Structure and expression of a novel, neuronal protein kinase C (PKC1B) from Caenorhabditis elegans. PKC1B is expressed selectively in neurons that receive, transmit, and process environmental signals

The nematode Caenorhabditis elegans provides an advantageous system for investigating the regulation, expression, and functions of protein kinase C (PKC) isoforms. We cloned and characterized cDNAs encoding a novel C. elegans PKC designated PKC1B. The predicted PKC1B polypeptide contains features characteristic of the nPKC subfamily of PKC isoforms. The levels of PKC1B and its cognate mRNA vary over a 7-fold range during C. elegans postembryonic development. PKC1B protein and mRNA are abundant at the earliest larval stage, but their relative concentrations decrease coordinately in late larvae. Embryos, which are enriched in PKC1B mRNA, contain little PKC1B protein. Thus, PKC1B expression is regulated at a translational or post-translational level during early development. Cells engaged in PKC1B gene transcription were identified in transgenic C. elegans that carry the lacZ gene under the regulation of the PKC1B promoter. Staining for beta-galactosidase revealed PKC1B promoter activity exclusively in sensory neurons and interneurons. Immunofluorescence microscopy disclosed that the PKC1B polypeptide is located in the processes (axons and dendrites) and perinuclear regions of approximately 75 neurons that constitute the sensory circuitry of the nematode. The intracellular localization of PKC1B and the enzyme's differential solubility in ionic and nonionic detergents suggest that the kinase is associated with membranes and the cytoskeleton.

Crystallization and preliminary X-ray analysis of the auto-inhibited twitchin kinase

An auto-inhibited fragment of twitchin kinase (residues 5890 to 6262) has been crystallized by vapor diffusion techniques using polyethylene glycol 4000 as the precipitant at pH 7.25 to 7.5 at 4 degrees C. We have found that MgSO4 and glycerol were essential for large crystal growth. The crystals belong to the orthorhombic space group P2(1)2(1)2, with unit cell dimensions of a = 144.1 A, b = 168.3 A and c = 60.6 A. They are suitable for X-ray analysis and diffract to a resolution of at least 2.8 A.

Trypanosoma brucei RNA polymerase II is phosphorylated in the absence of carboxyl-terminal domain heptapeptide repeats

Formation of an RNA polymerase II transcription initiation complex requires binding of a polymerase that contains a non-phosphorylated largest subunit carboxyl-terminal domain (CTD). Polymerase binding is followed by elongation after phosphorylation of the CTD by a CTD kinase. Phosphorylation sites are within the repeating heptapeptide motifs which characterize the CTD of all eukaryotic RNA polymerase IIs. In contrast to all other eukaryotes studied, the trypanosome genome contains two genetic loci which encode the large subunit of RNA polymerase II; both genes lack CTD heptapeptide repeat structures. We have examined whether Trypanosoma brucei RNA polymerase II, despite its unique CTD domain, is phosphorylated when isolated from elongating transcription complexes. Elongating trypanosome RNA polymerases were photoaffinity labeled during nuclear run-on assays. The identity of the labeled proteins was established by immunoblotting and immunoprecipitation using polymerase-specific antisera. Analysis of the largest subunit of RNA polymerase II revealed the expected 195-kDa species and an additional larger 220-kDa species. The apparent molecular weight of this larger form of RNA polymerase II decreased incrementally as a function of incubation with increasing concentrations of calf intestinal phosphatase. These results show that extensive phosphorylation of the largest subunit of RNA polymerase-II is a conserved feature between trypanosomes and higher eukaryotes despite the absence of a typical CTD domain.

Suppression of activated Let-60 ras protein defines a role of Caenorhabditis elegans Sur-1 MAP kinase in vulval differentiation

The let-60 ras gene of Caenorhabditis elegans is one of the key players in a signal transduction pathway that controls the choice between vulval and epidermal differentiation in response to extracellular signals. To identify components acting downstream of let-60 ras in the vulval signaling pathway, we have identified a reduction-of-function mutation in the sur-1 gene that completely suppresses the multivulva phenotype of a hyperactive let-60 ras mutation. About 10% of animals homozygous for the sur-1 mutation also display a specific and intriguing vulval cell lineage defect. In addition, the sur-1 mutation results in a cold-sensitive egg-laying defective phenotype and a partial larval lethal phenotype. We have cloned the sur-1 gene by DNA-mediated transformation and have shown that it encodes a protein similar in overall structure to mammalian MAP kinases (ERKs). The functional homology between Sur-1 MAP kinase and mammalian MAP kinases was also demonstrated by the ability of a rat ERK2 kinase to rescue the sur-1 mutant phenotypes. Genetic double-mutant analyses place sur-1 downstream of let-60 ras but upstream of lin-1 in the vulval signaling pathway. Our results provide further evidence for the extreme conservation of Ras-mediated signaling pathway between worms and humans and for the function of MAP kinases in cell signaling processes that control cell differentiation and animal development.

The C. elegans cell death gene ced-3 encodes a protein similar to mammalian interleukin-1 beta-converting enzyme

We have cloned the C. elegans cell death gene ced-3. A ced-3 transcript is most abundant during embryogenesis, the stage during which most programmed cell deaths occur. The predicted CED-3 protein shows similarity to human and murine interleukin-1 beta-converting enzyme and to the product of the mouse nedd-2 gene, which is expressed in the embryonic brain. The sequences of 12 ced-3 mutations as well as the sequences of ced-3 genes from two related nematode species identify sites of potential functional importance. We propose that the CED-3 protein acts as a cysteine protease in the initiation of programmed cell death in C. elegans and that cysteine proteases also function in programmed cell death in mammals.

Two novel transmembrane protein tyrosine kinases expressed during Caenorhabditis elegans hypodermal development

We describe our characterization of kin-15 and kin-16, a tandem pair of homologous Caenorhabditis elegans genes encoding transmembrane protein tyrosine kinases (PTKs) with an unusual structure: the predicted extracellular domain of each putative gene product is only about 50 amino acids, and there are no potential autophosphorylation sites in the C-terminal domain. Using lacZ fusions, we found that kin-15 and kin-16 both appear to be expressed during postembryonic development in the large hypodermal syncytium (hyp7) around the time that specific hypodermal cells fuse with hyp7. kin-15 and kin-16 were positioned on the genetic and physical maps, but extrachromosomal arrays containing wild-type kin-15 and/or kin-16 genes were unable to complement candidate lethal mutations. The results suggest that kin-15 and kin-16 may be specifically involved in cell-cell interactions regulating cell fusions that generate the hypodermis during postembryonic development.

The daf-4 gene encodes a bone morphogenetic protein receptor controlling C. elegans dauer larva development

The bone morphogenetic protein (BMP) family is a conserved group of signalling molecules within the transforming growth factor-beta (TGF-beta) superfamily. This group, including the Drosophila decapentaplegic (dpp) protein and the mammalian BMPs, mediates cellular interactions and tissue differentiation during development. Here we show that a homologue of human BMPs controls a developmental switch in the life cycle of the free-living soil nematode Caenorhabditis elegans. Starvation and overcrowding induce C. elegans to form a developmentally arrested, third-stage dauer larva. The daf-4 gene, which acts to inhibit dauer larva formation and promote growth, encodes a receptor protein kinase similar to the daf-1, activin and TGF-beta receptor serine/threonine kinases. When expressed in monkey COS cells, the daf-4 receptor binds human BMP-2 and BMP-4. The daf-4 receptor is the first to be identified for any growth factor in the BMP family.

Cloning and characterization of the C. elegans histidyl-tRNA synthetase gene

In this paper, we report the cloning and sequencing of the C. elegans histidyl-tRNA synthetase gene. The complete genomic sequence, and most of the cDNA sequence, of this gene is now determined. The gene size including flanking and coding regions is 2230 nucleotides long. Three small introns (45-50 bp long) are found to interrupt the open reading frame. The open reading frame translates to 523 amino acids. This putative protein sequence shows extensive homology with the human and yeast histidyl-tRNA the histidyl-tRNA synthetase gene is a single copy gene. Hence, it is very likely that it encodes both the cytoplasmic and the mitochondrial histidyl-tRNA synthetases. It is likely to be trans-spliced since it contains a trans-splice site in its 5' untranslated region.

Genetics of eukaryotic RNA polymerases I, II, and III

The transcription of nucleus-encoded genes in eukaryotes is performed by three distinct RNA polymerases termed I, II, and III, each of which is a complex enzyme composed of more than 10 subunits. The isolation of genes encoding subunits of eukaryotic RNA polymerases from a wide spectrum of organisms has confirmed previous biochemical and immunological data indicating that all three enzymes are closely related in structures that have been conserved in evolution. Each RNA polymerase is an enzyme complex composed of two large subunits that are homologous to the two largest subunits of prokaryotic RNA polymerases and are associated with smaller polypeptides, some of which are common to two or to all three eukaryotic enzymes. This remarkable conservation of structure most probably underlies a conservation of function and emphasizes the likelihood that information gained from the study of RNA polymerases from one organism will be applicable to others. The recent isolation of many mutations affecting the structure and/or function of eukaryotic and prokaryotic RNA polymerases now makes it feasible to begin integrating genetic and biochemical information from various species in order to develop a picture of these enzymes. The picture of eukaryotic RNA polymerases depicted in this article emphasizes the role(s) of different polypeptide regions in interaction with other subunits, cofactors, substrates, inhibitors, or accessory transcription factors, as well as the requirement for these interactions in transcription initiation, elongation, pausing, termination, and/or enzyme assembly. Most mutations described here have been isolated in eukaryotic organisms that have well-developed experimental genetic systems as well as amenable biochemistry, such as Saccharomyces cerevisiae, Drosophila melanogaster, and Caenorhabditis elegans. When relevant, mutations affecting regions of Escherichia coli RNA polymerase that are conserved among eukaryotes and prokaryotes are also presented. In addition to providing information about the structure and function of eukaryotic RNA polymerases, the study of mutations and of the pleiotropic phenotypes they imposed has underscored the central role played by these enzymes in many fundamental processes such as development and cellular differentiation.

Oxygen dependency of life-span in the nematode

1. The mean and maximum life-spans of both wild type Caenorhabditis elegans and the mev-1(kn1) mutant, whose cytoplasmic superoxide dismutase activity level is about half of the wild type, were increased and decreased under low and high concentrations of oxygen, respectively. 2. The Gompertz component, a parameter of ageing rate, of the wild type was smaller under 1% oxygen than under 2% or more oxygen. Further, the Gompertz component of the mutant increased with an increase in oxygen concentration. 3. The oxygen-dependent modulation of life-span and ageing rate seems to be enhanced by a genetic defect of the mutant in antioxidant defence.

Characterization of the Caenorhabditis elegans Tc1 transposase in vivo and in vitro

We have investigated the function of the Tc1A gene of the mobile element Tc1 of Caenorhabditis elegans. Tc1 is a member of a family of transposons found in several animal phyla, such as nematodes, insects, and vertebrates. Two lines of evidence show that Tc1A encodes the transposase of Tc1. First, forced expression of the Tc1A protein in transgenic nematodes results in an enhanced level of transposition of endogenous Tc1 elements. Second, DNase I footprinting and gel retardation assays show that Tc1A binds specifically to the inverted repeats at the ends of the element and that the Tc1A recognition site is located between base pairs 5 and 26 from the ends of Tc1. Functional dissection of the transposase shows the presence of two distinct DNA-binding domains. A site-specific DNA-binding domain is contained within the amino-terminal 63 residues of Tc1A; this region shows sequence similarity to the prokaryotic IS30 transposase. A second, general DNA-binding domain is located between amino acids 71 and 207. Our results suggest that Tc1 is more similar to prokaryotic insertion elements than to eukaryotic transposons such as P elements in Drosophila or Ac and En-1 in plants.

Oxidative stress and ageing in Caenorhabditis elegans

Mutations in the age-1 gene double both the mean and maximum life span of Caenorhabditis elegans. They also result in an age-specific increase of catalase and Cu/Zn superoxide dismutase activity levels. The higher superoxide dismutase activity levels in age-1 mutants confer hyperresistance to the superoxide-anion-generating drug paraquat. The rate of superoxide anion production by microsome fractions declines linearly with age in age-1(+) worms, but, after an initial decline, is stabilized at a higher level in senescent age-1 mutant nematodes. These results clearly show that oxidative stress resistance and potential life span are correlated in this organism, and they suggest that the natural product of age-1 either directly or indirectly downregulates the activities of several other genes as a function of age.

Mobilization of quiet, endogenous Tc3 transposons of Caenorhabditis elegans by forced expression of Tc3 transposase

The commonly studied Caenorhabditis elegans strain Bristol N2 contains approximately 15 copies per genome of the transposon Tc3. However, Tc3 is not active in Bristol N2. Tc3 contains one major open reading frame (Tc3A). We have fused this open reading frame to an inducible promoter and expressed it in a transgenic Bristol N2 line. Tc3A expression resulted in frequent excision and transposition of endogenous Tc3 elements. This shows that the Bristol N2 genome contains Tc3 transposons that are cis proficient for transposition, but are immobile because Tc3A is absent. We demonstrate that recombinant Tc3A binds specifically to the terminal nucleotides of the Tc3 inverted repeat, indicating that Tc3A is the Tc3 transposase. Activation of Tc3 transposition in vivo was accompanied by the appearance of extrachromosomal, linear copies of Tc3. These may be intermediates in Tc3 transposition.

Expression and biochemical characterization of the DNA binding activity of TcA, the putative transposase of Caenorhabditis elegans transposable element Tc1

The TcA protein is one of the proteins essential for Tc1 transposition. In order to study the biochemical parameters of Tc1 transposition mechanism, we used TcA protein overproduced in baculovirus system for DNA binding experiments. We show that, despite its relatively strong non specific affinity for DNA, TcA exhibits a better affinity for its Tc1 specific binding sites. The K0.5 is 3.8 nM for the Tc1 whereas in the same type of experiment the K0.5 is 24 nM for calf thymus DNA. The ratio value between specific and non specific DNA binding activity of the TcA protein was also exhibited by other transposases such as those of the bacteriophage Mu, Tn 10 and the Drosophila P element. This nonspecific DNA binding activity may be involved in determining sites of transposable element insertion.

C. elegans lin-45 raf gene participates in let-60 ras-stimulated vulval differentiation

Vulval differentiation in Caenorhabditis elegans is controlled by intercellular signalling mediated by a receptor tyrosine kinase and a ras gene product. The lin-45 gene encodes a homologue of the raf family of serine/threonine kinases and is necessary for vulval differentiation. The lin-45 raf gene product appears to act downstream of the ras protein in this pathway. A proto-oncogene-mediated signalling pathway may be a common feature of metazoan development.

The baculovirus Autographa californica encodes a protein tyrosine phosphatase

The genome of the baculovirus Autographa californica encodes a 19-kDa protein (BVP) containing an active site sequence motif ((I/V)HCXAGXXR(S/T)G) that characterizes a large family of protein tyrosine phosphatases (PTPs). The baculoviral protein was expressed in Escherichia coli and purified so that its enzymatic properties could be examined. We have demonstrated that recombinant BVP has intrinsic protein tyrosine phosphatase activity. Like VH1, a PTP encoded by vaccinia virus, BVP also dephosphorylates seryl or threonyl residues. However, the similarity of BVP to VH1 or the catalytic domains from PTPs of eukaryotic origin is restricted to a small region surrounding the active site motif. In contrast, the similarity of BVP to two putative PTPs encoded by the CDC14 gene of Saccharomyces cerevisiae and a gene of unknown function from Caenorhabditis elegans extends throughout its sequence. We postulate that BVP and its two homologs constitute a unique subfamily that may differ from other PTPs in having a specialized function, mode of regulation, or substrate preference.

The ubc-2 gene of Caenorhabditis elegans encodes a ubiquitin-conjugating enzyme involved in selective protein degradation

The ubiquitin-protein conjugation system is involved in a variety of eukaryotic cell functions, including the degradation of abnormal and short-lived proteins, chromatin structure, cell cycle progression, and DNA repair. The ubiquitination of target proteins is catalyzed by a ubiquitin-activating enzyme (E1) and ubiquitin-conjugating enzymes (E2s) and in some cases also requires auxiliary substrate recognition proteins (E3s). Multiple E2s have been found, and these likely possess specificity for different classes of target proteins. Here we report the cloning and characterization of a gene (ubc-2) encoding a ubiquitin-conjugating enzyme which is involved in the selective degradation of abnormal and short-lived proteins in the nematode Caenorhabditis elegans. The nematode ubc-2 gene encodes a 16.7-kDa protein with striking amino acid sequence similarity to Saccharomyces cerevisiae UBC4 and UBC5 and Drosophila UbcD1. When driven by the UBC4 promoter, ubc-2 can functionally substitute for UBC4 in yeast cells; it rescues the slow-growth phenotype of ubc4 ubc5 mutants at normal temperature and restores their ability to grow at elevated temperatures. Western blots (immunoblots) of ubc4 ubc5 yeast cells transformed with ubc-2 reveal a protein of the expected size, which cross-reacts with anti-Drosophila UbcD1 antibody. C. elegans ubc-2 is constitutively expressed at all life cycle stages and, unlike yeast UBC4 and UBC5, is not induced by heat shock. Both trans and cis splicing are involved in the maturation of the ubc-2 transcript. These data suggest that yeast UBC4 and UBC5, Drosophila UbcD1, and C. elegans ubc-2 define a highly conserved gene family which plays fundamental roles in all eukaryotic cells.

The gut esterase gene (ges-1) from the nematodes Caenorhabditis elegans and Caenorhabditis briggsae

The ges-1 gene codes for a non-specific carboxylesterase that is normally expressed only in the intestine of the nematode Caenorhabditis elegans. In the current paper, we describe the cloning and characterization of the ges-1 gene from C. elegans, as well as the homologous gene from the nematode Caenorhabditis briggsae. The ges-1 esterases from the two nematodes are 83% identical at the amino acid level and contain regions of significant similarity to insect and mammalian esterases; these conserved regions can be identified with residues believed to be necessary for esterase function. The ges-1 mRNAs from both C. elegans and C. briggsae are trans-spliced. The coding regions, the codon bias and the splicing signals of the two ges-1 genes are quite similar and most (6/7) of the intron positions are retained precisely. Yet, the flanking sequences of the two ges-1 genes appear to have diverged almost completely. For example, the C. elegans ges-1 5'-flanking region (as well as several introns) contains copies of three different SINE-like sequences, previously identified near the hsp-16 genes, near the unc-22 gene and in a repetitive element CeRep-3; none of these elements are found in the C. briggsae ges-1 gene. We show that: (1) the C. elegans ges-1 gene can be used to transform C. briggsae, whereupon expression of the exogenous ges-1 gene is confined to the C. briggsae intestine; (2) the ges-1 homologue cloned from C. briggsae can be transformed into C. elegans, whereupon it is expressed largely in the C. elegans intestine; and (3) a 5'-deletion of the C. elegans ges-1 gene that we have previously shown to be expressed in the C. elegans pharynx is also expressed in the pharynx of C. briggsae (either in the presence or absence of vector sequences). These results suggest that the ges-1 gene control circuits have been maintained between the two nematode species, despite the divergent 5'-flanking sequences of the gene. This raises the question of the evolutionary distance between C. elegans and C. briggsae and we attempt to estimate the C. elegans-C. briggsae divergence time by analysing the rate of synonymous substitutions in coding regions of ges-1 and six other C. elegans-C. briggsae gene pairs. We propose a new method of analysis, which attempts to remove rate differences found between different genes by extrapolating to zero codon bias.(ABSTRACT TRUNCATED AT 400 WORDS)

Post-transcriptional regulation of RNA polymerase II levels in Caenorhabditis elegans

To investigate the regulation of RNA polymerase II levels in Caenorhabditis elegans, we have constructed nematode strains having one, two, or three copies of ama-1, the gene for the largest subunit of RNA polymerase II. Steady-state levels of RNA polymerase II polypeptides and solubilized enzyme activity are invariant with gene dosage, indicating regulatory compensation. However, steady-state levels of ama-1 mRNA are directly proportional to gene dosage. These results imply that RNA polymerase II levels in C. elegans are regulated post-transcriptionally.

Molecular characterization in the dpy-14 region identifies the adenosylhomocysteine hydrolase gene in Caenorhabditis elegans

The region around dpy-14 on chromosome 1 of Caenorhabditis elegans has been extensively studied genetically, with regard to essential gene organization. This region was one of the first for which cloned DNA was available as a result of restriction fragment length polymorphism mapping. To examine the information content of the cloned DNA in this region, evolutionarily conserved sequences were identified by cross-species hybridization. Ten regions of conservation have been identified and characterized with regard to mRNA abundance and DNA sequence. cDNAs were obtained for seven of these conserved regions and sequence from the cDNAs were used to search the SWISS protein and EMBL nucleotide data banks. Two coding regions shared DNA identifies with existing sequences, the opa repeat family of Drosophila and the S-adenosylhomocysteine hydrolase gene. Of the three for which no corresponding cDNA were found, one corresponds to the snRNA U1-1. The other two did not detect transcripts on Northern analysis and are either conserved, but not coding, or code for low abundance transcripts. The density of conserved coding regions in this study was one per 15 kbp of genomic DNA, three times lower than that reported on chromosome 3 by the genome sequencing project.

cDNA sequence, gene structure, and cholinesterase-like domains of an esterase from Caenorhabditis elegans mapped to chromosome V

The structure of an esterase gene from Caenorhabditis elegans has been determined by comparison of the sequences in genomic and cDNA clones. The gene was mapped close to the center of chromosome V (1.7 centimorgans to the left of dpy-11) and is therefore distinct from the gut esterase gene ges-1. It possessed 7 short introns. The 5' splice site of intron 3 presented the sequence GC instead of the usual GT that was found in the other six introns. The cDNA was trans-spliced with the short leader SL1. The open reading frame indicated that a protein of 557 aminoacids was encoded. The deduced aminoacid sequence did not present a signal peptide at the N-terminal but a potential N-myristoylation site (GXXXS) provided that the initiator methionine was removed. This protein should therefore remain intracellular. Comparison of this C. elegans sequence to other protein sequences in databases, as well as the analysis of the secondary structure in the protein showed that it belongs to the subgroup of esterases in the alpha/beta hydrolase fold family.

Histochemical techniques for locating Escherichia coli beta-galactosidase activity in transgenic organisms

Escherichia coli beta-galactosidase is a commonly used reporter molecule for analyzing gene expression. Recently, beta-galactosidase fusions have been applied to a variety of eukaryotic systems. The techniques for constructing and introducing beta-galactosidase fusion constructs as well as soluble assays for total enzyme function have been described in detail elsewhere. This article describes histochemical techniques for analyzing organisms that contain a functional beta-galactosidase fusion construct. The object is to determine semiquantitatively which cells are expressing the beta-galactosidase fusion protein, as well as the subcellular localization of the protein. Due to its prevalence in the author's laboratory, Caenorhabditis elegans is used as a canonical organism for the detailed methods described.