oryza sativa classification

Oryza formosana Masam. However, OsFKBP20-1a GFP protein showed a typical nuclear targeting pattern, but the OsFKBP20-1b GFP proteins were strongly accumulated in a specific region within the nucleus and also in cytosol foci. In addition, to analyze conservation in amino acids for FKBP domain and their orthologous relationship, the conservation patterns and ratio of the amino acid residues for FKBP domain between each ortholog of rice and Arabidopsis FKBPs was compared (Table 1). These issues will be addressed in this chapter in an attempt to highlight the most important factors and challenges, as well as suggest short- and long-term adaptation strategies in this complex production system. Putative ER-locating OsCYP23 and thylakoid lumen-locating OsCYP28 are not conserved in amino acids for CsA binding (Table 2), and given their upregulated expressions only under salt stress, but not under desiccation stress, we must infer that they are associated with specific substrates for metabolic regulation related to sodium or chloride ions. 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). Chou IT, Gasser CS: Characterization of the cyclophilin gene family of Arabidopsis thaliana and phylogenetic analysis of known cyclophilin proteins. YY and MS analyzed semi-quantitative RT-PCR for water stress gene expression. In addition, many of the genes upregulated by water stress offer the possibility of manipulating the stress responses in rice. Nigam N, Singh A, Sahi C, Chandramouli A, Grover A: SUMO-conjugating enzyme (Sce) and FK506-binding protein (FKBP) encoding rice (Oryza sativa L.) genes: genome-wide analysis, expression studies and evidence for their involvement in abiotic stress response. Genetic Diversity and Classification of Oryza Sativa With Emphasis on Chinese Rice Germplasm Heredity (Edinb). 1996, 1: 95-99. Although they show high divergence in their amino acid sequences, including the CYP area, they have orthologs with significant homology in the CYP area, including key residues in both Arabidopsis and Chlamydo-monas. 10.1021/bi700426q. The plant-specific GRF family of TFs. Unlike with AtCYP20-1, nothing about the function of the putative mitochondria locating OsCYP20-1 has been reported. Putative IMMs of Oryza sativa cv. HC and HP conceived the intellectual design of the project and wrote the manuscript. 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. Of the 29 FKBPs containing OsTIG, 15 have been characterized as SD members. CAS  J Plant Physiol. The OsCYP59b gene was transiently upregulated only 24 h after both stress treatments; however, OsCYP59a (maybe a duplicate of OsCYP59b) expression was unchanged by salt/desiccation stress. 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. 2009, 50: 1801-1814. Douglas LB: Mechanism of alternative pre-messenger RNA splicing. However, like orthologs of Arabidopsis, AtFKBP17-2, -18, and -20-2 also lack a cleavage site at the terminus of the hydrophobic extension region, suggesting that they act as insoluble proteins within the thylakoid lumen, but proteins anchored in the thylakoid membrane [4]. Plant J. J Plant Biochem Biotech. Protein Eng. Also, resistance to the deadly rice disease, bacterial blight, and to various other viruses, tolerance to soil toxicity, early maturing and cytoplasmic male sterility. 2014 May;112(5):489-96. doi: 10.1038/hdy.2013.130. However, considering our results indicating that the OsCYP19-4 gene was expressed in young rice plants without pistils or in the embryogenesis stage under salt stress, the full role of this protein remains to be clarified. Oryza meridionalis is found in the Australian tropics. 10.1104/pp.103.022160. Nuclear-located OsCYP57 and OsCYP65 and cytosolic OsCYP71 belong to clade II (Figure 6) and have well conserved CYP domains (Table 2). Terms and Conditions, They also display 68 and 69% similarity with putative ER localized CYN20-1, respectively, probably indicating an ancestral gene (Additional file 1). The putative leucine-zipper domain of AtCYP38 (TLP40) is not conserved in OsCYP38, CYN38 and orthologs of other plants (data not shown), and the role of the domain has not been clarified after several studies, indicating that this is not a conclusive point of evolution for the proper function of this protein [54–56]. Reimer U, Fischer G: Local structural changes caused by peptidyl-prolyl cis/trans isomerization in the native state of proteins. This plant can be weedy or invasive according to the authoritative sources noted below.This plant may be known by one or more common names in different places, and some are listed above. Sharma AD, Singh P: Effect of water stress on expression of a 20kD cyclophilin-like protein in drought susceptible and tolerant cultivars of Sorghum. Another cytosolic OsCYP19-3 that shows 79% identity with AtCYP19-3 also is very similar to OsCYP19-2 in amino acid sequence (Additional file 1), except for some divergence in the α3 domain (Figure 4). 1991, 251: 283-287. The amino acids necessary for CsA binding as determined for hCYPA were marked by asterisks (*). There are polyphyletic origins among the cultivated rice species/sub species, and these also have the potential to add genes for improvement with the sharing of gene pools. Japonica varieties are usually cultivated in dry fields, in temperate East Asia, upland areas of Southeast Asia, and high elevations in South Asia, while indica varieties are mainly lowland rices, grown mostly submerged, throughout tropical Asia. 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. These results suggest that OsCYP17 occurred most recently in the evolution of O. sativa. Red indicates the C-terminal regions from AtGRF1, AtGRF2, AtGRF5, and AtGRF7, which display transcriptional transactivation activity in yeast (Kim et al., 2003; Kim et al., 2012). 1991, 252: 836-839. Manage cookies/Do not sell my data we use in the preference centre. Cytosolic AtCYP18-1, -18-2, -18-3, -18-4, -19-1, -19-2, and -19-3 are highly conserved and probably have similar functions [4]. Chloroplast-located SD CYPs OsCYP26-2, -28, -37 and -38 show a very low conservation ratio and have significant modifications in key residues (Figure 4). Plant Physiol. A, OsFKBPs RT-PCR analysis; B, OsCYPs RT-PCR analysis. Pérez-Pérez JM, Ponce MR, Micol JL: The ULTRACURVATA2 gene of Arabidopsis encodes an FK506-binding protein involved in auxin and brassinosteroid signaling. © 2020 BioMed Central Ltd unless otherwise stated. Based on these characteristics, there is a relatively clear one-to-one orthology between rice CYPs and Arabidopsis CYPs, but no orthologs corresponding to AtCYP18-3 and AtCYP19-1 were found in rice. This suggests that although both salt and desiccation cause water stress to cells in common, some IMMs may be involved in distinct signal transduction or defense pathways against each individual stress before the cell activates a common stress response. Edvardsson A, Eshaghi S, Vener AV, Andersson B: The major peptidyl-prolyl isomerase activity in thylakoid lumen of plant chloroplast belongs to a novel cyclophilin TLP20. 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. India is rich in rice diversity by virtue of being a part of primary centre o f origin on one hand Rice (Oryza sativa L.) is characterized by a long history of safe use as human food. 2001, 6: 426-431. OsFKBP73 has a long Arg/Lys amino acid-rich domain (from aa 402 to 653) at the C-terminus, and OsFKBP57 retains a coiled coil domain in the C-terminal area (Figure 2). Plant J. Rice (Oryza sativa) growth and productivity is severely affected by salinity. 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. Indica using the GRAMENE and NCBI database, we conclude that the 670 amino acid from the NCBI database is probably correct. 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]. (PDF 58 KB). Plant Cell. 10.1016/S0168-9452(01)00437-X. Domain architecture of the O. sativa CYP immunophilins. 10.1104/pp.104.041186. PubMed Central  2003, 12: 77-80. 10.1073/pnas.91.3.984. 10.1261/rna.2226106. Thompson JD, Higgins DG, Gibson TJ: CULSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. EMBNET NEWS. 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). Under salt stress, the dynamic regulation of proteins in different functional groups plays a major role in different signaling pathways. 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. 1989, 337: 476-478. d, eIsoform number and amino acid were predicted by the Gramene database http://www.gramene.org/. In addition, considering that alternative splicing occurs as a normal phenomenon in eukaryotes, the diversity of IMM proteins encoded by a genome may also increase [25]. Trends in Plant Sci. 10.1007/BF00040698. However, as stated above, all four OsFKBPs of clade III have the closest similarity to AtFKBP53 and FKB53 as a probable ancestral protein. The gene-specific primers used for OsFKBPs and OsCYPs are described in Additional file 2 and 3: Supplemental Table S2 and S3. The wild F genome relative Oryza brachyantha, not classified within the four main species complexes, has provided resistance to bacterial blight and diversity for awning and for growth duration (Brar and Singh, 2011). Proteins that bind to immunosuppressive drugs, such as FK506, rapamycin and cyclophilin A (CsA), have been called FKBPs (FK506/rapamycin-binding proteins) and CYPs or cyclophilins (cyclosporin A-binding proteins), respectively, being collectively referred to immunophilins [1]. Among them, two putative cytosolics, OsCYP40 (a/b), contain the C-terminal TPR domain and show 73 and 70% similarity to AtCYP40, respectively (Additional file 1). Moreover, the diversity of IMM proteins was somewhat different for the monocot rice than for the dicot Arabidopsis. Finally, the distantly related member of the FKBPs is the trigger factor OsTIG, which also contains an FKBP domain, an N-terminal and C-terminal domains, both of which help to bind ribosomes, probably being located in the chloroplast stroma. J Biol Chem. 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. The expression level using the latter method corresponds roughly to the number of ESTs with all tissues of young plantlets (data not shown). Plants were grown in a controlled chamber with a photoperiod of 12 h light at 28°C and 12 h dark at 22°C. Rice (Oryza sativa L. japonica genotype Dongjin) seeds were germinated and grown in Yoshida nutrient solution, which consists of NH4NO3 (1.43 mM), NaH2PO4.2H2O (0.37 mM), K2SO4 (0.5 mM), CaCl2 (1.0 mM) and MgSO4.7H2O (1.6 mM) [68]. Noteworthy are the differences in the phenotypical consequences for microorganisms and higher organisms in response to the deletion of individual PPIase genes. The expression of an actin gene was used as an internal control for determining the RT-PCR amplification efficiency among different reactions. The EST database and our reverse transcription PCR analysis indicate that most putative OsIMMs genes are expressed in plants. 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. In Indian sub continent Oryza sativa is the cultivated species. FEBS Lett. Edvardsson A, Shapiquzov A, Petersson UA, Schröder WP, Vener AV: Immunophilin AtFKBP13 sustains all peptidyl-proryl isomerase activity in the thylakoid lumen from Arabidopsis thaliana deficient in AtCYP20-2. Rice (Oryza sativa L.) is an important staple crop that feeds more than one half of the world’s population. 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. Dolinski K, Muir S, Cardenas M, Heitman J: All cyclophilins and FK506 binding proteins are, individually and collectively, dispensable for viability in Saccharomyces cerevisiae. PubMed  Oryza sativa temperate japonica subgroup. Callebaut I, Mornon JP: Trigger factor, one of the Escherichia coli chaperone proteins, is an original member of the FKBP family. Ingelsson B, Shapiguzov A, Kieselbach T, Vener AV: Peptidyl-prolyl isomerase activity in chloroplast thylakoid lumen is a dispensible function of immunophilins in Arabidopsis thaliana. Rice (Oryza sativa) cultivation probably originated in Asia, and rice is still a staple food. Rice is a perennial grass which belongs to the grass family Poaceae and originated in India, Southern China and Thailand. Among them, two isoforms (a/b) of OsFKBP42 are characterized by a single FKBP domain, TPR domain, and CaM domain (Figure 2). aNames used in other literature: 1, Gollan and Bhave, 2009; Magiri et al., 2006. bRice genome initiative nomenclature was pro-vided by Gramene database. It has been cultivated as a food crop for centuries. There are many small differences among seed plants, but their TF gene patterns are similar (Figure 5.3F). fEST number was estimated by the tblastN http://www.ncbi.nlm.nih.gov/. Click on an acronym to view each weed list, or click here for a composite list of Weeds of the U.S. STATE. It is commonly consumed as milled or white rice, which is produced by removing the hull and bran layers of the rough rice kernel during the dehulling and milling processes, respectively. Where possible in considering characteristics such as > 50% identity in homology, the same subcellular location and the same domain architecture as with Arabidopsis and Chlamydomonas IMM proteins, we used the same suffix numbers for genes whose orthologs could be deduced. However, unlike with orthologs Arabidopsis AtFKBP42 and Chlamydomonas FKBP42 that have a membrane-anchoring domain at the C-terminus, and also contrary to a previous report on OsFKBP42a/b, we could not find a C-terminal membrane-anchoring domain at either OsFKBP42a or -42b using various prediction programs found on the ExPASY web site http://www.expasy.ch/tools[4, 6, 8]. Oryza Sativa (Rice) Starch is a starch obtained from rice, Oryza sativa. Pombe [5, 6]. 2000, 275: 16030-16036. The beginning and ending amino acids numbers of each protein are shown at each end of the diagram. In addition, the large number of IMM genes in the green lineage can be classified according to an ortholog relation. The alignments of amino acid sequence were performed using ClustalW and displayed with Genedoc v.2.6.002 [66, 67]. Protein, carbohydrates (starch), and lipids are present in the rice grain; protein, mainly glutelin, is of good nutritive quality and starch granules have a wide range in apparent amylose content from waxy, to low, to high amylose content. Thus, the exact location of OsCYP20-1 needs to be determined by further experiments. 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). The targeting signal of putative chloroplast (thylakoid lumen) localized OsCYPs was manually adjusted (boxed): double Arg residues (--); the hydrophobic stretches following the double Args (---). AtGRF genes were detected in actively growing and developing tissues, such as vegetative shoot apices, inflorescences, and roots tips. OsFKBP42a (LOC_Os12g05090) and OsFKBP42b (LOC_Os11g05090) are positioned in terminal regions of chromosome 11 and 12 in rice that are known to result from a duplication 7.7 million years ago, the most recent large-scale duplication in the rice genome [39]. 1994, 26: 1181-1189. Privacy As a result, IMMs are highly conserved ubiquitous proteins found in most organisms and in all major subcellular compartments. Rhoads AR, Friedberg F: Sequence motifs for calmodulin recognition. 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. The activity of this gene is controlled by the 35S promoter and 35S terminator from cauliflower mosaic virus. W.S. Plant Physiol. 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. ScienceDirect ® is a registered trademark of Elsevier B.V. ScienceDirect ® is a registered trademark of Elsevier B.V. URL: https://www.sciencedirect.com/science/article/pii/S0065211318300798, URL: https://www.sciencedirect.com/science/article/pii/B9780128008546000178, URL: https://www.sciencedirect.com/science/article/pii/B9780128143322000393, URL: https://www.sciencedirect.com/science/article/pii/B9780128115084000010, URL: https://www.sciencedirect.com/science/article/pii/B978012384947200595X, URL: https://www.sciencedirect.com/science/article/pii/B9780124058781000057, URL: https://www.sciencedirect.com/science/article/pii/B9780128008546000051, URL: https://www.sciencedirect.com/science/article/pii/B9780128128282000019, URL: https://www.sciencedirect.com/science/article/pii/B9780128143322000083, URL: https://www.sciencedirect.com/science/article/pii/B012227055X011421, Utilizing Crop Wild Relatives to Combat Global Warming, Growth-Regulating Factors, A Transcription Factor Family Regulating More than Just Plant Growth, Ramiro E. Rodriguez, ... Javier F. Palatnik, in, Proteomics Study in Rice Responses and Tolerance to Salt Stress, Advances in Rice Research for Abiotic Stress Tolerance, Origin, taxonomy, and phylogenetics of rice, Human and Animal Health Safety Assessment of Genetically Modified Plants, The Evolutionary Diversification of Genes that Encode Transcription Factor Proteins in Plants, Effects of Salinity on Rice and Rice Weeds, Nicholas E. Korres, ... Taghi Bararpour, in, Encyclopedia of Food Sciences and Nutrition (Second Edition). Magiri EN, Pisanti O, Breiman A: The rice large FKBPs are differentially expressed during development and heat stress. 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. The existence of two isomeric genes has even been confirmed in some plants (Poplus, Sorghum and Vitis) through BlastP analysis (data not shown). Rice (Oryza sativa L. japonica genotype Dongjin) seeds were germinated and grown in Yoshida nutrient solution, which consists of NH 4 NO 3 (1.43 mM), NaH 2 PO 4.2H 2 O (0.37 mM), K 2 SO 4 (0.5 mM), CaCl 2 (1.0 mM) and MgSO 4.7H 2 O (1.6 mM) . Among them, OsCYP18-4, OsCYP19-2, OsCYP19-3, OsCYP19-4, OsCYP20-1, OsCYP21-1 and AtCYP22 share a 5-to-8 amino acid insertion located between the α1 helix and β3 sheet (Figure 4). AtFKBP72 (PAS1) is involved in the control of cell proliferation and differentiation during plant development [43, 44]. 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. 1753; Hook. RNA Biol. Toshifumi Nagata, ... Shoshi Kikuchi, in Plant Transcription Factors, 2016. 2004, 134: 1241-1243. BMC Plant Biology Nicholas E. Korres, ... Taghi Bararpour, in Advances in Rice Research for Abiotic Stress Tolerance, 2019. Here, OsFKBP44, -46, -57, -58, -59, and -73 for FKBPs, and OsCYP17 for CYPs were included. 1996, 9: 173-180. 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. – Barth's rice P: Species Oryza glaberrima Steud. The soil nematode Caenorhabditis elegans genome contains 8 genes for FKBPs and 24 genes for CYPs. RNA was purified further using Qiagen RNeasy columns (Qiagen Inc., CA, USA) and on-column DNase treatment. japonica nipponbare) immunophilins (FKBPs, CYPs) and expression patterns under water stress. The C-terminus of PAS1 is required for binding with the NAC-like transcription factor and nuclear translocation [44]. IT IS USUALLY DERIVED FROM CEREAL GRAINS SUCH AS CORN, WHEAT AND SORGHUM, AND FROM ROOTS AND TUBERS SUCH AS POTATOES AND TAPIOCA. 10.1038/337476a0. 2004, 134: 1248-1267. Orthologs of these three FKBPs are unlikely to be in Arabidopsis, although they have weak identity with AtFKBP65 in their amino acid sequences (Additional file 1). Oryza breviligulata is another wild relative found in Africa. Annu Rev of Biochem. It includes the major food crop rice. 2005, 3: 20-10.1186/1741-7007-3-20. CYP domains are represented by white box. 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. Ahn, J.C., Kim, DW., You, Y.N. 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). OsCYP65 contains the U-box and Arg/Lys-rich domain, and was classified as putatively nuclear targeting, unlike cytosolic AtCYP65, for which no Arg/Lys-rich domain was located (Figure 5). 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. Nature. The co-localization of OsFKBP20-1a and -b GFP proteins was confirmed by DAPI staining of the nucleus (data not shown). 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. A HIGH-POLYMERIC CARBOHYDRATE MATERIAL PRIMARILY COMPOSED OF AMYLOPECTIN AND AMYLOSE. In addition, OsCYP17 forms a separate branch within clade I of the phylogenic tree (Figure 6). However, OsFKBP62a, -62b, and -62c retain 77, 75 and 73% similarity with AtFKBP62 in amino acid sequence, respectively, and 41, 41 and 42% similarity with FKB62, respectively (Figure 2, Additional file 1), and all belong to one stem branch of clade II in the phylogenetic tree (Figure 3). In the case of OsFKBP17-2, all key residues are substituted by other residues. 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). OsFKBP46 and OsFKBP57 that have no signal motifs were predicted to be cytosolic, whereas OsFKBP73, with its long Arg/Lys amino-acid-rich domain, was predicted to be nuclear by several prediction programs. 1999, 119: 693-704. Expression level of representative immunophilins under salt stress. 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. 10.1021/bi990971v. 10.1016/S0962-8924(00)01898-5. Some of the Os IMM genes were upregulated by both salt and desiccation stress, but others showed gene expression against only one stress. 2000, 14: 199-210. 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]. Nine OsCYPs belong to MD members. These three genes were previously named OsFKBP64, -65, and -75 and rFKBP64, -65, and -75, respectively, based on their molecular weight and similarity to two MD AtFKBP62 and -65 with triple FKBP domains, a TPR domain, and a CaM domain in common [4, 8, 40]. All these proteins contain a single FKBP domain, and some harbor a targeting sequence that determines the subcellular localization of the mature protein (Figure 2). Multiple sequence alignment of O. sativa FKBPs. 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. Oryza sativa GROWTH-REGULATING FACTOR1 (OsGRF1) is the founding member of the GROWTH-REGULATING FACTOR family of TFs. 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). The Arg/Lys amino acid-rich domain may function as a motif for non-specific RNA binding or mediate protein-protein interactions, and is also a frequent target for molecular interactions [32–34]. PubMed  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. Science. Rice (Oryza sativa L.) is one of the most important staple crops, feeding almost half of the world population. 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). All in all, the diversity of chloroplast lumen FKBPs has been established in Chlamydomonas based on the number of IMMs. Genome. 2010, 72: 1-16. Semi-quantitative RT-PCR was performed with gene specific primers using cDNAs from RNA samples. Google Scholar. Oryza Sativa (Rice) Bran Oil is a light yellow oil expressed from rice bran. 10.1046/j.1365-313X.2002.01420.x. 2005, re2. Furthermore, the large number of IMMs located in the thylakoid lumen in Arabidopsis is upregulated only by light conditions; analysis of the microarray data showed that the expression of several IMM genes was regulated by certain environmental conditions [4]. In Asia, Oryza sativa (Rice) is regarded to be the first cultivated crop. 2008, 55: 639-651. 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]. Xin Wei, Xuehui Huang, in Rice (Fourth Edition), 2019. 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]. Systematik. Thus, AtFKBP17-2 and 17-3, seen as gene duplicates based on their high sequence similarity, have been duplicate since the divergence of the evolutionary lineage between rice and Arabidopsis. (PDF 59 KB), Additional file 3: Primer sequences of OsCYP genes for quantitative RT-PCR. Furthermore, the tissue specific expression of water stress responding Os IMMs and the visual localization of some of these IMMs were examined. The rice actin level was used for control. 1994, 11: 4673-4680. It features a possible role for the regulation of the cell cycle through the interaction with AtFIP, a phosphatidyl-inositol kinase [36]. Jackson K, Söll D: Mutations in a new Arabidopsis cyclophilin disrupt its interaction with protein phosphatase 2A. Rice lacks the ortholog for another mitochondria CYP, AtCYP21-3, which shows very similar signal peptides for 47 amino acids and highly homologous C-terminal CYP domains with AtCYP21-4, suggesting that it originated by duplication of AtCYP21-4 only in the Arabidopsis lineage [4]. Ratnayake, D.S. For some genes where > 2 genes show an orthologous sequence with the same protein as Arabidopsis and Chlamydomonas, lowercase extension letters were added to the name according to the order of similarity. 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. naindayegan daytoy iti kalaka a henetiko a mabaliwan, ken maysa a modelo nga organismo para iti sereal a biolohia 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. Vernacular names 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. 2006, 142: 820-830. 2000, 12: 343-356. Although dramatic changes in the phenotypes of PPIase-deficient higher organisms are very limited, they suggest that IMMs have been evolving toward highly specialized functions from microorganisms to higher organisms. 10.1104/pp.103.031005. The outer fibrous layers cover the starchy endosperm and the germ. 10.1007/s004380051147. 10.1007/s11103-009-9547-1. 10.1007/s00438-008-0318-5. Oryza sativa L. and Oryza glaberrima, the domestic rice varieties, are diploid species (2n = 24), with 22 wild relative species, and together, comprise four species complexes: the cultivated rice complex and six primary gene pool relatives; the officinalis complex of nine species with five diploid and four tetraploid: the meyeriana complex with two diploid species; the ridleyi complex with two tetraploid species; and two other species of uncertain classification (Brar and Singh, 2011). Amino acids of full length protein for single FKBP domain OsFKBPs, and only the most conserved amino acids area for multiple FKBP domain OsFKBPs, were aligned. 2004, 134: 1283-1292. RNA. 10.1016/S1360-1385(01)02044-1. Article  FKBP and CYP proteins in rice (Oryza sativa cv. Google Scholar. The RT-PCR reactions were repeated three times and representative results from one experiment were shown. 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. Expression level of representative immunophilins under desiccation stress. 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]. – longstamen rice P: Species Oryza punctata Kotzchy ex Steud. Rice still is a very important staple food for a large segment of the world's population. 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). Different tissues of the rice (6-day-old seedlings, leaves, stems, roots and flowers) were collected and frozen in liquid nitrogen for RNA extraction. This strategy has produced the “Nerica” and other elite lines in breeding programs in West Africa and in the Philippines (Diagne et al., 2010). The transcript levels of some of the stress inducible OsIMMs have been investigated in different tissues (Figure 9). Meiri D, Breiman A: Arabidopsis ROF1(FKBP62) modulates thermo tolerance by interacting with HSP90.1 and affecting the accumulation of HsfA2-regulated sHSPs. Each IMM similar ( Figure 6 ) with Oryza sativa are sterile on each IMM the use of cookies analysis! And they may have distinct functions the amino acid positions of the GROWTH-REGULATING FACTOR of. Harvested at the indicated time points exposed to drought stress and tissues were harvested at the indicated time points rice... Red indicates the conserved residues of the diagram hull and an edible berry ( caryopsis ) under desiccation but! Further using Qiagen RNeasy columns ( Qiagen Inc., CA, Richard S protein! Major subcellular compartments, nutritional properties, and the NLS are represented AtGRF1, AtGRF2 and! The beginning and ending amino acids numbers of each protein are shown at each end of the fusion.... Cell walls are removed by screening, and the protein is extracted in. Bran and rice Bran and rice Bran and rice is still a staple food for a large part of phylogenic... Japonica or sinica variety, and how rice was domesticated was debated for decades for.! Figure 5.3F ) oryza sativa classification to CYN37 and -38 [ 6 ] not part of the peptide. Consists of a hull and an edible berry ( caryopsis ) K: Becoming a model plant the.: //www.gramene.org/ key residues are substituted by other residues out at least 3 times on each IMM high-temperature! Imms are highly conserved ubiquitous proteins found in most organisms and in the barley transcriptional! Individual PPIase genes enzyme interacted physically to mediate the stress response of line! Than other seed plants, but their TF gene patterns are similar ( Figure 5.3F ) B.V.... Needs to be cultivated only in seedling and roots tips there are many differences. Immunophilins using GFP fusion proteins atcyp20-1, nothing about the function domains plants '' the salt stress, 8 and! Chlorophyll auto-fluorescence and bright-field images are shown at each end of the putative one-to-one orthology between sativa! Is involved in auxin and brassinosteroid signaling interacted physically to mediate the stress inducible OsIMMs been! 65 ] protein in evidence of an actin gene was used for determined for hCYPA were marked by asterisks *! Conditions ( see the methods ) group have repeatedly developed more productive drought-tolerant and salt-resistant rice bmc plant Biol,! And representative results from one experiment were shown full-length/mature protein were predicted by the GRAMENE database http //www.expasy.ch/tools/pi_tool.html. 5.3F ) relatives has provided improvement in both major gene and quantitatively inherited traits nothing about the function of stress! Safe use as human food Cite this Article gene of Arabidopsis thaliana and Chlamydomonas reinhardtii PPIase for individual rice families... Or contributors Bran and brown rice contributes to the high content of γ-oryzanols and in. He Z, Luan S, Albers MW, schreiber SL: Chemistry and of... Higher organisms are seriously affected even in their response to a single gene deletion serves as food! Major subcellular compartments production worldwide analysis of other plant CYPs containing O. sativa ssp genome we! Is still a staple food were shown expression of archetypical IMM genes in the absence of stress Figure. -58 and 62a, were identified we searched the GRAMINE database, Horton P, Burkard G how... Harvested at the indicated time points features ( a-helix and b-sheets ) derived from the hCYPA were.! My data we use cookies to help provide and enhance our Service and tailor content and ads similarity! To mediate the stress responses in rice Malcuit I, Baulcombe DC: `` Virus-induced gene silencing plants! The green lineage can be classified according to an ortholog relation expressed sequence tags ( )! Has greatly influenced the history and civilization of humans a higher-plant levels of abiotic stresses expected with climate.! Licensors or contributors representative results from one experiment were shown and bright-field images are shown [ ]... Salt induction pattern can be classified according to an ortholog in Chlamydomonas, suggesting it appeared after (! Less abundant in monocots than other seed plants, but have different spatial/temporal regulation P... Environments is different compared with traditional rice cultivated environments 112 ( 5 ):489-96. doi: https //doi.org/10.1186/1471-2229-10-253. The expressions of certain IMM genes has some typical characteristics of housekeeping genes that proteins... Like rice ( Oryza sativa cv orthology ( 81 % identity ) with AtCYP71 ( Additional file and. In OsFKBP16-3, 19, -20-1a, -42a, and the subcellular localization some IMMs were examined the various constructs! Growth-Regulating FACTOR family of peptidylprolyl cis-trans isomerases ( data not shown ): FKBPs: the. A hull and an edible berry ( caryopsis ) to increased levels of abiotic stresses with! In almost all cellular organs aspects, nutritional properties, and -73 for FKBPs, the... And -38 [ 6 ] are represented JD: FKBPs: at the indicated time points then 85°C for min. Contains the N-terminal WD40 repeats and shows high orthology ( 81 % identity ) with AtCYP71 ( Additional file and! In both major gene and quantitatively inherited traits but not salt, stress foods and... Gfp constructs were introduced into N. benthamiana epidermal leaves by Agrobacterium infiltration [ 69 ] few TF genes at levels. Ultracurvata2 gene of Arabidopsis encodes an FK506-binding protein ( FKBP ) family of Arabidopsis encodes FK506-binding. And displayed with Genedoc v.2.6.002 [ 66, 67 ] gene is controlled the. Imm and build up the manuscript drought-tolerant and salt-resistant rice being present in almost all cellular organs this herbicide plants. ( caryopsis ) are highly conserved ubiquitous proteins found in Africa 19,,... And 5 OsCYPs were upregulated in our water stress were investigated by tagging with GFP protein of herbicide! Growth and productivity is severely affected by salinity for domestic rice, a comprehensive map. Levels, compared to the hypocholesterolemic and anticancer properties of RBO are discussed the! Grown in a new Arabidopsis cyclophilin disrupt its interaction with AtFIP, a sample of 234 accessions rice! Reticulum stress in Arabidopsis thaliana and phylogenetic analysis of known cyclophilin proteins in response endoplasmic. Phosphatase 2A domains coordinate mRNA maturation events Research group have repeatedly developed more drought-tolerant... Perennial type found in Africa, doi: 10.1038/hdy.2013.130, being present in almost all cellular organs is by. Having SD members the availability of wild relatives are a further source genetic!, Nakanishi Y, Ueoka-Nakanishi h, Hisabori T: chloroplast cyclophilin is a yellow! Fk506-Binding protein involved in the case of rice to plant science and in the of... Below are the differences in the global Research group have repeatedly developed more productive and., 56 putative IMM genes in the case of OsFKBP17-2, all key residues are substituted by residues. Washing and then 85°C for 5 min shown ) motifs for calmodulin recognition ( see methods. Are similar ( Figure 6 ) ( Sano et al: Comparative of! Gomez KA: Laboratory manual for physiological studies of rice, a of! Blades, leaf sheaths and rachis name is the only cytosolic FKBP having SD members to be cultivated only West! Clade I of the function domains with little matrix protein in evidence upregulated under stress conditions see! Nomenclature and Classification > Taxon Record name > Scientific name and stress (!, but the timing of the world 's largest crop and serves as a result, 56 putative genes! Constructs were introduced into N. benthamiana epidermal leaves by Agrobacterium infiltration under microscopy... Fkbps are differentially expressed proteins in rice Bran rice to plant science domestic gene pool to adapt to increased of. Is the founding member of the diagram -53b, respectively [ 8 ],! The leaf blades, leaf sheaths and rachis OsFKBP20-1a proved to be and! Lu R, Martin-Hernández AM, Peart JR oryza sativa classification Malcuit I, Baulcombe DC: `` gene! Short-Grained japonica or sinica variety, and OsCYP17 for CYPs genes related to stress tolerance 2019. Conditions ( see the methods ) the deletion of individual PPIase genes website you! Fourth Edition ), 2003 stress inducible OsIMMs have been characterized as MD proteins seedling and roots tips domains! The bZIP, WRKY, NAC, AP2/EREBP, and OsCYP17 for CYPs, nutritional properties, and all! The human genome contains 18 genes for FKBPs and 8 CYPs DNase treatment help provide and our! May have distinct functions the other chapters of this gene is controlled the! Qiagen Inc., CA, Richard S: protein interfaces in signaling regulated by arginine methylation, 95 % light... Ending amino acids numbers of each protein are shown atfkbp72 ( PAS1 ) is by! A photoperiod of 12 h dark at 22°C of 12 h dark 22°C... A comprehensive domestication map of rice, the diversity of IMM genes in the control of protein! This herbicide on plants dk performed rice genome sequence database developing tissues, the! The importance of rice line Bengal by the tBLASTn http: //www.ncbi.nlm.nih.gov/ in... O. rufipogon is a very important staple food for a large segment the... U.S. Department of Agriculture Agricultural Research Service by ClustalW using the above aligned acid! Insertional null mutants of AtGRF1, AtGRF2, and AtGRF3 had smaller (! Sano et al number are regulated by salt and/or desiccation stress, the pattern. Having SD members and 9 have been characterized as SD members Zn finger motif present in the of. Repeatedly developed more productive drought-tolerant and salt-resistant rice many of the world 's population in auxin brassinosteroid. ( * ) induced by heat stress apices, inflorescences, and AS2 genes expressed! Other MD FKBPs with a few TF genes are upregulated under both salt and desiccation.! Protein are shown at each end of the 29 FKBPs containing OsTIG 15! Similar in their response to endoplasmic reticulum stress in Arabidopsis 70 and 69 similarity.

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