Novel ubiquitin-like ribosomal protein fusion genes from the nematodes Caenorhabditis elegans and Caenorhabditis briggsae

Unusually Divergent Ubiquitin Genes and Proteins in Plasmodium Species

Ubiquitin is an extraordinarily highly conserved 76 amino acid protein encoded by three different types of gene, where the primary translation products are fusions either of ubiquitin with one of two ribosomal proteins (RPs) or of multiple ubiquitin monomers from head to tail. Here, we investigate the evolution of ubiquitin genes in mammalian malaria parasites (Plasmodium species). The ubiquitin encoded by the RPS27a fusion gene is highly divergent, as previously found in a variety of protists. However, we also find that two other forms of divergent ubiquitin sequence, each previously thought to be extremely rare, have arisen recently during the divergence of Plasmodium subgenera. On two occasions, in two distinct lineages, the ubiquitin encoded by the RPL40 fusion gene has rapidly diverged. In addition, in one of these lineages, the polyubiquitin genes have undergone a single codon insertion, previously considered a unique feature of Rhizaria. There has been disagreement whether the multiple ubiquitin coding repeats within a genome exhibit concerted evolution or undergo a birth-and-death process; the Plasmodium ubiquitin genes show clear signs of concerted evolution, including the spread of this codon insertion to multiple repeats within the polyubiquitin gene.

Ubiquitination pathway model for the barber's pole worm - Haemonchus contortus

The ubiquitin-mediated pathway has been comprehensively explored in the free-living nematode Caenorhabditis elegans, but very little is known about this pathway in parasitic nematodes. Here, we inferred the ubiquitination pathway for an economically significant and pathogenic nematode - Haemonchus contortus - using abundant resources available for C. elegans. We identified 215 genes encoding ubiquitin (Ub; n = 3 genes), ubiquitin-activating enzyme (E1; one), -conjugating enzymes (E2s; 21), ligases (E3s; 157) and deubiquitinating enzymes (DUBs; 33). With reference to C. elegans, Ub, E1 and E2 were relatively conserved in sequence and structure, and E3s and DUBs were divergent, likely reflecting functional and biological uniqueness in H. contortus. Most genes encoding ubiquitination pathway components exhibit high transcription in the egg compared with other stages, indicating marked protein homeostasis in this early developmental stage. The ubiquitination pathway model constructed for H. contortus provides a foundation to explore the ubiquitin-proteasome system, crosstalk between autophagy and the proteasome system, and the parasite-host interactions. Selected E3 and DUB proteins which are very divergent in sequence and structure from host homologues or entirely unique to H. contortus and related parasitic nematodes may represent possible anthelmintic targets.

The Ubiquitin Moiety of Ubi1 Is Required for Productive Expression of Ribosomal Protein eL40 in Saccharomyces cerevisiae

Ubiquitin is a highly conserved small eukaryotic protein. It is generated by proteolytic cleavage of precursor proteins in which it is fused either to itself, constituting a polyubiquitin precursor of head-to-tail monomers, or as a single N-terminal moiety to ribosomal proteins. Understanding the role of the ubiquitin fused to ribosomal proteins becomes relevant, as these proteins are practically invariably eS31 and eL40 in the different eukaryotes. Herein, we used the amenable yeast Saccharomyces cerevisiae to study whether ubiquitin facilitates the expression of the fused eL40 (Ubi1 and Ubi2 precursors) and eS31 (Ubi3 precursor) ribosomal proteins. We have analyzed the phenotypic effects of a genomic ubi1∆ub-HA ubi2∆ mutant, which expresses a ubiquitin-free HA-tagged eL40A protein as the sole source of cellular eL40. This mutant shows a severe slow-growth phenotype, which could be fully suppressed by increased dosage of the ubi1∆ub-HA allele, or partially by the replacement of ubiquitin by the ubiquitin-like Smt3 protein. While expression levels of eL40A-HA from ubi1∆ub-HA are low, eL40A is produced practically at normal levels from the Smt3-S-eL40A-HA precursor. Finally, we observed enhanced aggregation of eS31-HA when derived from a Ubi3∆ub-HA precursor and reduced aggregation of eL40A-HA when expressed from a Smt3-S-eL40A-HA precursor. We conclude that ubiquitin might serve as a cis-acting molecular chaperone that assists in the folding and synthesis of the fused eL40 and eS31 ribosomal proteins.

Bioinformatics analysis of ubiquitin expression protein gene from Heterodera latipons

Ubiquitin expression protein DNA clone (Hl-UBI) was isolated from Heterodera latipons collected from North Jordan. Its sequence of 285 nucleotides was also determined and deposited in the GeneBank. The 285-bp open reading frame coded for 76-amino acid protein having two domains; the ubiquitin domain and the C terminal extension. The first 59 amino acids were predicted with the ubiquitin domain with identity percentages of 78% to ubiquitin of H. schachtii, 77% to polyubiquitin of Globodera pallida, 74% to ubiquitin of Globodera rostochiensis and 72% to ubiquitin of Heterodera glycines. The other domain at the C-terminus, containing 17 amino acids, showed no homology to any known protein. Sequence analysis showed a calculated encoding amino acids molecular weight of 8.77 kDa, theoretical isoelectric point = 4.76, negatively charged residues = 12, positively charged residues = 9, extinction coefficient = 1490, estimated half-life = 30 h, instability index = 32.51 and grand average of hydropathicity = -0.537. The demonstrated subcellular localization analysis of cytoplasm, cell nucleus, mitochondrion, cell skeleton and plasma membrane of Hl-UBI protein occupied about 52.20, 21.70, 17.40, 4.30 and 4.30%, respectively. Sequence, homology and structural analysis confirmed that Hl-UBI gene was highly conserved during evolution and belonged to ubiquitin gene family.

Analysis of UB and L40 resistance related to deltamethrin in Drosophila kc cells

Pests have been subjected to heavy selection pressure, and the development of resistance to pyrethroid has been recorded. It is extremely valuable to identify the resistance genes that are relevant for pest control. In our previous studies, we reported that UBL40 is the deltamethrin resistance-associated gene. UBL40 is cleaved by specific endopeptidases to release UB and L40. Whether UB or L40 participates in deltamethrin resistance requires further study. In this study, quantitative real-time PCR was applied to reveal that UB and L40 were both overexpressed in Drosophila kc cells after deltamethrin stimulation. To investigate the roles of UB and L40 further, RNA interferences (RNAi) and cell transfections were utilized. UB and L40 knockdown both significantly reduced the level of resistance of RNAi-treated cells after 48 h, and the overexpressions of UB and L40 in Drosophila kc cells conferred a degree of protection against deltamethrin. These results represent the first evidence that UB and L40 both play roles in the regulation of deltamethrin resistance and that this study could help us to elucidate the resistance mechanisms and identify new target genes associated with resistance.

The ubiquitin proteasome system in Caenorhabditis elegans and its regulation

Protein degradation constitutes a major cellular function that is responsible for maintenance of the normal cellular physiology either through the degradation of normal proteins or through the elimination of damaged proteins. The Ubiquitin–Proteasome System (UPS)¹ is one of the main proteolytic systems that orchestrate protein degradation. Given that up- and down- regulation of the UPS system has been shown to occur in various normal (such as ageing) and pathological (such as neurodegenerative diseases) processes, the exogenous modulation of the UPS function and activity holds promise of (a) developing new therapeutic interventions against various diseases and (b) establishing strategies to maintain cellular homeostasis. Since the proteasome genes are evolutionarily conserved, their role can be dissected in simple model organisms, such as the nematode, Caenorhabditis elegans. In this review, we survey findings on the redox regulation of the UPS in C. elegans showing that the nematode is an instrumental tool in the identification of major players in the UPS pathway. Moreover, we specifically discuss UPS-related genes that have been modulated in the nematode and in human cells and have resulted in similar effects thus further exhibiting the value of this model in the study of the UPS.

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UPS is one of the main proteolytic systems that orchestrate protein degradation.

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Proteasome function can be dissected in Caenorhabditis elegans.

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Nematodes can be used in the identification of major players in the UPS pathway.

Gene cloning and expression analysis of ubiquitin derived from Musca domestica

Ubiquitin (Ub) is a highly conserved 8-kDa protein that was first identified as a tag for protein degradation. Recently, its role in nonproteolytic cellular processes such as DNA repair and endocytosis has also been reported. An ubiquitin-fusion gene was cloned from Musca domestica. The complete length of this ubiquitin-fusion gene is 531 bp, of which 471 bp is an open reading frame (ORF) encoding a 156-amino acid peptide, and 60 bp is a 3'-untranslated region with the polyadenylation sequence AATAAA and a poly(A) tail. The ubiquitin-fusion protein includes an ubiquitin monomer of 76 amino acids with a 6-amino acid motif (LRLRGG) and 3 conserved lysine functional sites, which participate in the formation of the ubiquitin-protease complex. The ubiquitin-fusion protein also contains an 80-amino acid carboxyl extension protein, namely, ribosomal protein S27 with a classical zinc finger motif C-X(4)-C-X(14)-C-X(2)-C. Because of its carboxyl extension protein S27, the M. domestica ubiquitin-fusion protein was named Mub(S27). It has a predicted molecular weight of 18 kDa and a theoretical isoelectric point of 9.82. No signal peptides were predicted for the protein. Northern blot analysis revealed that Mub(S27) transcript level is higher at the embryo stage than that at any other developmental stages. When houseflies develop into 5-day pupae, the Ub mRNA level is relatively low. After infection with gram-negative and gram-positive bacteria, Mub(S27) transcript level was upregulated. Mub(S27) transcript level was also regulated by heat or cold stress.

Accurate structural correlations from maximum likelihood superpositions

The cores of globular proteins are densely packed, resulting in complicated networks of structural interactions. These interactions in turn give rise to dynamic structural correlations over a wide range of time scales. Accurate analysis of these complex correlations is crucial for understanding biomolecular mechanisms and for relating structure to function. Here we report a highly accurate technique for inferring the major modes of structural correlation in macromolecules using likelihood-based statistical analysis of sets of structures. This method is generally applicable to any ensemble of related molecules, including families of nuclear magnetic resonance (NMR) models, different crystal forms of a protein, and structural alignments of homologous proteins, as well as molecular dynamics trajectories. Dominant modes of structural correlation are determined using principal components analysis (PCA) of the maximum likelihood estimate of the correlation matrix. The correlations we identify are inherently independent of the statistical uncertainty and dynamic heterogeneity associated with the structural coordinates. We additionally present an easily interpretable method (“PCA plots”) for displaying these positional correlations by color-coding them onto a macromolecular structure. Maximum likelihood PCA of structural superpositions, and the structural PCA plots that illustrate the results, will facilitate the accurate determination of dynamic structural correlations analyzed in diverse fields of structural biology.

Biological macromolecules comprise extensive networks of interconnected atoms. These complex coupled networks result in correlated structural dynamics, where atoms and residues move and evolve together as concerted conformational changes. The availability of a wealth of macromolecular structures necessitates the use of robust strategies for analyzing the correlated modes of motion found in molecular ensembles. Current strategies use a combination of least-squares superpositions and statistical analysis of the structural covariance matrix. However, the least-squares treatment implicitly requires that atoms are uncorrelated and that each atom has the same positional uncertainty, two assumptions which are violated in structural ensembles. For example, the atoms in the proteins are connected by chemical bonds, covalent and non-covalent, resulting in strong correlations. Furthermore, different atoms have different variances, because some atoms are known with less precision or have greater mobility. Using maximum likelihood (ML) analysis, we have developed a technique that is markedly more accurate than the classical least-squares approach by accounting for both correlations and heterogeneous variances. The improved ability to accurately analyze the major modes of dynamic structural correlations will benefit a diverse range of biological disciplines, including nuclear magnetic resonance (NMR) spectroscopy, crystallography, molecular dynamics, and molecular evolution.

Do we need many genes for phylogenetic inference?

Fifty-six nuclear protein coding genes from Taxonomically Broad EST Database and other databases were selected for phylogenomic-based examination of alternative phylogenetic hypotheses concerning intergroup relationship between multicellular animals (Metazoa) and other representatives of Opisthokonta. The results of this work support sister group relationship between Metazoa and Choanoflagellata. Both of these groups form the taxon Holozoa along with the monophyletic Ichthyosporea or Mesomycetozoea (a group that includes Amoebidium parasiticum, Sphaeroforma arctica, and Capsaspora owczarzaki). These phylogenetic hypotheses receive high statistical support both when utilizing whole alignment and when only 5000 randomly selected alignment positions are used. The presented results suggest subdivision of Fungi into Eumycota and lower fungi, Chytridiomycota. The latter form a monophyletic group that comprises Chytridiales+Spizellomycetales+Blastocladiales (Batrachochytrium, Spizellomyces, Allomyces, Blastocladiella), contrary to the earlier reports based on the analysis of 18S rRNA and a limited set of protein coding genes. The phylogenetic distribution of genes coding for a ubiquitin-fused ribosomal protein S30 implies at least three independent cases of gene fusion: in the ancestors of Holozoa, in heterotrophic Heterokonta (Oomycetes and Blastocystis) and in the ancestors of Cryptophyta and Glaucophyta. Ubiquitin-like sequences fused with ribosomal protein S30 outside of Holozoa are not FUBI orthologs. Two independent events of FUBI replacement by the ubiquitin sequence were detected in the lineage of C. owczarzaki and in the monophyletic group of nematode worms Tylenchomorpha+Cephalobidae. Bursaphelenchus xylophilus (Aphelenchoidoidea) retains a state typical of the rest of the Metazoa. The data emphasize the fact that the reliability of phylogenetic reconstructions depends on the number of analyzed genes to a lesser extent than on our ability to recognize reconstruction artifacts.

Sequence and structure evolved separately in a ribosomal ubiquitin variant

Encoded by a multigene family, ubiquitin is expressed in the form of three precursor proteins, two of which are fusions to the ribosomal subunits S27a and L40. Ubiquitin assists in ribosome biogenesis and also functions as a post-translational modifier after its release from S27a or L40. However, several species do not conserve the ribosomal ubiquitin domains. We report here the solution structure of a distant variant of ubiquitin, found at the N-terminus of S27a in Giardia lamblia, referred to as GlUb(S27a). Despite the considerable evolutionary distance that separates ubiquitin from GlUb(S27a), the structure of GlUb(S27a) is largely identical to that of ubiquitin. The variant domain remains attached to S27a and is part of the assembled holoribosome. Thus, conservation of tertiary structure suggests a role of this variant as a chaperone, while conservation of the primary structure--necessary for ubiquitin's function as a post-translational modifier--is no longer required. Based on these observations, we propose a model to explain the origin of the widespread ubiquitin superfold in eukaryotes.

Ubiquitin--conserved protein or selfish gene?

The posttranslational modifier ubiquitin is encoded by a multigene family containing three primary members, which yield the precursor protein polyubiquitin and two ubiquitin moieties, Ub(L40) and Ub(S27), that are fused to the ribosomal proteins L40 and S27, respectively. The gene encoding polyubiquitin is highly conserved and, until now, those encoding Ub(L40) and Ub(S27) have been generally considered to be equally invariant. The evolution of the ribosomal ubiquitin moieties is, however, proving to be more dynamic. It seems that the genes encoding Ub(L40) and Ub(S27) are actively maintained by homologous recombination with the invariant polyubiquitin locus. Failure to recombine leads to deterioration of the sequence of the ribosomal ubiquitin moieties in several phyla, although this deterioration is evidently constrained by the structural requirements of the ubiquitin fold. Only a few amino acids in ubiquitin are vital for its function, and we propose that conservation of all three ubiquitin genes is driven not only by functional properties of the ubiquitin protein, but also by the propensity of the polyubiquitin locus to act as a 'selfish gene'.

A new class of ubiquitin extension proteins secreted by the dorsal pharyngeal gland in plant parasitic cyst nematodes

By performing cDNA AFLP on pre- and early parasitic juveniles, we identified genes encoding a novel type of ubiquitin extension proteins secreted by the dorsal pharyngeal gland in the cyst nematode Heterodera schachtii. The proteins consist of three domains, a signal peptide for secretion, a mono-ubiquitin domain, and a short C-terminal positively charged domain. A gfp-fusion of this protein is targeted to the nucleolus in tobacco BY-2 cells. We hypothesize that the C-terminal peptide might have a regulatory function during syncytium formation in plant roots.

Conservation of sequence and function of the pag-3 genes from C. elegans and C. briggsae

The Caenorhabditis briggsae homologue of the Caenorhabditis elegans pag-3 gene was cloned and sequenced. When transformed into a C. elegans pag-3 mutant, the C. briggsae pag-3 gene rescued the pag-3 reverse kinker and lethargic phenotypes. The C. elegans pag-3 gene fused to lacZ was expressed in the same pattern in C. elegans and C. briggsae. Unlike many gene homologues compared between C. elegans and C. briggsae, extensive sequence conservation was found in the non-coding regions upstream of the pag-3 exons, in several of the introns and in the downstream non-coding region. Furthermore, the splice acceptor and splice donor sites were conserved, and the size of the introns and exons was surprisingly similar. The predicted protein sequence of C. briggsae PAG-3 was 85% identical to the protein sequence of C. elegans PAG-3. Because so much of the non-coding region of pag-3 was conserved, the control of pag-3 may be quite complex, involving the binding of many trans-acting factors. These results suggest the evolutionary conservation of the pag-3 gene sequence, its expression and function.

Sex and the single worm: sex determination in the nematode C. elegans

The study of sex determination in model organisms has been especially fruitful in increasing our understanding of developmental biology, gene regulation and evolutionary mechanisms. The free living nematode, Caenorhabditis elegans, can develop as one of two sexes; male or self-fertilizing hermaphrodite. Here we discuss the progress toward a genetic and molecular understanding of that decision. Numerous genetic loci have been identified that affect sexual fate, and epistasis analysis of these genes has led to a model of a regulatory hierarchy with stepwise negative interactions. It is becoming evident that many of the genes have numerous levels of regulation. We also discuss the apparent rapid rate of evolution that many of the sex determination proteins have undergone. Protein sequences of homologues from closely related species are more divergent than homologues of proteins involved in other developmental processes. Rapid evolution of sex determination genes may be a common theme throughout the animal kingdom.

The rub family of ubiquitin-like proteins. Crystal structure of Arabidopsis rub1 and expression of multiple rubs in Arabidopsis

Several proteins with significant identity to ubiquitin have been characterized recently. In contrast to ubiquitin's main role in targeting proteins for degradation, a described function of one family of ubiquitin-related proteins, the Rub family, is to serve as a stable post-translational modification of a complex involved in the G1-to-S cell cycle transition. Rub proteins have been found in animals, plants, and fungi and consist of 76 residues with 52-63% identity to ubiquitin. In this study three different RUB proteins within the plant Arabidopsis are identified; two differ by only 1 amino acid, while the third is only 77.6% identical to the other two. Genes encoding all three are expressed in multiple organs. In addition, we report the crystal structure of higher plant RUB1 at 1.7-A resolution to help elucidate the functional differences between Rub and ubiquitin. RUB1 contains a single globular domain with a flexible COOH-terminal extension. The overall RUB1 structure is very similar to ubiquitin. The majority of the amino acid differences between RUB1 and ubiquitin map to the surface. These changes alter the electrostatic surface potential in two regions and likely confer specificity between ubiquitin and RUB1 and their ubiquitin-activating enzyme (E1) or E1-like activating enzymes.

Intracellular proteinases of invertebrates: calcium-dependent and proteasome/ubiquitin-dependent systems

Cytosolic proteinases carry out a variety of regulatory functions by controlling protein levels and/or activities within cells. Calcium-dependent and ubiquitin/proteasome-dependent pathways are common to all eukaryotes. The former pathway consists of a diverse group of Ca(2+)-dependent cysteine proteinases (CDPs; calpains in vertebrate tissues). The latter pathway is highly conserved and consists of ubiquitin, ubiquitin-conjugating enzymes, deubiquitinases, and the proteasome. This review summarizes the biochemical properties and genetics of invertebrate CDPs and proteasomes and their roles in programmed cell death, stress responses (heat shock and anoxia), skeletal muscle atrophy, gametogenesis and fertilization, development and pattern formation, cell-cell recognition, signal transduction and learning, and photoreceptor light adaptation. These pathways carry out bulk protein degradation in the programmed death of the intersegmental and flight muscles of insects and of individuals in a colonial ascidian; molt-induced atrophy of crustacean claw muscle; and responses of brine shrimp, mussels, and insects to environmental stress. Selective proteolysis occurs in response to specific signals, such as in modulating protein kinase A activity in sea hare and fruit fly associated with learning; gametogenesis, differentiation, and development in sponge, echinoderms, nematode, ascidian, and insects; and in light adaptation of photoreceptors in the eyes of squid, insects, and crustaceans. Proteolytic activities and specificities are regulated through proteinase gene expression (CDP isozymes and proteasomal subunits), allosteric regulators, and posttranslational modifications, as well as through specific targeting of protein substrates by a diverse assemblage of ubiquitin-conjugases and deubiquitinases. Thus, the regulation of intracellular proteolysis approaches the complexity and versatility of transcriptional and translational mechanisms.

Unique structural features of a novel class of small heat shock proteins

Small heat shock proteins (smHSPs) and alpha-crystallins constitute a family of related molecular chaperones that exhibit striking variability in size, ranging from 16 to 43 kDa. Structural studies on these proteins have been hampered by their tendency to form large, often dynamic and heterogeneous oligomeric complexes. Here we describe the structure and expression of HSP12.6, a member of a novel class of smHSPs from the nematode Caenorhabditis elegans. Like other members of its class, HSP12.6 possesses a conserved alpha-crystallin domain but has the shortest N- and C-terminal regions of any known smHSP. Expression of HSP12.6 is limited to the first larval stage of C. elegans and is not significantly up-regulated by a wide range of stressors. Unlike other smHSPs, HSP12.6 does not form large oligomeric complexes in vivo. HSP12.6 was produced in Escherichia coli as a soluble protein and purified. Cross-linking and sedimentation velocity analyses indicate that the recombinant HSP12.6 is monomeric, making it an ideal candidate for structure determination. Interestingly, HSP12.6 does not function as a molecular chaperone in vitro, since it is unable to prevent the thermally induced aggregation of a test substrate. The structural and functional implications of these findings are discussed.

Conservation of function and expression of unc-119 from two Caenorhabditis species despite divergence of non-coding DNA

The Caenorhabditis briggsae homologue of the Caenorhabditis elegans neuronal gene unc-119 has been cloned by low-stringency hybridization. Genomic clones containing the C. briggsae gene are able to completely rescue the unc-119 phenotype in transgenic C. elegans mutants. The open reading frame (ORF) of the predicted C. briggsae cDNA is 90% identical to that of C. elegans. Although the splice donor and acceptor sites are conserved, the untranslated regions, and the introns, differ greatly. For this gene, the average intron size in C. elegans is over 600 base pairs (bp); in C. briggsae it is only 113 bp. Their upstream control regions share limited sequence similarities; however, reporter gene fusions of the two species show strongly similar expression in C. elegans. These results are consistent with the maintenance not only of the function of the unc-119 gene but also the transcriptional control of the gene through tens of millions of years of evolution.

The yeast homolog of mammalian ribosomal protein S30 is expressed from a duplicated gene without a ubiquitin-like protein fusion sequence. Evolutionary implications

In mammals, the 59-residue ribosomal protein S30 (rpS30) is synthesized as a fusion to a 74-residue ubiquitin-like protein, which is cleaved to yield mature rpS30. An artificial fusion of this ubiquitin-like protein to E. coli beta-galactosidase was not cleaved when expressed in yeast (Saccharomyces cerevisiae), indicating that yeast lack this cleaving activity. The yeast rpS30 homolog (yrpS30) was purified and sequenced to reveal a 63-residue protein with 61% sequence identity to mammalian rpS30. Degenerate oligonucleotides based on the yrpS30 sequence were used to isolate full-length yrpS30 cDNAs. Sequence analysis of five cDNA clones revealed that yrpS30 is not synthesized as a fusion to a ubiquitin-like protein but is extended at its N terminus by a single methionine residue. The corresponding gene was identified in the GenBankTM data base by sequence alignment and termed RPS30A. The gene consists of two exons separated by a 430-base pair intron, which contains consensus splicing elements. Exon 1 encodes the initiator methionine residue and is preceded by canonical yeast ribosomal protein gene promoter elements. Exon 2 encodes the 62-residue mature yrpS30. Genomic hybridization reveals that the RPS30A gene is duplicated. Disruption of the RPS30A gene is not lethal but confers a slow growth phenotype. Ribosomes in the mutant strains contain an authentic yrpS30 protein, indicating that a functional yrpS30 is expressed from the duplicated gene but that the reduced capacity for yrpS30 synthesis restricted the growth rate. Analysis of available DNA sequence data bases reveals that rpS30 is synthesized as a fusion to a ubiquitin-like protein in nematodes and mammals but unfused in yeast, plants, and protazoa.

Structure of the ubiquitin-encoding genes of Cryptococcus neoformans

Cryptococcus neoformans (Cn) contains two ubiquitin (UBI)-encoding genes located on separate chromosomes. The UBI1 gene consists of UBI fused to a 53-amino-acid (aa) tail and is 95% identical to the Saccharomyces cerevisiae (Sc) UBI1 which codes for an UBI-CEP52 ribosomal protein fusion. UBI4 is a polyubiquitin gene that contains five UBI repeats. The UBI4 aa sequences differ from Sc UBI by a single aa. UBI1 contains two introns in the UBI-encoding portion and two introns in the tail. Single introns are present in three of the repeats in UB14 and are located at the same positions as those in UBII. There was also an average of 15% nt differences among UBI repeats. The results provide evidence of extensive recombination and/or conversion events between repeated genes in Cn.

Molecular analysis of Caenorhabditis elegans tcp-1, a gene encoding a chaperonin protein

A Caenorhabditis elegans (Ce) homologue to the eukaryotic tcp-1 gene (encoding t-complex polypeptide-1) has been mapped, isolated and sequenced. Ce tcp-1 is a single-copy gene located on chromosome II. Nucleotide sequence analysis of the gene reveals the presence of four introns in the coding region and repetitive elements upstream from the start codon. The predicted Ce TCP-1 protein displays more than 60% amino-acid sequence identity to other eukaryotic TCP-1, suggesting a common origin and function for these proteins. The primary tcp-1 transcript undergoes trans-splicing to the spliced leader SL1 RNA, in addition to cis-splicing, to yield a single mRNA species of 1.9 kb. Northern blot analysis shows that unlike the evolutionarily related Hsp60 chaperonin genes, tcp-1 is not upregulated at elevated temperatures, but instead appears to be down-regulated. Additionally, the overall level of the tcp-1 transcript is approximately constant throughout the development of the nematode. The Ce chaperonin-containing TCP-1 (CCT) was identified. A protein extract made from Ce embryos was subjected to sucrose gradient fractionation and ATP-agarose chromatography. Western blot analysis of the purified protein fractions, using anti-mouse TCP-1 monoclonal antibody and antibodies raised against Ce TCP-1, reveals that Ce TCP-1 is a 57-kDa protein subunit of a high-molecular-mass complex capable of binding ATP.

The bli-4 locus of Caenorhabditis elegans encodes structurally distinct kex2/subtilisin-like endoproteases essential for early development and adult morphology

Many secreted proteins are excised from inactive proproteins by cleavage at pairs of basic residues. Recent studies have identified several serine endoproteases that catalyze this cleavage in the secretory pathways of yeast and metazoans. These enzymes belong to the kex2/subtilisin-like family of proprotein convertases. In this paper we describe the molecular characterization of the bli-4 gene from Caenorhabditis elegans, which was shown previously by genetic analysis of lethal mutants to be essential for the normal development of this organism. Sequencing of cDNA and genomic clones has revealed that bli-4 encodes gene products related to the kex2/subtilisin-like family of proprotein convertases. Analysis of bli-4 cDNAs has predicted four protein products, which we have designated blisterases A, B, C, and D. These protein products share a common amino terminus, but differ at the carboxyl termini, and are most likely produced from alternatively spliced transcripts. We have determined the molecular lesions for three bli-4 alleles (h199, h1010, and q508) that result in developmental arrest during late embryogenesis. In each case, the molecular lesions are within exons common to all of the BLI-4 isoforms. The original defining allele of bli-4, e937, is completely viable yet exhibits blistering of the adult cuticle. Molecular analysis of this allele revealed a deletion that removes exon 13, which is unique to blisterase A. No RNA transcript corresponding to exon 13 is detectable in the blistered mutants. These findings suggest that blisterase A is required for the normal function of the adult cuticle.(ABSTRACT TRUNCATED AT 250 WORDS)

Expression of the Leishmania tarentolae ubiquitin-encoding and mini-exon genes

To develop models for transcription and trans-splicing in kinetoplastid protozoa, we have characterized ubiquitin (Ubi) gene organization and mRNA processing in Leishmania tarentolae (Lt). Three ubi loci were characterized: two discrete Ubi-extension protein 52 (EP52)-encoding genes (ubiA and ubiB) and a polymorphic polyubiquitin-encoding gene (ubiC). The three loci resided on chromosomes of 2.05 Mb, 630 kb and 2.9 Mb, respectively. On the basis of upstream flanking gene identity, ubiB appears to be the homologue of the tandemly repeated ubi-EP52/1 and 2 in Trypanosoma brucei (Tb). Similar to Trypanosoma cruzi, Lt did not contain a homologue of the ubi-EP76 that has been found in Saccharomyces cerevisiae and multicellular organisms. All three Lt ubi loci were transcribed. The primary transcripts from the ubi loci were processed at the 5'-end by trans-splicing with the mini-exon. A Lt mini-exon gene (min) that gave rise to a 95-nt primary transcript, which is the second template in the trans-splicing reaction, was also characterized.