Maturation of the major ubiquitin gene transcript in Caenorhabditis elegans involves the acquisition of a trans-spliced leader

Neurotoxic unc-8 mutants encode constitutively active DEG/ENaC channels that are blocked by divalent cations

Ion channels of the DEG/ENaC family can induce neurodegeneration under conditions in which they become hyperactivated. The Caenorhabditis elegans DEG/ENaC channel MEC-4(d) encodes a mutant channel with a substitution in the pore domain that causes swelling and death of the six touch neurons in which it is expressed. Dominant mutations in the C. elegans DEG/ENaC channel subunit UNC-8 result in uncoordinated movement. Here we show that this unc-8 movement defect is correlated with the selective death of cholinergic motor neurons in the ventral nerve cord. Experiments in Xenopus laevis ooctyes confirm that these mutant proteins, UNC-8(G387E) and UNC-8(A586T), encode hyperactivated channels that are strongly inhibited by extracellular calcium and magnesium. Reduction of extracellular divalent cations exacerbates UNC-8(G387E) toxicity in oocytes. We suggest that inhibition by extracellular divalent cations limits UNC-8 toxicity and may contribute to the selective death of neurons that express UNC-8 in vivo.

Cross-validated methods for promoter/transcription start site mapping in SL trans-spliced genes, established using the Ciona intestinalis troponin I gene

In conventionally-expressed eukaryotic genes, transcription start sites (TSSs) can be identified by mapping the mature mRNA 5'-terminal sequence onto the genome. However, this approach is not applicable to genes that undergo pre-mRNA 5'-leader trans-splicing (SL trans-splicing) because the original 5'-segment of the primary transcript is replaced by the spliced leader sequence during the trans-splicing reaction and is discarded. Thus TSS mapping for trans-spliced genes requires different approaches. We describe two such approaches and show that they generate precisely agreeing results for an SL trans-spliced gene encoding the muscle protein troponin I in the ascidian tunicate chordate Ciona intestinalis. One method is based on experimental deletion of trans-splice acceptor sites and the other is based on high-throughput mRNA 5'-RACE sequence analysis of natural RNA populations in order to detect minor transcripts containing the pre-mRNA's original 5'-end. Both methods identified a single major troponin I TSS located ∼460 nt upstream of the trans-splice acceptor site. Further experimental analysis identified a functionally important TATA element 31 nt upstream of the start site. The two methods employed have complementary strengths and are broadly applicable to mapping promoters/TSSs for trans-spliced genes in tunicates and in trans-splicing organisms from other phyla.

Characterization of beta-tubulin genes in hookworms and investigation of resistance-associated mutations using real-time PCR

Human hookworms (Ancylostoma duodenale, Necator americanus) are a major cause of malnutrition and anemia, particularly in children, and high worm burdens can lead to stunted growth and mental retardation. Mass drug administration (MDA) with benzimidazole (BZ) anthelmintics has the potential to greatly reduce morbidity and infection prevalence. However, such treatment strategies may apply significant selection pressure on resistance alleles. In several Strongylid parasites of livestock, resistance to BZ drugs is associated with single nucleotide polymorphisms (SNPs) in the beta-tubulin isotype-1 gene at codons 167 and 200. As an initial investigation into the possible development of BZ resistance in hookworms, we have cloned and sequenced the beta-tubulin isotype-1 genes of the canine hookworm Ancylostoma caninum and the two human hookworm species A. duodenale and N. americanus. The genomic sequences are highly conserved as evidenced by a similar structure of exons and introns; the 10 exons are of the same length in all three species and code for the same amino acids. The genomic sequences were then used to develop a real-time PCR assay for detecting polymorphisms in codons 167 and 200 in all three species. Hookworm specimens previously obtained from Pemba Island school children who had demonstrated a reduced response to treatment with mebendazole were then examined using the real-time PCR assay. None of the samples revealed significant levels of polymorphisms at these loci. If BZ resistance is present in the hookworm populations examined, the results do not support the hypothesis that changes in codons 167 and 200 of beta-tubulin isotype-1 are responsible for any resistance.

Repetitious structure and transcription control of a polyubiquitin gene in Volvox carteri

Southern analysis indicated the presence of at least four ubiquitin gene loci in the Volvox carteri genome. Three of these, a polyubiquitin gene described here and a non-segregating ubiquitin gene pair, were assigned to two different linkage groups by RFLP mapping; the non-polymorphic fourth gene locus remained unassigned. The polyubiquitin gene was cloned and its 2,116-bp sequence determined. It contains six exons each interrupted by an intron at Gly35, and it encodes a pentameric polyubiquitin polypeptide consisting of five runs of 76 identical amino-acid residues and a C-terminal extension of one leucine. The five tandem repeats of coding units plus introns exhibit an unusually high degree of overall sequence identity indicating an efficient process of gene homogenization in this region of the V. carteri genome. S1 mapping revealed two closely-spaced transcription starts, 24 and 28 nucleotides downstream from a putative TATA sequence. Preceding the TATA box are two 14-bp conserved heat-shock elements (HSEs) and two octameric sequences closely resembling an yesat HSE. Consistent with a 1.6-kb transcript seen on Northern blots are two polyadenylation signals (TGTAA) located 99 bp and 169 bp downstream from the TGA translational stop. The polyubiquitin gene was transcribed throughout the Volvox life cycle with peaks in the 1.6-kb mRNA levels during pre-cleavage, cleavage, and post-inversion. In contrast, an 0.6-kb monoubiquitin transcript was abundant only at the pre-cleavage stage suggesting a different type of gene control. Heat shock increased the level of polyubiquitin mRNA, whereas the level of monoubiquitin mRNA was down-regulated.

The intron of Arabidopsis thaliana polyubiquitin genes is conserved in location and is a quantitative determinant of chimeric gene expression

We have isolated and determined DNA sequence for the 5'-flanking regions of three Arabidopsis thaliana polyubiquitin genes, UBQ3, UBQ10, and UBQ11. Comparison to cDNA sequences revealed the presence of an intron in the 5'-untranslated region at the same position immediately upstream of the initiator methionine codon in each of the three genes. An intron at this position is also present in two sunflower and two maize polyubiquitin genes. An intron is also found in the 5'-untranslated regions of several animal polyubiquitin genes, although the exact intron position is not conserved among them, and none are in the same position as those in the higher plant polyubiquitin genes. Chimeric genes containing the 5'-flanking regions of UBQ3, UBQ10, and UBQ11 in front of the coding regions for the reporter enzyme Escherichia coli beta-glucuronidase (GUS) were constructed. When introduced transiently into Arabidopsis leaves via microprojectile bombardment, all resulted in readily detectable levels of GUS activity that were quantitatively similar. The introns of UBQ3 and UBQ10 in the corresponding promoter fragments were removed by replacement with flanking cDNA sequences and chimeric genes constructed. These constructs resulted in 2.5- to 3-fold lower levels of marker enzyme activity after transient introduction into Arabidopsis leaves. The UBQ10 promoter without the 5' intron placed upstream of firefly luciferase (LUX) resulted in an average of 3-fold lower LUX activity than from an equivalent construct with the UBQ10 intron. A UBQ3 promoter cassette was constructed for the constitutive expression of open reading frames in dicot plants and it produced readily detectable levels of GUS activity in transient assays.

Trans-splicing of an early embryo mRNA in Litomosoides carinii, coding for the major microfilarial sheath protein gp22

Both genomic and cDNA clones have been isolated encoding the major sheath glycoprotein, gp22, of Litomosoides carinii microfilariae. The mature gp22 mRNA is shown to result from both trans-splicing of a 22-nucleotide 5'-leader sequence to an acceptor site at position 313 of the pre-mRNA, immediately upstream from the start codon, and from cis-splicing of a 117-nt intron located within the coding sequence. Cis-splicing precedes the trans-splicing reaction. The gp22 reading frame of 148 codons has the inferred structure of a prepro-protein and includes a leader peptide and a pro-segment ahead of the known N terminus of the mature, extracellular protein of 105 amino acids. The N-terminal part of that protein contains five repeats of an elastin-related pentapeptide sequence, which, together with a proline-threonine segment between two Cys clusters in the center and at its C terminus, may cause an elongated conformation with an apparent molecular size of 22 kDa in contrast to the calculated M(r) of 11,200.

Expression of the polyubiquitin-encoding gene (ubq-1) in transgenic Caenorhabditis elegans

The expression of the polyubiquitin-encoding gene (ubq-1) of Caenorhabditis elegans was analysed using transgenic nematode lines carrying translational ubq-1::lacZ fusions. Animals carrying a construct consisting of 938 bp of ubq-1 upstream sequences fused to lacZ (ubq938::lacZ) expressed beta Gal in embryos and in a tissue-general manner in 20% of L1 larvae. Somatic expression in later stages was usually confined to body muscle. Progressively larger deletions extending from the 5' end of ubq938::lacZ did not significantly alter the pattern of expression until 827 bp of sequence had been removed. Thus, sequences upstream from the transcription start point, including a G+C-rich block and a sequence resembling a TATA box (GAATAA), are not required to generate the expression pattern seen with ubq938::lacZ. Moreover, a basal level of expression was maintained in embryos when 903 bp were deleted. These results suggest that the promoter elements required for efficient expression of ubq-1 may reside within the transcribed region of the gene; alternatively, they must lie more than 1.7 kb upstream or 0.8 kb downstream from this region. Polymerase chain reaction analysis indicates that RNA molecules transcribed from the ubq938::lacZ and ubq delta 827::lacZ transgenes are trans-spliced to SL1, as is ubq-1 RNA.

Identification of a novel Brugia pahangi beta-tubulin gene (beta 2) and a 22-nucleotide spliced leader sequence on beta 1-tubulin mRNA

We have examined the expression of beta-tubulin genes in the parasitic nematode, Brugia pahangi. A genomic library was constructed and screened by hybridization with a Haemonchus contortus beta-tubulin cDNA fragment which recognizes several B. pahangi beta-tubulin sequences, including sequences which correspond to the previously characterized beta 1-tubulin gene. The B. pahangi beta 2-tubulin gene was isolated by selecting clones which hybridize to the H. contortus beta-tubulin gene but which do not hybridize to the beta 1-tubulin gene. A partial sequence of the beta 2-tubulin gene confirms that it codes for a distinct beta-tubulin. Southern hybridization analyses show that the beta 2-tubulin sequence exists as a single copy gene within the B. pahangi genome. Expression of the beta 2-tubulin gene is developmentally regulated and the message is found predominantly in adult male worms, whereas the beta 1-tubulin gene is expressed in microfilariae and approximately equal levels of the transcript are found in male and female adult worms. During mRNA maturation the beta 1-tubulin mRNA of microfilariae and adult worms acquires a trans-spliced leader identical to the SL1 of Caenorhabditis elegans.

Polyubiquitin RNA characteristics and conditional induction in sea urchin embryos

A cDNA of the sea urchin Strongylocentrotus purpuratus was identified as encoding polyubiquitin and used to detect a single gene with transcripts containing multiple ubiquitin coding units. Polyubiquitin transcripts exist as a 3.2-kb RNA in polyribosomes and as three higher molecular weight RNAs in purified nuclei. The amount of polyubiquitin RNA is essentially constant at 10(4) -10(5) transcripts per embryo during the egg-to-blastula period and then declines during further development. Heat shock elicits a transient increase in the level of polyubiquitin RNA, while Zn(II) ions induce a sustained accumulation, that is influenced by developmental parameters: One round of Zn(II) induction elicits the accumulation of the nuclear 7.6- and 5.6-kb RNAs, as well as the 3.2-kb polysomal RNA; however, a second round of induction yields only the 5.6- and 3.2-kb RNAs, suggestive of a change in pre-mRNA size or processing. Polyubiquitin RNA is expressed equally in ectodermal and mesoendodermal tissues and is induced in both tissue fractions by treatment of pluteus larvae with Zn(II). However, in isolated and cultured tissue fractions, polyubiquitin RNA is not inducible by Zn(II), in contrast to the full inducibility of metallothionein mRNAs. Polyubiquitin RNA induction thus appears to be conditioned by the integrity of the embryo, as well as by previous exposure to inducer.

A comparison of trans-RNA splicing in trypanosomes and nematodes

Many aspects of the biology of kinetoplastids are unique, so it is surprising that they share with nematodes an unusual post-transcriptional process called trans-splicing. During this process, a small conserved RNA sequence is added to the 5' non-translated ends of transcribed RNAs of protein-encoding genes. Trypanosomes and nematodes are the only organisms to date in which these sequences have been described, and the biological significance of trans-splicing remains a mystery but may be of wider occurrence in invertebrates. In this review, John Donelson and Wenlin Zeng compare the process in nematodes and trypanosomes and speculate on its raison d'être.

Presence of the Caenorhabditis elegans spliced leader on different mRNAs and in different genera of nematodes

Several different mRNAs from Caenorhabditis elegans contain the same 22-nucleotide leader sequence at their 5' ends that is acquired in a trans-splicing reaction. About 10 to 15% of the major proteins are translated from mRNAs that contain the spliced leader, among them two ribosomal proteins, ubiquitin, GAPDH, a heat shock protein (hsp70a), and three actins. The same spliced leader sequence is present in mRNAs isolated from nematodes from several different genera; but it is not present in mRNAs from other organisms. The spliced leader is encoded as a spliced leader (SL) RNA about 100 nucleotides long. The gene for the SL RNA is located in the 5S rDNA repeat in C. elegans; however, this association with the 5S repeat is not preserved in other genera. The 22-nucleotide spliced leader sequence is conserved in three genera of nematodes.