451
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Gissot L, Polge C, Bouly JP, Lemaitre T, Kreis M, Thomas M. AKINbeta3, a plant specific SnRK1 protein, is lacking domains present in yeast and mammals non-catalytic beta-subunits. PLANT MOLECULAR BIOLOGY 2004; 56:747-59. [PMID: 15803412 DOI: 10.1007/s11103-004-5111-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2004] [Accepted: 10/18/2004] [Indexed: 05/23/2023]
Abstract
The SNF1/AMPK/SnRK1 heterotrimeric kinase complex is involved in the adaptation of cellular metabolism in response to diverse stresses in yeast, mammals and plants. Following a model proposed in yeast, the kinase targets are likely to bind the complex via the non-catalytic beta-subunits. These proteins currently identified in yeast, mammals and plants present a common structure with two conserved interacting domains named Kinase Interacting Sequence (KIS) and Association with SNF1 Complex (ASC), and a highly variable N-terminal domain. In this paper we describe the characterisation of AKINbeta3, a novel protein related to AKINbeta subunits of Arabidopsis thaliana, containing a truncated KIS domain and no N-terminal extension. Interestingly the missing region of the KIS domain corresponds to the glycogen-binding domain (beta-GBD) identified in the mammalian AMPKbeta1. In spite of its unusual features, AKINbeta3 complements the yeast sip1Deltasip2Deltagal83Delta mutant. Moreover, interactions between AKINbeta3 and other AKIN complex subunits from A. thaliana were detected by two-hybrid experiments and in vitro binding assays. Taken together these data demonstrate that AKINbeta3 is a beta-type subunit. A search for beta-type subunits revealed the existence of beta3-type proteins in other plant species. Furthermore, we suggest that the AKINbeta3-type subunits could be plant specific since no related sequences have been found in any of the other completely sequenced genomes. These data suggest the existence of novel SnRK1 complexes including AKINbeta3-type subunits, involved in several functions among which some could be plant specific.
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Affiliation(s)
- Lionel Gissot
- Laboratoire de Biologie du Développement des Plantes, Institut de Biotechnologie des Plantes (IBP), UMR CNRS 8618, Bâtiment 630, Université Paris-Sud, F-91405 Orsay Cedex, France
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452
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Martínez Zamora MG, Castagnaro AP, Díaz Ricci JC. Isolation and diversity analysis of resistance gene analogues (RGAs) from cultivated and wild strawberries. Mol Genet Genomics 2004; 272:480-7. [PMID: 15565466 DOI: 10.1007/s00438-004-1079-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2004] [Accepted: 10/05/2004] [Indexed: 10/26/2022]
Abstract
Degenerate oligonucleotide primers, designed based on conserved regions of Nucleotide Binding Site (NBS) domains from previously cloned plant resistance genes, were used to isolate Resistance Gene Analogues (RGAs) from wild and cultivated strawberries. Seven distinct families of RGAs of the NBS-LRR type were identified from two related wild species, Fragaria vesca and F. chiloensis, and six different Fragaria x ananassa cultivars. With one exception (GAV-3), the deduced amino acid sequences of strawberry RGAs showed strong similarity to TIR (Toll Interleukin I Receptor)-type R genes from Arabidopsis, tobacco and flax, suggesting the existence of common ancestors. GAV-3 seemed to be more closely related to the non-TIR type. Further studies showed that the recombination level and the ratio of non-synonymous to synonymous substitutions within families were low. These data suggest that NBS-encoding sequences of RGAs in strawberry are subject to a gradual accumulation of mutations leading to purifying selection, rather than to a diversifying process. The present paper is the first report on RGAs in strawberry.
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Affiliation(s)
- M G Martínez Zamora
- Dpto. de Bioquímica de la Nutrición, Instituto de Química Biológica "Dr. Bernabé Bloj" (UNT), INSIBIO (CONICET-UNT), Chacabuco 461, 4000 Tucumán, Argentina
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453
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Chen TM, Lu CC, Li WH. Prediction of splice sites with dependency graphs and their expanded bayesian networks. Bioinformatics 2004; 21:471-82. [PMID: 15374869 DOI: 10.1093/bioinformatics/bti025] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Owing to the complete sequencing of human and many other genomes, huge amounts of DNA sequence data have been accumulated. In bioinformatics, an important issue is how to predict the complete structure of genes from the genomic DNA sequence, especially the human genome. A crucial part in the gene structure prediction is to determine the precise exon-intron boundaries, i.e. the splice sites, in the coding region. RESULTS We have developed a dependency graph model to fully capture the intrinsic interdependency between base positions in a splice site. The establishment of dependency between two position is based on a chi2-test from known sample data. To facilitate statistical inference, we have expanded the dependency graph (which is usually a graph with cycles that make probabilistic reasoning very difficult, if not impossible) into a Bayesian network (which is a directed acyclic graph that facilitates statistical reasoning). When compared with the existing models such as weight matrix model, weight array model, maximal dependence decomposition, Cai et al.'s tree model as well as the less-studied second-order and third-order Markov chain models, the expanded Bayesian networks from our dependency graph models perform the best in nearly all the cases studied. AVAILABILITY Software (a program called DGSplicer) and datasets used are available at http://csrl.ee.nthu.edu.tw/bioinf/ CONTACT cclu@ee.nthu.edu.tw.
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Affiliation(s)
- Te-Ming Chen
- Department of Electrical Engineering, National Tsing Hua University Hsinchu 30013, Taiwan
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454
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Talbert PB, Bryson TD, Henikoff S. Adaptive evolution of centromere proteins in plants and animals. J Biol 2004; 3:18. [PMID: 15345035 PMCID: PMC549713 DOI: 10.1186/jbiol11] [Citation(s) in RCA: 183] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2004] [Revised: 07/20/2004] [Accepted: 07/22/2004] [Indexed: 11/25/2022] Open
Abstract
Background Centromeres represent the last frontiers of plant and animal genomics. Although they perform a conserved function in chromosome segregation, centromeres are typically composed of repetitive satellite sequences that are rapidly evolving. The nucleosomes of centromeres are characterized by a special H3-like histone (CenH3), which evolves rapidly and adaptively in Drosophila and Arabidopsis. Most plant, animal and fungal centromeres also bind a large protein, centromere protein C (CENP-C), that is characterized by a single 24 amino-acid motif (CENPC motif). Results Whereas we find no evidence that mammalian CenH3 (CENP-A) has been evolving adaptively, mammalian CENP-C proteins contain adaptively evolving regions that overlap with regions of DNA-binding activity. In plants we find that CENP-C proteins have complex duplicated regions, with conserved amino and carboxyl termini that are dissimilar in sequence to their counterparts in animals and fungi. Comparisons of Cenpc genes from Arabidopsis species and from grasses revealed multiple regions that are under positive selection, including duplicated exons in some grasses. In contrast to plants and animals, yeast CENP-C (Mif2p) is under negative selection. Conclusions CENP-Cs in all plant and animal lineages examined have regions that are rapidly and adaptively evolving. To explain these remarkable evolutionary features for a single-copy gene that is needed at every mitosis, we propose that CENP-Cs, like some CenH3s, suppress meiotic drive of centromeres during female meiosis. This process can account for the rapid evolution and the complexity of centromeric DNA in plants and animals as compared to fungi.
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Affiliation(s)
- Paul B Talbert
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA 98109-1024, USA
| | - Terri D Bryson
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA 98109-1024, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, Seattle, WA 98109-1024, USA
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455
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Zhou Y, Zhou C, Ye L, Dong J, Xu H, Cai L, Zhang L, Wei L. Database and analyses of known alternatively spliced genes in plants. Genomics 2004; 82:584-95. [PMID: 14611800 DOI: 10.1016/s0888-7543(03)00204-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Alternative splicing is an important cellular mechanism that increases the diversity of gene products. The number of alternatively spliced genes reported so far in plants is much smaller than that in mammals, but is increasing as a result of the explosive growth of available EST and genomic sequences. We have searched for all alternatively spliced genes reported in GenBank and PubMed in all plant species under Viridiplantae. After careful merging and manual review of the search results, we obtained a comprehensive, high-quality collection of 168 genes reported to be alternatively spliced in plants, spanning 44 plant species (March 22, 2003 update). We developed a relational database with Web-based user interface to store and present the data, named the Plant Alternative Splicing Database (PASDB), freely available at http://pasdb.genomics.org.cn. We analyzed the functional categories that these genes belong to using the Gene Ontology. We also analyzed in detail the biological roles and gene structures of the four genes that are known to be alternatively spliced in more than one plant species. Finally, we studied the structural features of the splice sites in the alternatively spliced genes.
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Affiliation(s)
- Yan Zhou
- Hangzhou Genomics Institute, Key Laboratory of Bioinformatics of Zhejiang Province, Zhejiang University, Hangzhou, Zhejiang 310007, China
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456
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Morales ME, Kalinna BH, Heyers O, Mann VH, Schulmeister A, Copeland CS, Loukas A, Brindley PJ. Genomic organization of the Schistosoma mansoni aspartic protease gene, a platyhelminth orthologue of mammalian lysosomal cathepsin D. Gene 2004; 338:99-109. [PMID: 15302411 DOI: 10.1016/j.gene.2004.05.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2004] [Revised: 05/06/2004] [Accepted: 05/17/2004] [Indexed: 10/26/2022]
Abstract
Schistosomes are considered the most important of the helminth parasites of humans in terms of morbidity and mortality. Schistosomes employ proteolytic enzymes to digest host hemoglobin from ingested human blood, including a cathepsin D-like, aspartic protease that is overexpressed in the gut of the adult female schistosome. Because of its key role in parasite nutrition, this enzyme represents a potential intervention target. To continue exploration of this potential, here we have determined the sequence, structure and genomic organization of the cathepsin D gene locus of Schistosoma mansoni. Using the cDNA encoding S. mansoni cathepsin D as a probe, we isolated several positive bacterial artificial chromosomes (BAC) from a BAC library that represents an approximately 8-fold coverage of the schistosome genome. Sequencing of BAC clone 25-J-24 revealed that the cathepsin D gene locus was approximately 13 kb in length, and included seven exons interrupted by six introns. The exons ranged in length from 49 to 294 bp, and the introns from 30 to 5025 bp. The genomic organization of schistosome cathepsin D was similar in sequence, structure and complexity to human cathepsin D, including to a greater or lesser extent the conservation of all six exon/intron boundaries of the schistosome gene. It was less similar to aspartic protease genes of the nematodes Caenorhabditis elegans and Haemonchus contortus, and dissimilar to those of plasmepsins from malarial parasites. Examination of the introns revealed the presence of endogenous mobile genetic elements including SR2, the ASL-associated retrotransposon, and the SINE-like element, SMalpha. Phylogenetically, schistosome cathepsin D appeared to be more closely related to mammalian cathepsin D than to other sub-families of eukaryotic aspartic proteases known from mammals. Taken together, these features indicated that schistosome cathepsin D is a platyhelminth orthologue of mammalian lysosomal cathepsin D.
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Affiliation(s)
- Maria E Morales
- Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
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457
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Graham MA, Silverstein KAT, Cannon SB, VandenBosch KA. Computational identification and characterization of novel genes from legumes. PLANT PHYSIOLOGY 2004; 135:1179-97. [PMID: 15266052 PMCID: PMC519039 DOI: 10.1104/pp.104.037531] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2003] [Revised: 04/01/2004] [Accepted: 04/03/2004] [Indexed: 05/18/2023]
Abstract
The Fabaceae, the third largest family of plants and the source of many crops, has been the target of many genomic studies. Currently, only the grasses surpass the legumes for the number of publicly available expressed sequence tags (ESTs). The quantity of sequences from diverse plants enables the use of computational approaches to identify novel genes in specific taxa. We used BLAST algorithms to compare unigene sets from Medicago truncatula, Lotus japonicus, and soybean (Glycine max and Glycine soja) to nonlegume unigene sets, to GenBank's nonredundant and EST databases, and to the genomic sequences of rice (Oryza sativa) and Arabidopsis. As a working definition, putatively legume-specific genes had no sequence homology, below a specified threshold, to publicly available sequences of nonlegumes. Using this approach, 2,525 legume-specific EST contigs were identified, of which less than three percent had clear homology to previously characterized legume genes. As a first step toward predicting function, related sequences were clustered to build motifs that could be searched against protein databases. Three families of interest were more deeply characterized: F-box related proteins, Pro-rich proteins, and Cys cluster proteins (CCPs). Of particular interest were the >300 CCPs, primarily from nodules or seeds, with predicted similarity to defensins. Motif searching also identified several previously unknown CCP-like open reading frames in Arabidopsis. Evolutionary analyses of the genomic sequences of several CCPs in M. truncatula suggest that this family has evolved by local duplications and divergent selection.
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Affiliation(s)
- Michelle A Graham
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108, USA
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458
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Mehli L, Schaart JG, Kjellsen TD, Tran DH, Salentijn EMJ, Schouten HJ, Iversen TH. A gene encoding a polygalacturonase-inhibiting protein (PGIP) shows developmental regulation and pathogen-induced expression in strawberry. THE NEW PHYTOLOGIST 2004; 163:99-110. [PMID: 33873779 DOI: 10.1111/j.1469-8137.2004.01088.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
• Polygalacturonase-inhibiting proteins (PGIPs) have been demonstrated to play a role in host defence in several plants. • The PGIP now cloned from strawberry (Fragaria × ananassa) showed a high degree of homology to other fruit PGIPs. The gene expression of strawberry PGIP was monitored in healthy leaves, flowers and fruit at different maturity stages. PGIP transcript levels were also analysed following fruit inoculation with the fungal pathogen Botrytis cinerea in strawberry cultivars displaying variation in susceptibility. • Healthy mature berries showed the highest constitutive PGIP gene expression levels compared with leaves, flowers and immature fruit, indicating that the gene is developmentally regulated. Among the cultivars studied ('Elsanta', 'Korona', 'Polka', 'Senga sengana', 'Tenira'), 'Polka' had the highest constitutive expression level of PGIP. After inoculation with B. cinerea, all five cultivars displayed a significant induction of PGIP gene expression, but the differences between them were not statistically significant. • The high induction of the PGIP gene after inoculation with B. cinerea indicates that PGIP has a role in defence of strawberry.
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Affiliation(s)
- Lisbeth Mehli
- Plantebiosenteret, Department of Biology, NTNU, 7491 Trondheim, Norway
- Present address: Sør-Trøndelag University College, Department of Food Science, Trondheim, Norway
| | - Jan G Schaart
- Plant Research International, Business Unit Biodiversity and Breeding, Post box 16, 6700 AA Wageningen, The Netherlands
| | - Trygve D Kjellsen
- Plantebiosenteret, Department of Biology, NTNU, 7491 Trondheim, Norway
| | - Diem Hong Tran
- Plant Research International, Business Unit Biodiversity and Breeding, Post box 16, 6700 AA Wageningen, The Netherlands
| | - Elma M J Salentijn
- Plant Research International, Business Unit Biodiversity and Breeding, Post box 16, 6700 AA Wageningen, The Netherlands
| | - Henk J Schouten
- Plant Research International, Business Unit Biodiversity and Breeding, Post box 16, 6700 AA Wageningen, The Netherlands
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459
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Cooper JL, Henikoff S. Adaptive evolution of the histone fold domain in centromeric histones. Mol Biol Evol 2004; 21:1712-8. [PMID: 15175412 DOI: 10.1093/molbev/msh179] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Centromeric DNA, being highly repetitive, has been refractory to molecular analysis. However, centromeric structural proteins are encoded by single-copy genes, and these can be analyzed by using standard phylogenetic tools. The centromere-specific histone, CenH3, replaces histone H3 in centromeric nucleosomes, and is required for the proper distribution of chromosomes during cell division. Whereas histone H3s are nearly identical between species, CenH3s are divergent, with an N-terminal tail that is highly variable in length and sequence. Both the N-terminal tail and histone fold domain (HFD) are subject to adaptive evolution in Drosophila. Similarly, comparisons between Arabidopsis thaliana and Arabidopsis arenosa detected adaptive evolution, but only in the N-terminal tail. We have extended our evolutionary analyses of CenH3s to other members of the Brassicaceae, which allowed the detection of positive selection in both the N-terminal tail and in the HFD. We find that adaptively evolving sites in the HFD can potentially interact with DNA, including sites in the loop 1 region of the HFD that are required for centromeric targeting in Drosophila. Other adaptively evolving sites in the HFD can be localized on the structure of the nucleosome core particle, revealing an extended surface in addition to loop 1 in which conformational changes might alter histone-DNA contacts or water bridges. The identification of adaptively evolving sites provides a structural basis for the interaction between centromeric DNA and the protein that is thought to underlie the evolution of centromeres and the accumulation of pericentric heterochromatin.
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Affiliation(s)
- Jennifer L Cooper
- Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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460
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Guitton AE, Page DR, Chambrier P, Lionnet C, Faure JE, Grossniklaus U, Berger F. Identification of new members of Fertilisation Independent Seed Polycomb Group pathway involved in the control of seed development in Arabidopsis thaliana. Development 2004; 131:2971-81. [PMID: 15151989 DOI: 10.1242/dev.01168] [Citation(s) in RCA: 154] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In higher plants, double fertilisation initiates seed development. One sperm cell fuses with the egg cell and gives rise to the embryo, the second sperm cell fuses with the central cell and gives rise to the endosperm. The endosperm develops as a syncytium with the gradual organisation of domains along an anteroposterior axis defined by the position of the embryo at the anterior pole and by the attachment to the placenta at the posterior pole. We report that ontogenesis of the posterior pole in Arabidopsis thaliana involves oriented migration of nuclei in the syncytium. We show that this migration is impaired in mutants of the three founding members of the FERTILIZATION INDEPENDENT SEED (FIS) class, MEDEA (MEA), FIS2 and FERTILIZATION INDEPENDENT ENDOSPERM (FIE). A screen based on a green fluorescent protein (GFP) reporter line allowed us to identify two new loci in the FIS pathway, medicis and borgia. We have cloned the MEDICIS gene and show that it encodes the Arabidopsis homologue of the yeast WD40 domain protein MULTICOPY SUPRESSOR OF IRA (MSI1). The mutations at the new fis loci cause the same cellular defects in endosperm development as other fis mutations, including parthenogenetic development, absence of cellularisation, ectopic development of posterior structures and overexpression of the GFP marker.
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Affiliation(s)
- Anne-Elisabeth Guitton
- EMBO YIP Team, Unité Mixte de Recherche 5667, IFR128 BioSciences Lyon-Gerland, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, F-69364 Lyon cedex 07, France
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461
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Gemignani F, Moreno V, Landi S, Moullan N, Chabrier A, Gutiérrez-Enríquez S, Hall J, Guino E, Peinado MA, Capella G, Canzian F. A TP53 polymorphism is associated with increased risk of colorectal cancer and with reduced levels of TP53 mRNA. Oncogene 2004; 23:1954-6. [PMID: 14647431 DOI: 10.1038/sj.onc.1207305] [Citation(s) in RCA: 159] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We undertook a case-control study to examine the possible associations of the TP53 variants Arg > Pro at codon 72 and p53PIN3, a 16 bp insertion/duplication in intron 3, with the risk of colorectal cancer (CRC). The p53PIN3 A2 allele (16 bp duplication) was associated with an increased risk (OR 1.55, 95% CI 1.10-2.18, P = 0.012), of the same order of magnitude as that observed in previous studies for other types of cancer. The Pro72 allele was weakly associated with CRC (OR = 1.34, 95% CI 0.98-1.84, P = 0.066). The possible functional role of p53PIN3 was investigated by examining the TP53 mRNA transcripts in 15 lymphoblastoid cell lines with different genotypes. The possibility that the insertion/deletion could lead to alternatively spliced mRNAs was excluded. However, we found reduced levels of TP53 mRNA associated with the A2 allele. In conclusion, the epidemiological study suggests a role for p53PIN3 in tumorigenesis, supported by the in vitro characterization of this variant.
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462
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Castelli V, Aury JM, Jaillon O, Wincker P, Clepet C, Menard M, Cruaud C, Quétier F, Scarpelli C, Schächter V, Temple G, Caboche M, Weissenbach J, Salanoubat M. Whole genome sequence comparisons and "full-length" cDNA sequences: a combined approach to evaluate and improve Arabidopsis genome annotation. Genome Res 2004; 14:406-13. [PMID: 14993207 PMCID: PMC353228 DOI: 10.1101/gr.1515604] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
To evaluate the existing annotation of the Arabidopsis genome further, we generated a collection of evolutionary conserved regions (ecores) between Arabidopsis and rice. The ecore analysis provides evidence that the gene catalog of Arabidopsis is not yet complete, and that a number of these annotations require re-examination. To improve the Arabidopsis genome annotation further, we used a novel "full-length" enriched cDNA collection prepared from several tissues. An additional 1931 genes were covered by new "full-length" cDNA sequences, raising the number of annotated genes with a corresponding "full-length" cDNA sequence to about 14,000. Detailed comparisons between these "full-length" cDNA sequences and annotated genes show that this resource is very helpful in determining the correct structure of genes, in particular, those not yet supported by "full-length" cDNAs. In addition, a total of 326 genomic regions not included previously in the Arabidopsis genome annotation were detected by this cDNA resource, providing clues for new gene discovery. Because, as expected, the two data sets only partially overlap, their combination produces very useful information for improving the Arabidopsis genome annotation.
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Affiliation(s)
- Vanina Castelli
- Genoscope-Centre National de Séquençage and Centre National de la Recherche Scientifique Unité Mixte de Recherche-3080, 91000 Evry, France
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463
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Chantret N, Cenci A, Sabot F, Anderson O, Dubcovsky J. Sequencing of the Triticum monococcum Hardness locus reveals good microcolinearity with rice. Mol Genet Genomics 2004; 271:377-86. [PMID: 15014981 DOI: 10.1007/s00438-004-0991-y] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2003] [Accepted: 02/16/2004] [Indexed: 11/25/2022]
Abstract
The Hardness ( Ha) locus on chromosome 5D is the main determinant of grain texture in hexaploid wheat. The related genes Puroindoline-a and -b ( Pina-D1, Pinb-D1) and Grain Softness Protein ( Gsp-D1) are tightly linked at this locus. Mutations in the Pina-D1 and Pinb-D1 genes are associated with increased grain hardness. We report here the complete sequence of a 101-kb BAC clone from Triticum monococcum (A(m ) genome) which includes these three genes, and its comparison with the orthologous region in rice. The genes Gsp-A(m) 1, Pina-A(m) 1 and Pinb-A(m) 1 are separated by 37 kb and 32 kb, respectively, and are organized in the same transcriptional orientation. Four additional genes, including a pair of duplicated genes, were identified upstream of Gsp-A(m) 1 within a high-density gene island. These additional genes were found in the same order and orientation, and the same relative distances apart as similar genes previously annotated on rice chromosome 12. An interesting discovery was a small unannotated putative rice gene that was similar to the Gsp-A(m) 1 gene of T. monococcum (65% similarity at the protein level), and that was disposed in the same orientation, and located in the same position relative to the other orthologous genes. The high gene density observed in this BAC (1 gene per 14 kb) was expected for a distal chromosome region, but the level of microcolinearity with rice was higher than that reported in similar distal regions of other wheat chromosomes. Most of the BAC sequence (40%) was represented by repetitive elements, mainly concentrated in regions adjacent to the genes Pina-A(m) 1 and Pinb-A(m) 1. Rearrangements among these repetitive elements might provide an explanation for the frequent deletions observed at this locus in the genomes of the polyploid wheat species.
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Affiliation(s)
- N Chantret
- INRA, CIRAD-AMIS-Biotrop, Av. Agropolis, TA 40/30, 34398 Cedex 5, Montpellier, France
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464
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Copeland CS, Heyers O, Kalinna BH, Bachmair A, Stadler PF, Hofacker IL, Brindley PJ. Structural and evolutionary analysis of the transcribed sequence of Boudicca, a Schistosoma mansoni retrotransposon. Gene 2004; 329:103-14. [PMID: 15033533 DOI: 10.1016/j.gene.2003.12.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2003] [Revised: 12/09/2003] [Accepted: 12/23/2003] [Indexed: 10/26/2022]
Abstract
Boudicca is a gypsy-like, long terminal repeat (LTR) retrotransposon that has colonized the genome of the human blood fluke, Schistosoma mansoni. Previous studies have indicated that more than 1000 copies of Boudicca reside within the S. mansoni genome, although many of them may be degenerate and inactive. Messenger RNAs transcribed from genomic copies of Boudicca were investigated by reverse transcription PCR. Overlapping RT-PCR products corresponding to the gag and pol polyproteins of Boudicca, along with relevant sequences of genomic fragments of Boudicca, were assembled into contigs. Consensus sequences from these contigs were used to predict the sequence and structure of transpositionally active copies of the Boudicca retrotransposon. They verified that Boudicca has a kabuki-like Cys-His box motif at the active site of its gag protein, a classic DTG motif as the active site of the protease domain of the pol ORF2, and indicated a contiguous integrase domain at the C-terminus of pol with strong identity to integrase from the LTR retrotransposons CsRn1 and kabuki, as well as to the conserved integrase core domain, GenBank rve (). Models of the secondary structure of the Boudicca transcript suggested that the first AUG was occluded by a stem loop structure, which in turn suggested a method of regulation of expression, at the level of translation, of Boudicca proteins. In addition, phylogenetic analysis targeting discrete domains of Boudicca revealed a generalized radiation in sequences among the multiple copies of Boudicca resident in the schistosome genome.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Chromosomes, Artificial, Bacterial/genetics
- Cloning, Molecular
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Helminth/chemistry
- DNA, Helminth/genetics
- Evolution, Molecular
- Gene Dosage
- Gene Expression Regulation
- Gene Products, gag/genetics
- Genome
- Molecular Sequence Data
- Nucleic Acid Conformation
- Phylogeny
- Polyproteins/genetics
- Protein Biosynthesis/genetics
- RNA, Helminth/chemistry
- RNA, Helminth/genetics
- Retroelements/genetics
- Schistosoma mansoni/genetics
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
- Transcription, Genetic/genetics
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Affiliation(s)
- Claudia S Copeland
- Department of Molecular Parasitology, Institute for Biology, Humboldt University Berlin, Berlin, Germany
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465
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Jeffares DC, Phillips MJ, Moore S, Veit B. A description of the Mei2-like protein family; structure, phylogenetic distribution and biological context. Dev Genes Evol 2004; 214:149-58. [PMID: 14986133 DOI: 10.1007/s00427-004-0384-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2003] [Accepted: 12/21/2003] [Indexed: 10/26/2022]
Abstract
The Schizosaccharomyces pombe Mei2 gene encodes an RNA recognition motif (RRM) protein that stimulates meiosis upon binding a specific non-coding RNA and subsequent accumulation in a "mei2-dot" in the nucleus. We present here the first systematic characterization of the family of proteins with characteristic Mei2-like amino acid sequences. Mei2-like proteins are an ancient eukaryotic protein family with three identifiable RRMs. The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is the most highly conserved of the three RRMs. RRM3 also contains conserved sequence elements at its C-terminus not found in other RRM domains. Single copy Mei2-like genes are present in some fungi, in alveolates such as Paramecium and in the early branching eukaryote Entamoeba histolytica, while plants contain small families of Mei2-like genes. While the C-terminal RRM is highly conserved between plants and fungi, indicating conservation of molecular mechanisms, plant Mei2-like genes have changed biological context to regulate various aspects of developmental pattern formation.
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Affiliation(s)
- Daniel C Jeffares
- Department of Evolutionary Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark.
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466
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Eden E, Brunak S. Analysis and recognition of 5' UTR intron splice sites in human pre-mRNA. Nucleic Acids Res 2004; 32:1131-42. [PMID: 14960723 PMCID: PMC373407 DOI: 10.1093/nar/gkh273] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2003] [Revised: 10/21/2003] [Accepted: 12/16/2003] [Indexed: 12/23/2022] Open
Abstract
Prediction of splice sites in non-coding regions of genes is one of the most challenging aspects of gene structure recognition. We perform a rigorous analysis of such splice sites embedded in human 5' untranslated regions (UTRs), and investigate correlations between this class of splice sites and other features found in the adjacent exons and introns. By restricting the training of neural network algorithms to 'pure' UTRs (not extending partially into protein coding regions), we for the first time investigate the predictive power of the splicing signal proper, in contrast to conventional splice site prediction, which typically relies on the change in sequence at the transition from protein coding to non-coding. By doing so, the algorithms were able to pick up subtler splicing signals that were otherwise masked by 'coding' noise, thus enhancing significantly the prediction of 5' UTR splice sites. For example, the non-coding splice site predicting networks pick up compositional and positional bias in the 3' ends of non-coding exons and 5' non-coding intron ends, where cytosine and guanine are over-represented. This compositional bias at the true UTR donor sites is also visible in the synaptic weights of the neural networks trained to identify UTR donor sites. Conventional splice site prediction methods perform poorly in UTRs because the reading frame pattern is absent. The NetUTR method presented here performs 2-3-fold better compared with NetGene2 and GenScan in 5' UTRs. We also tested the 5' UTR trained method on protein coding regions, and discovered, surprisingly, that it works quite well (although it cannot compete with NetGene2). This indicates that the local splicing pattern in UTRs and coding regions is largely the same. The NetUTR method is made publicly available at www.cbs.dtu.dk/services/NetUTR.
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Affiliation(s)
- E Eden
- Center for Biological Sequence Analysis, Biocentrum-DTU Building 208, Technical University of Denmark, DK-2800 Lyngby, Denmark
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467
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Zhang X, Jiang N, Feschotte C, Wessler SR. PIF- and Pong-Like Transposable Elements: Distribution, Evolution and Relationship With Tourist-Like Miniature Inverted-Repeat Transposable Elements. Genetics 2004. [DOI: 10.1093/genetics/166.2.971] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Miniature inverted-repeat transposable elements (MITEs) are short, nonautonomous DNA elements that are widespread and abundant in plant genomes. Most of the hundreds of thousands of MITEs identified to date have been divided into two major groups on the basis of shared structural and sequence characteristics: Tourist-like and Stowaway-like. Since MITEs have no coding capacity, they must rely on transposases encoded by other elements. Two active transposons, the maize P Instability Factor (PIF) and the rice Pong element, have recently been implicated as sources of transposase for Tourist-like MITEs. Here we report that PIF- and Pong-like elements are widespread, diverse, and abundant in eukaryotes with hundreds of element-associated transposases found in a variety of plant, animal, and fungal genomes. The availability of virtually the entire rice genome sequence facilitated the identification of all the PIF/Pong-like elements in this organism and permitted a comprehensive analysis of their relationship with Tourist-like MITEs. Taken together, our results indicate that PIF and Pong are founding members of a large eukaryotic transposon superfamily and that members of this superfamily are responsible for the origin and amplification of Tourist-like MITEs.
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Affiliation(s)
- Xiaoyu Zhang
- Departments of Plant Biology and Genetics, University of Georgia, Athens, Georgia 30602
| | - Ning Jiang
- Departments of Plant Biology and Genetics, University of Georgia, Athens, Georgia 30602
| | - Cédric Feschotte
- Departments of Plant Biology and Genetics, University of Georgia, Athens, Georgia 30602
| | - Susan R Wessler
- Departments of Plant Biology and Genetics, University of Georgia, Athens, Georgia 30602
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468
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MHC Class I Epitope Binding Prediction Trained on Small Data Sets. LECTURE NOTES IN COMPUTER SCIENCE 2004. [DOI: 10.1007/978-3-540-30220-9_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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469
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Stellari GM, Jaramillo MA, Kramer EM. Evolution of the APETALA3 and PISTILLATA lineages of MADS-box-containing genes in the basal angiosperms. Mol Biol Evol 2003; 21:506-19. [PMID: 14694075 DOI: 10.1093/molbev/msh044] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The B class genes, including homologs of the Arabidopsis loci APETALA3 (AP3) and PISTILLATA (PI ), appear to play a conserved role in the determination of petal and stamen identity across core eudicot angiosperms. Understanding how and when these functions evolved is a critical component of elucidating the evolution of flowers, particularly the appearance of petaloid perianth organs. Before comparisons of gene expression patterns or functions can be made, however, it is necessary to establish the orthology of AP3 and PI homologs from basal angiosperms. Here, we report the identification and analysis of 29 new representatives of the B gene lineage from basal ANITA and magnoliid dicot angiosperms. These studies indicate that gene duplications have occurred at every phylogenetic level, both before and after the duplication that produced the separate AP3 and PI lineages. Comparison of genomic structure among PI homologs indicates that a 12-nucleotide deletion that had been considered synapomorphic for the whole PI lineage actually arose within the ANITA grade, after the split of the Nymphaeales but before the separation of the Austrobaileyales. Evidence for alternative splicing of the Nymphaea AP3 homolog is also presented. The implications of these findings for angiosperm systematics, the conservation of AP3 and PI gene function, and the evolution of the ABC program are discussed.
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Affiliation(s)
- Giulia M Stellari
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
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470
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Zhang L, Luo L. Splice site prediction with quadratic discriminant analysis using diversity measure. Nucleic Acids Res 2003; 31:6214-20. [PMID: 14576308 PMCID: PMC275452 DOI: 10.1093/nar/gkg805] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Based on the conservation of nucleotides at splicing sites and the features of base composition and base correlation around these sites we use the method of increment of diversity combined with quadratic discriminant analysis (IDQD) to study the dependence structure of splicing sites and predict the exons/introns and their boundaries for four model genomes: Caenorhabditis elegans, Arabidopsis thaliana, Drosophila melanogaster and human. The comparison of compositional features between two sequences and the comparison of base dependencies at adjacent or non-adjacent positions of two sequences can be integrated automatically in the increment of diversity (ID). Eight feature variables around a potential splice site are defined in terms of ID. They are integrated in a single formal framework given by IDQD. In our calculations 7 (8) base region around the donor (acceptor) sites have been considered in studying the conservation of nucleotides and sequences of 48 bp on either side of splice sites have been used in studying the compositional and base-correlating features. The windows are enlarged to 16 (donor), 29 (acceptor) and 80 bp (either side) to improve the prediction for human splice sites. The prediction capability of the present method is comparable with the leading splice site detector--GeneSplicer.
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Affiliation(s)
- Lirong Zhang
- Laboratory of Theoretical Biophysics, Faculty of Science and Technology, Inner Mongolia University, Hohhot, 010021 China
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471
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Venkataraman G, Goswami M, Tuteja N, Reddy MK, Sopory SK. Isolation and characterization of a phospholipase C delta isoform from pea that is regulated by light in a tissue specific manner. Mol Genet Genomics 2003; 270:378-86. [PMID: 14564506 DOI: 10.1007/s00438-003-0925-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2003] [Accepted: 08/19/2003] [Indexed: 01/21/2023]
Abstract
Phosphoinositide-specific phospholipases C (PLCs) play an important role in many cellular responses and are involved in the production of secondary messengers. We report the cloning and characterization of a cDNA encoding a PLC-delta from Pisum sativum (PsPLC). The amino acid sequence deduced from the cDNA sequence showed 75-80% identity to other plant PLCs and contained the characteristic X, Y and C2 domains. The genomic PLC clone from pea was also characterized and found to contain eight introns. The protein was expressed in Escherichia coli, but the recombinant product did not show any phosphoinositide (PI)- or phosphatidylinositol-4, 5-bisphosphate (PIP2)-specific activity, despite having all known residues required for such activity, and in spite of the fact that its C2 domain was shown to bind calcium. Under similar in vitro assay conditions the recombinant tobacco PLC used as a control showed calcium-dependent PI- and PIP2-specific activity. Though PsPLC did not show enzyme activity in vitro, and may represent an inactive form of PLC, such as those reported in some mammalian systems, analysis of the transcription of PsPLC showed that the gene is expressed in all pea tissues, and is regulated by light in a tissue-specific manner. Roots showed higher expression of PsPLC than shoots. A putative PsPLC promoter region (792 bp) was also cloned and found to contain root-specific and light-responsive cis elements, suggesting that this form of PLC may be involved in important functions in plants.
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Affiliation(s)
- G Venkataraman
- International Centre for Genetic Engineering and Biotechnology (ICEGEB), Aruna Asaf Ali Marg, 110 067 New Delhi, India
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472
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Sehgal A, Kumar N, Carruthers VB, Sharma S. Translocation of ribosomal protein P0 onto the Toxoplasma gondii tachyzoite surface. Int J Parasitol 2003; 33:1589-94. [PMID: 14636674 DOI: 10.1016/s0020-7519(03)00267-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A ribosomal phosphoprotein P0 detected on the surface of the human malarial parasite Plasmodium falciparum (PfP0) has been shown to be recognised by invasion blocking antibodies. Using cross-reactive polyclonal antibodies against PfP0, the surface localisation has also been demonstrated on certain mammalian cells, yeast and Toxoplasma gondii. We sought to characterise the phenomenon of surface localisation in Toxoplasma using T. gondii P0 protein. Sequence analysis of a cDNA clone isolated from a T. gondii library showed marked similarity to PfP0, suggesting that T. gondii expresses an orthologous gene, TgP0. The expression of TgP0 was corroborated by Northern blot analysis revealing a transcript of 1.8 kb in size. Immunofluorescence analysis using anti-PfP0 indicated surface localisation of TgP0. To confirm surface translocation of the TgP0, tachyzoites were transfected with the HA-tagged TgP0 gene followed by immunofluorescence detection of the HA-tag. Surface translocation of transiently expressed TgP0 and blocking of tachyzoite invasion of human foreskin fibroblasts by anti-PfP0 antibodies suggest that P0 protein plays an important role in T. gondii invasion of human cells.
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Affiliation(s)
- Alfica Sehgal
- Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
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473
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Neumann P, Pozárková D, Macas J. Highly abundant pea LTR retrotransposon Ogre is constitutively transcribed and partially spliced. PLANT MOLECULAR BIOLOGY 2003; 53:399-410. [PMID: 14750527 DOI: 10.1023/b:plan.0000006945.77043.ce] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
We have isolated and characterized a novel giant retroelement, named Ogre, which is over 22 kb long and makes up at least 5% of the pea (Pisum sativum L.) genome. This element can be classified as a Ty3/gypsy-like LTR retrotransposon based on the presence of long terminal repeats (LTRs) and the order of the domains coding for typical retrotransposon proteins. In addition to its extreme length, it has several features which make it unique among the retroelements described so far: (1) the sequences coding for gag and prot proteins are separated from the rt/rh-int domains by several stop codons; (2) the region containing these stop codons is removed from the element transcripts by splicing which results in reconstitution of the complete gag-pol coding sequence; (3) only a part of the transcripts is spliced which probably determines the ratio of translated proteins; (4) the element contains an extra ORF located upstream the gag-pol coding sequences, potentially coding for a protein of 546-562 amino acids with unknown function. The transcriptional activity of the Ogre elements has been detected in all organs tested (leaves, roots, flowers) as well as in wounded leaves and protoplasts. Considering this retroelement's constitutive expression and observed high mutual similarity of the element genomic sequences, it is possible to speculate about its recent amplification in the genomes of pea and other legume plants.
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Affiliation(s)
- Pavel Neumann
- Institute of Plant Molecular Biology, Laboratory of Molecular Cytogenetics, Branisovská 31, Ceské Budejovice, 37005 Czech Republic.
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474
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Pritham EJ, Zhang YH, Feschotte C, Kesseli RV. An Ac -like Transposable Element Family With Transcriptionally Active Y-Linked Copies in the White Campion, Silene latifolia. Genetics 2003; 165:799-807. [PMID: 14573489 PMCID: PMC1462803 DOI: 10.1093/genetics/165.2.799] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
An RFLP genomic subtraction was used to isolate male-specific sequences in the species Silene latifolia. One isolated fragment, SLP2, shares similarity to a portion of the Activator (Ac) transposase from Zea mays and to related proteins from other plant species. Southern blot analysis of male and female S. latifolia genomic DNA shows that SLP2 belongs to a low-copy-number repeat family with two Y-linked copies. Screening of a S. latifolia male genomic library using SLP2 as a probe led to the isolation of five clones, which were partially sequenced. One clone contains two large open reading frames that can be joined into a sequence encoding a putative protein of 682 amino acids by removing a short intron. Database searches and phylogenetic analysis show that this protein belongs to the hAT superfamily of transposases, closest to Tag2 (Arabidopsis thaliana), and contains all of the defined domains critical for the activity of these transposases. PCR with genomic and cDNA templates from S. latifolia male, female, and hermaphrodite individuals revealed that one of the Y-linked copies is transcriptionally active and alternatively spliced. This is the first report of a transcriptionally active transposable element (TE) family in S. latifolia and the first DNA transposon residing on a plant Y chromosome. The potential activity and regulation of this TE family and its use for Y chromosome gene discovery is discussed.
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Affiliation(s)
- Ellen J Pritham
- Department of Biology, University of Massachusetts, Boston, Massachusetts 02125, USA
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475
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Le Bras M, Bensaad K, Soussi T. Data mining the p53 pathway in the Fugu genome: evidence for strong conservation of the apoptotic pathway. Oncogene 2003; 22:5082-90. [PMID: 12902991 DOI: 10.1038/sj.onc.1206424] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The p53 tumour suppressor gene belongs to a small family of related proteins that includes two other members, p63 and p73. Phylogenetic and functional studies suggest that p63 and p73 are ancient genes that have essential roles in normal development, whereas p53 seems to have evolved more recently to prevent cell transformation. In mammalian cells, a plethora of proteins have been found to specifically regulate p53 activity. The genome of the fish Fugu rubripes has been recently published. It is the second vertebrate genome for which the entire sequence is now available. Phylogenetic studies are essential in order to analyse and define signalling pathways important for cell cycle regulation. The presence or absence of a critical member in any pathway can shed light about the evolution of these pathways. The Fugu genome databank has been analysed for several members of the p53 network, including p53, p63 and p73. A good conservation of the network that regulates p53 stability and apoptosis has been found. We also discovered that some cofactors that cooperate with p53 for apoptosis are also well conserved and belong to multigene families not detected in the human genome.
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Affiliation(s)
- Morgane Le Bras
- Laboratoire de Génotoxicologie des Tumeurs, Institut Curie, 26 rue d'Ulm, 75005 Paris, France
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476
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Toledo-Ortiz G, Huq E, Quail PH. The Arabidopsis basic/helix-loop-helix transcription factor family. THE PLANT CELL 2003; 15:1749-1770. [PMID: 12897250 DOI: 10.1105/tpc.013839.et] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The basic/helix-loop-helix (bHLH) proteins are a superfamily of transcription factors that bind as dimers to specific DNA target sites and that have been well characterized in nonplant eukaryotes as important regulatory components in diverse biological processes. Based on evidence that the bHLH protein PIF3 is a direct phytochrome reaction partner in the photoreceptor's signaling network, we have undertaken a comprehensive computational analysis of the Arabidopsis genome sequence databases to define the scope and features of the bHLH family. Using a set of criteria derived from a previously defined consensus motif, we identified 147 bHLH protein-encoding genes, making this one of the largest transcription factor families in Arabidopsis. Phylogenetic analysis of the bHLH domain sequences permits classification of these genes into 21 subfamilies. The evolutionary and potential functional relationships implied by this analysis are supported by other criteria, including the chromosomal distribution of these genes relative to duplicated genome segments, the conservation of variant exon/intron structural patterns, and the predicted DNA binding activities within subfamilies. Considerable diversity in DNA binding site specificity among family members is predicted, and marked divergence in protein sequence outside of the conserved bHLH domain is observed. Together with the established propensity of bHLH factors to engage in varying degrees of homodimerization and heterodimerization, these observations suggest that the Arabidopsis bHLH proteins have the potential to participate in an extensive set of combinatorial interactions, endowing them with the capacity to be involved in the regulation of a multiplicity of transcriptional programs. We provide evidence from yeast two-hybrid and in vitro binding assays that two related phytochrome-interacting members in the Arabidopsis family, PIF3 and PIF4, can form both homodimers and heterodimers and that all three dimeric configurations can bind specifically to the G-box DNA sequence motif CACGTG. These data are consistent, in principle, with the operation of this combinatorial mechanism in Arabidopsis.
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Affiliation(s)
- Gabriela Toledo-Ortiz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
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477
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Toledo-Ortiz G, Huq E, Quail PH. The Arabidopsis basic/helix-loop-helix transcription factor family. THE PLANT CELL 2003; 15:1749-70. [PMID: 12897250 PMCID: PMC167167 DOI: 10.1105/tpc.013839] [Citation(s) in RCA: 884] [Impact Index Per Article: 42.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2003] [Accepted: 06/02/2003] [Indexed: 05/18/2023]
Abstract
The basic/helix-loop-helix (bHLH) proteins are a superfamily of transcription factors that bind as dimers to specific DNA target sites and that have been well characterized in nonplant eukaryotes as important regulatory components in diverse biological processes. Based on evidence that the bHLH protein PIF3 is a direct phytochrome reaction partner in the photoreceptor's signaling network, we have undertaken a comprehensive computational analysis of the Arabidopsis genome sequence databases to define the scope and features of the bHLH family. Using a set of criteria derived from a previously defined consensus motif, we identified 147 bHLH protein-encoding genes, making this one of the largest transcription factor families in Arabidopsis. Phylogenetic analysis of the bHLH domain sequences permits classification of these genes into 21 subfamilies. The evolutionary and potential functional relationships implied by this analysis are supported by other criteria, including the chromosomal distribution of these genes relative to duplicated genome segments, the conservation of variant exon/intron structural patterns, and the predicted DNA binding activities within subfamilies. Considerable diversity in DNA binding site specificity among family members is predicted, and marked divergence in protein sequence outside of the conserved bHLH domain is observed. Together with the established propensity of bHLH factors to engage in varying degrees of homodimerization and heterodimerization, these observations suggest that the Arabidopsis bHLH proteins have the potential to participate in an extensive set of combinatorial interactions, endowing them with the capacity to be involved in the regulation of a multiplicity of transcriptional programs. We provide evidence from yeast two-hybrid and in vitro binding assays that two related phytochrome-interacting members in the Arabidopsis family, PIF3 and PIF4, can form both homodimers and heterodimers and that all three dimeric configurations can bind specifically to the G-box DNA sequence motif CACGTG. These data are consistent, in principle, with the operation of this combinatorial mechanism in Arabidopsis.
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Affiliation(s)
- Gabriela Toledo-Ortiz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
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478
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Asselta R, Montefusco MC, Duga S, Malcovati M, Peyvandi F, Mannucci PM, Tenchini ML. Severe factor V deficiency: exon skipping in the factor V gene causing a partial deletion of the C1 domain. J Thromb Haemost 2003; 1:1237-44. [PMID: 12871325 DOI: 10.1046/j.1538-7836.2003.00160.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Severe factor V (FV) deficiency is a rare coagulation disorder, characterized by very low or unmeasurable plasma levels of functional and immunoreactive FV. Among rare inherited coagulopathies, FV deficiency is the least characterized from a molecular point of view (only 12 mutations have been reported). OBJECTIVES The aim of this work was to investigate, at the molecular level, the pathogenetic mechanisms responsible for a case of severe FV deficiency. PATIENTS AND METHODS A 19-year-old Iranian man showing unmeasurable FV activity and severely reduced FV antigen level in plasma was studied. Mutation screening was performed by sequencing. The effect of the identified mutation was investigated both at the mRNA and at the protein level. RESULTS Molecular analysis of the factor V (FV) gene identified a novel homozygous A-->T transversion at position + 3 of the donor splice site of intron 19 (IVS19 + 3A-->T). Production of mutant mRNA in HeLa cells demonstrated that this mutation causes the entire exon 19 to be skipped from the FV mRNA. The mutant processed transcript codes for a deleted FV, lacking the first 24 amino acids of the C1 domain. Expression of the mutant FV protein in COS-1 cells showed that the deleted protein was synthesized but not secreted; moreover, the intracellular amount of deleted FV was reduced compared to wild type, suggesting intracellular degradation of mutant FV. CONCLUSIONS This work reports the molecular characterization of the first mutation causing a partial deletion in the FV molecule, resulting in a severe impairment of protein secretion.
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Affiliation(s)
- R Asselta
- Department of Biology and Genetics for Medical Sciences, University of Milan, via Viotti 3/5, 20133 Milan, Italy
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479
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Wortman JR, Haas BJ, Hannick LI, Smith RK, Maiti R, Ronning CM, Chan AP, Yu C, Ayele M, Whitelaw CA, White OR, Town CD. Annotation of the Arabidopsis genome. PLANT PHYSIOLOGY 2003; 132:461-8. [PMID: 12805579 PMCID: PMC166989 DOI: 10.1104/pp.103.022251] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2003] [Revised: 03/07/2003] [Accepted: 03/18/2003] [Indexed: 05/18/2023]
Affiliation(s)
- Jennifer R Wortman
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
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480
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Schoof H, Karlowski WM. Comparison of rice and Arabidopsis annotation. CURRENT OPINION IN PLANT BIOLOGY 2003; 6:106-112. [PMID: 12667865 DOI: 10.1016/s1369-5266(03)00003-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Several versions of the rice genome were published in 2002, providing a first overview of the genome content of this model monocot. At the same time, the genome of the model dicot, Arabidopsis thaliana, reached a new level of annotation as thousands of full-length cDNA sequences were integrated with the genome sequence.
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Affiliation(s)
- Heiko Schoof
- Technical University of Munich, Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany.
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481
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Roudier F, Fedorova E, Lebris M, Lecomte P, Györgyey J, Vaubert D, Horvath G, Abad P, Kondorosi A, Kondorosi E. The Medicago species A2-type cyclin is auxin regulated and involved in meristem formation but dispensable for endoreduplication-associated developmental programs. PLANT PHYSIOLOGY 2003; 131:1091-103. [PMID: 12644661 PMCID: PMC166874 DOI: 10.1104/pp.102.011122] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Phytohormones as well as temporal and spatial regulation of the cell cycle play a key role in plant development. Here, we investigated the function and regulation of an alfalfa (Medicago sativa) A2-type cyclin in three distinct root developmental programs: in primary and secondary root development, nodule development, and nematode-elicited gall formation. Using transgenic plants carrying the Medsa;cycA2;2 promoter-beta-glucuronidase gene fusion, in combination with other techniques, cycA2;2 expression was localized in meristems and proliferating cells in the lateral root and nodule primordia. Rapid induction of cycA2;2 by Nod factors demonstrated that this gene is implicated in cell cycle activation of differentiated cells developing to nodule primordia. Surprisingly, cycA2;2 was repressed in the endoreduplicating, division-arrested cells both during nodule development and formation of giant cells in nematode-induced galls, indicating that CycA2;2 was dispensable for S-phase in endoreduplication cycles. Overexpression of cycA2;2 in transgenic plants corresponded to wild type protein levels and had no apparent phenotype. In contrast, antisense expression of cycA2;2 halted regeneration of somatic embryos, suggesting a role for CycA2;2 in the formation or activity of apical meristems. Expression of cycA2;2 was up-regulated by auxins, as expected from the presence of auxin response elements in the promoter. Moreover, auxin also affected the spatial expression pattern of this cyclin by shifting the cycA2;2 expression from the phloem to the xylem poles.
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Affiliation(s)
- François Roudier
- Institut des Sciences du Végétale, Centre National de la Recherche Scientiique Unité Propre de Recherche, Gi-sur-Yvette, France
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482
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Knappe S, Flügge UI, Fischer K. Analysis of the plastidic phosphate translocator gene family in Arabidopsis and identification of new phosphate translocator-homologous transporters, classified by their putative substrate-binding site. PLANT PHYSIOLOGY 2003; 131:1178-90. [PMID: 12644669 PMCID: PMC166879 DOI: 10.1104/pp.016519] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2002] [Revised: 11/12/2002] [Accepted: 11/12/2002] [Indexed: 05/17/2023]
Abstract
Analysis of the Arabidopsis genome revealed the complete set of plastidic phosphate translocator (pPT) genes. The Arabidopsis genome contains 16 pPT genes: single copies of genes coding for the triose phosphate/phosphate translocator and the xylulose phosphate/phosphate translocator, and two genes coding for each the phosphoenolpyruvate/phosphate translocator and the glucose-6-phosphate/phosphate translocator. A relatively high number of truncated phosphoenolpyruvate/phosphate translocator genes (six) and glucose-6-phosphate/phosphate translocator genes (four) could be detected with almost conserved intron/exon structures as compared with the functional genes. In addition, a variety of PT-homologous (PTh) genes could be identified in Arabidopsis and other organisms. They all belong to the drug/metabolite transporter superfamily showing significant similarities to nucleotide sugar transporters (NSTs). The pPT, PTh, and NST proteins all possess six to eight transmembrane helices. According to the analysis of conserved motifs in these proteins, the PTh proteins can be divided into (a) the lysine (Lys)/arginine group comprising only non-plant proteins, (b) the Lys-valine/alanine/glycine group of Arabidopsis proteins, (c) the Lys/asparagine group of Arabidopsis proteins, and (d) the Lys/threonine group of plant and non-plant proteins. None of these proteins have been characterized so far. The analysis of the putative substrate-binding sites of the pPT, PTh, and NST proteins led to the suggestion that all these proteins share common substrate-binding sites on either side of the membrane each of which contain a conserved Lys residue.
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Affiliation(s)
- Silke Knappe
- Botanisches Institut der Universität zu Köln, Lehrstuhl II, Gyrhofstrasse 15, D-50931 Cologne, Germany
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483
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484
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van Leeuwen H, Monfort A, Zhang HB, Puigdomènech P. Identification and characterisation of a melon genomic region containing a resistance gene cluster from a constructed BAC library. Microcolinearity between Cucumis melo and Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2003; 51:703-18. [PMID: 12678558 DOI: 10.1023/a:1022573230486] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
A bacterial artificial chromosome (BAC) library from the dihaploid melon line 'PIT92' was constructed with a 6 times coverage of the haploid melon genome. A contig of four BACs around the MRGH63 resistance gene homologue fragment was created. The complete sequence of a 117-kb BAC clone allowed to determine two clearly defined regions, the first one containing a cluster of three resistance gene homologues. Separated by a retrotransposon, that contains large long terminal repeats, the second region presents a group of genes with a conserved distribution in two regions of the Arabidopsis genome. The detailed analysis of this region provides a description of the gene structure and the presence of repetitive sequences in a defined fragment of the genome of Cucumis melo.
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MESH Headings
- Amino Acid Sequence
- Arabidopsis/genetics
- Base Sequence
- Chromosomes, Artificial, Bacterial/genetics
- Chromosomes, Plant/genetics
- Cloning, Molecular
- Cucumis/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- Genes, Plant/genetics
- Genome, Plant
- Genomic Library
- Immunity, Innate/genetics
- Molecular Sequence Data
- Multigene Family/genetics
- Repetitive Sequences, Nucleic Acid/genetics
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Synteny
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Affiliation(s)
- Hans van Leeuwen
- Department de Genètica Molecular, Institut de Biologia Molecular de Barcelona, CID-CSIC, Jordi Girona 18, 08034, Barcelona, Spain
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485
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Abstract
The phylogeny of highly divergent multigene families is often difficult to validate but can be substantiated by inclusion of data outside of the phylogeny, such as signature motifs, intron splice site conservation, unique substitutions of conserved residues, similar gene functions, and out groups. The Family 1 Glycosyltransferases (UGTs) comprises such a highly divergent, polyphyletic multigene family. Phylogenetic comparisons of UGTs from plants, animals, fungi, bacteria, and viruses reveal that plant UGTs represent three distinct clades. The majority of the plant sequences appears to be monophyletic and have diverged after the bifurcation of the animal/fungi/plant kingdoms. The two minor clades contain the sterol and lipid glycosyltransferases and each show more homology to non-plant sequences. The lipid glycosyltransferase clade is homologous to bacterial lipid glycosyltransferases and reflects the bacterial origin of chloroplasts. The fully sequenced Arabidopsis thaliana genome contains 120 UGTs including 8 apparent pseudogenes. The phylogeny of plant glycosyltransferases is substantiated with complete phylogenetic analysis of the A. thaliana UGT multigene family, including intron-exon organization and chromosomal localization.
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Affiliation(s)
- Suzanne Paquette
- Department of Biological Structure, HSBG-514, Box 357420, University of Washington Medical School, Seattle, WA 98145-9420, USA
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486
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Goubet F, Misrahi A, Park SK, Zhang Z, Twell D, Dupree P. AtCSLA7, a cellulose synthase-like putative glycosyltransferase, is important for pollen tube growth and embryogenesis in Arabidopsis. PLANT PHYSIOLOGY 2003; 131:547-57. [PMID: 12586879 PMCID: PMC166831 DOI: 10.1104/pp.014555] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2002] [Revised: 10/25/2002] [Accepted: 11/14/2002] [Indexed: 05/18/2023]
Abstract
The cellulose synthase-like proteins are a large family of proteins in plants thought to be processive polysaccharide beta-glycosyltransferases. We have characterized an Arabidopsis mutant with a transposon insertion in the gene encoding AtCSLA7 of the CSLA subfamily. Analysis of the transmission efficiency of the insertion indicated that AtCSLA7 is important for pollen tube growth. Moreover, the homozygous insertion was embryo lethal. A detailed analysis of seed developmental progression revealed that mutant embryos developed more slowly than wild-type siblings. The mutant embryos also showed abnormal cell patterning and they arrested at a globular stage. The defective embryonic development was associated with reduced proliferation and failed cellularization of the endosperm. AtCSLA7 is widely expressed, and is likely to be required for synthesis of a cell wall polysaccharide found throughout the plant. Our results suggest that this polysaccharide is essential for cell wall structure or for signaling during plant embryo development.
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Affiliation(s)
- Florence Goubet
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge CB2 1QW, United Kingdom
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487
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Samson D, Legeai F, Karsenty E, Reboux S, Veyrieras JB, Just J, Barillot E. GénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics. Nucleic Acids Res 2003; 31:179-82. [PMID: 12519976 PMCID: PMC165507 DOI: 10.1093/nar/gkg060] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Génoplante is a partnership program between public French institutes (INRA, CIRAD, IRD and CNRS) and private companies (Biogemma, Bayer CropScience and Bioplante) that aims at developing genome analysis programs for crop species (corn, wheat, rapeseed, sunflower and pea) and model plants (Arabidopsis and rice). The outputs of these programs form a wealth of information (genomic sequence, transcriptome, proteome, allelic variability, mapping and synteny, and mutation data) and tools (databases, interfaces, analysis software), that are being integrated and made public at the public bioinformatics resource centre of Génoplante: GénoPlante-Info (GPI). This continuous flood of data and tools is regularly updated and will grow continuously during the coming two years. Access to the GPI databases and tools is available at http://genoplante-info.infobiogen.fr/.
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Affiliation(s)
- Delphine Samson
- Génoplante-Info, Unité de Recherche Génomique-Info, INRA, Infobiogen, 523 Place des Terrasses, F-91000 Evry, France.
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488
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Welinder KG, Justesen AF, Kjaersgård IVH, Jensen RB, Rasmussen SK, Jespersen HM, Duroux L. Structural diversity and transcription of class III peroxidases from Arabidopsis thaliana. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:6063-81. [PMID: 12473102 DOI: 10.1046/j.1432-1033.2002.03311.x] [Citation(s) in RCA: 175] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Understanding peroxidase function in plants is complicated by the lack of substrate specificity, the high number of genes, their diversity in structure and our limited knowledge of peroxidase gene transcription and translation. In the present study we sequenced expressed sequence tags (ESTs) encoding novel heme-containing class III peroxidases from Arabidopsis thaliana and annotated 73 full-length genes identified in the genome. In total, transcripts of 58 of these genes have now been observed. The expression of individual peroxidase genes was assessed in organ-specific EST libraries and compared to the expression of 33 peroxidase genes which we analyzed in whole plants 3, 6, 15, 35 and 59 days after sowing. Expression was assessed in root, rosette leaf, stem, cauline leaf, flower bud and cell culture tissues using the gene-specific and highly sensitive reverse transcriptase-polymerase chain reaction (RT-PCR). We predicted that 71 genes could yield stable proteins folded similarly to horseradish peroxidase (HRP). The putative mature peroxidases derived from these genes showed 28-94% amino acid sequence identity and were all targeted to the endoplasmic reticulum by N-terminal signal peptides. In 20 peroxidases these signal peptides were followed by various N-terminal extensions of unknown function which are not present in HRP. Ten peroxidases showed a C-terminal extension indicating vacuolar targeting. We found that the majority of peroxidase genes were expressed in root. In total, class III peroxidases accounted for an impressive 2.2% of root ESTs. Rather few peroxidases showed organ specificity. Most importantly, genes expressed constitutively in all organs and genes with a preference for root represented structurally diverse peroxidases (< 70% sequence identity). Furthermore, genes appearing in tandem showed distinct expression profiles. The alignment of 73 Arabidopsis peroxidase sequences provides an easy access to the identification of orthologous peroxidases in other plant species and will provide a common platform for combining knowledge of peroxidase structure and function relationships obtained in various species.
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Affiliation(s)
- Karen G Welinder
- Department of Protein Chemistry, University of Copenhagen, Denmark.
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489
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Pandey R, Müller A, Napoli CA, Selinger DA, Pikaard CS, Richards EJ, Bender J, Mount DW, Jorgensen RA. Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids Res 2002; 30:5036-55. [PMID: 12466527 PMCID: PMC137973 DOI: 10.1093/nar/gkf660] [Citation(s) in RCA: 527] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2002] [Accepted: 10/06/2002] [Indexed: 12/26/2022] Open
Abstract
Sequence similarity and profile searching tools were used to analyze the genome sequences of Arabidopsis thaliana, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans and Drosophila melanogaster for genes encoding three families of histone deacetylase (HDAC) proteins and three families of histone acetyltransferase (HAT) proteins. Plants, animals and fungi were found to have a single member of each of three subfamilies of the GNAT family of HATs, suggesting conservation of these functions. However, major differences were found with respect to sizes of gene families and multi-domain protein structures within other families of HATs and HDACs, indicating substantial evolutionary diversification. Phylogenetic analysis identified a new class of HDACs within the RPD3/HDA1 family that is represented only in plants and animals. A similar analysis of the plant-specific HD2 family of HDACs suggests a duplication event early in dicot evolution, followed by further diversification in the lineage leading to Arabidopsis. Of three major classes of SIR2-type HDACs that are found in animals, fungi have representatives only in one class, whereas plants have representatives only in the other two. Plants possess five CREB-binding protein (CBP)-type HATs compared with one to two in animals and none in fungi. Domain and phylogenetic analyses of the CBP family proteins showed that this family has evolved three distinct types of CBPs in plants. The domain architecture of CBP and TAF(II)250 families of HATs show significant differences between plants and animals, most notably with respect to bromodomain occurrence and their number. Bromodomain-containing proteins in Arabidopsis differ strikingly from animal bromodomain proteins with respect to the numbers of bromodomains and the other types of domains that are present. The substantial diversification of HATs and HDACs that has occurred since the divergence of plants, animals and fungi suggests a surprising degree of evolutionary plasticity and functional diversification in these core chromatin components.
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Affiliation(s)
- Ritu Pandey
- Department of Plant Sciences, University of Arizona, Tucson, AZ 85721-0036, USA
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490
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Graham MA, Marek LF, Shoemaker RC. Organization, expression and evolution of a disease resistance gene cluster in soybean. Genetics 2002; 162:1961-77. [PMID: 12524363 PMCID: PMC1462381 DOI: 10.1093/genetics/162.4.1961] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
PCR amplification was previously used to identify a cluster of resistance gene analogues (RGAs) on soybean linkage group J. Resistance to powdery mildew (Rmd-c), Phytophthora stem and root rot (Rps2), and an ineffective nodulation gene (Rj2) map within this cluster. BAC fingerprinting and RGA-specific primers were used to develop a contig of BAC clones spanning this region in cultivar "Williams 82" [rps2, Rmd (adult onset), rj2]. Two cDNAs with homology to the TIR/NBD/LRR family of R-genes have also been mapped to opposite ends of a BAC in the contig Gm_Isb001_091F11 (BAC 91F11). Sequence analyses of BAC 91F11 identified 16 different resistance-like gene (RLG) sequences with homology to the TIR/NBD/LRR family of disease resistance genes. Four of these RLGs represent two potentially novel classes of disease resistance genes: TIR/NBD domains fused inframe to a putative defense-related protein (NtPRp27-like) and TIR domains fused inframe to soybean calmodulin Ca(2+)-binding domains. RT-PCR analyses using gene-specific primers allowed us to monitor the expression of individual genes in different tissues and developmental stages. Three genes appeared to be constitutively expressed, while three were differentially expressed. Analyses of the R-genes within this BAC suggest that R-gene evolution in soybean is a complex and dynamic process.
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Affiliation(s)
- Michelle A Graham
- Department of Agronomy, Iowa State University, Ames, Iowa 50010, USA
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491
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Xiao YL, Malik M, Whitelaw CA, Town CD. Cloning and sequencing of cDNAs for hypothetical genes from chromosome 2 of Arabidopsis. PLANT PHYSIOLOGY 2002; 130:2118-28. [PMID: 12481096 PMCID: PMC166724 DOI: 10.1104/pp.010207] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2002] [Revised: 08/25/2002] [Accepted: 09/09/2002] [Indexed: 05/19/2023]
Abstract
About 25% of the genes in the fully sequenced and annotated Arabidopsis genome have structures that are predicted solely by computer algorithms with no support from either nucleic acid or protein homologs from other species or expressed sequence matches from Arabidopsis. These are referred to as "hypothetical genes." On chromosome 2, sequenced by The Institute for Genomic Research, there are approximately 800 hypothetical genes among a total of approximately 4,100 genes. To test their expression under various growth conditions and in specific tissues, we used six cDNA populations prepared from cold-treated, heat-treated, and pathogen (Xanthomonas campestris pv campestris)-infected plants, callus, roots, and young seedlings. To date, 169 hypothetical genes were tested, and 138 of them are found to be expressed in one or more of the six cDNA populations. By sequencing multiple clones from each 5'- and 3'-rapid amplification of cDNA ends (RACE) product and assembling the sequences, we generated full-length sequences for 16 of these genes. For 14 genes, there was one full-length assembly that precisely supported the intron-exon boundaries of their gene predictions, adding only 5'- and 3'-untranslated region sequences. However, for three of these genes, the other assemblies represent additional exons and alternatively spliced or unspliced introns. For the remaining two genes, the cDNA sequences reveal major differences with predicted gene structures. In addition, a total of six genes displayed more than one polyadenylation site. These data will be used to update gene models in The Institute for Genomic Research annotation database ATH1.
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Affiliation(s)
- Yong-Li Xiao
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA.
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492
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Roberts AW, Roberts EM, Delmer DP. Cellulose synthase (CesA) genes in the green alga Mesotaenium caldariorum. EUKARYOTIC CELL 2002; 1:847-55. [PMID: 12477785 PMCID: PMC138757 DOI: 10.1128/ec.1.6.847-855.2002] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Cellulose, a microfibrillar polysaccharide consisting of bundles of beta-1,4-glucan chains, is a major component of plant and most algal cell walls and is also synthesized by some prokaryotes. Seed plants and bacteria differ in the structures of their membrane terminal complexes that make cellulose and, in turn, control the dimensions of the microfibrils produced. They also differ in the domain structures of their CesA gene products (the catalytic subunit of cellulose synthase), which have been localized to terminal complexes and appear to help maintain terminal complex structure. Terminal complex structures in algae range from rosettes (plant-like) to linear forms (bacterium-like). Thus, algal CesA genes may reveal domains that control terminal complex assembly and microfibril structure. The CesA genes from the alga Mesotaenium caldariorum, a member of the order Zygnematales, which have rosette terminal complexes, are remarkably similar to seed plant CesAs, with deduced amino acid sequence identities of up to 59%. In addition to the putative transmembrane helices and the D-D-D-QXXRW motif shared by all known CesA gene products, M. caldariorum and seed plant CesAs share a region conserved among plants, an N-terminal zinc-binding domain, and a variable or class-specific region. This indicates that the domains that characterize seed plant CesAs arose prior to the evolution of land plants and may play a role in maintaining the structures of rosette terminal complexes. The CesA genes identified in M. caldariorum are the first reported for any eukaryotic alga and will provide a basis for analyzing the CesA genes of algae with different types of terminal complexes.
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Affiliation(s)
- Alison W Roberts
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island 02881, USA
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493
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Gupta R, Ting JTL, Sokolov LN, Johnson SA, Luan S. A tumor suppressor homolog, AtPTEN1, is essential for pollen development in Arabidopsis. THE PLANT CELL 2002; 14:2495-507. [PMID: 12368500 PMCID: PMC151231 DOI: 10.1105/tpc.005702] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2002] [Accepted: 07/29/2002] [Indexed: 05/18/2023]
Abstract
Although it is well known that Tyr phosphatases play a critical role in signal transduction in animal cells, little is understood of the functional significance of Tyr phosphatases in higher plants. Here, we describe the functional analysis of an Arabidopsis gene (AtPTEN1) that encodes a Tyr phosphatase closely related to PTEN, a tumor suppressor in animals. The recombinant AtPTEN1 protein, like its homologs in animals, is an active phosphatase that dephosphorylates phosphotyrosine and phosphatidylinositol substrates. RNA gel blot analysis and examination of promoter-reporter constructs in transgenic Arabidopsis plants revealed that the AtPTEN1 gene is expressed exclusively in pollen grains during the late stage of development. Suppression of AtPTEN1 gene expression by RNA interference caused pollen cell death after mitosis. We conclude that AtPTEN1 is a pollen-specific phosphatase and is essential for pollen development.
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Affiliation(s)
- Rajeev Gupta
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
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494
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Mathé C, Sagot MF, Schiex T, Rouzé P. Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res 2002; 30:4103-17. [PMID: 12364589 PMCID: PMC140543 DOI: 10.1093/nar/gkf543] [Citation(s) in RCA: 209] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2002] [Revised: 08/07/2002] [Accepted: 08/07/2002] [Indexed: 11/14/2022] Open
Abstract
While the genomes of many organisms have been sequenced over the last few years, transforming such raw sequence data into knowledge remains a hard task. A great number of prediction programs have been developed that try to address one part of this problem, which consists of locating the genes along a genome. This paper reviews the existing approaches to predicting genes in eukaryotic genomes and underlines their intrinsic advantages and limitations. The main mathematical models and computational algorithms adopted are also briefly described and the resulting software classified according to both the method and the type of evidence used. Finally, the several difficulties and pitfalls encountered by the programs are detailed, showing that improvements are needed and that new directions must be considered.
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Affiliation(s)
- Catherine Mathé
- Institut de Pharmacologie et Biologie Structurale, UMR 5089, 205 route de Narbonne, F-31077 Toulouse Cedex, France.
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495
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Agashe B, Prasad CK, Siddiqi I. Identification and analysis ofDYAD: a gene required for meiotic chromosome organisation and female meiotic progression inArabidopsis. Development 2002; 129:3935-43. [PMID: 12135930 DOI: 10.1242/dev.129.16.3935] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The dyad mutant of Arabidopsis was previously identified as being defective in female meiosis. We report here the analysis of the DYAD gene. In ovules and anthers DYAD RNA is detected specifically in female and male meiocytes respectively, in premeiotic interphase/meiotic prophase. Analysis of chromosome spreads in female meiocytes showed that in the mutant, chromosomes did not undergo synapsis and formed ten univalents instead of five bivalents. Unlike mutations in AtDMC1 and AtSPO11 which also affect bivalent formation as the univalent chromosomes segregate randomly, the dyad univalents formed an ordered metaphase plate and underwent an equational division. This suggests a requirement for DYAD for chromosome synapsis and centromere configuration in female meiosis. The dyad mutant showed increased and persistent expression of a meiosis-specific marker, pAtDMC1::GUS during female meiosis, indicative of defective meiotic progression. The sequence of the putative protein encoded by DYAD did not reveal strong similarity to other proteins. DYAD is therefore likely to encode a novel protein required for meiotic chromosome organisation and female meiotic progression.
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Affiliation(s)
- Bhavna Agashe
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500007, India
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496
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Ostergaard L, Petersen M, Mattsson O, Mundy J. An Arabidopsis callose synthase. PLANT MOLECULAR BIOLOGY 2002; 49:559-66. [PMID: 12081364 DOI: 10.1023/a:1015558231400] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Beta-1,3-glucan polymers are major structural components of fungal cell walls, while cellulosic beta-1,4-glucan is the predominant polysaccharide in plant cell walls. Plant beta-1,3-glucan, called callose, is produced in pollen and in response to pathogen attack and wounding, but it has been unclear whether callose synthases can also produce cellulose and whether plant cellulose synthases may also produce beta-1,3-glucans. We describe here an Arabidopsis gene, AtGsl5, encoding a plasma membrane-localized protein homologous to yeast beta-1,3-glucan synthase whose expression partially complements a yeast beta-1,3-glucan synthase mutant. AtGsl5 is developmentally expressed at highest levels in flowers, consistent with flowers having high beta-1,3-glucan synthase activities for deposition of callose in pollen. A role for AtGsl5 in callose synthesis is also indicated by AtGsl5 expression in the Arabidopsis mpk4 mutant which exhibits systemic acquired resistance (SAR), elevated beta-1,3-glucan synthase activity, and increased callose levels. In addition, AtGsl5 is a likely target of salicylic acid (SA)-dependent SAR, since AtGsl5 mRNA accumulation is induced by SA in wild-type plants, while expression of the nahG salicylate hydroxylase reduces AtGsl5 mRNA levels in the mpk4 mutant. These results indicate that AtGsl5 is likely involved in callose synthesis in flowering tissues and in the mpk4 mutant.
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Affiliation(s)
- Lars Ostergaard
- Department of Plant Physiology, Institute of Molecular Biology, University of Copenhagen, Denmark
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497
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Bouché N, Scharlat A, Snedden W, Bouchez D, Fromm H. A novel family of calmodulin-binding transcription activators in multicellular organisms. J Biol Chem 2002; 277:21851-61. [PMID: 11925432 DOI: 10.1074/jbc.m200268200] [Citation(s) in RCA: 193] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Screening of cDNA expression libraries derived from plants exposed to stress, with 35S-labeled recombinant calmodulin as a probe, revealed a new family of proteins containing a transcription activation domain and two types of DNA-binding domains designated the CG-1 domain and the transcription factor immunoglobulin domain, ankyrin repeats, and a varying number of IQ calmodulin-binding motifs. Based on domain organization and amino acid sequence comparisons, similar proteins, with the same domain organization, were identified in the genomes of other multicellular organisms including human, Drosophila, and Caenorhabditis, whereas none were found in the complete genomes of single cell eukaryotes and prokaryotes. This family of proteins was designated calmodulin-binding transcription activators (CAMTAs). Arabidopsis thaliana contains six CAMTA genes (AtCAMTA1-AtCAMTA6). The transcription activation domain of AtCAMTA1 was mapped by testing a series of protein fusions with the DNA-binding domain of the bacterial LexA transcription factor and two reporter genes fused to LexA recognition sequences in yeast cells. Two human proteins designated HsCAMTA1 and HsCAMTA2 were also shown to activate transcription in yeast using the same reporter system. Subcellular fractionation of Arabidopsis tissues revealed the presence of CAMTAs predominantly in the nucleus. Calmodulin binding assays identified a region of 25 amino acids capable of binding calmodulin with high affinity (K(d) = 1.2 nm) in the presence of calcium. We suggest that CAMTAs comprise a conserved family of transcription factors in a wide range of multicellular eukaryotes, which possibly respond to calcium signaling by direct binding of calmodulin.
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Affiliation(s)
- Nicolas Bouché
- School of Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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498
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Feschotte C, Wessler SR. Mariner-like transposases are widespread and diverse in flowering plants. Proc Natl Acad Sci U S A 2002; 99:280-5. [PMID: 11756687 PMCID: PMC117552 DOI: 10.1073/pnas.022626699] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Complete and partial sequences of mariner-like elements (MLEs) have been reported for hundreds of species of animals, but only two have been identified in plants. On the basis of these two plant MLEs and several related sequences identified by database searches, plant-specific degenerate primers were derived and used to amplify a conserved region of MLE transposase genes from a variety of plant genomes. Positive products were obtained for 6 dicots and 31 monocots of 54 plant species tested. Phylogenetic analysis of 68 distinct MLE transposase sequences from 25 grass species is consistent with vertical transmission and rapid diversification of multiple lineages of transposases. Surprisingly, the evolution of MLEs in grasses was accompanied by repeated and independent acquisition of introns in a localized region of the transposase gene.
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Affiliation(s)
- Cédric Feschotte
- Department of Botany and Genetics, University of Georgia, Athens, GA 30602, USA.
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499
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Wright DA, Voytas DF. Athila4 of Arabidopsis and Calypso of soybean define a lineage of endogenous plant retroviruses. Genome Res 2002; 12:122-31. [PMID: 11779837 PMCID: PMC155253 DOI: 10.1101/gr.196001] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2001] [Accepted: 07/15/2001] [Indexed: 11/24/2022]
Abstract
The Athila retroelements of Arabidopsis thaliana encode a putative envelope gene, suggesting that they are infectious retroviruses. Because most insertions are highly degenerate, we undertook a comprehensive analysis of the A. thaliana genome sequence to discern their conserved features. One family (Athila4) was identified whose members are largely intact and share >94% nucleotide identity. As a basis for comparison, related elements (the Calypso elements) were characterized from soybean. Consensus Calypso and Athila4 elements are 12-14 kb in length and have long terminal repeats of 1.3-1.8 kb. Gag and Pol are encoded on a single open reading frame (ORF) of 1801 (Calypso) and 1911 (Athila4) amino acids. Following the Gag-Pol ORF are noncoding regions of ~0.7 and 2 kb, which, respectively, flank the env-like gene. The env-like ORF begins with a putative splice acceptor site and encodes a protein with a predicted central transmembrane domain, similar to retroviral env genes. RNA of Athila elements was detected in an A. thaliana strain with decreased DNA methylation (ddm1). Additionally, a PCR survey identified related reverse transcriptases in diverse angiosperm genomes. Their ubiquitous nature and the potential for horizontal transfer by infection implicates these endogenous retroviruses as important vehicles for plant genome evolution.
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Affiliation(s)
- David A Wright
- Department of Zoology and Genetics, Iowa State University, Ames, Iowa 50011, USA
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500
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Pertea M, Salzberg SL. Computational gene finding in plants. PLANT MOLECULAR BIOLOGY 2002; 48:39-48. [PMID: 11860211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Automated methods for identifying protein coding regions in genomic DNA have progressed significantly in recent years, but there is still a strong need for more accurate computational solutions to the gene finding problem. Large-scale genome sequencing projects depend greatly on gene finding to generate accurate and complete gene annotation. Improvements in gene finding software are being driven by the development of better computational algorithms, a better understanding of the cell's mechanisms for transcription and translation, and the enormous increases in genomic sequence data. This paper reviews some of the most widely used algorithms for gene finding in plants, including technical descriptions of how they work and recent measurements of their success on the genomes of Arabidopsis thaliana and rice.
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Affiliation(s)
- Mihaela Pertea
- Institute for Genome Research, Rockville, MD 20850, USA.
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