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We are interested in identifying Drosophila melanogaster RNA-binding proteins involved in important developmental decisions made at the level of mRNA processing, stability, localization or translational control. A large subset of the proteins known to interact with specific RNA sequences shares an evolutionarily conserved 80-90-amino-acid (aa) domain referred to as an RNA-recognition motif (RRM),...
We have previously reported the isolation and preliminary characterisation of a full-length cDNA sequence derived from the human BBC1 gene, a gene which displays differential expression in tumours of the female breast [Adams et al., Hum. Mol. Genet. 1 (1992) 91-96]. Here, we report the isolation and characterisation of the Drosophila melanogaster (Dm) homologue of this human gene. The Dmbbcl cDNA...
A novel method is described for the rapid concentration of particular cDNAs and their mapping to specific regions of a genome. The strategy for cDNA scanning is based on the hybridization of an entire library of cDNAs to a large fragment of genomic DNA that is covalently bound to latex particles. The hybridized cDNAs are eluted, amplified by PCR and cloned into a λ vector. Selected cDNAs that...
A Drosophila melanogaster (Dm) cDNA (vha14) encoding the 14-kDa F-subunit of the vacuolar H + -ATPase (V-ATPase) has been cloned via homology with the corresponding Manduca sexta (Ms) gene. Its deduced translation product is a 124-amino-acid polypeptide sharing 90% identity with the Ms polypeptide and 50% identity with an analogous polypeptide of Saccharomyces cerevisiae, and a more distant...
In the framework of the complete genome sequencing programme of the crucifer Arabidopsis thaliana, a 23.9-kb fragment from the long arm of chromosome IV has been analysed. This paper presents a methodological approach, integrating computerized predictions, database screening, the sequencing of cognate cDNAs and a PCR-based detection of expression that allows the accumulation of an important amount...
The human gene XPB, defective in xeroderma pigmentosum patients complementation group B, encodes a DNA helicase involved in several DNA metabolic pathways, including DNA repair and transcription. The high conservation of this gene has allowed the cloning of homologs in various species, such as mouse, yeast and Drosophila. Not much information on the molecular basis of nucleotide excision repair in...
We isolated two copia-type retrotransposons from Arabidopsis thaliana. We named these elements AtRE1 (Arabidopsis thaliana Retro Element 1) and AtRE2. Nucleotide sequence analysis revealed that both elements have long terminal repeats (LTRs), and that their internal sequences include one large open reading frame that could encode Gag protein, protease, integrase, reverse transcriptase, and RNaseH...
Transporter-mediated Ca 2+ efflux from the cytoplasm is an important component of plant signal transduction. To elucidate the diversity and role of Ca 2+ /H + in controlling plant cytosolic Ca 2+ concentrations, homologs of CAX (for calcium exchanger) genes were cloned from Zea mays and Arabidopsis thaliana cDNA libraries. The A. thaliana homolog of CAX...
Using a transposon insertion line of the Drosophila Genome Project we have cloned the black-pearl gene (blp), analyzed cDNA clones, generated various mutants, and characterized their phenotypes. The blp gene codes for a protein of 15.7 kDa calculated molecular weight that has been conserved from yeast to plants and mammals with high homology. A domain of these new proteins shows distant similarity...
NF-Y is a CCAAT-specific binding factor composed of three distinct subunits. In vertebrates and fungi all three subunits are encoded by evolutionary conserved single copy genes. In this report we have cloned twenty-three NF-Y genes in A. thaliana, assessed their mRNA expression levels in a large number of tissues and confirmed that indeed multiple CCAAT-binding activities are present. Alignments of...
Nuclear factor Y (NF-Y) is a highly conserved trimeric activator that recognizes with high specificity and affinity the widespread CCAAT box promoter element. We previously cloned the genes of 23 NF-Y genes of Arabidopsis thaliana (Gene 264 (2001) 173). Now that the Arabidopsis genome sequencing project is complete, we present the cloning, alignments and expression profiles of the remaining six genes...
A tRNALeu-like sequence is located within a probable enhancer region of the RNA polymerase II-dependent gene encoding an RNA-binding protein, Atgrp7, in Arabidopsis (Mol. Gen. Genet. 261 (1999) 811). To examine whether this sequence is transcribed, we used our in vitro transcription system from tobacco cell nuclei. In vitro assays demonstrated that this tRNA-like sequence is transcribed by RNA polymerase...
Homologues of the bacterial cell division protein FtsZ are found in higher plants where they function as key components of the chloroplast division complex. In contrast to most bacteria that encode a single FtsZ protein, plants encode multiple proteins that group into two families, FtsZ1 and FtsZ2. Using new sequence data from a broad range photosynthetic organisms, we performed a series of analyses...
We have developed a new tool, named the plant exon finder (PEF), for identifying exons in plant genome sequences as an applied technique of T-DNA insertional mutagenesis. The T-DNA constructs contain a heat-shock gene promoter or the cauliflower mosaic virus (CaMV) 35S promoter, followed by the first exon of an Arabidopsis gene with its start codon and the intron donor sequence facing the T-DNA left...
Ankyrin repeats are present in a great variety of proteins of eukaryotes, prokaryotes and some viruses and they function as protein-protein interaction domains. We have search for all the ankyrin repeats present in Arabidopsis proteins and determined their consensus sequence. We identified a total of 509 ankyrin repeats present in 105 proteins. Ankyrin repeat containing proteins can be classified...
MicroRNAs (miRNAs) are a class of non-coding RNAs that regulate gene post-transcriptional expression in animals and plants. Comparatively genomic computational methods have been developed to predict new miRNAs in worms, humans, and Arabidopsis. Here we present an EST (Expressed Sequence Tags) — and GSS (Genomic Survey Sequences)-based combined approach for the detection of novel miRNAs in Gossypium...
To come to a better understanding of the evolution and function of the SBP-box transcription factor family in plants, we identified, isolated and characterized 13 of its members from the moss Physcomitrella patens. For the majority of the moss SBP-box genes, clear orthologous relationships with family members of flowering plants could be established by phylogenetic analysis based on the conserved...
Lateral gene transfer (LGT) can facilitate the acquisition of new functions in recipient lineages, which may enable them to colonize new environments. Several recent publications have shown that gene transfer between prokaryotes and eukaryotes occurs with appreciable frequency. Here we present a study of interdomain gene transfer of cutinases – well documented virulence factors in fungi – between...
Soil salinity severely affects plant growth and agricultural productivity. AtbZIP24 encodes a bZIP transcription factor that is induced by salt stress in Arabidopsis thaliana but suppressed in the salt-tolerant relative Lobularia maritima. Transcriptional repression of AtbZIP24 using RNA interference improved salt tolerance in A. thaliana. Under non-stress growth conditions, transgenic A. thaliana...
Cytokinin is an essential regulator of numerous plant growth and developmental processes. However, less is known about the mechanisms of cytokinin-regulated floral development. In the present study, we found that flower-specific elevation of cytokinin through transgenic expression of an Arabidopsis ATP/ADP isopentenyltransferase 4 (AtIPT4) gene under the control of the APETALA1 (AP1) promoter lead...
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