoms . 10.1023/A:1005930024796. Oryza officinalis complex with nine species—the B, C, D and E genomes variously in diploid and tetraploid combinations—have contributed resistance to the dreaded brown leaf hopper, bacterial blight disease, blast, and also to yield-enhancing traits from Oryza grandiglumis (CCDD) (Yoon et al., 2006). Callebaut I, Mornon JP: Trigger factor, one of the Escherichia coli chaperone proteins, is an original member of the FKBP family. This information added broader evidence in favor of the theory that the diversity of IMMs was already established in their last common ancestor, probably close to the root of the "green" lineage of plants, but they may have continued to change and become more diverse since the completion of the "green" lineage. Cite this article. Kay JE: Structure-function relationships in FK506-binding protein (FKBP) family of peptidylprolyl cis-trans isomerases. The rice actin level was used for control. 10.1111/j.1365-313X.2008.03532.x. 10.1139/gen-42-4-646. Rice has been cultivated as a major crop for > 7000 years, and currently sustains more than half of the world's population [22]. Gopalan G, He Z, Balmer Y, Romano P, Gupta R, Héroux A, Buchanan BB, Swaminathan K, Luan S: Structural analysis uncovers a role for redox in regulating FKBP13, an immnunophilin of the chloroplast thylakoid lumen. However, few studies and little detailed and accurate information of root characteristics were reported in fine-rooted plants like rice (Oryza sativa L.). Lu R, Martin-Hernández AM, Peart JR, Malcuit I, Baulcombe DC: "Virus-induced gene silencing in plants". As a putative ER-targeting protein, OsFKBP15-1-GFP protein seemed to be localized in the ER, but we were unable to use a specific marker protein in this study. 2000, 68: 167-178. Rice roots function as the primary site for salinity perception, transmitting salt signals to the shoots for proper salt response and adaptation of the entire plant. As with OsCYPs induced under salt stress, desiccation inducing OsCYPs also are composed of CYPs targeted to the various cellular organs. 10.1128/EC.4.2.230-241.2005. Rubin GM, et al: Comparative genomics of the eukaryotes. In addition, their expression levels responding to the water-stress have been analyzed in different tissues, and some subcellular IMMs located by means of tagging with GFP protein. Cell. naindayegan daytoy iti kalaka a henetiko a mabaliwan, ken maysa a modelo nga organismo para iti sereal a biolohia The precise function of the trigger factor in the chloroplast remains unknown, but it is a PPIase and chaperone associated with the ribosome that is involved in the early steps of protein folding [45]. Nature. AtFKBP72 (PAS1) is involved in the control of cell proliferation and differentiation during plant development [43, 44]. From these results, we suggest that At/OsCYP20-2 maintains the homeostatic state of thylakoid lumen under stress, although it may be unrelated to its PPIase activity. The human genome contains 42 (18 FKBPs and 24 CYPs). O. rufipogon is a perennial type found in tropical and subtropical Asia, South America and Australia. The protein targeting signal and subcellular location of the IMMs were predicted using several programs, such as PSORT http://psort.ims.u-tokyo.ac.jp, TargetP http://www.cbs.dtu.dk/services/TargetP/, SignalP http://www.cbs.dtu.dk/services/SignalP/, ChloroP http://www.cbs.dtu.dk/services/ChloroP/, and PredictNLS http://www.predictprotein.org/ for cross-confirmation. Sequence analysis of OsGRF1 homologs highlighted two highly conserved protein domains: the QLQ (Gln, Leu, Gln), involved in protein–protein interactions, and the WRC (Trp, Arg, Cys), containing a putative nuclear localization signal and a DNA-binding domain (Figure 17.1A and C). g, hThe Mr and isoelectric point of the full-length/mature protein were predicted by Compute pI/Mw tool http://www.expasy.ch/tools/pi_tool.html. EMBNET NEWS. In addition, many of the genes upregulated by water stress offer the possibility of manipulating the stress responses in rice. FKBP and CYP proteins in rice (Oryza sativa cv. 10.1146/annurev.biochem.72.121801.161720. OsFKBP44 has a long N-terminal area containing two internal repeat domains and a FKBP domain, showing some degree of similarity to AtFKBP15-3 (data not shown). In addition, OsCYP17 forms a separate branch within clade I of the phylogenic tree (Figure 6). 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. Japonica were identified via BLAST searching of the Rice Genome Annotation Project database http://rice.plantbiology.msu.edu using the amino acid sequence of AtFKBP12 for FKBPs and AtCYP18-1 for CYPs as the query. Furthermore, most of the chloroplast IMMs in both plants has a putative ortholog relation, which indicates that they may have a conserved function in relation to photosynthesis. The strongest salt induction pattern can be seen on OsFKBP20-1b, which is rarely expressed in the absence of stress (Figure 7A). Fisher G, Wittmann-Liebold B, Lang K, Kiefhaber T, Schmid FX: Cyclophilin and the peptidyl-prolyl cis-trans isomerase are probably identical proteins. Article  Google Scholar. 10.1126/science.1068275. A HIGH-POLYMERIC CARBOHYDRATE MATERIAL PRIMARILY COMPOSED OF AMYLOPECTIN AND AMYLOSE. PubMed Central  Indica using the GRAMENE and NCBI database, we conclude that the 670 amino acid from the NCBI database is probably correct. MD AtFKBP53 and a SD AtFKBP15-3 showed high sequence similarity, but also that rice lacks an ortholog of AtFKBP15-3, suggesting that these proteins (OsFKBP44 and AtFKBP15-3) also originated from Chlamydomonas FKB53, but that duplication of two proteins occurred after the lineage divergence of the two plants from a common ancestor. 333 1753 . Among the desiccation affected OsCYPs, OsCYP19-2, -20-2, -21-4, and -57 showed increased expression 6 h after stress, but only OsCYP59b showed a change in the induced expression at 24 h after desiccation, being notably similar to salt stress response (Figure 8B). However, the number of IMMs in different organisms differs greatly. Different tissues of the rice (6-day-old seedlings, leaves, stems, roots and flowers) were collected and frozen in liquid nitrogen for RNA extraction. Oryza sativa - Taxon details on Integrated Taxonomic Information System (ITIS). They are collectively referred to as immunophilin (IMM), being present in almost all cellular organs. 1999, 42: 646-655. 1999, 262: 830-838. Bedford MT, Frankel A, Yaffe MB, Clarke S, Leder P, Richard S: Arginine methylation inhibits the binding of proline-rich ligands to Src homology 3, but not WW, domains. RNA Biol. Plant Mol Biol. 1753; Hook. Stoller G, Rücknagel KP, Nierhaus KH, Schmid FX, Fischer G, Rahfeld JU: A ribosome-associated peptidyl-prolyl cis/trans isomerase identified as the trigger factor. 2004, 134: 101-117. CAS  As the OsCYP19-2 sequence has not any a signal peptide for subcellular localization (according to the database), the GFP fusion protein was also located in the cytosol. The other functional domains such as tetrapeptide repeats (TPR), Arg/Lys amino acids rich domain (gray background box), coiled coil domain (CCD), internal repeats (RPT) and Calmodulin-binding motif (CaM) are indicated separately. P62937) was used for comparison. 10.1074/jbc.M909368199. 10.1046/j.1365-313X.2002.01420.x. Google Scholar. 1997, 11: 331-340. Privacy Among them, OsFKBP53 and -58 contain highly charged domains, putative nuclear targeting signals in the N-terminal regions, and a single FKBP domain (Figure 2). Unrooted phylogenetic trees of O. sativa CYP proteins. 10.1007/s11103-009-9547-1. The OsIMMs FKBP15-1, FKBP20-1a and FKBP20-1b, CYP19-2, and CYP20-2 cDNA fragments corresponding to the 154, 186, 185, 171, 247, and amino acids were cloned into the pCAMBIA1302 plasmids using BglII and SpeI sites to generate the OsIMMs-GFP fusion proteins respectively. Escherichia coli contains 6 IMMs, the yeast genome contains 12 (4 genes for FKBPs and 8 genes for CYPs), Drosophila melanogaster contains 21 ones (7 FKBPs and 14 CYPs), and Caenorhabditis elegans contains 25 (8 FKBPs and 17 CYPs). The 2 cultivated species are Oryza sativa and Oryza glaberrima. 10.1016/S0014-5793(98)01028-X. 2002, 296: 92-100. j, kOrthologous immunophilin and % identity (ID) were analysed by blastp http://www.ncbi.nlm.nih.gov/ of the NCBI database of the complete proteome of A. thaliana and C. reinhardtii: IP, immunophilin. Brink S, Bogsch EG, Edwards WR, Hynds PJ, Robinson C: Targeting of thylakoid proteins by the ΔpH-driven twin-arginine transduction pathway requires a specific signal in the hydrophobic domain in conjunction with the twin-arginine motif. Furthermore, the tissue specific expression of water stress responding Os IMMs and the visual localization of some of these IMMs were examined. Crude Rice Bran Oil is non-edible due to the large amounts of … It also does not have an ortholog in Chlamydomonas, suggesting it appeared after Chlamydomonas (Additional file 1 and Table 2). The targeting signal of putative chloroplast (thylakoid lumen) localized OsFKBPs was manually adjusted (boxed): double Arg residues (--); the hydrophobic stretches following the double Args (---). Plant Physiol. Oryza sativa temperate japonica subgroup. Plants were grown in a controlled chamber with a photoperiod of 12 h light at 28°C and 12 h dark at 22°C. 1996, 1: 95-99. indica and O. sativa var japonica ecotype in temperate regions are clearly separated having diverged around 7 million years ago with different ancestral gene pools (Brar and Singh, 2011). Among SD CYPs showing significant phylogenic diversity in amino acids for CsA binding mitochondria-located, OsCYP21-4 is not conserved in 7 amino acids for PPIase and shows 54% identity in the amino acid sequence with AtCYP21-4. The rice grain consists of a hull and an edible berry (caryopsis). The analysis indicated many of the genes (OsFKBP 20-1a, -20-1b, -58, -42a, and OsCYP18-1, -21-4, -19-3, -17 and -20-1) are expressed in all tissues, including 6-day seedlings, leaves, stems, roots and flowers, in agreement with previous Arabidopsis orthologs results [4]. In clade III, four MD FKBPs (OsFKBP44, -53, -58, and -59) were grouped as 4 branches of the same node (Figure 3) and were analyzed to the highest identity with AtFKBP53 and FKB53 (Additional file 1) via blastP analysis. But some of the stress-inducible OsIMMs (OsFKBP15-1, -16-1, -62a, and OsCYP19-4, -28, -57, -59b) are not consistent with the Arabidopsis orthologs results: OsFKBP15-1 is expressed only weakly in leaf, compared to the AtFKBP15-1 which is expressed strongly in all tissues. Biochem J. Science. Sharma AD, Singh P: Effect of water stress on expression of a 20kD cyclophilin-like protein in drought susceptible and tolerant cultivars of Sorghum. Putative ER targeting SD OsCYPs, OsCYP19-4 and -21-1 show 70 and 69% similarity to the ER proteins AtCYP19-4 and AtCYP21-1, respectively. 2004, 134: 1241-1243. 10.1038/337476a0. Magiri EN, Pisanti O, Breiman A: The rice large FKBPs are differentially expressed during development and heat stress. Saito T, Niwa Y, Ashida H, Tanaka K, Kawamukai M, Matsuda H, Nakagawa T: Expression of a gene for cyclophilin which contains an amino-terminal endoplasmic reticulum-targeting signal. RNAs were isolated from RNA samples isolated from different tissues. It has been cultivated as a food crop for centuries. Despite their lack of structural similarity, these two families share a common peptidyl-prolyl isomerase (PPIase), catalyzing the cis/trans isomerization of proline imidic peptide bonds [2]. Ti Oryza sativa, kadawyan nga ammo a kas ti pagay ti Asia, ket ti sebbangan ti mula a kaaduan a maibagbaga iti Ilokano a kas bagas.Ti Oryza sativa ket maysa a ruot nga agraman iti henoma a buklen dagiti 430Mb iti ballasiw dagiti 12 a kromosoma. Xin Wei, Xuehui Huang, in Rice (Fourth Edition), 2019. Classification Oryza sativa contains two major subspecies: the sticky, short-grained japonica or sinica variety, and the nonsticky, long-grained indica variety. Oryza sativa Japonica Group (Japanese rice) Click on organism name to get more information. In reality, the amino acids at the C-terminus in which the membrane-anchoring domain is positioned showed significant changes between AtFKBP42 and OsFKBP42a/b (data not shown). (PDF 58 KB). CYP5 may regulate the function of the GNOM protein during embryogenesis [63]. A35780) was used for determined for hFKBP12 were marked by asterisks (*). Pathogen : Disease incited by a fungus, Pyricularia oryzae. These include OsFKBP12, -13, -15-1, -15-2, -16-1, -16-2, -16-3, -16-4, -17-1, -17-2, -18, -19, -20-2, -53, and -72 for FKBPs, and OsCYP18-1, -18-2, -18-4, -19-2, -19-3, -19-4, -20-1, -20-2, -20-3, -21-1, -21-4, -22, -23, -26-2, -28, -37, -38, -57, -63, -65, -71, and -95 for CYPs. As a result, IMMs are highly conserved ubiquitous proteins found in most organisms and in all major subcellular compartments. Taxonomy ID 39946. Temperate japonica is cultivated in East Asia (China, Japan, Korea, Vietnam, and Taiwan), while tropical japonica is in Indonesia , Madagascar , and also the Americas where it was brought to with slave trade. Colgan J, Asmal M, Luban J: Isolation, characterization and Targeted Disruption of Mouse Ppia: Cyclophilin A is Not Essential for Mammalian Cell Viability. Regarding desiccation stress, 8 OsFKBPs and 5 OsCYPs were upregulated in our water stress conditions (see the methods). Rice is a perennial grass which belongs to the grass family Poaceae and originated in India, Southern China and Thailand. The numbers above the boxes denote the amino acid positions of the function domains. Ferbitz L, Maier T, Patzelt H, Bukau B, Deuerling E, Ban N: Trigger factor in complex with the ribosome forms a molecular cradle for nascent proteins. Oryza longistaminata occurring in Africa is closely related to the West African Oryza barthii sometimes in sympatric communities, which has a tall (~ 2 m), erect, rhizomatous phenotype and is outcrossing. Another two CYPs, the putative mitochondrial OsCYP21-4 and nuclear OsCYP57, were positively regulated in response to both salt and desiccation stress; none of the functions of the two proteins and their other plant orthologs are known. O. sativa has a diphyletic origin, and the two sub species, namely, O. sativa var. 10.1104/pp.103.031005. According to the prediction database, OsFKBP15-1 is localized to ER; OsFKBP20-1a and -b are localized to nucleus (Figure 2);OsCYP19-2 is cytosolic; and OsCYP20-2 is located in the chloroplast lumen (Figure 5). Notably, photosynthetic organisms harbor a remarkably large number of IMMs, with 52 genes (23 FKBPs and 29 CYPs) in Arabidopsis, 49 (23 FKBPs and 26 CYPs) in Chlamydomonas, and 29 FKBPs in rice [4, 6, 8, 9]. In this chapter, we discuss recent genetic work that is related to the origin, taxonomy, and phylogenetics of rice, and we describe the genomic research into the domestication of indica and japonica. Gullerova M, Barta A, Lorkovic ZJ: AtCyp59 is a multi-domain cyclophilin from Arabidopsis thaliana that interacts with SR proteins and the C-terminal domain of the RNA polymerase II. 10.1074/jbc.M601815200. Plant Cell Physiol. Plant Cell. Classification of rice (Oryza satival. Vespa L, Vachon G, Berger F, Perazza D, Faure JD, Herzog M: The immnuophilin-interacting protein AtFIP37 from Arabidopsis is essential for plant development and is involved in trichome endoreduplication. Genetic Diversity and Classification of Oryza Sativa With Emphasis on Chinese Rice Germplasm Heredity (Edinb). 1999, 155: 212-219. – longstamen rice P: Species Oryza punctata Kotzchy ex Steud. The full length ORF of Os immunophilins FKBP15-2, FKBP20-1a, FKBP20-1b, CYP19-2 and CYP20-2 were fused to the N-terminal mGFP5 in pCAMBIA1302 and expressed in N. benthamiana leaf cell transformed using Agrobacterium. PubMed  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). Expression of some IMMs has been induced by both biotic and abiotic stresses, including HgCl2, viral infection, salicylic acid, salt stress, heat and cold shock, light and drought [15–21]. Oryza sativa contains two major subspecies: the sticky, short-grained japonica or sinica variety, and the nonsticky, long-grained indica rice [ja] variety. Plant Physiol. Under the salt stress of 200 mM NaCl, OsFKBP20-1b, -58, -16-1, and -62a mRNA levels were increased. It is the grain with the second highest worldwide production after Zea mays. Jackson K, Söll D: Mutations in a new Arabidopsis cyclophilin disrupt its interaction with protein phosphatase 2A. PubMed  The Rice Chromosomes 11 and 12 Sequencing Consortia: The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. RNAs were isolated from two-week-old seedlings were exposed to 200 mM NaCl and tissues were harvested at the indicated time points. OsCYP18-1 and -18-2 retain 89 and 82% identity with AtCYP18-1 and -18-2 in amino acid sequence, and 70 and 75% with CYN18-1 and -18-2, respectively (Additional file 1). The filter set were used (excitation 450-490 nm, emission 500-550 nm) and Texas Red (excitation 530-585 nm, emission 650 nm longpass) for green fluorescent proteins and autofluorescence of chlorophyll, respectively. PubMed Central  This work was supported by the Biogreen 21 Project (PJ0066472010) of RDA NAAS to HS Cho, and partially supported by 2010 Postdoctoral Fellowship Program of RDA NAAS to H Hwang. PubMed Google Scholar. The other functional domains such as tetrapeptide repeats (TPR), Arg/Lys amino acids rich domain (gray background box), U-box, WD repeats (WD), RRM, Leu-zipper, and zinc-finger are indicated separately. Other MD FKBPs with a TPR domain are OsFKBP62a, -62b, and -62c. – broadleaf rice P: Species Oryza longistaminata A. Chev. It is wet hammer-milled, the cell walls are removed by screening, and the protein is extracted. Toshifumi Nagata, ... Shoshi Kikuchi, in Plant Transcription Factors, 2016. 10.1007/BF00040698. 2000, 275: 16030-16036. Additionally, the ROF1-HSP90.1 complex was localized in the nucleus during exposure to heat stress, whereas it was localized in the cytoplasm under normal conditions [19]. Motohashi K, Koyama F, Nakanishi Y, Ueoka-Nakanishi H, Hisabori T: Chloroplast cyclophilin is a target protein of thioredoxin. Methods. Goulas E, Schubert M, Kieselbach T, Kleczkowski LA, Gardeström P, Schröder W, Hurry V: The chloroplast lumen and stromal proteomics of Arabidopsis thaliana show differential sensitivity to short- and long-term exposure to low temperature. AtCYP20-1, the ortholog of OsCYP20-1, interacted with the regulatory subunit RCN1 of a Ser/Thr-specific protein phosphatase, which suggests that AtCYP20-1 and the RCN1 complex is required for the control of root cell proliferation [64]. The signal sequences of all chloroplast FKBPs have double arginine residues and follow the hydrophobic region needed for chloroplast lumen translocation via the Tat (twin arginine translocase) pathway [37]. 2005, 17: 269-275. беларуская: Рыс English: Rice suomi: Riisit français: Riz தமிழ்: நெல் 中文: 稻属 Cookies policy. 2009, 59: 387-399. Nucleic Acids Res. Plant Disease in Rice - Oryza sativa . Oryza sativa is a major and important crop of Asia, especially southern, eastern, and South-East Asia, and also important in Southern Europe, like France, and the Americas, while Oryza glaberrima is distributed as a semi-upland (non irrigated largely, but, irrigated partially, as well) land type found in high rainfall areas. Secondary structure features (a-helix and b-sheets) derived from the hFKBP12 were displayed. It has been suggested that two pairs of Arabidopsis CYPs, AtCYP18-3 and AtCYP19-1, and AtCYP18-4 and AtCYP19-2, arose by gene duplication, implying that the gene duplication occurred only in the Arabidopsis lineage because of divergence of the lineage between O. sativa and Arabidopsis, and these two pair of genes may entail redundancy [15, 46]. Below are the links to the authors’ original submitted files for images. Secondary structure features (a-helix and b-sheets) derived from the hCYPA were displayed. 2006, 142: 820-830. Fulgosi H, Vener AV, Altschmied L, Herrmann RG, Andersson B: A novel multi-functional chloroplast protein: identification of a 40 kDa immunophilin-like protein located in the thylakoid lumen. Expression levels of some immunophilins (especially, showing changes in mRNA expression levels under water stress) in different tissues. volume 10, Article number: 253 (2010) It includes the major food crop rice. Yoshida S, Forno DA, Cock JH, Gomez KA: Laboratory manual for physiological studies of rice. Romano PG, Horton P, Gray JE: The Arabidopsis cyclophilin gene family. hFKBP12 identifies the 14 amino acid residues for the FK506 binding and PPIase activity [27–29]. The rice actin level was used for control. (C) Multiple sequence alignments of the QLQ and WRC domains. The targeting signal of putative chloroplast (thylakoid lumen) localized OsCYPs was manually adjusted (boxed): double Arg residues (--); the hydrophobic stretches following the double Args (---). Thus, we named only OsFKBP53 as an ortholog of AtFKBP53, and the others were referred to by molecular weight because there were no adequate orthologs in Arabidopsis. The OsCYP19-3 may have a distinct function from OsCYP19-2, considering that OsCYP19-3 has been survived a long period of evolution in most plants, including Arabidopsis and rice (data not shown). 1997, 4: 1-4. Duplication probably occurred immediately after the rice and Arabidopsis lineages separated. Proc Natl Acad Sci. J Biol Chem. AtCYP20-1 was identified as an unfolded protein response (UPR) gene following endoplasmic reticulum stress [65]. Article  A, OsFKBPs RT-PCR analysis; B, OsCYPs RT-PCR analysis. 1994, 26: 1181-1189. A total of 10 μL of PCR samples was separated by agarose gel electrophoresis and visualized with ethidium bromide staining. (PDF 97 KB). The human genome contains 18 genes for FKBPs and 24 genes for CYPs. Rice still is a very important staple food for a large segment of the world's population. FEBS Lett. Plant Cell Physiol. The expression of most of rice's IMMs was identified by the presence of ESTs in the NCBI O. sativa EST database. JP gave suggestions for the manuscript writing. rice. Genomics. However, about half the rice-growing areas in the world do not have sufficient water to maintain flooded conditions, and yield is also reduced to some extent by various abiotic stresses, including drought and salinity. The wide range in amylose content reflects different preferences for cooked rice texture in Asia and elsewhere. Classification kingdom Plantae phylum Tracheophyta class Liliopsida order ... Oryza sativa Name Homonyms Oryza sativa subsp. 2004, 134: 1283-1292. 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. Systematic position : The fungus belongs to class: Deuteromycetes. It was also shown that Arabidopsis thaliana GRFs (AtGRFs) have transcriptional transactivation activity in yeast, further confirming their role as TFs (Kim and Kende, 2004). OsFKBP72 also shows considerable similarity with AtFKBP72 in the C-terminal area. In addition, these two proteins belong to clade II, which is comprised of the two SD CYPs (OsCYP18-1 and -18-2), as well as 3 MD CYPs (OsCYP57, -65 and -71), and OsCYP18-1 and OsCYP65 share the same branch (Figure 6). There are many small differences among seed plants, but their TF gene patterns are similar (Figure 5.3F). India is rich in rice diversity by virtue of being a part of primary centre o f origin on one hand cPredicted localization and prediction obtained using TargetP http://www.cbs.dtu.dk/services/TargetP/, ChloroP http://www.cbs.dtu.dk/services/ChloroP/ and PredictNLS http://www.predictprotein.org: TL, thylakoid lumen; S, stroma; ER, endoplasmic reticulum; Vac, vacuole. The transmembrane domains (TM) that are not part of the signal peptide are labeled. This plant hormone promotes the growth of rice stems after flooding by activating cell proliferation in the intercalary meristem (Kende et al., 1998), a region at the base of internodes where new cells are produced. Two OsFKBPs (20-1a and 20-1b) are characterized as putative nuclear targeting paralogous proteins by the presence of nuclear localization signals (NLS) in the C-terminal region (Figure 2). Pombe [5, 6]. Annu Rev of Biochem. The aims of this study were to quantitatively classify fine lateral roots (FLRs), thick lateral roots (TLRs), and nodal roots (NRs) and analyze their dynamics of mean diameter (MD), lengths and … 2000, 12: 343-356. The Biology and Ecology of Rice (Oryza sativa L.) in Australia The Office of the Gene Technology Regulator O. sativa has a relatively small (430 million base pairs) diploid genome (2n = 24). To compare the conservation patterns of the amino acid residues for CsA binding/PPIase activity and secondary structural details, the full length of the single domain of CYPs and a truncated CYP domain for the MD CYPs were used for the amino acid alignment. 2001, 11: 82-88. Interestingly, only OsCYP59a includes the long insertion between the α1/β3 and β4/β5 domains, and they may have distinct functions. Two OsFKBPs (OsFKBP15-1 and OsFKBP15-2) contain putative ER targeting sequences at the N-terminus and have possible C-terminal endoplasmic reticulum (ER) retention signals (DSEL and NSEL for OsFKBP15-1 and OsFKBP15-2, respectively) (Figure 1 and 2), although it will need to be confirmed whether they function as real anchors in the ER membrane. Despite the primacy of rice, when, where, and how rice was domesticated was debated for decades. Rice belongs to the genus Oryza, of the tribe Oryzeae, of the subfamily Bambusoideae or Ehrhartoideae, of the family Poaceae or Gramineae. Plant J. 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). Reactions were incubated at 65°C for 5 min, 50°C for 50 min, and then 85°C for 5 min. They are closely related in sequence, and they are 81% similar to AtFKBP15-1 and 76% similar to AtFKBP15-2 in their amino acid sequences (Additional file 1). The bipartite chloroplast/thylakoid targeting signal, ER Targeting signal, and the NLS are represented. Putative IMMs of Oryza sativa cv. Unlike other MD FKBPs, which are composed of triple FKBP domains, the second FKBP domain of OsFKBP72 is the most highly conserved domain and shows remarkable differences in terms of key residues of hFKBP12 for ISD binding/PPIase activity. Rice (Oryza sativa) cultivation probably originated in Asia, and rice is still a staple food. 2014 May;112(5):489-96. doi: 10.1038/hdy.2013.130. The high content of γ-oryzanols and tocols in rice bran and brown rice contributes to the hypocholesterolemic and anticancer properties of rice. Meiri D, Breiman A: Arabidopsis ROF1(FKBP62) modulates thermo tolerance by interacting with HSP90.1 and affecting the accumulation of HsfA2-regulated sHSPs. 10.1074/jbc.M304258200. Like other photosynthetic organisms encoding the putative 52 genes of Arabidopsis, 49 genes of Chlamydomonas, putative 27 genes for FKBPs and 36 genes for CYPs of Sorghum bicolor, and putative 26 genes for FKBPs and 25 genes for CYPs of Vitis vinifera (our unpublished data), rice also has one of the largest IMM families in organisms whose genomes have been completely sequenced [4, 6]. Another thylakoid IMM, OsFKBP19, which has two cysteine residues in the loop regions between the β2 and β3 domains, is also upregulated by desiccation stress, whereas thylakoid lumen OsFKBP13 and OsFKBP16-2 that have two coupled cysteine residues forming a disulfide bond and upregulated by light irradiation, did not respond to salt and desiccation stress [4]. Further analysis of grf mutants indicated that their smaller leaves contain fewer cells, which implicated a link between GRFs and the control of cell proliferation (Horiguchi et al., 2005; Kim and Kende, 2004; Kim et al., 2003). Despite the high level of conservation of the PPIases throughout eukaryotes and prokaryotes, they do not have a function within many cells under normal growth conditions, but may become essential in the absence of other cellular factors [5]. 10.1006/geno.2000.6295. Plant Mol Biol. The expression level using the latter method corresponds roughly to the number of ESTs with all tissues of young plantlets (data not shown). Oryza sativa or Oryza glaberrima is a grass species from which rice is produced. Article  However, some genes were novel, did not match with those of Arabidopsis and Chlamydomonas, and several genes were paralogs by genetic duplication.

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oryza sativa classification

Oryza formosana Masam. Finally, the full length of the amino acid sequences of all FKBPs was used to generate a phylogenetic tree in order to assay the evolutionary relationships among the OsFKBPs (Figure 3). 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. We have identified 2 rice IMM families, FK506 binding proteins and cyclophilins, using the rice genome sequence database. Rice is the world's largest crop and serves as a staple food for a large part of the world's human population. CAS  10.1016/S1360-1385(96)80041-0. 1998, 17: 1577-1587. Rice (Oryza sativa L.) is one of the most important staple crops, feeding almost half of the world population. Plant Physiol. OsCYP20-2 GFP protein, which contains double arginine residues and hydrophobic regions as a putative chloroplast lumenal protein, was clearly localized in chloroplasts. These results suggest that OsCYP17 occurred most recently in the evolution of O. sativa. Manage cookies/Do not sell my data we use in the preference centre. Plant Physiol. OsFKBP58 has 36% similarity to AtFKBP53 (Additional file 1) and retains 8 - 20 mer of amino acid insertion in 3 areas besides the FKBP domain, and thus the CCD domain was predicted to be between amino acids 353 and 381 (Figure 2). Vernacular names More to the point, Escherichia coli possesses 6 IMMs, including 3 FKBPs and 2 cyclophilins. 2006, 47: 720-734. Data source Beijing Genomics Institute OsFKBP44 and OsCYP17 did not show ESTs, but their expression was confirmed by RT-PCR analysis (Additional file 1). Nicholas E. Korres, ... Taghi Bararpour, in Advances in Rice Research for Abiotic Stress Tolerance, 2019. 10.1126/science.1702904. Notably, monocots and dicots are highly similar in their TF gene patterns. Otherwise, as in the case of PAS1, we infer that it is a cytosol/nucleus shuttle protein. However, the phenotype and protein composition of the thylakoid lumen in AtCYP20-2 mutants seems indistinguishable from that of the wild type plants, and it is concluded therefore that AtCYP20-2 is unrelated to its PPIase capacity [52, 53]. However, many IMMs in plants may serve a more diverse array of functions, especially in relation to photosynthesis, but may also involve a significant amount of redundancy [4]. The sequence alignment of Figure 4 (OsCYPs) was used and the phylogenetic analysis was based on the sequence alignments by ClustalX http://align.genome.jp. 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. From the analysis of other plant CYPs containing O. sativa ssp. The 29 OsFKBPs identified could be classified into single-domain (SD) members with a FKBP catalytic domain, and multiple-domain (MD) members with other functional domains in addition to a single or multiple FKBP domains (Figure 2). Most strikingly, of all genes encoding FKBPs and CYPs, a total of 12 can be deleted without seriously affecting the viability of Saccharomyces cerevisiae [11]. Plant Cell. Science. Two μg of RNA were transcribed reversely in a 20 μl reaction volume using oligo dT 14 to 18 primer (Invitrogen Life Technologies) and reverse transcriptase (SuperScript III, Invitrogen Life Technologies). The soil nematode Caenorhabditis elegans genome contains 8 genes for FKBPs and 24 genes for CYPs. 2007, 46: 9432-9442. Pl. Moreover, the diversity of IMM proteins was somewhat different for the monocot rice than for the dicot Arabidopsis. 10.1073/pnas.91.3.984. By continuing you agree to the use of cookies. (B) The Arabidopsis triple mutant grf1–grf2–grf3 has small leaves. In the case of rice, introgression from wild relatives has provided improvement in both major gene and quantitatively inherited traits. RNAs were isolated from two-week-old seedlings were exposed to drought stress and tissues were harvested at the indicated time points. In addition, a comprehensive analysis of rice IMM FKBPs and CYPs, including putative domain architecture, amino acid alignment, the conservation ratio of key amino residues for binding of immunosuppressive drugs, and phylogenetic relationships between family members, was also conducted. B.O. 10.1104/pp.118.4.1395. Semi-quantitative RT-PCR was performed with gene specific primers using cDNAs from RNA samples. 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. The GFP fusion proteins of OsFKBP20-1a and -b, predicted to be nuclear due to the C-terminal NLS sequences, were distinctly localized within the nucleus. PubMed  For the salt stress treatment, two-week-old rice seedlings were subjected to 200 mM NaCl and harvested at time courses of 0, 1, 3, 6, 12, 24, 48 and 72 hours after treatment. Japonica and ssp. 2005, 3: 20-10.1186/1741-7007-3-20. It is noteworthy that except for O. sativa ssp. Plant Physiol. This number compares well with the 29 AtCYPs for Arabidopsis and the 26 genes for Chlamydomonas, indicating that the diversity of CYPs has been maintained or even slightly increased since they were established in the photosynthetic green ancestor. 2004, 134: 1268-1282. Copyright © 2020 Elsevier B.V. or its licensors or contributors. The conservation patterns of OsFKBPs with the 14 amino acid residues of hFKBP12 were very similar to those of the Arabidopsis (Table 1) and Chlamydomonas orthologs [6]. Ultimately, the classification of putative FKBPs and CYPs in rice provides information about the evolutionary/functional significance of each FKBP and CYP based on a comparison with the relatively well studied Arabidopsis and Chlamydomonas IMMs. He Z, Li L, Luan S: Immunophilins and parvulins. Among 27 OsCYPs, 26 members could have matching orthology with a protein among Arabidopsis CYPs, whereas for only OsCYP17, we could find no obvious orthology with Arabidopsis CYPs. Rhoads AR, Friedberg F: Sequence motifs for calmodulin recognition. FEBS Lett. Also by investigating the expression of all OsFKBPs and OsCYPs under salt and desiccation stress conditions, we found that a significant number of genes were up-regulated in response to water stress. BMC Plant Biol 10, 253 (2010). Plant Physiol. Differentially expressed proteins in rice roots and shoots serve as marker groups for salt tolerance in rice. 10.1073/pnas.0405240101. Scholze C, Peterson A, Diettrich B, Luckner M: Cyclophilin isoforms from Digitalis lanata: sequences and expression during embryogenesis and stress. OsFKBP62a is expressed in leaves, stems and flowers, but not in seedlings and is extremely low in roots, whereas AtFKBP62 is expressed in all tissues. Symptoms . 10.1023/A:1005930024796. Oryza officinalis complex with nine species—the B, C, D and E genomes variously in diploid and tetraploid combinations—have contributed resistance to the dreaded brown leaf hopper, bacterial blight disease, blast, and also to yield-enhancing traits from Oryza grandiglumis (CCDD) (Yoon et al., 2006). Callebaut I, Mornon JP: Trigger factor, one of the Escherichia coli chaperone proteins, is an original member of the FKBP family. This information added broader evidence in favor of the theory that the diversity of IMMs was already established in their last common ancestor, probably close to the root of the "green" lineage of plants, but they may have continued to change and become more diverse since the completion of the "green" lineage. Cite this article. Kay JE: Structure-function relationships in FK506-binding protein (FKBP) family of peptidylprolyl cis-trans isomerases. The rice actin level was used for control. 10.1111/j.1365-313X.2008.03532.x. 10.1139/gen-42-4-646. Rice has been cultivated as a major crop for > 7000 years, and currently sustains more than half of the world's population [22]. Gopalan G, He Z, Balmer Y, Romano P, Gupta R, Héroux A, Buchanan BB, Swaminathan K, Luan S: Structural analysis uncovers a role for redox in regulating FKBP13, an immnunophilin of the chloroplast thylakoid lumen. However, few studies and little detailed and accurate information of root characteristics were reported in fine-rooted plants like rice (Oryza sativa L.). Lu R, Martin-Hernández AM, Peart JR, Malcuit I, Baulcombe DC: "Virus-induced gene silencing in plants". As a putative ER-targeting protein, OsFKBP15-1-GFP protein seemed to be localized in the ER, but we were unable to use a specific marker protein in this study. 2000, 68: 167-178. Rice roots function as the primary site for salinity perception, transmitting salt signals to the shoots for proper salt response and adaptation of the entire plant. As with OsCYPs induced under salt stress, desiccation inducing OsCYPs also are composed of CYPs targeted to the various cellular organs. 10.1128/EC.4.2.230-241.2005. Rubin GM, et al: Comparative genomics of the eukaryotes. In addition, their expression levels responding to the water-stress have been analyzed in different tissues, and some subcellular IMMs located by means of tagging with GFP protein. Cell. naindayegan daytoy iti kalaka a henetiko a mabaliwan, ken maysa a modelo nga organismo para iti sereal a biolohia The precise function of the trigger factor in the chloroplast remains unknown, but it is a PPIase and chaperone associated with the ribosome that is involved in the early steps of protein folding [45]. Nature. AtFKBP72 (PAS1) is involved in the control of cell proliferation and differentiation during plant development [43, 44]. From these results, we suggest that At/OsCYP20-2 maintains the homeostatic state of thylakoid lumen under stress, although it may be unrelated to its PPIase activity. The human genome contains 42 (18 FKBPs and 24 CYPs). O. rufipogon is a perennial type found in tropical and subtropical Asia, South America and Australia. The protein targeting signal and subcellular location of the IMMs were predicted using several programs, such as PSORT http://psort.ims.u-tokyo.ac.jp, TargetP http://www.cbs.dtu.dk/services/TargetP/, SignalP http://www.cbs.dtu.dk/services/SignalP/, ChloroP http://www.cbs.dtu.dk/services/ChloroP/, and PredictNLS http://www.predictprotein.org/ for cross-confirmation. Sequence analysis of OsGRF1 homologs highlighted two highly conserved protein domains: the QLQ (Gln, Leu, Gln), involved in protein–protein interactions, and the WRC (Trp, Arg, Cys), containing a putative nuclear localization signal and a DNA-binding domain (Figure 17.1A and C). g, hThe Mr and isoelectric point of the full-length/mature protein were predicted by Compute pI/Mw tool http://www.expasy.ch/tools/pi_tool.html. EMBNET NEWS. In addition, many of the genes upregulated by water stress offer the possibility of manipulating the stress responses in rice. FKBP and CYP proteins in rice (Oryza sativa cv. 10.1146/annurev.biochem.72.121801.161720. OsFKBP44 has a long N-terminal area containing two internal repeat domains and a FKBP domain, showing some degree of similarity to AtFKBP15-3 (data not shown). In addition, OsCYP17 forms a separate branch within clade I of the phylogenic tree (Figure 6). 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. Japonica were identified via BLAST searching of the Rice Genome Annotation Project database http://rice.plantbiology.msu.edu using the amino acid sequence of AtFKBP12 for FKBPs and AtCYP18-1 for CYPs as the query. Furthermore, most of the chloroplast IMMs in both plants has a putative ortholog relation, which indicates that they may have a conserved function in relation to photosynthesis. The strongest salt induction pattern can be seen on OsFKBP20-1b, which is rarely expressed in the absence of stress (Figure 7A). Fisher G, Wittmann-Liebold B, Lang K, Kiefhaber T, Schmid FX: Cyclophilin and the peptidyl-prolyl cis-trans isomerase are probably identical proteins. Article  Google Scholar. 10.1126/science.1068275. A HIGH-POLYMERIC CARBOHYDRATE MATERIAL PRIMARILY COMPOSED OF AMYLOPECTIN AND AMYLOSE. PubMed Central  Indica using the GRAMENE and NCBI database, we conclude that the 670 amino acid from the NCBI database is probably correct. MD AtFKBP53 and a SD AtFKBP15-3 showed high sequence similarity, but also that rice lacks an ortholog of AtFKBP15-3, suggesting that these proteins (OsFKBP44 and AtFKBP15-3) also originated from Chlamydomonas FKB53, but that duplication of two proteins occurred after the lineage divergence of the two plants from a common ancestor. 333 1753 . Among the desiccation affected OsCYPs, OsCYP19-2, -20-2, -21-4, and -57 showed increased expression 6 h after stress, but only OsCYP59b showed a change in the induced expression at 24 h after desiccation, being notably similar to salt stress response (Figure 8B). However, the number of IMMs in different organisms differs greatly. Different tissues of the rice (6-day-old seedlings, leaves, stems, roots and flowers) were collected and frozen in liquid nitrogen for RNA extraction. Oryza sativa - Taxon details on Integrated Taxonomic Information System (ITIS). They are collectively referred to as immunophilin (IMM), being present in almost all cellular organs. 1999, 42: 646-655. 1999, 262: 830-838. Bedford MT, Frankel A, Yaffe MB, Clarke S, Leder P, Richard S: Arginine methylation inhibits the binding of proline-rich ligands to Src homology 3, but not WW, domains. RNA Biol. Plant Mol Biol. 1753; Hook. Stoller G, Rücknagel KP, Nierhaus KH, Schmid FX, Fischer G, Rahfeld JU: A ribosome-associated peptidyl-prolyl cis/trans isomerase identified as the trigger factor. 2004, 134: 101-117. CAS  As the OsCYP19-2 sequence has not any a signal peptide for subcellular localization (according to the database), the GFP fusion protein was also located in the cytosol. The other functional domains such as tetrapeptide repeats (TPR), Arg/Lys amino acids rich domain (gray background box), coiled coil domain (CCD), internal repeats (RPT) and Calmodulin-binding motif (CaM) are indicated separately. P62937) was used for comparison. 10.1074/jbc.M909368199. 10.1046/j.1365-313X.2002.01420.x. Google Scholar. 1997, 11: 331-340. Privacy Among them, OsFKBP53 and -58 contain highly charged domains, putative nuclear targeting signals in the N-terminal regions, and a single FKBP domain (Figure 2). Unrooted phylogenetic trees of O. sativa CYP proteins. 10.1007/s11103-009-9547-1. The OsIMMs FKBP15-1, FKBP20-1a and FKBP20-1b, CYP19-2, and CYP20-2 cDNA fragments corresponding to the 154, 186, 185, 171, 247, and amino acids were cloned into the pCAMBIA1302 plasmids using BglII and SpeI sites to generate the OsIMMs-GFP fusion proteins respectively. Escherichia coli contains 6 IMMs, the yeast genome contains 12 (4 genes for FKBPs and 8 genes for CYPs), Drosophila melanogaster contains 21 ones (7 FKBPs and 14 CYPs), and Caenorhabditis elegans contains 25 (8 FKBPs and 17 CYPs). The 2 cultivated species are Oryza sativa and Oryza glaberrima. 10.1016/S0014-5793(98)01028-X. 2002, 296: 92-100. j, kOrthologous immunophilin and % identity (ID) were analysed by blastp http://www.ncbi.nlm.nih.gov/ of the NCBI database of the complete proteome of A. thaliana and C. reinhardtii: IP, immunophilin. Brink S, Bogsch EG, Edwards WR, Hynds PJ, Robinson C: Targeting of thylakoid proteins by the ΔpH-driven twin-arginine transduction pathway requires a specific signal in the hydrophobic domain in conjunction with the twin-arginine motif. Furthermore, the tissue specific expression of water stress responding Os IMMs and the visual localization of some of these IMMs were examined. Crude Rice Bran Oil is non-edible due to the large amounts of … It also does not have an ortholog in Chlamydomonas, suggesting it appeared after Chlamydomonas (Additional file 1 and Table 2). The targeting signal of putative chloroplast (thylakoid lumen) localized OsFKBPs was manually adjusted (boxed): double Arg residues (--); the hydrophobic stretches following the double Args (---). Plant Physiol. Oryza sativa temperate japonica subgroup. Plants were grown in a controlled chamber with a photoperiod of 12 h light at 28°C and 12 h dark at 22°C. 1996, 1: 95-99. indica and O. sativa var japonica ecotype in temperate regions are clearly separated having diverged around 7 million years ago with different ancestral gene pools (Brar and Singh, 2011). Among SD CYPs showing significant phylogenic diversity in amino acids for CsA binding mitochondria-located, OsCYP21-4 is not conserved in 7 amino acids for PPIase and shows 54% identity in the amino acid sequence with AtCYP21-4. The rice grain consists of a hull and an edible berry (caryopsis). The analysis indicated many of the genes (OsFKBP 20-1a, -20-1b, -58, -42a, and OsCYP18-1, -21-4, -19-3, -17 and -20-1) are expressed in all tissues, including 6-day seedlings, leaves, stems, roots and flowers, in agreement with previous Arabidopsis orthologs results [4]. In clade III, four MD FKBPs (OsFKBP44, -53, -58, and -59) were grouped as 4 branches of the same node (Figure 3) and were analyzed to the highest identity with AtFKBP53 and FKB53 (Additional file 1) via blastP analysis. But some of the stress-inducible OsIMMs (OsFKBP15-1, -16-1, -62a, and OsCYP19-4, -28, -57, -59b) are not consistent with the Arabidopsis orthologs results: OsFKBP15-1 is expressed only weakly in leaf, compared to the AtFKBP15-1 which is expressed strongly in all tissues. Biochem J. Science. Sharma AD, Singh P: Effect of water stress on expression of a 20kD cyclophilin-like protein in drought susceptible and tolerant cultivars of Sorghum. Putative ER targeting SD OsCYPs, OsCYP19-4 and -21-1 show 70 and 69% similarity to the ER proteins AtCYP19-4 and AtCYP21-1, respectively. 2004, 134: 1241-1243. 10.1038/337476a0. Magiri EN, Pisanti O, Breiman A: The rice large FKBPs are differentially expressed during development and heat stress. Saito T, Niwa Y, Ashida H, Tanaka K, Kawamukai M, Matsuda H, Nakagawa T: Expression of a gene for cyclophilin which contains an amino-terminal endoplasmic reticulum-targeting signal. RNAs were isolated from RNA samples isolated from different tissues. It has been cultivated as a food crop for centuries. Despite their lack of structural similarity, these two families share a common peptidyl-prolyl isomerase (PPIase), catalyzing the cis/trans isomerization of proline imidic peptide bonds [2]. Ti Oryza sativa, kadawyan nga ammo a kas ti pagay ti Asia, ket ti sebbangan ti mula a kaaduan a maibagbaga iti Ilokano a kas bagas.Ti Oryza sativa ket maysa a ruot nga agraman iti henoma a buklen dagiti 430Mb iti ballasiw dagiti 12 a kromosoma. Xin Wei, Xuehui Huang, in Rice (Fourth Edition), 2019. Classification Oryza sativa contains two major subspecies: the sticky, short-grained japonica or sinica variety, and the nonsticky, long-grained indica variety. Oryza sativa Japonica Group (Japanese rice) Click on organism name to get more information. In reality, the amino acids at the C-terminus in which the membrane-anchoring domain is positioned showed significant changes between AtFKBP42 and OsFKBP42a/b (data not shown). (PDF 58 KB). CYP5 may regulate the function of the GNOM protein during embryogenesis [63]. A35780) was used for determined for hFKBP12 were marked by asterisks (*). Pathogen : Disease incited by a fungus, Pyricularia oryzae. These include OsFKBP12, -13, -15-1, -15-2, -16-1, -16-2, -16-3, -16-4, -17-1, -17-2, -18, -19, -20-2, -53, and -72 for FKBPs, and OsCYP18-1, -18-2, -18-4, -19-2, -19-3, -19-4, -20-1, -20-2, -20-3, -21-1, -21-4, -22, -23, -26-2, -28, -37, -38, -57, -63, -65, -71, and -95 for CYPs. As a result, IMMs are highly conserved ubiquitous proteins found in most organisms and in all major subcellular compartments. Taxonomy ID 39946. Temperate japonica is cultivated in East Asia (China, Japan, Korea, Vietnam, and Taiwan), while tropical japonica is in Indonesia , Madagascar , and also the Americas where it was brought to with slave trade. Colgan J, Asmal M, Luban J: Isolation, characterization and Targeted Disruption of Mouse Ppia: Cyclophilin A is Not Essential for Mammalian Cell Viability. Regarding desiccation stress, 8 OsFKBPs and 5 OsCYPs were upregulated in our water stress conditions (see the methods). Rice is a perennial grass which belongs to the grass family Poaceae and originated in India, Southern China and Thailand. The numbers above the boxes denote the amino acid positions of the function domains. Ferbitz L, Maier T, Patzelt H, Bukau B, Deuerling E, Ban N: Trigger factor in complex with the ribosome forms a molecular cradle for nascent proteins. Oryza longistaminata occurring in Africa is closely related to the West African Oryza barthii sometimes in sympatric communities, which has a tall (~ 2 m), erect, rhizomatous phenotype and is outcrossing. Another two CYPs, the putative mitochondrial OsCYP21-4 and nuclear OsCYP57, were positively regulated in response to both salt and desiccation stress; none of the functions of the two proteins and their other plant orthologs are known. O. sativa has a diphyletic origin, and the two sub species, namely, O. sativa var. 10.1104/pp.103.031005. According to the prediction database, OsFKBP15-1 is localized to ER; OsFKBP20-1a and -b are localized to nucleus (Figure 2);OsCYP19-2 is cytosolic; and OsCYP20-2 is located in the chloroplast lumen (Figure 5). Notably, photosynthetic organisms harbor a remarkably large number of IMMs, with 52 genes (23 FKBPs and 29 CYPs) in Arabidopsis, 49 (23 FKBPs and 26 CYPs) in Chlamydomonas, and 29 FKBPs in rice [4, 6, 8, 9]. In this chapter, we discuss recent genetic work that is related to the origin, taxonomy, and phylogenetics of rice, and we describe the genomic research into the domestication of indica and japonica. Gullerova M, Barta A, Lorkovic ZJ: AtCyp59 is a multi-domain cyclophilin from Arabidopsis thaliana that interacts with SR proteins and the C-terminal domain of the RNA polymerase II. 10.1074/jbc.M601815200. Plant Cell Physiol. Plant Cell. Classification of rice (Oryza satival. Vespa L, Vachon G, Berger F, Perazza D, Faure JD, Herzog M: The immnuophilin-interacting protein AtFIP37 from Arabidopsis is essential for plant development and is involved in trichome endoreduplication. Genetic Diversity and Classification of Oryza Sativa With Emphasis on Chinese Rice Germplasm Heredity (Edinb). 1999, 155: 212-219. – longstamen rice P: Species Oryza punctata Kotzchy ex Steud. The full length ORF of Os immunophilins FKBP15-2, FKBP20-1a, FKBP20-1b, CYP19-2 and CYP20-2 were fused to the N-terminal mGFP5 in pCAMBIA1302 and expressed in N. benthamiana leaf cell transformed using Agrobacterium. PubMed  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). Expression of some IMMs has been induced by both biotic and abiotic stresses, including HgCl2, viral infection, salicylic acid, salt stress, heat and cold shock, light and drought [15–21]. Oryza sativa contains two major subspecies: the sticky, short-grained japonica or sinica variety, and the nonsticky, long-grained indica rice [ja] variety. Plant Physiol. Under the salt stress of 200 mM NaCl, OsFKBP20-1b, -58, -16-1, and -62a mRNA levels were increased. It is the grain with the second highest worldwide production after Zea mays. Jackson K, Söll D: Mutations in a new Arabidopsis cyclophilin disrupt its interaction with protein phosphatase 2A. PubMed  The Rice Chromosomes 11 and 12 Sequencing Consortia: The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. RNAs were isolated from two-week-old seedlings were exposed to 200 mM NaCl and tissues were harvested at the indicated time points. OsCYP18-1 and -18-2 retain 89 and 82% identity with AtCYP18-1 and -18-2 in amino acid sequence, and 70 and 75% with CYN18-1 and -18-2, respectively (Additional file 1). The filter set were used (excitation 450-490 nm, emission 500-550 nm) and Texas Red (excitation 530-585 nm, emission 650 nm longpass) for green fluorescent proteins and autofluorescence of chlorophyll, respectively. PubMed Central  This work was supported by the Biogreen 21 Project (PJ0066472010) of RDA NAAS to HS Cho, and partially supported by 2010 Postdoctoral Fellowship Program of RDA NAAS to H Hwang. PubMed Google Scholar. The other functional domains such as tetrapeptide repeats (TPR), Arg/Lys amino acids rich domain (gray background box), U-box, WD repeats (WD), RRM, Leu-zipper, and zinc-finger are indicated separately. Other MD FKBPs with a TPR domain are OsFKBP62a, -62b, and -62c. – broadleaf rice P: Species Oryza longistaminata A. Chev. It is wet hammer-milled, the cell walls are removed by screening, and the protein is extracted. Toshifumi Nagata, ... Shoshi Kikuchi, in Plant Transcription Factors, 2016. 10.1007/BF00040698. 2000, 275: 16030-16036. Additionally, the ROF1-HSP90.1 complex was localized in the nucleus during exposure to heat stress, whereas it was localized in the cytoplasm under normal conditions [19]. Motohashi K, Koyama F, Nakanishi Y, Ueoka-Nakanishi H, Hisabori T: Chloroplast cyclophilin is a target protein of thioredoxin. Methods. Goulas E, Schubert M, Kieselbach T, Kleczkowski LA, Gardeström P, Schröder W, Hurry V: The chloroplast lumen and stromal proteomics of Arabidopsis thaliana show differential sensitivity to short- and long-term exposure to low temperature. AtCYP20-1, the ortholog of OsCYP20-1, interacted with the regulatory subunit RCN1 of a Ser/Thr-specific protein phosphatase, which suggests that AtCYP20-1 and the RCN1 complex is required for the control of root cell proliferation [64]. The signal sequences of all chloroplast FKBPs have double arginine residues and follow the hydrophobic region needed for chloroplast lumen translocation via the Tat (twin arginine translocase) pathway [37]. 2005, 17: 269-275. беларуская: Рыс English: Rice suomi: Riisit français: Riz தமிழ்: நெல் 中文: 稻属 Cookies policy. 2009, 59: 387-399. Nucleic Acids Res. Plant Disease in Rice - Oryza sativa . Oryza sativa is a major and important crop of Asia, especially southern, eastern, and South-East Asia, and also important in Southern Europe, like France, and the Americas, while Oryza glaberrima is distributed as a semi-upland (non irrigated largely, but, irrigated partially, as well) land type found in high rainfall areas. Secondary structure features (a-helix and b-sheets) derived from the hFKBP12 were displayed. It has been suggested that two pairs of Arabidopsis CYPs, AtCYP18-3 and AtCYP19-1, and AtCYP18-4 and AtCYP19-2, arose by gene duplication, implying that the gene duplication occurred only in the Arabidopsis lineage because of divergence of the lineage between O. sativa and Arabidopsis, and these two pair of genes may entail redundancy [15, 46]. Below are the links to the authors’ original submitted files for images. Secondary structure features (a-helix and b-sheets) derived from the hCYPA were displayed. 2006, 142: 820-830. Fulgosi H, Vener AV, Altschmied L, Herrmann RG, Andersson B: A novel multi-functional chloroplast protein: identification of a 40 kDa immunophilin-like protein located in the thylakoid lumen. Expression levels of some immunophilins (especially, showing changes in mRNA expression levels under water stress) in different tissues. volume 10, Article number: 253 (2010) It includes the major food crop rice. Yoshida S, Forno DA, Cock JH, Gomez KA: Laboratory manual for physiological studies of rice. Romano PG, Horton P, Gray JE: The Arabidopsis cyclophilin gene family. hFKBP12 identifies the 14 amino acid residues for the FK506 binding and PPIase activity [27–29]. The rice actin level was used for control. (C) Multiple sequence alignments of the QLQ and WRC domains. The targeting signal of putative chloroplast (thylakoid lumen) localized OsCYPs was manually adjusted (boxed): double Arg residues (--); the hydrophobic stretches following the double Args (---). Thus, we named only OsFKBP53 as an ortholog of AtFKBP53, and the others were referred to by molecular weight because there were no adequate orthologs in Arabidopsis. The OsCYP19-3 may have a distinct function from OsCYP19-2, considering that OsCYP19-3 has been survived a long period of evolution in most plants, including Arabidopsis and rice (data not shown). 1997, 4: 1-4. Duplication probably occurred immediately after the rice and Arabidopsis lineages separated. Proc Natl Acad Sci. J Biol Chem. AtCYP20-1 was identified as an unfolded protein response (UPR) gene following endoplasmic reticulum stress [65]. Article  A, OsFKBPs RT-PCR analysis; B, OsCYPs RT-PCR analysis. 1994, 26: 1181-1189. A total of 10 μL of PCR samples was separated by agarose gel electrophoresis and visualized with ethidium bromide staining. (PDF 97 KB). The human genome contains 18 genes for FKBPs and 24 genes for CYPs. Rice still is a very important staple food for a large segment of the world's population. FEBS Lett. Plant Cell Physiol. The expression of most of rice's IMMs was identified by the presence of ESTs in the NCBI O. sativa EST database. JP gave suggestions for the manuscript writing. rice. Genomics. However, about half the rice-growing areas in the world do not have sufficient water to maintain flooded conditions, and yield is also reduced to some extent by various abiotic stresses, including drought and salinity. The wide range in amylose content reflects different preferences for cooked rice texture in Asia and elsewhere. Classification kingdom Plantae phylum Tracheophyta class Liliopsida order ... Oryza sativa Name Homonyms Oryza sativa subsp. 2004, 134: 1283-1292. 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. Systematic position : The fungus belongs to class: Deuteromycetes. It was also shown that Arabidopsis thaliana GRFs (AtGRFs) have transcriptional transactivation activity in yeast, further confirming their role as TFs (Kim and Kende, 2004). OsFKBP72 also shows considerable similarity with AtFKBP72 in the C-terminal area. In addition, these two proteins belong to clade II, which is comprised of the two SD CYPs (OsCYP18-1 and -18-2), as well as 3 MD CYPs (OsCYP57, -65 and -71), and OsCYP18-1 and OsCYP65 share the same branch (Figure 6). There are many small differences among seed plants, but their TF gene patterns are similar (Figure 5.3F). India is rich in rice diversity by virtue of being a part of primary centre o f origin on one hand cPredicted localization and prediction obtained using TargetP http://www.cbs.dtu.dk/services/TargetP/, ChloroP http://www.cbs.dtu.dk/services/ChloroP/ and PredictNLS http://www.predictprotein.org: TL, thylakoid lumen; S, stroma; ER, endoplasmic reticulum; Vac, vacuole. The transmembrane domains (TM) that are not part of the signal peptide are labeled. This plant hormone promotes the growth of rice stems after flooding by activating cell proliferation in the intercalary meristem (Kende et al., 1998), a region at the base of internodes where new cells are produced. Two OsFKBPs (20-1a and 20-1b) are characterized as putative nuclear targeting paralogous proteins by the presence of nuclear localization signals (NLS) in the C-terminal region (Figure 2). Pombe [5, 6]. Annu Rev of Biochem. The aims of this study were to quantitatively classify fine lateral roots (FLRs), thick lateral roots (TLRs), and nodal roots (NRs) and analyze their dynamics of mean diameter (MD), lengths and … 2000, 12: 343-356. The Biology and Ecology of Rice (Oryza sativa L.) in Australia The Office of the Gene Technology Regulator O. sativa has a relatively small (430 million base pairs) diploid genome (2n = 24). To compare the conservation patterns of the amino acid residues for CsA binding/PPIase activity and secondary structural details, the full length of the single domain of CYPs and a truncated CYP domain for the MD CYPs were used for the amino acid alignment. 2001, 11: 82-88. Interestingly, only OsCYP59a includes the long insertion between the α1/β3 and β4/β5 domains, and they may have distinct functions. Two OsFKBPs (OsFKBP15-1 and OsFKBP15-2) contain putative ER targeting sequences at the N-terminus and have possible C-terminal endoplasmic reticulum (ER) retention signals (DSEL and NSEL for OsFKBP15-1 and OsFKBP15-2, respectively) (Figure 1 and 2), although it will need to be confirmed whether they function as real anchors in the ER membrane. Despite the primacy of rice, when, where, and how rice was domesticated was debated for decades. Rice belongs to the genus Oryza, of the tribe Oryzeae, of the subfamily Bambusoideae or Ehrhartoideae, of the family Poaceae or Gramineae. Plant J. 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). Reactions were incubated at 65°C for 5 min, 50°C for 50 min, and then 85°C for 5 min. They are closely related in sequence, and they are 81% similar to AtFKBP15-1 and 76% similar to AtFKBP15-2 in their amino acid sequences (Additional file 1). The bipartite chloroplast/thylakoid targeting signal, ER Targeting signal, and the NLS are represented. Putative IMMs of Oryza sativa cv. Unlike other MD FKBPs, which are composed of triple FKBP domains, the second FKBP domain of OsFKBP72 is the most highly conserved domain and shows remarkable differences in terms of key residues of hFKBP12 for ISD binding/PPIase activity. Rice (Oryza sativa) cultivation probably originated in Asia, and rice is still a staple food. 2014 May;112(5):489-96. doi: 10.1038/hdy.2013.130. The high content of γ-oryzanols and tocols in rice bran and brown rice contributes to the hypocholesterolemic and anticancer properties of rice. Meiri D, Breiman A: Arabidopsis ROF1(FKBP62) modulates thermo tolerance by interacting with HSP90.1 and affecting the accumulation of HsfA2-regulated sHSPs. 10.1074/jbc.M304258200. Like other photosynthetic organisms encoding the putative 52 genes of Arabidopsis, 49 genes of Chlamydomonas, putative 27 genes for FKBPs and 36 genes for CYPs of Sorghum bicolor, and putative 26 genes for FKBPs and 25 genes for CYPs of Vitis vinifera (our unpublished data), rice also has one of the largest IMM families in organisms whose genomes have been completely sequenced [4, 6]. Another thylakoid IMM, OsFKBP19, which has two cysteine residues in the loop regions between the β2 and β3 domains, is also upregulated by desiccation stress, whereas thylakoid lumen OsFKBP13 and OsFKBP16-2 that have two coupled cysteine residues forming a disulfide bond and upregulated by light irradiation, did not respond to salt and desiccation stress [4]. Further analysis of grf mutants indicated that their smaller leaves contain fewer cells, which implicated a link between GRFs and the control of cell proliferation (Horiguchi et al., 2005; Kim and Kende, 2004; Kim et al., 2003). Despite the high level of conservation of the PPIases throughout eukaryotes and prokaryotes, they do not have a function within many cells under normal growth conditions, but may become essential in the absence of other cellular factors [5]. 10.1006/geno.2000.6295. Plant Mol Biol. The expression level using the latter method corresponds roughly to the number of ESTs with all tissues of young plantlets (data not shown). Oryza sativa or Oryza glaberrima is a grass species from which rice is produced. Article  However, some genes were novel, did not match with those of Arabidopsis and Chlamydomonas, and several genes were paralogs by genetic duplication. How To Make Aloe Vera Gel With Gelatin, Buy Now Pay Later Beauty Sites, Amanita Bisporigera Facts, Best Face Wash For Open Pores And Blackheads, Bic Venturi V1020, Perennial Identification By Color, Italian Fried Cheese Sandwich, Best Buttermilk Biscuits,

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