Rapid transcriptional regulation by phytochrome of the genes for phytochrome and chlorophyll a/b-binding protein in Avena sativa.

We have examined phytochrome-regulated transcription of phytochrome (phy) and chlorophyll a/b binding protein (cab) genes in dark-grown Avena seedlings by using run-on transcription in isolated nuclei. Kinetic analysis of phy transcription following pulse-light treatments to produce various amounts of Pfr, the active form of phytochrome, leads to these conclusions. (i) Transcription decreases rapidly (discernible within 5 min) after Pfr formation, reaching an essentially undetectable level by 1 h. (ii) The response is very sensitive; less than 1% Pfr is sufficient to produce maximum feedback repression over the first 30 min. (iii) The duration of transcriptional repression is proportional to the Pfr concentration; derepression begins once the concentration falls below some saturation level because of degradation of Pfr. Concurrent analysis of cab transcription leads to these conclusions. (i) After Pfr formation, transcription increases approximately 10-fold by 3 h, but this response is not detectable until after a 30-min lag. (ii) Detectable induction of cab requires a greater than 30-fold-higher Pfr level than is needed to repress phy expression. (iii) Transcription returns to the preirradiation level considerably sooner than does phy transcription (less than 12 h versus greater than 24 h respectively), indicating that a high level of Pfr is needed to sustain the increased transcription of cab. Taken together, these results suggest that differences in the phytochrome signal transduction pathway are responsible for the distinct patterns of regulation of these genes. Full repression of phy occurs even when protein synthesis is inhibited greater than 90% by cycloheximide and chloramphenicol. In conjunction with the rapidity of the response to Pfr, this result provides evidence that feedback repression of phy gene transcription does not require expression of an intervening regulatory gene(s). Thus, phy is the first gene for which there is evidence for direct control of transcription by the phytochrome signal transduction chain.

Intragenic dominant suppressors of glp-1, a gene essential for cell-signaling in Caenorhabditis elegans, support a role for cdc10/SWI6/ankyrin motifs in GLP-1 function.

The glp-1 gene product mediates cell-cell interactions required for cell fate specification during development in Caenorhabditis elegans. To identify genes that interact with glp-1, we screened for dominant suppressors of two temperature-sensitive glp-1 alleles and recovered 18 mutations that suppress both germline and embryonic glp-1 phenotypes. These dominant suppressors are tightly linked to glp-1 and do not bypass the requirement for a distal tip cell, which is thought to be the source of a signal that is received and transduced by the GLP-1 protein. Using single-strand conformation polymorphism (SSCP) analysis and DNA sequencing, we found that at least 17 suppressors are second-site intragenic revertants. The suppressors, like the original glp-1(ts) mutations, are all located in the cdc10/SWI6/ankyrin domain of GLP-1. cdc10/SWI6/ankyrin motifs have been shown to mediate specific protein-protein interactions in other polypeptides. We propose that the glp-1(ts) mutations disrupt contact between GLP-1 and an as yet unidentified target protein(s) and that the dominant suppressor mutations restore appropriate protein-protein interactions.

Enhancers of glp-1, a gene required for cell-signaling in Caenorhabditis elegans, define a set of genes required for germline development.

The distal tip cell (DTC) regulates the proliferation or differentiation choice in the Caenorhabditis elegans germline by an inductive mechanism. Cell signaling requires a putative receptor in the germline, encoded b y the glp-1 gene, and a putative signal from the DTC, encoded by the lag-2 gene. Both glp-1 and lag-2 belong to multigene gene families whose members are essential for cell signaling during development of various tissues in insects and vertebrates as well as C. elegans. Relatively little is known about how these pathways regulate cell fate choice. To identify additional genes involved in the glp-1 signaling pathway, we carried out screens for genetic enhancers of glp-1. We recovered mutations in five new genes, named ego (enhancer of glp-1), and two previously identified genes, lag-1 and glp-4, that strongly enhance a weak glp-1 loss-of-function phenotype in the germline. Ego mutations cause multiple phenotypes consistent with the idea that gene activity is required for more than one aspect of germline and, in some cases, somatic development. Based on genetic experiments, glp-1 appears to act upstream of ego-1 and ego-3. We discuss the possible functional relationships among these genes in light of their phenotypes and interactions with glp-1.

Nucleotide and amino acid sequence of a Cucurbita phytochrome cDNA clone: identification of conserved features by comparison with Avena phytochrome.

The amino acid (aa) sequence of Cucurbita phytochrome has been deduced from the nucleotide (nt) sequence of a cDNA clone which was initially identified by hybridization to an Avena phytochrome cDNA clone. Cucurbita, a dicot, and Avena, a monocot, represent evolutionarily divergent groups of plants. The Cucurbita phytochrome polypeptide is 1123 aa in length, corresponding to 125 kDa. Overall, the Cucurbita and Avena phytochrome sequences are 65% homologous at both the nt and aa levels but this sequence conservation is not evenly distributed. Most of the N-terminal two-thirds of the aligned polypeptide chains exhibits localized regions of high conservation, while the extreme N terminus and the C-terminal one-third are less homologous. Comparison of the predicted hydropathic properties of these polypeptides also indicates conservation of domains of phytochrome structure. The possible correlation of these conserved structural features with previously identified functional domains of phytochrome is discussed.

Green fluorescent protein as a quantitative reporter of relative promoter activity in E. coli.

Green fluorescent protein (GFP) has become a valuable tool for the detection of gene expression in prokaryotes and eukaryotes. To evaluate its potential for quantitation of relative promoter activity in E. coli, we have compared GFP with the commonly used reporter gene lacZ, encoding beta-galactosidase. We cloned a series of previously characterized synthetic E. coli promoters into GFP and beta-galactosidase reporter vectors. Qualitative and quantitative assessments of these constructs show that (a) both reporters display similar sensitivities in cells grown on solid or liquid media and (b) GFP is especially well suited for quantitation of promoter activity in cells grown on agar. Thus, GFP provides a simple, rapid and sensitive tool for measuring relative promoter activity in intact E. coli cells.

Phylogenetic analysis of vertebrate and invertebrate Delta/Serrate/LAG-2 (DSL) proteins.

Delta/Serrate/LAG-2 (DSL) proteins are putative transmembrane signaling molecules that regulate cell differentiation in metazoans. DSL proteins are characterized by the presence of a motif unique to these proteins, the DSL motif, and a variable number of tandemly repeated copies of an epidermal growth factor-like (EGF) motif. We have completed a phylogenetic analysis of 15 DSL proteins from eight species. Our findings reveal that at least one gene duplication occurred prior to the divergence of the Drosophila melanogaster and vertebrate lineages, with subsequent duplications in vertebrates. The three known Caenorhabditis elegans proteins likely arose by two independent duplications in the nematode lineage. Analysis of EGF repeats suggests that EGF 2 has been conserved among DSL proteins in vertebrates and D. melanogaster. The sequences of two EGF repeats have been perfectly conserved in vertebrate orthologs: EGF 2 in Delta and EGF 15 in Jagged/Serrate. Finally, the linear order of EGF repeats has been conserved in the vertebrate Jagged/Serrate orthologs and vertebrate Delta orthologs.

Cloning of cDNA for phytochrome from etiolated Cucurbita and coordinate photoregulation of the abundance of two distinct phytochrome transcripts.

We have isolated several cDNA clones for phytochrome from a dicot, Cucurbita pepo L. cv. Black Beauty (zucchini), and have used them to study the regulation of Cucurbita phytochrome mRNA levels. A cDNA library was constructed from poly(A)(+) RNA isolated from etiolated Cucurbita hypocotyl hooks and enriched for phytochrome mRNA by size fractionation. This library was screened with a (32)P-labeled fragment isolated from an Avena phytochrome cDNA clone. Several putative phytochrome clones were isolated and mapped by restriction endonuclease analysis. On the basis of this analysis there is no evidence for the expression of multiple phytochrome genes in Cucurbita. Recent sequence analysis has confirmed that the largest of these clones, pFMD1 (∼3.6 kb), does indeed encode phytochrome and that it contains the entire amino acid coding sequence for Cucurbita phytochrome (33). RNA blot analysis has revealed that two polyadenylated phytochrome transcripts (∼5.6 kb and ∼4.2 kb) are present in both cotyledons and hypocotyl hooks of Cucurbita. In etiolated Cucurbita seedlings given a saturating pulse of red light, the abundance of both transcripts coordinately declines to 50-60% of the dark levels within 3 h and reaccumulates to dark levels within 24 h. Reversal of induction of this response by a far-red light pulse immediately following red light treatment is not observed, which is in contrast to the far-red reversibility of the red light promoted decrease in phytochrome mRNA abundance observed in Avena (6). Etiolated seedlings transferred to continuous white light also show a coordinate decrease in the levels of the two RNAs to ∼40% of the dark levels within 3 h. The magnitude of the light-induced decline in phytochrome mRNA abundance in Cucurbita is substantially less than the decrease previously reported for Avena (6).

A phylogenetic analysis of vertebrate and invertebrate Notch-related genes.

Members of the Notch gene family are thought to mediate inductive cell-cell interactions during development of a wide variety of vertebrates and invertebrates. These genes encoded transmembrane proteins that appear to act as receptors and contain three repeated sequence motifs. Two of these motifs (an epidermal growth factor-like sequence and a cdc10/SWI6/ankyrin sequence) have been found in a large number of unrelated proteins, while the third motif (a lin-12/Notch/glp-1 sequence) is unique to proteins of the Notch family. We present a phylogenetic analysis of 17 Notch-related genes from eight species that has implications as to the origins and relative functions of these genes in different species. Several independent gene duplications have occurred and at least one such duplication in the vertebrate lineage preceded the avian/mammalian divergence. Significantly, the overall organization of individual members of each internally repeated motif appears to have been conserved among species, suggesting that each repeat plays a unique role in protein function. Yet, where sequence divergence does occur among genes in vertebrate, dipteran, and nematode lineages, it may signify functional differences for specific regions in Notch-related proteins.

Alternative splicing of fructose 1,6-bisphosphate aldolase transcripts in Drosophila melanogaster predicts three isozymes.

The genes that encode fructose 1,6-bisphosphate aldolase of Drosophila melanogaster have been isolated and characterized. These genes exist in a single copy 8-kilobase pair locus in the Drosophila genome which is located at cytogenetic position 97A-B. The nucleotide sequence and transcript mapping suggest that three overlapping protein isozyme genes may be encoded at this locus. These isozyme genes all share a single promoter, a 5'-untranslated first exon, and two other protein coding exons. The isozyme-specific carboxyl-terminal amino acids are encoded by one of three alternatively utilized fourth exons: 4A, 4B, or 4C by alternative splicing. The transcript containing exon 4C, whose sequence has been reported previously, is abundant throughout development and has a developmental profile similar to other glycolytic gene transcripts; however, it shows developmental specificity in the alternative use of two polyadenylation signals which result in a 2.4-kilobase and a 1.9-kilobase transcript. The transcript containing exon 4B is 1.6 kilobases in size and is most abundant during the larval stages and during the time of eclosion. The transcript containing exon 4A is in low abundance and found only during the adult stage. Sequence comparisons of the alternative fourth exons indicate that the duplication leading to the multiple exons is quite old and preceded the origin of the genus Drosophila.

Structure and expression of the triose phosphate isomerase (Tpi) gene of Drosophila melanogaster.

We report the isolation of the genomic sequence that encodes the enzyme triose phosphate isomerase of Drosophila melanogaster. There is a single copy of the Tpi sequence in the genome of Drosophila, as judged by Southern blots and in situ hybridization to salivary gland chromosomes. The sequence of 3414 nucleotides from the Tpi region was determined. The gene has an intron in the 5' untranslated region of the transcript and a second intron in the coding region at an evolutionarily conserved position. Transcripts initiate at a single site which does not have a TATA box in the usual position. Northern blot analysis of RNA prepared from different developmental stages revealed that Tpi mRNA is present in substantial amounts in oocytes, declines in abundance in early embryos, and begins to increase during mid-embryogenesis. Transcript abundance follows a pattern typical of enzymes involved in intermediate metabolism. A peak is found during third instar followed by a decline during pupal stages and then a second rise near the time of eclosion.