Abstract:
:Arabidopsis is currently the reference genome for higher plants. A new, more detailed statistical analysis of Arabidopsis gene structure is presented including intron and exon lengths, intergenic distances, features of promoters, and variant 5'-ends of mRNAs transcribed from the same transcription unit. We also provide a statistical characterization of Arabidopsis transcripts in terms of their size, UTR lengths, 3'-end cleavage sites, splicing variants, and coding potential. These analyses were facilitated by scrutiny of our collection of sequenced full-length cDNAs and much larger collection of 5'-ESTs, together with another set of full-length cDNAs from Salk/Stanford/Plant Gene Expression Center/RIKEN. Examples of alternative splicing are observed for transcripts from 7% of the genes and many of these genes display multiple spliced isoforms. Most splicing variants lie in non-coding regions of the transcripts. Non-canonical splice sites constitute less than 1% of all splice sites. Genes with fewer than four introns display reduced average mRNA levels. Putative alternative transcription start sites were observed in 30% of highly expressed genes and in more than 50% of the genes with low expression. Transcription start sites correlate remarkably well with a CG skew peak in the DNA sequences. The intergenic distances vary considerably, those where genes are transcribed towards one another being significantly shorter. New transcripts, missing in the current TIGR genome annotation and ESTs that are non-coding, including those antisense to known genes, are derived and cataloged in the Supplementary Material. They identify 148 new loci in the Arabidopsis genome. The conclusions drawn provide a better understanding of the Arabidopsis genome and how the gene transcripts are processed. The results also allow better predictions to be made for, as yet, poorly defined genes and provide a reference for comparisons with other plant genomes whose complete sequences are currently being determined. Some comparisons with rice are included in this paper.
journal_name
Plant Mol Bioljournal_title
Plant molecular biologyauthors
Alexandrov NN,Troukhan ME,Brover VV,Tatarinova T,Flavell RB,Feldmann KAdoi
10.1007/s11103-005-2564-9subject
Has Abstractpub_date
2006-01-01 00:00:00pages
69-85issue
1eissn
0167-4412issn
1573-5028journal_volume
60pub_type
杂志文章abstract::We describe the molecular and functional characterization of three closely related S-adenosyl-L-methionine synthetase (SAMS) isoenzymes from Catharanthus roseus (Madagascar periwinkle). The genes are differentially expressed in cell cultures during growth of the culture and after application of various stresses (elici...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1023/a:1005711720930
更新日期:1997-01-01 00:00:00
abstract::Nodules of tropical legumes generally export symbiotically fixed nitrogen in the form of ureides that are produced by oxidation of de novo synthesized purines. To investigate the regulation of de novo purine biosynthesis in these nodules, we have isolated cDNA clones encoding 5-aminoimidazole ribonucleotide (AIR) carb...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00020176
更新日期:1994-01-01 00:00:00
abstract::Seed dormancy is an important developmental process that prevents pre-harvest sprouting in many grains and other seeds. Abscisic acid (ABA), a plant hormone, plays a crucial role in regulating dormancy but the underlying molecular regulatory mechanisms are not fully understood. An Arabidopsis zinc-finger gene, MEDIATO...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1023/B:PLAN.0000028730.10834.e3
更新日期:2004-01-01 00:00:00
abstract::Homospermidine synthase is the first specific enzyme in the biosynthesis of pyrrolizidine alkaloids. Whereas the substrates putrescine and spermidine are part of the highly dynamic polyamine pool of plants, the product homospermidine is incorporated exclusively into the necine base moiety of pyrrolizidine alkaloids. R...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-009-9514-x
更新日期:2009-09-01 00:00:00
abstract::Heterokont algae such as diatoms, brown seaweeds and the raphidophyte Heterosigma akashiwo acquired their chloroplasts via a secondary endosymbiosis involving a red algal endosymbiont and a eukaryote host, resulting in chloroplasts surrounded by four membranes rather than two. The precursor of a nuclear-encoded thylak...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1023/a:1023900100803
更新日期:2003-05-01 00:00:00
abstract::The cis-regulatory elements that confer cell cycle-dependent expression to the wheat histone H3 gene were investigated in rice cells (Oc strain) transformed with H3/GUS chimeric genes. 5' deletion mutants of the H3 promoter region (from -1711, -908 or -185 to +57 relative to the transcription start site) were joined t...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00019303
更新日期:1993-11-01 00:00:00
abstract::Repetitive DNA sequences were detected directly on somatic metaphase chromosome spreads from soybean root tips using fluorescent in situ hybridization. Methods to spread the forty small metaphase chromosomes substantially free of cellular material were developed using protoplasts. The specific DNA probe was a 1.05 kb ...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00036810
更新日期:1991-07-01 00:00:00
abstract::Type I signal peptidases are a widespread family of enzymes which remove the presequences from proteins translocated across cell membranes, including thylakoid and cytoplasmic membranes of cyanobacteria and thylakoid membranes of chloroplasts. We have cloned and sequenced a signal peptidase gene from the thermophilic ...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00019191
更新日期:1995-01-01 00:00:00
abstract::Bacteroids of Rhizobium leguminosarum in root nodules of Pisum sativum are enclosed by a plant-derived peribacteriod membrane (PBM). The contents of the interstitial peribacteroid space (PBS) between bacteroid membrane and PBM were isolated by a controlled osmotic shock of PBM-enclosed bacteroids and analysed by two-d...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00015670
更新日期:1988-03-01 00:00:00
abstract::We identified a novel nucleoplasm localized protein in Arabidopsis called AT-hook motif nuclear localized protein 1 (AHL1), which was isolated by visual screening of transformants using random GFP::cDNA fusions. AHL1 contains an AT-hook motif and unknown conserved PPC (plants and prokaryotes conserved) domain that inc...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-004-3249-5
更新日期:2004-09-01 00:00:00
abstract::A full-length cDNA encoding the 206 amino acid open reading frame of a trypsin/chymotrypsin inhibitor abundant in the corms of giant taro (Alocasia macrorrhiza) was isolated. An internal fragment was cloned using degenerate primers corresponding to a region of the mature protein sequence and the 'rapid amplification o...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00020813
更新日期:1996-03-01 00:00:00
abstract::Plant cell suspension cultures are invaluable models for the study of cellular processes. Here we develop the recently described Arabidopsis suspension culture MM2d as a transcript profiling platform by means of Affymetrix ATH1 microarrays. Analysis of gene expression profiles during normal culture growth, during sync...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1023/B:PLAN.0000019059.56489.ca
更新日期:2003-11-01 00:00:00
abstract::The soybean leghemoglobin lba gene promoter sequence was determined and aligned with the promoter sequence of the soybean lbc3 gene from the same gene family. Five highly conserved regions were found. There are two large conserved regions, one of which overlaps the basic promoter while the other defines a minimal enha...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00027380
更新日期:1993-08-01 00:00:00
abstract::Golgins are a family of coiled-coil proteins that are associated with the Golgi apparatus. They are necessary for tethering events in membrane fusion and may act as structural support for Golgi cisternae. Here we report on the identification of an Arabidopsis golgin which is a homologue of CASP, a known transmembrane ...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-005-4618-4
更新日期:2005-05-01 00:00:00
abstract::When dark-grown aurea mutant tomato seedlings which lack more than 95% of the phytochrome present in isogenic wild-type seedlings are kept in white or blue light, four nuclear-encoded transcripts coding for plastidic proteins (the light-harvesting chlorophyll a/b-binding protein of photosystem I and II [cab-PSII], pla...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00020560
更新日期:1991-02-01 00:00:00
abstract::Higher-plant, green and red algal chloroplasts are surrounded by a double membrane envelope. The glaucocystophyte plastid (cyanelle) has retained a prokaryotic cell wall between the two envelope membranes. The complex chloroplasts of Euglena and dinoflagellates are surrounded by three membranes while the complex chlor...
journal_title:Plant molecular biology
pub_type: 杂志文章,评审
doi:
更新日期:1998-09-01 00:00:00
abstract::The monoterpene indole alkaloids (MIAs) from Madagascar periwinkle (Catharanthus roseus) are secondary metabolites of high interest due to their therapeutical values. Secologanin, the monoterpenoid moiety incorporated into MIAs, is derived from the plastidial methyl-D: -erythritol 4-phosphate (MEP) pathway. Here, we h...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-007-9190-7
更新日期:2007-09-01 00:00:00
abstract::Miniature inverted-repeat transposable elements (MITEs) are short, non autonomous DNA elements that are widespread and abundant in plant genomes. The high sequence and size conservation observed in many MITE families suggest that they have spread recently throughout their respective host genomes. Here we present a mai...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-009-9511-0
更新日期:2009-09-01 00:00:00
abstract::In beans, expression of the beta-phaseolin gene (phas), encoding the major seed storage protein of bean (Phaseolus vulgaris) is confined to the cotyledons of developing embryos. Phaseolin has not been detected in the endosperm, which remains liquid and is lost early in development. However, fusion constructs between t...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00020199
更新日期:1996-11-01 00:00:00
abstract::Pyruvate orthophosphate dikinase (PPDK) is a critical enzyme for C(4) photosynthesis, providing the primary acceptor for fixation of bicarbonate in mesophyll cells. Although first isolated in C(4) plants, it is also present in C(3) species. We report that the single gene encoding PPDK in Arabidopsis thaliana possesses...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-006-9023-0
更新日期:2006-10-01 00:00:00
abstract::We have characterized a gene (Ltp1) encoding a barley lipid transfer protein. Northern blot analysis showed that Ltp1 mRNA accumulates specifically in the aleurone layer of developing and germinating seeds. Southern blot analysis indicated that LTP1 protein is encoded by a single gene in barley. Sequence analysis of L...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00040674
更新日期:1992-02-01 00:00:00
abstract::A drought- and abscisic acid (ABA)-inducible gene, His1, was isolated from Lycopersicon pennellii, a drought-resistant relative of cultivated tomato, and the gene structure was defined experimentally. The nucleotide sequence of His1 predicts a protein of 202 amino acid residues, with a significant sequence homology to...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00020112
更新日期:1996-01-01 00:00:00
abstract::Arabidopsis thaliana encodes four Dicer-like (DCL) proteins and five dsRNA-binding (DRB) proteins. We have previously demonstrated that DCL4 specifically interacts with DRB4 in vitro. Here we describe the interaction between DCL4 and DRB4 in vivo. The phenotype of a mutant with a defect in DCL4 (dcl4-2) was similar to...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-006-9125-8
更新日期:2007-04-01 00:00:00
abstract::Analysis of the structure of chromatin in cereal species using micrococcal nuclease (MNase) cleavage showed nucleosomal organization and a ladder with typical nucleosomal spacing of 175-185 bp. Probing with a set of DNA probes localized in the authentic telomeres, subtelomeric regions and bulk chromatin revealed that ...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1023/a:1005912822671
更新日期:1998-01-01 00:00:00
abstract::Proline-rich protein (PRP), a cell wall protein of plant, has been studied in many plant species. Yet, none of the PRPs has been functionally elucidated. Here we report a novel flower-specific PRP designated OsPRP3 from rice. Expression analysis showed that the OsPRP3 transcript was mainly present in rice flower and a...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-009-9557-z
更新日期:2010-01-01 00:00:00
abstract::Considerable progress in tomato molecular biology has been made over the past five years. At least 19 different mRNAs which increase in amount during tomato fruit ripening have been cloned and genes for enzymes involved in cell wall degradation (polygalacturonase and pectinesterase) and ethylene synthesis (ACC synthas...
journal_title:Plant molecular biology
pub_type: 杂志文章,评审
doi:10.1007/BF00015607
更新日期:1992-05-01 00:00:00
abstract::The amounts of a 1.9 kb mitochondrial plasmid relative to sequences in another mitochondrial DNA replicon and also to nuclear ribosomal DNA sequences have been compared in maize leaves and anthers. Similar comparisons have been made between plants with the same nuclear genotype but containing normal, S, or T cytoplasm...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF02418241
更新日期:1985-07-01 00:00:00
abstract:KEY MESSAGE:IEF, a novel plasma plasma membrane protein, is important for exine formation in Arabidopsis. Exine, an important part of pollen wall, is crucial for male fertility. The major component of exine is sporopollenin which are synthesized and secreted by tapetum. Although sporopollenin synthesis has been well st...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-020-01114-8
更新日期:2021-01-22 00:00:00
abstract::The expression of the alpha' and beta subunit genes of beta-conglycinin is differentially regulated during soybean embryo development. Although both are expressed solely in developing seeds during mid to late stages of embryo development, the alpha' subunit is expressed more highly on a per gene basis, and alpha' subu...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/BF00023991
更新日期:1991-03-01 00:00:00
abstract::The PR-like proteins, class I beta-1,3-glucanase (GLU I) and chitinase (CHN I), are induced as part of a stereotypic response that can provide protection against viral, bacterial, and fungal pathogens. We have identified two Nicotiana plumbaginifolia ankyrin-repeat proteins, designated Glucanohydrolase Binding Protein...
journal_title:Plant molecular biology
pub_type: 杂志文章
doi:10.1007/s11103-004-4679-9
更新日期:2004-11-01 00:00:00