Genomes and Genes
Summary: Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.
- Mendes M, Guerra R, Berns M, Manzo C, Masiero S, Finzi L, et al. MADS domain transcription factors mediate short-range DNA looping that is essential for target gene expression in Arabidopsis. Plant Cell. 2013;25:2560-72 pubmed publisher..Our in vivo data show that the size and position of this loop, determined by the choice of CArG element usage, is essential for correct expression. Our studies provide solid in vivo evidence for the floral quartet model. ..
- Parrilla Doblas J, Ponferrada Marín M, Roldan Arjona T, Ariza R. Early steps of active DNA demethylation initiated by ROS1 glycosylase require three putative helix-invading residues. Nucleic Acids Res. 2013;41:8654-64 pubmed publisher..Altogether, our results suggest that ROS1 uses three predicted helix-invading residues to actively interrogate DNA in search for 5-meC. ..
- Bonnet S, Knoll A, Hartung F, Puchta H. Different functions for the domains of the Arabidopsis thaliana RMI1 protein in DNA cross-link repair, somatic and meiotic recombination. Nucleic Acids Res. 2013;41:9349-60 pubmed publisher..The OB-fold domain 2 is not necessary for either somatic or meiotic HR, but it seems to have a minor function in DNA cross-link repair. ..
- Posé D, Verhage L, Ott F, Yant L, Mathieu J, Angenent G, et al. Temperature-dependent regulation of flowering by antagonistic FLM variants. Nature. 2013;503:414-7 pubmed publisher..A better understanding of how temperature controls the molecular mechanisms of flowering will be important to cope with current changes in global climate. ..
- Kong Y, Zhou G, Abdeen A, Schafhauser J, Richardson B, Atmodjo M, et al. GALACTURONOSYLTRANSFERASE-LIKE5 is involved in the production of Arabidopsis seed coat mucilage. Plant Physiol. 2013;163:1203-17 pubmed publisher..These data provide evidence that AtGATL5 might function in the regulation of the final size of the mucilage rhamnogalacturonan I. ..
- Hu Y, Jiang L, Wang F, Yu D. Jasmonate regulates the inducer of cbf expression-C-repeat binding factor/DRE binding factor1 cascade and freezing tolerance in Arabidopsis. Plant Cell. 2013;25:2907-24 pubmed publisher..Taken together, our study provides evidence that jasmonate functions as a critical upstream signal of the ICE-CBF/DREB1 pathway to positively regulate Arabidopsis freezing tolerance...
- Geng Y, Wu R, Wee C, Xie F, Wei X, Chan P, et al. A spatio-temporal understanding of growth regulation during the salt stress response in Arabidopsis. Plant Cell. 2013;25:2132-54 pubmed publisher..Together, our data reveal a sophisticated assortment of regulatory programs acting together to coordinate spatially patterned biological changes involved in the immediate and long-term response to a stressful shift in environment. ..
- Yang C, Bratzel F, Hohmann N, Koch M, Turck F, Calonje M. VAL- and AtBMI1-mediated H2Aub initiate the switch from embryonic to postgerminative growth in Arabidopsis. Curr Biol. 2013;23:1324-9 pubmed publisher..Furthermore, we show different mechanisms to achieve PcG repression in plants, as the repression of genes involved in other processes has different requirements for H2Aub and H3K27me3 marking...
- Derkacheva M, Steinbach Y, Wildhaber T, Mozgová I, Mahrez W, Nanni P, et al. Arabidopsis MSI1 connects LHP1 to PRC2 complexes. EMBO J. 2013;32:2073-85 pubmed publisher..The LHP1-MSI1 interaction forms a positive feedback loop to recruit PRC2 to chromatin that carries H3K27me3. Consequently, this can provide a mechanism for the faithful inheritance of local epigenetic information through replication. ..
- Cruz Ramírez A, Diaz Trivino S, Wachsman G, Du Y, Arteaga Vazquez M, Zhang H, et al. A SCARECROW-RETINOBLASTOMA protein network controls protective quiescence in the Arabidopsis root stem cell organizer. PLoS Biol. 2013;11:e1001724 pubmed publisher..Analysis of the in vivo role of quiescence in the root stem cell niche reveals that slow cycling within the QC is not needed for structural integrity of the niche but allows the growing root to cope with DNA damage. ..
- Sukumar P, Maloney G, Muday G. Localized induction of the ATP-binding cassette B19 auxin transporter enhances adventitious root formation in Arabidopsis. Plant Physiol. 2013;162:1392-405 pubmed publisher..These experiments are consistent with localized synthesis of ABCB19 protein after hypocotyl excision leads to enhanced IAA transport and local IAA accumulation driving adventitious root formation. ..
- Pinosa F, Buhot N, Kwaaitaal M, Fahlberg P, Thordal Christensen H, Ellerstr m M, et al. Arabidopsis phospholipase d? is involved in basal defense and nonhost resistance to powdery mildew fungi. Plant Physiol. 2013;163:896-906 pubmed publisher..In conclusion, we propose that PLD is involved in defense signaling in nonhost resistance against powdery mildew fungi and put PLD? forward as the main isoform participating in this process...
- Koen E, Besson Bard A, Duc C, Astier J, Gravot A, Richaud P, et al. Arabidopsis thaliana nicotianamine synthase 4 is required for proper response to iron deficiency and to cadmium exposure. Plant Sci. 2013;209:1-11 pubmed publisher..Collectively, our data, together with recent studies, support the hypothesis that AtNAS4 displays an important role in iron distribution and is required for proper response to iron deficiency and to cadmium supply...
- Da Ines O, Degroote F, Goubely C, Amiard S, Gallego M, White C. Meiotic recombination in Arabidopsis is catalysed by DMC1, with RAD51 playing a supporting role. PLoS Genet. 2013;9:e1003787 pubmed publisher..Our data demonstrate that RAD51 plays a supporting role for DMC1 in meiotic recombination in the flowering plant, Arabidopsis. ..
- Niu Q, Liang Y, Zhou J, Dou X, Gao S, Chen L, et al. Pollen-expressed transcription factor 2 encodes a novel plant-specific TFIIB-related protein that is required for pollen germination and embryogenesis in Arabidopsis. Mol Plant. 2013;6:1091-108 pubmed publisher..These results suggest that PTF2 plays crucial roles in pollen germination and embryogenesis in Arabidopsis, possibly by regulating gene expression through interaction with TBP2 and the subunits of RNAPs. ..
- Leydon A, Beale K, Woroniecka K, Castner E, Chen J, Horgan C, et al. Three MYB transcription factors control pollen tube differentiation required for sperm release. Curr Biol. 2013;23:1209-14 pubmed publisher..Our data indicate that de novo transcription in the pollen tube nucleus during growth in the pistil leads to pollen tube differentiation required for release of sperm cells. ..
- Kapazoglou A, Drosou V, Argiriou A, Tsaftaris A. The study of a barley epigenetic regulator, HvDME, in seed development and under drought. BMC Plant Biol. 2013;13:172 pubmed publisher..The study of a barley DME gene will contribute to our understanding of epigenetic mechanisms operating during seed development and stress response in agronomically important cereal crops. ..
- Yángüez E, Castro Sanz A, Fernández Bautista N, Oliveros J, Castellano M. Analysis of genome-wide changes in the translatome of Arabidopsis seedlings subjected to heat stress. PLoS ONE. 2013;8:e71425 pubmed publisher..Among the differentially translated genes, master regulators of the stress response stand out, highlighting the main role of translation in the early establishment of the physiological response of plants to elevated temperatures. ..
- Stankovic N, Schloesser M, Joris M, Sauvage E, Hanikenne M, Motte P. Dynamic Distribution and Interaction of the Arabidopsis SRSF1 Subfamily Splicing Factors. Plant Physiol. 2016;170:1000-13 pubmed publisher..Altogether, our report extends our understanding of shuttling dynamics of Arabidopsis SR splicing factors. ..
- Sheng L, Hu X, Du Y, Zhang G, Huang H, Scheres B, et al. Non-canonical WOX11-mediated root branching contributes to plasticity in Arabidopsis root system architecture. Development. 2017;144:3126-3133 pubmed publisher..The discovery of WOX11-mediated root-derived roots reveals a previously uncharacterized pathway that confers plasticity during the generation of root system architecture in response to different inductive cues. ..
- Kamioka M, Takao S, Suzuki T, Taki K, Higashiyama T, Kinoshita T, et al. Direct Repression of Evening Genes by CIRCADIAN CLOCK-ASSOCIATED1 in the Arabidopsis Circadian Clock. Plant Cell. 2016;28:696-711 pubmed publisher..This study shows that direct binding by CCA1 in the morning provides strong repression of PRR5, and repression by CCA1 also temporally regulates an evening-expressed gene set that includes PRR5. ..
- Xu G, Yuan M, Ai C, Liu L, Zhuang E, Karapetyan S, et al. uORF-mediated translation allows engineered plant disease resistance without fitness costs. Nature. 2017;545:491-494 pubmed publisher..This broadly applicable strategy may lead to decreased pesticide use and reduce the selective pressure for resistant pathogens. ..
- Lazarus S, Tseng H, Lawrence F, Woodruff M, Duncan E, Pettit A. Characterization of Normal Murine Carpal Bone Development Prompts Re-Evaluation of Pathologic Osteolysis as the Cause of Human Carpal-Tarsal Osteolysis Disorders. Am J Pathol. 2017;187:1923-1934 pubmed publisher..Thus, abnormal peri-articular skeletal development and modeling, rather than excessive bone resorption, may be the underlying pathophysiology of these skeletal syndromes. ..
- Minas G, Momiji H, Jenkins D, Costa M, Rand D, Finkenstädt B. ReTrOS: a MATLAB toolbox for reconstructing transcriptional activity from gene and protein expression data. BMC Bioinformatics. 2017;18:316 pubmed publisher..The output from this software provides a useful analysis of time series data and can be incorporated into further modelling approaches or in hypothesis generation. ..
- Hameed M. Hypoxia up-regulates mitochondrial genome-encoded transcripts in Arabidopsis roots. Genes Genet Syst. 2016;90:325-34 pubmed publisher..Since no significant difference was detected in the expression of mitochondrial RNA polymerases or the mitochondrial DNA content per cell, we propose a transcriptional mode of induction of mitochondrial gene expression under hypoxia. ..
- Goñi O, Fort A, Quille P, McKeown P, Spillane C, O Connell S. Comparative Transcriptome Analysis of Two Ascophyllum nodosum Extract Biostimulants: Same Seaweed but Different. J Agric Food Chem. 2016;64:2980-9 pubmed publisher..The standardization of the composition of ANE biostimulants represents a challenge for providing consistent effects on plant gene expression and biostimulation. ..
- Gabruk M, Habina I, Kruk J, Dłużewska J, Szymańska R. Natural variation in tocochromanols content in Arabidopsis thaliana accessions - the effect of temperature and light intensity. Physiol Plant. 2016;157:147-60 pubmed publisher..Unexpectedly, the highest increase in the PC-OH/PC ratio was found for accessions originating from cold climate (Shigu, Krazo-1 and Lov-5), even though such plants could be expected to be more resistant to low temperature stress. ..
- Geng X, Shen M, Kim J, Mackey D. The Pseudomonas syringae type III effectors AvrRpm1 and AvrRpt2 promote virulence dependent on the F-box protein COI1. Plant Cell Rep. 2016;35:921-32 pubmed publisher..Collectively, these results indicate that type III effectors AvrRpm1 and AvrRpt2 promote bacterial virulence by targeting a COI1-dependent signaling pathway. ..
- Zanella M, Borghi G, Pirone C, Thalmann M, Pazmino D, Costa A, et al. Î²-amylase 1 (BAM1) degrades transitory starch to sustain proline biosynthesis during drought stress. J Exp Bot. 2016;67:1819-26 pubmed publisher..We propose the transitory-starch/proline interplay as an interesting trait to be tackled by breeding technologies aimingto improve drought tolerance in relevant crops. ..
- Pitzschke A, Xue H, Persak H, Datta S, Seifert G. Post-Translational Modification and Secretion of Azelaic Acid Induced 1 (AZI1), a Hybrid Proline-Rich Protein from Arabidopsis. Int J Mol Sci. 2016;17: pubmed publisher..In summary, the data point to AZI1 being a partially secreted protein and a likely new member of the group of hydroxyproline-rich glycoproteins. Its dual location suggests AZI1 to exert both intra- and extracellular functions. ..
- Herud O, Weijers D, Lau S, Jurgens G. Auxin responsiveness of the MONOPTEROS-BODENLOS module in primary root initiation critically depends on the nuclear import kinetics of the Aux/IAA inhibitor BODENLOS. Plant J. 2016;85:269-77 pubmed publisher..Our results suggest that the instability of the inhibitor BDL necessitates a fast nuclear uptake in order to reach the critical threshold level required for auxin responsiveness of the MP-BDL module in primary root initiation. ..
- Wang X, Liu L. Crystal Structure and Catalytic Mechanism of 7-Hydroxymethyl Chlorophyll a Reductase. J Biol Chem. 2016;291:13349-59 pubmed publisher..Furthermore, the trimeric form of HCAR provides a biological clue of its interaction with light-harvesting complex II. ..
- Holtkotte X, Ponnu J, Ahmad M, Hoecker U. The blue light-induced interaction of cryptochrome 1 with COP1 requires SPA proteins during Arabidopsis light signaling. PLoS Genet. 2017;13:e1007044 pubmed publisher..Similarly, ?CC-SPA1 interacted with CRY2, though with a much lower affinity than wild-type SPA1. In total, our results demonstrate that CRY1 and CRY2 strongly differ in their blue light-induced interaction with the COP1/SPA complex...
- Sankari M, Hemachandran H, Anantharaman A, Babu S, Madrid R, C G, et al. Identifying a Carotenoid Cleavage Dioxygenase 4a Gene and Its Efficient Agrobacterium-Mediated Genetic Transformation in Bixa orellana L. Appl Biochem Biotechnol. 2016;179:697-714 pubmed publisher..orellana was closely related to the CsCCD4 gene of C. sativus, which suggests this gene may have a role in various processes such as fragrance, insect attractant and pollination. ..
- Michaud M, Gros V, Tardif M, BrugiÃ¨re S, Ferro M, Prinz W, et al. AtMic60 Is Involved in Plant Mitochondria Lipid Trafficking and Is Part of a Large Complex. Curr Biol. 2016;26:627-39 pubmed publisher..Furthermore, AtMic60 promotes lipid desorption from membranes, likely as an initial step for lipid transfer, and binds to Tom40, suggesting that AtMic60 could regulate the tethering between the inner and outer membranes of mitochondria. ..
- VÃcha J, BabinskÃ½ M, Demo G, OtrusinovÃ¡ O, Jansen S, PekÃ¡rovÃ¡ B, et al. The influence of Mg2+ coordination on 13C and 15N chemical shifts in CKI1RD protein domain from experiment and molecular dynamics/density functional theory calculations. Proteins. 2016;84:686-99 pubmed publisher..A partial correlation between dominant geometry influence and torsion angle shifts upon the coordination has been observed. ..
- Chen X, Huang H, Qi T, Liu B, Song S. New perspective of the bHLH-MYB complex in jasmonate-regulated plant fertility in arabidopsis. Plant Signal Behav. 2016;11:e1135280 pubmed publisher..Here, we further discuss the different properties of the components of the bHLH-MYB complex in expression pattern and stamen regulation. ..
- Zhao B, Lv M, Feng Z, Campbell T, Liscum E, Li J. TWISTED DWARF 1 Associates with BRASSINOSTEROID-INSENSITIVE 1 to Regulate Early Events of the Brassinosteroid Signaling Pathway. Mol Plant. 2016;9:582-92 pubmed publisher..These results provide better understanding of the early events of the BR signaling pathway. ..
- Olivier M, Da Ines O, Amiard S, Serra H, Goubely C, White C, et al. The Structure-Specific Endonucleases MUS81 and SEND1 Are Essential for Telomere Stability in Arabidopsis. Plant Cell. 2016;28:74-86 pubmed publisher..SEND1 has at most a minor role in resolution of the Holliday junction but acts as an essential backup to MUS81 for resolution of toxic replication structures to ensure genome stability and to maintain telomere integrity. ..
- Takagi H, Ishiga Y, Watanabe S, Konishi T, Egusa M, Akiyoshi N, et al. Allantoin, a stress-related purine metabolite, can activate jasmonate signaling in a MYC2-regulated and abscisic acid-dependent manner. J Exp Bot. 2016;67:2519-2532 pubmed publisher..Overall, this study suggests a possible connection of purine catabolism with stress hormone homeostasis and signaling, and highlights the potential importance of allantoin in these interactions. ..
- Hetmann A, Wujak M, Kowalczyk S. Protein Transphosphorylation During the Mutual Interaction between Phytochrome A and a Nuclear Isoform of Nucleoside Diphosphate Kinase Is Regulated by Red Light. Biochemistry (Mosc). 2016;81:1153-1162 pubmed..The results presented in this work indicate that NDPK-In may function as a protein kinase regulated by light. ..
- Hwang S, Li H, Alavilli H, Lee B, Choi D. Molecular and physiological characterization of AtHIGD1 in Arabidopsis. Biochem Biophys Res Commun. 2017;487:881-886 pubmed publisher..Our results represent the first report of a biological function for an HIGD protein in plants and indicate that AtHIGD1 is a mitochondrial protein that plays an active role in mitigating the effects of hypoxia on plants. ..
- Dietrich D, Pang L, Kobayashi A, Fozard J, Boudolf V, Bhosale R, et al. Root hydrotropism is controlled via a cortex-specific growth mechanism. Nat Plants. 2017;3:17057 pubmed publisher..In addition, unlike its role in root gravitropism, the elongation zone performs a dual function during a hydrotropic response, both sensing a water potential gradient and subsequently undergoing differential growth. ..