Gene Ontology annotations and resources.

The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources.

Methylation of genomes and genes at the invertebrate-vertebrate boundary.

Patterns of DNA methylation in animal genomes are known to vary from an apparent absence of modified bases, via methylation of a minor fraction of the genome, to genome-wide methylation. Representative genomes from 10 invertebrate phyla comprise predominantly nonmethylated DNA and (usually but not always) a minor fraction of methylated DNA. In contrast, all 27 vertebrate genomes that have been examined display genome-wide methylation. Our studies of chordate genomes suggest that the transition from fractional to global methylation occurred close to the origin of vertebrates, as amphioxus has a typically invertebrate methylation pattern whereas primitive vertebrates (hagfish and lamprey) have patterns that are typical of vertebrates. Surprisingly, methylation of genes preceded this transition, as many invertebrate genes have turned out to be heavily methylated. Methylation does not preferentially affect genes whose expression is highly regulated, as several housekeeping genes are found in the heavily methylated fraction whereas several genes expressed in a tissue-specific manner are in the nonmethylated fraction.

Sequence, expression and evolution of the globins of the parasitic nematode Nippostrongylus brasiliensis.

The globins of the nematode parasite Nippostrongylus brasiliensis have oxygen affinities 100-fold higher than the rodent host's haemoglobins. Two isoforms are found, one located in the cuticle, and the other in the body of the nematode. Both isoforms have been cloned and analysed for clues as to function and evolution. The body globin isoform is first expressed upon invasion of the mammalian host. The abundant cuticular globin is expressed only by adult nematodes in the gut, and differs significantly from the body globin. Both globins are found as trans-spliced mRNAs: the developmental pattern of expression of the mRNA parallels the protein expression. The pattern of the nematode globin genes is complex. Comparison with other nematode globin sequences suggests that N. brasiliensis is more closely related to Caenorhabditis elegans than to ascarid species. At least two gene duplication events are predicted: gene duplication preceded the radiation of the important vertebrate-parasitic strongylid nematode species. Both N. brasiliensis globins have a central intron the exact position of which suggests that it arose from an independent insertion event in the strongylid-rhabditid line. The globins have been expressed in Escherichia coli as functional holenzymes as a prelude to studies to elucidate the origin of their extraordinary oxygen affinity.

Identification of serine/threonine protein kinases secreted by Trichinella spiralis infective larvae.

Serine/threonine protein kinase activity was identified in excretory/secretory (ES) products of Trichinella spiralis infective larvae, via phosphorylation of exogenous and endogenous substrates. Protein kinase activity was identified as an authentic secretory product via blockade of release into culture medium by brefeldin A. Enzyme activity was reductant-dependent, and the relative resistance to a panel of inhibitors suggested that it could not be readily assigned to any of the major documented subfamilies of serine/threonine protein kinases. There was no evidence for protein tyrosine kinase activity in ES products. The major phosphorylated proteins in this compartment resolved at 50 and 55 kDa by SDS-PAGE, and are therefore designated pp50/55. These proteins contained mainly phosphoserine, and appear to represent differentially glycosylated variants of a 35 kDa polypeptide, modified via the addition of three and four N-linked oligosaccharides, respectively. An autophosphorylation assay following separation by SDS-PAGE identified two protein kinases of 70 and 135 kDa in ES products.

Transcriptional noise and the evolution of gene number.

Several proposals are made to explain the apparent increase in complexity of certain lineages during evolution. The proposals (not made in this order) are: (1) that gene number is a valid measure of biological complexity; (2) that gene number has not increased continuously during evolution, but has risen in discrete steps; (3) that two of the biggest steps occurred at the transition from prokaryotes to eukaryotes and the transition from invertebrates to vertebrates; (4) that these steps were made possible by 'systemic' changes in the way that genetic information is managed in the genome; (5) that the ability to silence inappropriate promoters is the primary limitation on gene number; (6) that the invention of nucleosomes (and perhaps the nuclear membrane) facilitated the evolution of eukaryotes from prokaryotic ancestors; (7) that the spread of low density methylation throughout the genome facilitated the evolution of vertebrates from invertebrate ancestors.

Mouse carbonic anhydrase III: nucleotide sequence and expression studies.

A cDNA for the mouse carbonic anhydrase, CAIII, has been isolated from a lambda gt11 expression library. The cloned cDNA contains all of the coding region (777 bp) and both 5' untranslated (86-bp) and 3' untranslated (217-bp) sequences. The coding sequence shows 87% homology at the nucleotide level and 91% homology, when amino acid residues are compared, with human CAIII. Protein and mRNA analyses show that CAIII is present at low levels in cultured myoblasts and is abundant in adult skeletal muscle and in liver. The marked sex-related differences in CAIII distribution, described for rat liver, are not seen in the mouse. Restriction fragment length polymorphisms using TaqI and PstI are described which distinguish between Mus spretus and Mus musculus domesticus.

Carbonic anhydrase 3 (CA3), a mesodermal marker.

Carbonic anhydrase 3 (CA3) is an abundant muscle protein characteristic of adult type 1, slow-twitch, fibres. The protein plays an important role in facilitated CO2 diffusion and diverse processes involving H+ and HCO-3 transport. Nucleotide sequence comparisons have identified putative promoter and enhancer regions in the 5' flanking sequences of the CA3 gene. Functional assays show that 2.8kb of 5' flanking sequence efficiently promotes transcription of a reporter gene in a muscle specific manner. Removal of sequences 5' to -722bp leads to a major loss of activity and this result implies that the proximal promoter region which includes a GArG box and four potential MyoD1 binding sites is not adequate for maximal transcription. The longest CA3 promoter construct is also active in 10T1/2 cells, which are precursor mesodermal cells and do not normally express CA3. In situ hybridization to mRNA in developing mouse embryos reveals a pattern of expression in myotomes and pre-muscles masses of the limb buds which is consistent with the regulation of CA3 by myogenic determination factors. These studies also showed that CA3 expression is not confined to cells of the muscle lineage since it is expressed in primitive mesoderm prior to the onset of myogenesis. Later in embryogenesis CA3 defines a subset of mesodermal cell types which includes not only skeletal muscle but also notochord and adipocytes.

CAIII a marker for early myogenesis: analysis of expression in cultured myogenic cells.

Carbonic anhydrase III (CAIII) is an abundant muscle protein characteristic of adult type-1, slow-twitch, muscle fibers. We demonstrate that CAIII is not confined to mature muscle but is also expressed in cultured myogenic cells that were originally derived from adult and fetal limb muscle (G8 and C2C12) and by azacytidine treatment of 10T1/2 fibroblasts (23A2). Transcripts may accumulate in these cells to levels that correspond to 6.5% of that found in mature muscle. CAIII is expressed in mononucleate myoblasts and is abundant in those that preferentially fuse to form myotubes, and these findings contrast with those for many other muscle genes whose transcripts only accumulate on or after terminal differentiation. Preliminary promoter-function assays by transfection shows that 2.8 kb of sequence flanking the 5' end of the human CAIII gene efficiently promotes transcription of the bacterial chloramphenicol acetyltransferase gene in myogenic cells. However, none of the sequences within this region are sufficient to confer muscle-specific expression. Removal of sequences 5' to -715 bp leads to a major loss of transcriptional activity of the CAIII promoter. These results imply that the proximal CAIII promoter, which includes a putative CArG box and four potential MyoD binding sites, is not adequate for either myoblast-specific or maximal transcription.

Mapping of mouse carbonic anhydrase-3, Car-3: another locus in the homologous region of mouse chromosome 3 and human chromosome 8.

At least six separate genes determining tissue- and organelle-specific isoforms of carbonic anhydrase are known. We have determined the chromosome location of one of these genes, carbonic anhydrase-3 (Car-3), in the mouse and carried out a linkage analysis of Car-1, Car-2, and Car-3. Car-3 has been assigned to band 3A2 by in situ hybridization. We identified a PstI restriction fragment length polymorphism between Mus spretus and Mus mus domesticus and, by using an interspecific backcross, showed that Car-3 is 2.4 +/- 1.7% SE from both Car-1 and Car-2, calculating genetic distance as percentage recombination. No recombinants were found between Car-1 and Car-2 in 100 backcross offspring, and when these data are combined with earlier results, these two loci are estimated to be 1.2 cM from each other at the 95% confidence interval. The three homologous carbonic anhydrase loci in man had earlier been assigned to 8q22, and the finding of linkage of Car-3 to Car-1 and Car-2 in the mouse adds another locus to the conserved segments on mouse chromosome 3 and human chromosome 8.

Carbonic anhydrase III, an early mesodermal marker, is expressed in embryonic mouse skeletal muscle and notochord.

Carbonic anhydrase III (CAIII) is an abundant soluble protein in adult mammalian slow twitch skeletal muscle fibers. It is thought to be an early marker for myogenesis based upon its high level of expression in myoblasts in vitro prior to fusion. Using in situ hybridization, we have studied the in vivo distribution of CAIII gene transcripts in mouse embryos and fetuses from 7.25 days to 17.5 days post coitum (p.c.). CAIII mRNAs are first detected in the myotomes of somites between 9.5 and 10.5 days p.c. (20-30 somites). At 15.5 days p.c., CAIII begins to be restricted to developing slow muscle fibers. By two weeks post partum (p.p.), CAIII mRNAs are detected mainly in slow muscle fibers. CAIII transcripts are detected at an earlier stage (7.25 days p.c.) in the developing notochord. CAIII is expressed at a much higher level in the notochord than it is in developing skeletal muscle. As the notochord forms the nucleus pulposus in fetal mice, CAIII mRNA levels remain very high. Expression of CAIII in the notochord is of interest in the context of skeletal myogenesis because the notochord is thought to play an important role in somite formation. In addition to the notochord, CAIII transcripts are detected prenatally in several other non-muscle tissues: in cells of the choroid plexus, endocardial cushion and ureter, and in adipocytes.

Capturing novel mouse genes encoding chromosomal and other nuclear proteins.

The burgeoning wealth of gene sequences contrasts with our ignorance of gene function. One route to assigning function is by determining the sub-cellular location of proteins. We describe the identification of mouse genes encoding proteins that are confined to nuclear compartments by splicing endogeneous gene sequences to a promoterless betageo reporter, using a gene trap approach. Mouse ES (embryonic stem) cell lines were identified that express betageo fusions located within sub-nuclear compartments, including chromosomes, the nucleolus and foci containing splicing factors. The sequences of 11 trapped genes were ascertained, and characterisation of endogenous protein distribution in two cases confirmed the validity of the approach. Three novel proteins concentrated within distinct chromosomal domains were identified, one of which appears to be a serine/threonine kinase. The sequence of a gene whose product co-localises with splicesome components suggests that this protein may be an E3 ubiquitin-protein ligase. The majority of the other genes isolated represent novel genes. This approach is shown to be a powerful tool for identifying genes encoding novel proteins with specific sub-nuclear localisations and exposes our ignorance of the protein composition of the nucleus. Motifs in two of the isolated genes suggest new links between cellular regulatory mechanisms (ubiquitination and phosphorylation) and mRNA splicing and chromosome structure/function.

Human muscle carbonic anhydrase: gene structure and DNA methylation patterns in fetal and adult tissues.

We report the isolation and analysis of genomic clones comprising the entire gene coding for the human muscle carbonic anhydrase, CAIII. The gene spans 10.3 kb and has a seven-exon/six-intron structure. A noncanonical TATA box, a CCAAT motif, and two CCGCCC elements are present in the sequences upstream of exon 1. Although the expression of CAIII shows strict tissue specificity, the gene exhibits a number of features normally associated with housekeeping enzymes. For example, there is 48% homology with a 25-bp consensus sequence between the TATA box and the cap site and there is a CpG-rich island spanning a 469-bp sequence near to the origin of transcription. Methylation studies suggest that some CCGG sites clustered in the CpG-rich island are undermethylated in DNA from fetal and adult muscle and in other tissues irrespective of CAIII expression. In contrast, several nonclustered CCGG sites show a methylation pattern that correlates with gene expression. However DNA from differentiated type II adult muscle fibers is undermethylated at these sites even though CAIII is not expressed.

dSIR2 and dHDAC6: two novel, inhibitor-resistant deacetylases in Drosophila melanogaster.

We have identified new members of the histone deacetylase enzyme family in Drosophila melanogaster. dHDAC6 is a class II deacetylase with two active sites, and dSIR2 is an NAD-dependent histone deacetylase. These proteins, together with two class I histone deacetylases, dHDAC1 and dHDAC3, have been expressed and characterized as epitope-tagged recombinant proteins in Schneider SL2 cells. All these proteins have in vitro deacetylase activity and are able to deacetylate core histone H4 at all four acetylatable lysine residues (5, 8, 12, and 16). Recombinant dHDAC6 and dSIR2 are both insensitive to TSA and HC toxin and resistant, relative to dHDAC1 and dHDAC3, to inhibition by sodium butyrate. Indirect immunofluorescence microscopy of stably transfected SL2 lines reveals that dHDAC1 and dSIR2 are nuclear, dHDAC6 is cytosolic, and dHDAC3 is detectable in both cytosol and nucleus. dHDAC6 and dSIR2 elute from Superose 6 columns with apparent molecular weights of 90 and 200 kDa, respectively. In contrast, dHDAC1 and dHDAC3elute at 800 and 700 kDa, respectively, suggesting that they are components of multiprotein complexes. Consistent with this, recombinant dHDAC1 coimmunoprecipitates with components of the Drosophila NuRD complex and dHDAC3 with an as yet unknown 45-kDa protein.

Studies of DNA methylation in animals.

We have been studying the evolution and function of DNA methylation in vertebrate animals using three related approaches. The first is to further characterise proteins that bind to methylated DNA. Such proteins can be viewed as 'receptors' of the methyl-CpG 'ligand' that mediate downstream consequences of DNA modification. The second approach involves CpG islands. These patches of non-methylated DNA coincide with most gene promoters, but their origin and functional significance have only recently become the subject of intensive study. The third approach is to trace the evolution of DNA methylation. Genomic methylation patterns of vertebrates are strikingly different from those of invertebrates. By studying methylation in animals that diverged from common ancestors near to the invertebrate/vertebrate boundary, we will assess the possibility that changes in DNA methylation contributed causally to the evolution of the complex vertebrate lineage.

Brugia pahangi and Brugia malayi: a surface-associated glycoprotein (gp15/400) is composed of multiple tandemly repeated units and processed from a 400-kDa precursor.

The cuticle of filarial nematode parasites contains distinct and separable sets of soluble and structural proteins. Surface-labeling techniques have previously identified a soluble protein complex in adult stage Brugia which ranges in molecular weight from 15 to 200 kDa. Using an antiserum directed to the 15-kDa basal subunit of this complex, we show here that this complex is synthesized and processed from a single, very large precursor protein with a molecular weight of approximately 400 kDa. Molecular cloning, sequencing, and Southern analysis indicates that the protein is encoded by a single gene composed predominantly of approximately 20 tandemly repeated segments of 396 bp. The two complete copies of these repeated segments in our cDNA sequence are identical. Each subunit of 132 amino acids bears a consensus site for N-linked glycosylation, and glycosidase treatment indicates that this corresponds to an oligosaccharide side chain of 2 kDa. The protein displays no significant homology to sequences lodged in databases corresponding to molecules of known function. Nevertheless, a significant similarity (19/41 residues) is observed with the N-terminal sequence of a protein termed ABA-1, an allergen from Ascaris.

Molecular genealogy of some nematode taxa as based on cytochrome c and globin amino acid sequences.

We have begun to reconstruct the ancient history of the nematode phylum based on cytochrome c and globin amino acid sequences. The data suggest that the nematode ancestor diverged from a line leading to mammals about 1 billion years ago and that the most recent common ancestor of the extant species Caenorhabditis elegans, Trichostrongylus colubriformis, Nippostrongylus brasiliensis, Ascaris suum, and Pseudoterranova decipiens lived about 550 MY ago. The rhabditids and strongylids emerged as one offshoot of this ancestor, the ascarids as another. Rhabditids and strongylids diverged some 400 MY ago, whereas the genera Trichostrongylus and Nippostrongylus diverged slightly over 200 MY ago. A gene duplication event in the strongylid branch is predicted to have occurred around 250-335 MY ago. There are two globin genes in Nippostrongylus, expressed in anatomically distinct compartments (body and cuticle), and the single sequence from Trichostrongylus is most like the Nippostrongylus body globin gene. A strikingly different duplication event occurred within the same period in the line leading to the extant ascarid genera, creating a single polypeptide containing two globin domains. The genera Ascaris and Pseudoterranova diverged some 150-250 MY ago. Interestingly, the second globin repeat evolved at a faster rate in both species examined. This is possibly related to the acquisition of an unusual carboxyterminal extension, composed of alternating positively and negatively charged residues, that is necessary for the assembly of several monomers into the native polymeric molecules.