Sirpiö S, Khrouchtchova A, Allahverdiyeva Y, Hansson M, Fristedt R, Vener AV, Scheller HV, Jensen PE, Haldrup A, Aro EM: AtCYP38 ensures early biogenesis, correct assembly and sustenance of photosystem II. 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. RNAs were isolated from two-week-old seedlings were exposed to drought stress and tissues were harvested at the indicated time points. However, few studies and little detailed and accurate information of root characteristics were reported in fine-rooted plants like rice (Oryza sativa L.). Japonica) were identified and classified, and given the appropriate name for each IMM, considering the ortholog-relation with Arabidopsis and Chlamydomonas or molecular weight of the proteins. 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). 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). Yang X, Tuskan GA, Cheng MZ: Divergence of the Dof gene families in poplar, Arabidopsis, and rice suggests multiple modes of gene evolution after duplication. Oryza formosana Masam. However, we could not find the CaM domain C-terminal area of OsFKBP72 using a CaM prediction program, unlike with AtFKBP72 (PAS1), a putative CaM domain in the C-terminal area due to the binding of calmodulin in vitro [43]. Google Scholar. 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). This strategy has produced the “Nerica” and other elite lines in breeding programs in West Africa and in the Philippines (Diagne et al., 2010). Plants were grown in a controlled chamber with a photoperiod of 12 h light at 28°C and 12 h dark at 22°C. 1984). Three OsFKBPs, OsFKBP20-1b, -58 and 62a, were upregulated under both salt and desiccation stress. Expression of the fusion proteins were monitored at 48 h after Agrobacterium injection by an Axiophot fluorescence microscope (Zeiss, Germany). The majority of chloroplast FKBPs have a peptidase cleavage site, Ala-Xaa-Ala, at the terminus of the hydrophobic region (Figure 1), suggesting that all the chloroplast FKBPs target the thylakoid lumen like the chloroplast FKBPs of Arabidopsis and Chlamydomonas. Article  The ER location of AtCYP19-4 (CYP5) has been confirmed by N-terminal green fluorescent protein fusion, and may involve the modulation of a guanine nucleotide exchange factor essential for vesicle trafficking [48, 49]. Yoshida S, Forno DA, Cock JH, Gomez KA: Laboratory manual for physiological studies of rice. 1991, 251: 283-287. Terms and Conditions, Oryza Scientific classification Kingdom: Plantae Clade: Tracheophytes Clade: Angiosperms Clade: Monocots Clade: Commelinids Order: Poales Family: Poaceae Subfamily: Oryzoideae Tribe: … 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]. The paralog OsFKBP42a and 42b are ~90% identical, but they have slightly different EST numbers (Additional file 1) and distinct spatial expression profiles, with OsFKBP42a being expressed at the highest levels in crown tissue, whereas OsFKBP42b is expressed more highly in the roots [8]. 2006, 12: 631-643. The availability of wild relatives provides opportunities beyond the domestic gene pool to adapt to increased levels of abiotic stresses expected with climate change. 2005, 4: 230-241. 2000, 152: 123-134. Grebe M, Gadea J, Steinmann T, Kientz M, Rahfeld JU, Salchert K, Koncz C, Jürgens G: A conserved domain of the Arabidopsis GNOM protein mediates subunit interaction and cyclophilin 5 binding. Correspondence to 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. FK506 binding proteins (FKBPs) and cyclophilins (CYPs) are abundant and ubiquitous proteins belonging to the peptidyl-prolyl cis/trans isomerase (PPIase) superfamily, which regulate much of metabolism through a chaperone or an isomerization of proline residues during protein folding. 10.1104/pp.103.022160. Classification of the putative FKBPs and CYPs in rice provides the information about their evolutional/functional significance when comparisons are drawn with the relatively well studied genera, Arabidopsis and Chlamydomonas. These were OsFKBP20-1a, -20-1b, -42a, -42b, -62a, -62b, and -62c for FKBPs and OsCYP40a, -40b, -59a, and -59b for CYPs. The various GFP constructs were introduced into N. benthamiana epidermal leaves by Agrobacterium infiltration [69]. Also, the two proteins exhibit phylogenetic divergence due to a tetra- (18-2) or penta- (18-1) peptide deletion in the β2 domain (Figure 4 and Figure 6). 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]. 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. Biochemistry. – longstamen rice P: Species Oryza punctata Kotzchy ex Steud. In particular, a number of IMMs relate to environmental stresses. Data source Beijing Genomics Institute 2006, 142: 820-830. BMC Plant Biol 10, 253 (2010). The transcript levels of some of the stress inducible OsIMMs have been investigated in different tissues (Figure 9). fEST number was estimated by the tblastN http://www.ncbi.nlm.nih.gov/. (A) QLQ and WRC domain organization in representative GRFs from A. thaliana (AtGRF), O. sativa (OsGRF), and Zea mays (ZmGRF). 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]. Glycemic index correlates negatively with amylose content. He Z, Li L, Luan S: Immunophilins and parvulins. To access the validity of subcellular localization for predicted Os IMM proteins, OsFKBP15-1, -20-1a, -20-1b, OsCYP19-2 and -20-2 were fused with N-terminal GFP protein and then expressed in N. benthamiana, using Agrobacterium transiently (Figure 10). 2014 May;112(5):489-96. doi: 10.1038/hdy.2013.130. Japonica). Harrar Y, Bellini C, Faure JD: FKBPs: at the crossroads of folding and transduction. OsFKBP44 and OsCYP17 did not show ESTs, but their expression was confirmed by RT-PCR analysis (Additional file 1). EMBO J. 333 1753 . Article  The alignments of amino acid sequence were performed using ClustalW and displayed with Genedoc v.2.6.002 [66, 67]. 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. In particular, AtCYP21-1, the ortholog of OsCYP21-1, has yet to have its location verified, being either cytosolic or ER [4, 50]. Smyczynski C, Roudier F, Gissot L, Vaillant E, Grandjean O, Morin H, Masson T, Bellec Y, Geelen D, Faure JD: The C terminus of the immunophilin PASTICCINO1 is required for plant development and for interaction with a NAC-like transcription factor. 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]. Expression in OsFKBP20-1a, -58, and -42b was induced at 1 h after desiccation stress, but expression in OsFKBP16-3, -19, -20-1b, -42a, and OsFKBP62a was induced 24 h after desiccation (Figure 8A). 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. 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]. It is cultivated worldwide with a concentration in Asia. India 7: 92. 2001, 11: 82-88. OsFKBP20-1a proved to be nuclear-targeting and heat-inducible; its over-expression in yeast indicates a capacity for high-temperature tolerance [60]. 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]. 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). In the case of rice, introgression from wild relatives has provided improvement in both major gene and quantitatively inherited traits. Members of the genus grow as tall, wetland grasses, growing to 1–2 m tall; the genus includes both annual and perennial species. Oryza sativa temperate japonica subgroup. Pombe [5, 6]. DK performed rice genome database search and sorting the IMM gene family. 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]. 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. Google Scholar. Annu Rev of Biochem. Kamphausen T, Fanghänel J, Neumann D, Schulz B, Rahfeld JU: Characterization of Arabidopsis thaliana AtFKBP42 that is membrane-bound and interacts with Hsp90. 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. The calmodulin-binding motif (CaM) has been recognized as a major Ca2+ sensor and as a modulator of regulatory events through its interaction with a protein [35]. RNAs were isolated from two-week-old seedlings were exposed to 200 mM NaCl and tissues were harvested at the indicated time points. Plant Physiol. 10.1007/s00497-004-0238-4. Backgrounds indicate percentage of amino acid similarity: black, 95%; dark grey, 70%; light grey, 40%. PubMed Central  They are collectively referred to as immunophilin (IMM), being present in almost all cellular organs. Salinity has been a key abiotic plant stress damaging crop production worldwide. We have identified 2 rice IMM families, FK506 binding proteins and cyclophilins, using the rice genome sequence database. The Opaline limited edition lipglosses by Oryza is a bright polychromatic range of long-lasting metallic glosses that bring a bright iridescent shimmer to your lips! 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]. 1999, 119: 693-704. Specifically, most of the genes survived without degeneration or great modification during evolution, which suggests that most orthologous IMM genes may have a conserved function in cell metabolism. This is the smallest genome of all food crops and approximately 50% of the genome is composed of repetitive sequences (Chang 2003). 10.1111/j.1365-313X.2008.03532.x. Ahn, J.C., Kim, DW., You, Y.N. All chloroplast lumen-located OsCYPs also contain double arginine residues, and follow the hydrophobic region needed for chloroplast lumen targeting (the signal sequences of OsCYP37 and OsCYP38 are not shown here for adequate CYP domain alignment) in the extension signal of the N-terminus (Figure 4). Methods. In the sativa complex, the seven primary gene pool relatives, all diploids with the A genome as domestic rice, have diverse ecogeographic distribution, as follows: Oryza nivara, an annual, ranges from the Deccan Plateau in India to the Plateau regions of Myanmar, China and South-East Asia, sometimes cohabiting with Oryza rufipogon, a close relative. 1998, 118: 1395-1401. CYP domains are represented by white box. 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. Google Scholar. However, higher organisms are seriously affected even in their response to a single gene deletion. 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). 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. PubMed Central  Nicholas KB, Nicholas HB, Deerfield DW: GeneDoc: analysis and visualization of genetic variation. 2003, 30: 296-303. OsFKBP16-1 is expressed only in leaves and stems, but the AtFKBP16-1, a chloroplast lumen protein, is well expressed in most of tissues except roots. 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].