Genomes and Genes
Experts and Doctors on arabidopsis proteins in Sapporo, Hokkaido, Japan
Locale: Sapporo, Hokkaido, Japan
Topic: arabidopsis proteins
- Ohtomo I, Ueda H, Shimada T, Nishiyama C, Komoto Y, Hara Nishimura I, et al. Identification of an allele of VAM3/SYP22 that confers a semi-dwarf phenotype in Arabidopsis thaliana. Plant Cell Physiol. 2005;46:1358-65 pubmed..These findings suggest that VAM3/SYP22 and SYP23 have overlapping functions and that the vesicle transport mediated by these syntaxins is important for shoot morphogenesis. ..
- Tian C, Muto H, Higuchi K, Matamura T, Tatematsu K, Koshiba T, et al. Disruption and overexpression of auxin response factor 8 gene of Arabidopsis affect hypocotyl elongation and root growth habit, indicating its possible involvement in auxin homeostasis in light condition. Plant J. 2004;40:333-43 pubmed..ARF family genes seem to control both auxin sensitivity and homeostasis in Arabidopsis. ..
- Hanzawa Y, Takahashi T, Michael A, Burtin D, Long D, Pineiro M, et al. ACAULIS5, an Arabidopsis gene required for stem elongation, encodes a spermine synthase. EMBO J. 2000;19:4248-56 pubmed
- Yamashita Y, Kadokura Y, Sotta N, Fujiwara T, Takigawa I, Satake A, et al. Ribosomes in a stacked array: elucidation of the step in translation elongation at which they are stalled during S-adenosyl-L-methionine-induced translation arrest of CGS1 mRNA. J Biol Chem. 2014;289:12693-704 pubmed publisher..We propose that the anticodon end of peptidyl-tRNA resides in the A-site of the stacked ribosomes and that the stacked ribosomes are stalled at an early step of translocation, possibly at the P/E hybrid state...
- Matsushima N, Mikami T, Tanaka T, Miyashita H, Yamada K, Kuroki Y. Analyses of non-leucine-rich repeat (non-LRR) regions intervening between LRRs in proteins. Biochim Biophys Acta. 2009;1790:1217-37 pubmed publisher..The sequence analysis of IRs offers functional similarity in some LRR@IR protein families. This study suggests that various IRs and super motifs provide a great variety of structures and functions for LRRs. ..
- Fujioka Y, Noda N, Fujii K, Yoshimoto K, Ohsumi Y, Inagaki F. In vitro reconstitution of plant Atg8 and Atg12 conjugation systems essential for autophagy. J Biol Chem. 2008;283:1921-8 pubmed..The in vitro conjugation systems reported here will afford a tool with which to investigate the cross-talk mechanism between two conjugation systems. ..
- Sako K, Maki Y, Kanai T, Kato E, Maekawa S, Yasuda S, et al. Arabidopsis RPT2a, 19S proteasome subunit, regulates gene silencing via DNA methylation. PLoS ONE. 2012;7:e37086 pubmed publisher..Increased methylation was also found at transposon sequences, suggesting that the 19S proteasome containing AtRPT2a negatively regulates TGS at transgenes and at specific endogenous genes through DNA methylation. ..
- Nagane T, Tanaka A, Tanaka R. Involvement of AtNAP1 in the regulation of chlorophyll degradation in Arabidopsis thaliana. Planta. 2010;231:939-49 pubmed publisher..The concerted regulation of chlorophyll degradation is discussed in relation to the function of AtNAP1. ..
- Takano J, Tanaka M, Toyoda A, Miwa K, Kasai K, Fuji K, et al. Polar localization and degradation of Arabidopsis boron transporters through distinct trafficking pathways. Proc Natl Acad Sci U S A. 2010;107:5220-5 pubmed publisher..The present study of BOR1 and NIP5;1 demonstrates the importance of selective endocytic trafficking in polar localization and degradation of plant nutrient transporters for radial transport and homeostasis of plant mineral nutrients. ..
- Sasaki K, Kim M, Imai R. Arabidopsis COLD SHOCK DOMAIN PROTEIN2 is a RNA chaperone that is regulated by cold and developmental signals. Biochem Biophys Res Commun. 2007;364:633-8 pubmed..These data indicated that AtCSP2 is involved in developmental processes as well as cold adaptation. Localization of AtCSP2::GFP in nucleolus and cytoplasm suggested different nuclear and cytosolic RNA targets. ..
- Sato T, Maekawa S, Yasuda S, Domeki Y, Sueyoshi K, Fujiwara M, et al. Identification of 14-3-3 proteins as a target of ATL31 ubiquitin ligase, a regulator of the C/N response in Arabidopsis. Plant J. 2011;68:137-46 pubmed publisher..These results indicate that ATL31 targets and ubiquitinates 14-3-3 proteins for degradation via the ubiquitin-proteasome system during the response to cellular C/N status. ..
- Nakajima S, Ito H, Tanaka R, Tanaka A. Chlorophyll b reductase plays an essential role in maturation and storability of Arabidopsis seeds. Plant Physiol. 2012;160:261-73 pubmed publisher..Furthermore, NYC1 expression was repressed in the ABA-insensitive mutants during embryogenesis. These data indicate that chlorophyll degradation is induced by ABA during seed maturation to produce storable seeds. ..
- Yamanaka T, Ohta T, Takahashi M, Meshi T, Schmidt R, Dean C, et al. TOM1, an Arabidopsis gene required for efficient multiplication of a tobamovirus, encodes a putative transmembrane protein. Proc Natl Acad Sci U S A. 2000;97:10107-12 pubmed..Taken into account that the tobamovirus replication complex is associated with membranes, we propose that TOM1 participates in the in vivo formation of the replication complex by serving as a membrane anchor...
- Sonoda Y, Yao S, Sako K, Sato T, Kato W, Ohto M, et al. SHA1, a novel RING finger protein, functions in shoot apical meristem maintenance in Arabidopsis. Plant J. 2007;50:586-96 pubmed..These observations indicate that SHA1, a putative E3 ligase, is required for post-embryonic SAM maintenance by controlling proper cellular organization. ..
- Suzuki M, Kato A, Nagata N, Komeda Y. A xylanase, AtXyn1, is predominantly expressed in vascular bundles, and four putative xylanase genes were identified in the Arabidopsis thaliana genome. Plant Cell Physiol. 2002;43:759-67 pubmed..Of these, two also contain several regions with sequences similar to CBDs in their N-terminal regions. Comparison of the amino acid sequences of the five xylanases suggests a possible process for their molecular evolution. ..
- Takahashi K, Takabayashi A, Tanaka A, Tanaka R. Functional analysis of light-harvesting-like protein 3 (LIL3) and its light-harvesting chlorophyll-binding motif in Arabidopsis. J Biol Chem. 2014;289:987-99 pubmed publisher..Collectively, these results indicate that the LHC motif of LIL3 is involved in the complex formation of LIL3 and GGR, which might contribute to the GGR reaction. ..
- Abe M, Katsumata H, Komeda Y, Takahashi T. Regulation of shoot epidermal cell differentiation by a pair of homeodomain proteins in Arabidopsis. Development. 2003;130:635-43 pubmed..This suggests that PDF2 and ATML1 are functionally interchangeable and play a critical role in maintaining the identity of L1 cells, possibly by interacting with their L1 box and those of downstream target-gene promoters. ..
- Tatematsu K, Kumagai S, Muto H, Sato A, Watahiki M, Harper R, et al. MASSUGU2 encodes Aux/IAA19, an auxin-regulated protein that functions together with the transcriptional activator NPH4/ARF7 to regulate differential growth responses of hypocotyl and formation of lateral roots in Arabidopsis thaliana. Plant Cell. 2004;16:379-93 pubmed..These results suggest that MSG2/IAA19 and NPH4/ARF7 may constitute a negative feedback loop to regulate differential growth responses of hypocotyls and lateral root formation. ..
- Maruyama Y, Yamoto N, Suzuki Y, Chiba Y, Yamazaki K, Sato T, et al. The Arabidopsis transcriptional repressor ERF9 participates in resistance against necrotrophic fungi. Plant Sci. 2013;213:79-87 pubmed publisher..These results indicate that the transcriptional repressor ERF9 participates in plant defense mechanisms against necrotic fungi mediated by the DEAR1-dependent ethylene/JA signaling pathway...
- Tashiro S, Tian C, Watahiki M, Yamamoto K. Changes in growth kinetics of stamen filaments cause inefficient pollination in massugu2, an auxin insensitive, dominant mutant of Arabidopsis thaliana. Physiol Plant. 2009;137:175-87 pubmed publisher..Considering that MSG2 is likely to be a direct target of the auxin F-box receptors, MSG2 may be one of the master genes that control the transient growth increase of stamen filaments. ..
- Nakagawa M, Komeda Y. Flowering of Arabidopsis cop1 mutants in darkness. Plant Cell Physiol. 2004;45:398-406 pubmed..The delay in flowering in the double mutants was not strongly influenced by the light conditions, whereas that of the gi-2 cop1-6 double mutant was reduced in darkness. ..
- Xie G, Kato H, Sasaki K, Imai R. A cold-induced thioredoxin h of rice, OsTrx23, negatively regulates kinase activities of OsMPK3 and OsMPK6 in vitro. FEBS Lett. 2009;583:2734-8 pubmed publisher..This inhibition effects were redox-dependent and did not involve stable physical interaction. The data suggested a novel mechanism for redox regulation of MAPKs in plants...
- Matsunaga W, Kobayashi A, Kato A, Ito H. The effects of heat induction and the siRNA biogenesis pathway on the transgenerational transposition of ONSEN, a copia-like retrotransposon in Arabidopsis thaliana. Plant Cell Physiol. 2012;53:824-33 pubmed publisher..In contrast to vegetative tissue, high accumulation of the transcripts and amplified DNA copies of ONSEN were detected in callus. This result indicated that ONSEN activation is controlled by cell-specific regulatory mechanisms. ..
- Abe M, Takahashi T, Komeda Y. Cloning and characterization of an L1 layer-specific gene in Arabidopsis thaliana. Plant Cell Physiol. 1999;40:571-80 pubmed..Possible roles of the PDF1 gene in the SAM are discussed. ..
- Hayashi N, Sasaki S, Takahashi H, Yamashita Y, Naito S, Onouchi H. Identification of Arabidopsis thaliana upstream open reading frames encoding peptide sequences that cause ribosomal arrest. Nucleic Acids Res. 2017;45:8844-8858 pubmed publisher..thaliana protoplasts. These results suggest that the peptide sequences of the three uORFs identified in this study cause ribosomal arrest in the uORFs, thereby repressing the expression of proteins encoded by the main ORFs. ..
- Yamasato A, Tanaka R, Tanaka A. Loss of the N-terminal domain of chlorophyllide a oxygenase induces photodamage during greening of Arabidopsis seedlings. BMC Plant Biol. 2008;8:64 pubmed publisher..In conclusion, the A domain of CAO is essential in the control of chlorophyll biosynthesis and in the survival of seedlings during de-etiolation especially under strong illumination. ..
- Takahashi T, Matsuhara S, Abe M, Komeda Y. Disruption of a DNA topoisomerase I gene affects morphogenesis in Arabidopsis. Plant Cell. 2002;14:2085-93 pubmed
- Muto H, Watahiki M, Nakamoto D, Kinjo M, Yamamoto K. Specificity and similarity of functions of the Aux/IAA genes in auxin signaling of Arabidopsis revealed by promoter-exchange experiments among MSG2/IAA19, AXR2/IAA7, and SLR/IAA14. Plant Physiol. 2007;144:187-96 pubmed..These results showed functional differences among the msg2-1, axr2-1, and slr-1 proteins, though some phenotypes were determined by the promoter activity. ..
- Fujibe T, Saji H, Watahiki M, Yamamoto K. Overexpression of the RADICAL-INDUCED CELL DEATH1 (RCD1) gene of Arabidopsis causes weak rcd1 phenotype with compromised oxidative-stress responses. Biosci Biotechnol Biochem. 2006;70:1827-31 pubmed..Subcellular localization of RCD1 was examined by transiently expressing green fluorescent protein (GFP) fused with RCD1 in onion epidermal cells. GFP signals are observed as aggregated foci in the inner nuclear matrix-like region. ..
- Kato H, Motomura T, Komeda Y, Saito T, Kato A. Overexpression of the NAC transcription factor family gene ANAC036 results in a dwarf phenotype in Arabidopsis thaliana. J Plant Physiol. 2010;167:571-7 pubmed publisher..Microscopy revealed that cell sizes in leaves and stems of these plants were smaller than those in wild-type plants. These findings suggested that ANAC036 and its orthologues are involved in the growth of leaf cells. ..
- Sako K, Maki Y, Aoyama T, Goto D, Yamaguchi J. Control of endoreduplication of trichome by RPT2a, a subunit of the 19S proteasome in Arabidopsis. J Plant Res. 2010;123:701-6 pubmed publisher..Together, these data suggest that RPT2a functions to negatively regulate endocycle progression following completion of the third endoreduplication step mediated by RHL1 (8C-16C). ..
- Hagiwara Y, Komoda K, Yamanaka T, Tamai A, Meshi T, Funada R, et al. Subcellular localization of host and viral proteins associated with tobamovirus RNA replication. EMBO J. 2003;22:344-53 pubmed..These observations suggest that the formation of tobamoviral RNA replication complex occurs on TOM1-containing membranes and is facilitated by TOM2A...
- Kim M, Sasaki K, Imai R. Cold shock domain protein 3 regulates freezing tolerance in Arabidopsis thaliana. J Biol Chem. 2009;284:23454-60 pubmed publisher..Overexpression of AtCSP3 in transgenic plants conferred enhanced freezing tolerance over wild-type plants. Together, the data demonstrated an essential role of RNA chaperones for cold adaptation in higher plants. ..
- Muto H, Yabe N, Asami T, Hasunuma K, Yamamoto K. Overexpression of constitutive differential growth 1 gene, which encodes a RLCKVII-subfamily protein kinase, causes abnormal differential and elongation growth after organ differentiation in Arabidopsis. Plant Physiol. 2004;136:3124-33 pubmed..Taken together, CDG1 gene may interfere with signal transduction of BR when overexpressed, but is not an essential factor for it in the wild type. ..
- Tsuda K, Yamazaki K. Structure and expression analysis of three subtypes of Arabidopsis MBF1 genes. Biochim Biophys Acta. 2004;1680:1-10 pubmed..These findings suggest that AtMBF1c may be involved in stress response pathway. ..
- Muto H, Nagao I, Demura T, Fukuda H, Kinjo M, Yamamoto K. Fluorescence cross-correlation analyses of the molecular interaction between an Aux/IAA protein, MSG2/IAA19, and protein-protein interaction domains of auxin response factors of arabidopsis expressed in HeLa cells. Plant Cell Physiol. 2006;47:1095-101 pubmed..These results also show that FCCS is useful to examine protein-protein interactions especially for transcriptional regulators. ..
- Shimosaka E, Sasanuma T, Handa H. A wheat cold-regulated cDNA encoding an early light-inducible protein (ELIP): its structure, expression and chromosomal location. Plant Cell Physiol. 1999;40:319-25 pubmed..The data showed that the wcr12 gene or related homologues are located on the chromosomes of homoeologous group-5 in wheat...
- Yamanaka T, Imai T, Satoh R, Kawashima A, Takahashi M, Tomita K, et al. Complete inhibition of tobamovirus multiplication by simultaneous mutations in two homologous host genes. J Virol. 2002;76:2491-7 pubmed
- Miwa K, Wakuta S, Takada S, Ide K, Takano J, Naito S, et al. Roles of BOR2, a boron exporter, in cross linking of rhamnogalacturonan II and root elongation under boron limitation in Arabidopsis. Plant Physiol. 2013;163:1699-709 pubmed publisher..Thus, we propose that under B-limited conditions, transport of boric acid/borate by BOR2 from symplast to apoplast is required for effective cross linking of RG-II in cell wall and root cell elongation...
- Yoshinari A, Kasai K, Fujiwara T, Naito S, Takano J. Polar localization and endocytic degradation of a boron transporter, BOR1, is dependent on specific tyrosine residues. Plant Signal Behav. 2012;7:46-9 pubmed publisher..Here, we analyzed possible involvement of an additional tyrosine residue (Y414) in the loop region and discuss the pathway of the BOR1 trafficking for polar localization and endocytic degradation of BOR1. ..
- Nakagawara E, Sakuraba Y, Yamasato A, Tanaka R, Tanaka A. Clp protease controls chlorophyll b synthesis by regulating the level of chlorophyllide a oxygenase. Plant J. 2007;49:800-9 pubmed
- Onouchi H, Haraguchi Y, Nakamoto M, Kawasaki D, Nagami Yamashita Y, Murota K, et al. Nascent peptide-mediated translation elongation arrest of Arabidopsis thaliana CGS1 mRNA occurs autonomously. Plant Cell Physiol. 2008;49:549-56 pubmed publisher..In contrast, decay intermediates of CGS1 mRNA normally observed upon induction of CGS1 mRNA decay in plant systems were not detected in RRL, raising the possibility that CGS1 mRNA degradation involves a plant-specific mechanism. ..
- Onodera Y, Nakagawa K, Haag J, Pikaard D, Mikami T, Ream T, et al. Sex-biased lethality or transmission of defective transcription machinery in Arabidopsis. Genetics. 2008;180:207-18 pubmed publisher..As a result, the expected stringent selection against nonfunctional essential genes in the haploid state occurs in the female lineage but is relaxed in the male lineage. ..
- Hirashima M, Tanaka R, Tanaka A. Light-independent cell death induced by accumulation of pheophorbide a in Arabidopsis thaliana. Plant Cell Physiol. 2009;50:719-29 pubmed publisher..We discuss the possible mechanism of light-independent cell death and the involvement of pheophorbide a in the signaling pathway for programmed cell death. ..
- Ito H, Yoshida T, Tsukahara S, Kawabe A. Evolution of the ONSEN retrotransposon family activated upon heat stress in Brassicaceae. Gene. 2013;518:256-61 pubmed publisher..These results suggest that ONSEN has conserved transcriptional activation promoted by environmental heat stress in some Brassicaceae species...