Progress in Arabidopsis genome sequencing and functional genomics

Wambutt, R.; Murphy, G; Volckaert, Guido; Pohl, Thomas; Düsterhöft, Andreas; Stiekema, Willem J.; Entian, Karl‐Dieter; Terryn, Nancy; Harris, Barbara; Ansorge, Wilhelm; Brandt, Petra; Grivell, L.A.; Rieger, Michael A.; Weichselgartner, M.; Simone, Vincenzo De; Obermaier, B.; Mache, Régis; Müller, Manfred; Kreis, Martin E.; Delseny, Michel; Puigdomènech, Pere; Watson, Martin D.; Schmidtheini, T.; Reichert, B.; Portatelle, D.; Pérez-Alonso, Manuel; Boutry, Marc; Bancroft, Ian; Vos, Pieter; Hoheisel, Jörg D.; Zimmermann, Wolfgang; Wedler, Holger; Ridley, Peter T.; Langham, Sally; McCullagh, Bonnie S.; Bilham, Lorelei; Robben, Johan; Schueren, Jan van der; Grymonprez, Barbara; Chuang, Yu-Chen; Vandenbussche, Filip; Braeken, M.A.K.A.; Weltjens, I.; Voet, Marleen; Bastiaens, I.; Aert, Rita; Defoor, E.; Weitzenegger, Thomas; Bothe, Gordana; Ramsperger, Uwe; Hilbert, Helmut; Braun, Martha; Holzer, E.; Brandt, Amanda S.; Peters, Sabine; Staveren, M. van; Dirkse, W. G.; Mooijman, P.J.W.; Lankhorst, René Klein; Rose, Matthias; Hauf, J.; Kötter, Peter; Berneiser, S.; Hempel, Stefan; Feldpausch, Meghan N.; Lamberth, S.; Daele, Hilde Van den; Keyser, Annick De; Buysshaert, C.; Gielen, J.; Villarroel, Raimundo; Clercq, Rebecca De; Montagu, Marc Van; Rogers, Jane; Cronin, Ann; Quail, Michael A.; Bray-Allen, S.; Clark, Lynn M.; Doggett, Jon; Hall, Sarah E.; Kay, Mike; Lennard, Nicola; McLay, Kirsten; Mayes, Rebecca; Pettett, A.; Rajandream, Marie‐Adèle; Lyne, M.; Beneš, Vladimı́r; Rechmann, S.; Borkova, Dana; Blöcker, Helmut; Scharfe, Maren; Grimm, Marc Oliver; Löhnert, T H; Dose, S.; Haan, M. de; Maarse, Ammy C.; Schäfer, Melanie; Müller-Auer, S.; Gabel, C.; Fuchs, M.; Fartmann, Berthold; Granderath, K.; Dauner, D.; Herzl, A.; Neumann, Sebastian; Argiriou, Anagnostis; Vitale, Domenico; Liguori, Rosario; Piravandi, E.; Massenet, O.; Quigley, Françoise; Clabauld, G.; Mündlein, Axel; Felber, R.; Schnabl, Susanne; Hiller, Reinhard; Schmidt, Wolfgang; Lecharny, Alain; Aubourg, Santiago P.; Gy, Isabelle; Cooke, Richard; Berger, Christel; Monfort, Amparo; Casacuberta, Elena; Gibbons, Terry; Weber, Nico; Vandenbol, Micheline; Bargues, M.; Terol, Javier; Torres, A.; Pérez‐Pérez, Alejandro; Purnelle, Bénédicte; Bent, E.; Johnson, Samantha; Tacon, D.; Jesse, Taco; Heijnen, Leo; Schwarz, Štefan; Scholler, Patrik; Heber, Steffen; Bielke, C.; Frishmann, D; Haase, Dirk; Lemcke, Kai; Mewes, Hans‐Werner; Stöcker, Susanne; Zaccaria, Paolo; Mayer, Klaus; Schüller, Christine M.; Bevan, Michael W.

doi:10.1016/s0168-1656(00)00195-4

Cited by 15 publications

(4 citation statements)

References 34 publications

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“…A constitutive cyanase activity, similar to that of the E. coli enzyme, has been also reported in the cyanobacteria Synechococcus UTEX625, where the function may be related to providing CO 2 from bicarbonate and cyanate for photosynthesis [22], and Synechocystis PCC6803 [23,24]. Cyanase activity has been reported in some plant extracts [25,26] and the gene for cyanase has been identified in at least one plant species [27].…”

Section: Introductionmentioning

confidence: 89%

Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site

et al. 2000

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The cyanase monomer is composed of two domains. The N-terminal domain shows structural similarity to the DNA-binding alpha-helix bundle motif. The C-terminal domain has an 'open fold' with no structural homology to other proteins. The subunits of cyanase are arranged in a novel manner both at the dimer and decamer level. The dimer structure reveals the C-terminal domains to be intertwined, and the decamer is formed by a pentamer of these dimers. The active site of the enzyme is located between dimers and is comprised of residues from four adjacent subunits of the homodecamer. The structural data allow a conceivable reaction mechanism to be proposed.

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Section: Introductionmentioning

confidence: 89%

Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site

et al. 2000

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“…Initial estimates suggest that from 5% to 6% of Arabidopsis genes are rhythmically expressed (46a). This is a far cry from the apparent universality of circadian regulation of transcription in the cyanobacterium Synechococcus (85), but suggests that there are between ∼1250 and 1500 Arabidopsis CCGs, based on a current estimate of ∼25,000 Arabidopsis genes (154). Of course, the biological material used to generate the hybridization probes limits the detection of oscillating transcripts to those that are regulated in those tissues at the developmental stage under the specific growth conditions sampled, and it will take many iterations to exhaustively sample all possible developmental stages and environmental conditions.…”

Section: Rhythms In Gene Expressionmentioning

confidence: 99%

CIRCADIANRHYTHMS INPLANTS

McClung

2001

Annu. Rev. Plant. Physiol. Plant. Mol. Biol.

195

107

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Circadian rhythms, endogenous rhythms with periods of approximately 24 h, are widespread in nature. Although plants have provided many examples of rhythmic outputs and our understanding of photoreceptors of circadian input pathways is well advanced, studies with plants have lagged in the identification of components of the central circadian oscillator. Nonetheless, genetic and molecular biological studies, primarily in Arabidopsis, have begun to identify the components of plant circadian systems at an accelerating pace. There also is accumulating evidence that plants and other organisms house multiple circadian clocks both in different tissues and, quite probably, within individual cells, providing unanticipated complexity in circadian systems.

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“…Annotation of fully sequenced genomes also requires a search for the inherent marks, represented by speci¢c sequence motifs common to groups of functionally or phylogenetically related proteins [1]. Recently, a revolution in biosciences has begun by achieving a nearly complete sequence of human genome [2], Drosophila melanogaster, [3], Caenorhabditis elegans, [4] or plant Arabidopsis thaliana [5] genomes. Their detailed annotation (ascribing phenotypes to the revealed genes), namely in the case of human genome, will probably take years, however the ¢rst steps have already been taken [6,7].…”

Section: Introductionmentioning

confidence: 99%

Mitochondrial uncoupling proteins and phylogenesis – UCP4 as the ancestral uncoupling protein

Hanák

Ježek

2001

FEBS Letters

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We searched for the previously defined uncoupling protein (UCP) signatures [Jez ek, P. and Urbänkovä, E. (2000) IUBMB Life 49, 63^70] in genomes of Drosophila melanogaster, Caenorhabditis elegans, Dictyostelium discoideum, and Arabidopsis thaliana. We identified four UCPs in Drosophila and one in Caenorhabditis or Dictyostelium as close relatives of human UCP4 (BMCP), but distant from UCP1, UCP2, UCP3, and two plant UCPs of Arabidopsis. But the third Arabidopsis UCP is the closest UCP4 relative. This suggests that UCP4 represents the ancestral UCP from which other mammalian and plant UCPs diverged. Speculations on UCP4 participation in apoptosis are thus supported by its early phylogenetic occurrence. ß

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Progress in Arabidopsis genome sequencing and functional genomics

Cited by 15 publications

References 34 publications

Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site

Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site

CIRCADIANRHYTHMS INPLANTS

Mitochondrial uncoupling proteins and phylogenesis – UCP4 as the ancestral uncoupling protein

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