Sequence comparisons of developmentally regulated collagen genes of Caenorhabditis elegans

Novel elasticity measurements reveal C. elegans cuticle stiffens with age and in a long-lived mutant

Changes in biomechanical properties have profound impacts on human health. C. elegans might serve as a model for studying the molecular genetics of mammalian tissue decline. Previously, we found that collagens are required for insulin signaling mutants' long lifespan and that overexpression of specific collagens extends wild-type lifespan. However, whether these effects on lifespan are due to mechanical changes during aging has not yet been established. Here, we have developed two novel methods to study the cuticle: we measure mechanical properties of live animals using osmotic shock, and we directly perform the tensile test on isolated cuticles using microfluidic technology. Using these tools, we find that the cuticle, not the muscle, is responsible for changes in the "stretchiness" of C. elegans, and that cuticle stiffness is highly nonlinear and anisotropic. We also found that collagen mutations alter the integrity of the cuticle by significantly changing the elasticity. In addition, aging stiffens the cuticle under mechanical loads beyond the cuticle's healthy stretched state. Measurements of elasticity showed that long-lived daf-2 mutants were considerably better at preventing progressive mechanical changes with age. These tests of C. elegans biophysical properties suggest that the cuticle is responsible for their resilience.

Functional Annotation of Caenorhabditis elegans Genes by Analysis of Gene Co-Expression Networks

Caenorhabditis elegans (C. elegans) is a well-characterized metazoan, whose transcriptome has been profiled in different tissues, development stages, or other conditions. Large-scale transcriptomes can be reused for gene function annotation through systematic analysis of gene co-expression relationships. We collected 2101 microarray data from National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO), and identified 48 modules of co-expressed genes that correspond to tissues, development stages, and other experimental conditions. These modules provide an overview of the transcriptional organizations that may work under different conditions. By analyzing higher-order module networks, we found that nucleus and plasma membrane modules are more connected than other intracellular modules. Module-based gene function annotation may help to extend the candidate cuticle gene list. A comparison with other published data validates the credibility of our result. Our findings provide a new source for future gene discovery in C. elegans.

The pseudokinase NIPI-4 is a novel regulator of antimicrobial peptide gene expression

Hosts have developed diverse mechanisms to counter the pathogens they face in their natural environment. Throughout the plant and animal kingdoms, the up-regulation of antimicrobial peptides is a common response to infection. In C. elegans, infection with the natural pathogen Drechmeria coniospora leads to rapid induction of antimicrobial peptide gene expression in the epidermis. Through a large genetic screen we have isolated many new mutants that are incapable of upregulating the antimicrobial peptide nlp-29 in response to infection (i.e. with a Nipi or 'no induction of peptide after infection' phenotype). More than half of the newly isolated Nipi mutants do not correspond to genes previously associated with the regulation of antimicrobial peptides. One of these, nipi-4, encodes a member of a nematode-specific kinase family. NIPI-4 is predicted to be catalytically inactive, thus to be a pseudokinase. It acts in the epidermis downstream of the PKC∂ TPA-1, as a positive regulator of nlp antimicrobial peptide gene expression after infection. It also controls the constitutive expression of antimicrobial peptide genes of the cnc family that are targets of TGFß regulation. Our results open the way for a more detailed understanding of how host defense pathways can be molded by environmental pathogens.

EGF signalling activates the ubiquitin proteasome system to modulate C. elegans lifespan

Epidermal growth factor (EGF) signalling regulates growth and differentiation. Here, we examine the function of EGF signalling in Caenorhabditis elegans lifespan. We find that EGF signalling regulates lifespan via the Ras-MAPK pathway and the PLZF transcription factors EOR-1 and EOR-2. As animals enter adulthood, EGF signalling upregulates the expression of genes involved in the ubiquitin proteasome system (UPS), including the Skp1-like protein SKR-5, while downregulating the expression of HSP16-type chaperones. Using reporters for global UPS activity, protein aggregation, and oxidative stress, we find that EGF signalling alters protein homoeostasis in adults by increasing UPS activity and polyubiquitination, while decreasing protein aggregation. We show that SKR-5 and the E3/E4 ligases that comprise the ubiquitin fusion degradation (UFD) complex are required for the increase in UPS activity observed in adults, and that animals that lack SKR-5 or the UFD have reduced lifespans and indications of oxidative stress. We propose that as animals enter fertile adulthood, EGF signalling switches the mechanism for maintaining protein homoeostasis from a chaperone-based approach to an approach involving protein elimination via augmented UPS activity.

C. elegans peb-1 mutants exhibit pleiotropic defects in molting, feeding, and morphology

Caenorhabditis elegans PEB-1 is a novel DNA-binding protein expressed in most pharyngeal cell types and outside the pharynx in the hypodermis, hindgut, and vulva. Previous RNAi analyses indicated that PEB-1 is required for normal morphology of these tissues and growth; however, the peb-1 null phenotype was unknown. Here we describe the deletion mutant peb-1(cu9) that not only exhibits the morphological defects observed in peb-1(RNAi) animals, but also results in penetrant larval lethality characterized by defects in pharyngeal function and molting. Consistent with a function in molting, we found that PEB-1 was detectable in all hypodermal and hindgut cells underlying the cuticle. Comparison to molting-defective lrp-1(ku156) mutants revealed that the peb-1(cu9) mutants were particularly defective in shedding the pharyngeal cuticle, and this defect likely contributed to feeding defects and lethality. Most markers of pharyngeal cell differentiation examined were expressed normally in peb-1(cu9) mutants; however, g1 gland cell expression of a kel-1Colon, two colonsgfp reporter was reduced. As g1 gland cells have prominent functions during molting, we suggest defective gland cell differentiation contributes to peb-1(cu9) molting defects. In comparison, other peb-1 mutant phenotypes, including hindgut abnormalities, appeared independent of the molting defect. Similar phenotypes resulted from late loss of pha-4 function, suggesting that PEB-1 and PHA-4 have common functions in some tissues where they are co-expressed.

Isolation of a novel collagen gene (Mj-col-5) in Meloidogyne javanica and analysis of its expression pattern

Mj-col-5, isolated from the plant parasitic nematode Meloidogyne javanica, has a longer carboxy-terminus than other members of the Caenorhabditis elegans COL-6 subfamily of cuticle collagen, including an extra tyrosine residue, and may form altered nonreducible cross-linkages. By semiquantitative determination at different life stages, Mj-col-5 transcript was shown to be more abundant in eggs than in juveniles/young females and adult females. To characterize further this gene's contribution to the changing cuticle of the nematode, we expressed a fusion protein containing a nonconserved 58-amino-acid sequence from the putative Mj-col-5 gene product and raised rabbit antiserum against the fusion protein. The antiserum detected a strongly reacting band (36 kDa, designated MJE36) on western blots of M. javanica eggs extracted with beta-mercaptoethanol. MJE36 was sensitive to collagenase and was not detected on western blots of extracts from M. javanica second-stage juveniles or adult females. A band of the same molecular size was detected in Meloidogyne incognita egg extracts but not in those of Heterodera avenae. Immunoblot indicated that MJE36 is not present in egg shells of M. javanica.

Characterisation of a collagen gene subfamily from the potato cyst nematode Globodera pallida

We have isolated two full-length genomic DNA sequences, which encode the cuticle collagen proteins GP-COL-1 and GP-COL-2, from the potato cyst nematode Globodera pallida. A third, partial collagen gene ORF termed gp-col-t(t=truncated) has also been isolated and appears to represent an unexpressed pseudogene. The gp-col-1 and gp-col-2 genes both contain three short (<97 bp) introns which disrupt coding regions predicted to specify proteins with molecular weights of 33 and 32.7 kDa respectively. All three sequences show high similarity to each other and to the previously isolated G. pallida cDNA clone gp-col-8. The conserved pattern of cysteine residues and non-(Gly-X-Y)(n) region sequence similarity observed in all four G. pallida genes suggests that these molecules form part of the same subfamily of collagens. Southern analysis indicates that this subfamily is likely to contain further members. The G. pallida collagen sequences show striking similarity to twelve genes from Caenorhabditis elegans which collectively represent the recently classified Group 1a collagen subfamily. No data exists on the function of this subfamily in C. elegans. gp-col-1 and gp-col-2 are developmentally regulated with transcripts of both genes detected in adult virgin and gravid females but not in pre-parasitic second stage juveniles. A similar expression pattern is observed for the Group 1a collagen lemmi 5 from Meloidogyne incognita perhaps indicating a generic link between subfamily and function during the various changes in cuticular structure which accompany nematode growth and reproduction. Immunochemical studies indicate that the GP-COL-1 protein is specifically located in the hypodermis of G. pallida adult females.

Diverse Caenorhabditis elegans genes that are upregulated in dauer larvae also show elevated transcript levels in long-lived, aged, or starved adults

Under adverse conditions, the nematode Caenorhabditis elegans undergoes reversible developmental arrest as dauer larvae, an alternative third larval stage adapted for dispersal and long-term survival. Following such arrest, which may exceed three times their usual life-span, worms resume development to form reproductive adults of normal subsequent longevity. Mutations of genes in the dauer-formation (daf) pathway can extend life-span two- to fourfold, even in adults that mature without diapause. To identify transcript-level changes that might contribute to extended survival, we prepared a subtractive cDNA library of messages more abundant in dauer than in non-dauer (L3) larvae. Six genes were confirmed as three- to ninefold upregulated in dauer larvae, after correction for mRNA load: genes encoding poly(A)-binding protein (PABP), heat-shock proteins hsp70 and hsp90, and three novel genes of uncertain function. The novel genes encode a partial homologue of human activating signal cointegrator 1 (ASC-1), a GTP-binding homologue of a ribosomal protein, and an SH3-domain protein. Transcript levels for all except hsp70 increased during aging in two C. elegans strains, whereas the three novel genes (and possibly PABP) were also induced to varying degrees by starvation of adults. All six genes are expressed at higher levels in young adults of long-lived daf mutant strains than in normal-longevity controls, suggesting that increased expression of these genes may play a protective function, thus favoring survival in diverse contexts.

CHR3: a Caenorhabditis elegans orphan nuclear hormone receptor required for proper epidermal development and molting

CHR3 is a Caenorhabditis elegans orphan nuclear hormone receptor highly homologous to Drosophila DHR3, an ecdysone-inducible gene product involved in metamorphosis. Related vertebrate factors include RORalpha/RZRalpha, RZRbeta and RevErb. Gel-shift studies show that CHR3 can bind the DR5-type hormone response sequence. CHR3 is a nuclear protein present in all blastomeres during early embryogenesis. During morphogenesis, both CHR3 protein and zygotically active reporter genes are detectable in epidermal cells and their precursors. Inhibition of the gene encoding CHR3 results in several larval defects associated with abnormal epidermal cell function, including molting and body size regulation, suggesting that CHR3 is an essential epidermal factor required for proper postembryonic development.

The first isolated collagen gene of the root-knot nematode Meloidogyne javanica is developmentally regulated

The nematode's surface comprises a multilayered cuticle, which consists mainly of collagen proteins. We identified, cloned and characterized the first cuticular collagen gene, Mjcol-3, of the plant-parasitic nematode Meloidogyne javanica. The gene putatively encodes a 32.4-kDa collagen protein, including a propeptide which possesses a subtilisin-like protease-cleavage site. Six introns were identified in the gene sequence, with three slightly different acceptor-splicing sites. The basic structure of the predicted MJCOL-3 protein sequence is highly similar to that of the Caenorhabditis elegans DPY-7, with 65.9% identity between the two amino acid sequences. Relative to DPY-7, the putative MJCOL-3 protein has a shorter carboxy-terminus. This non-conserved feature may indicate different contributions of DPY-7 and MJCOL-3 collagens to the structure of the cuticle. Mjcol-3 is developmentally regulated: transcripts were found mainly in preparasitic developing eggs, less in parasitic third- and fourth-stage juveniles and young females shortly after the fourth molt, and much less in females before egg-laying.

cis regulatory requirements for hypodermal cell-specific expression of the Caenorhabditis elegans cuticle collagen gene dpy-7

The Caenorhabditis elegans cuticle collagens are encoded by a multigene family of between 50 and 100 members and are the major component of the nematode cuticular exoskeleton. They are synthesized in the hypodermis prior to secretion and incorporation into the cuticle and exhibit complex patterns of spatial and temporal expression. We have investigated the cis regulatory requirements for tissue- and stage-specific expression of the cuticle collagen gene dpy-7 and have identified a compact regulatory element which is sufficient to specify hypodermal cell reporter gene expression. This element appears to be a true tissue-specific promoter element, since it encompasses the dpy-7 transcription initiation sites and functions in an orientation-dependent manner. We have also shown, by interspecies transformation experiments, that the dpy-7 cis regulatory elements are functionally conserved between C. elegans and C. briggsae, and comparative sequence analysis supports the importance of the regulatory sequence that we have identified by reporter gene analysis. All of our data suggest that the spatial expression of the dpy-7 cuticle collagen gene is established essentially by a small tissue-specific promoter element and does not require upstream activator or repressor elements. In addition, we have found the DPY-7 polypeptide is very highly conserved between the two species and that the C. briggsae polypeptide can function appropriately within the C. elegans cuticle. This finding suggests a remarkably high level of conservation of individual cuticle components, and their interactions, between these two nematode species.

Isolation and characterization of a putative collagen gene from the potato cyst nematode Globodera pallida

A cDNA clone encoding a full length putative collagen has been isolated in a screen of a mixed stage Globodera pallida expression library. Comparison of the deduced amino acid sequence of this molecule with other collagens suggests it is a cuticular collagen and a member of the col-8 subfamily of collagen genes. Northern blots show the gene is expressed specifically in gravid, adult females of the parasite as compared to second (invasive) stage juveniles and virgin females. Preliminary immunocytochemical studies indicate this collagen is present in areas other than the cuticle; these findings and the potential functional role of this collagen are discussed.

Identification and sequence comparison of a cuticular collagen of Brugia pahangi

The cuticle of filarial nematodes is a specialized extracellular matrix that covers the parasite and protects it from adverse conditions of the environment. As a surface structure it is in direct contact with the host defence mechanisms and therefore plays an important role in the molecular host-parasite relationship. Using polyclonal antisera raised against the insoluble components of the cuticle of the adult filarial parasite Brugia pahangi, we have isolated cDNA clones encoding collagen molecules of the cuticle. The protein domain structure of cDNA clone Bpcol-1 was compared with the known structures of cuticular collagens of the nematodes Brugia malayi, Caenorhabditis elegans, Ascaris suum and Haemonchus contortus, confirming interspecies similarities. Using affinity-purified anti-Bpcol-1 antibodies we identified Bpcol-1 antigenic determinants in different nematode extracts, and determined the localization of such epitopes within the cuticle of B. pahangi.

The Caenorhabditis elegans heterochronic gene pathway controls stage-specific transcription of collagen genes

In Caenorhabditis elegans, the terminal differentiation of the hypodermal cells occurs at the larval-to-adult molt, and is characterized in part by the formation of a morphologically distinct adult cuticle. The timing of this event is controlled by a pathway of heterochronic genes that includes the relatively direct regulatory gene, lin-29, and upstream genes lin-4, lin-14 and lin-28. Using northern analysis to detect endogenous collagen mRNA levels and collagen/lacZ reporter constructs to monitor collagen transcriptional activity, we show that the stage-specific switch from larval cuticle to adult cuticle correlates with the transcriptional activation of adult-specific collagen genes and repression of larval-specific collagen genes. Heterochronic mutations that cause precocious formation of adult cuticle also cause precocious transcription of the adult-specific collagen genes, col-7 and col-19; heterochronic mutations that prevent the switch to adult cuticle cause continued expression of the larval collagen gene, col-17, in adults and prevent adult-specific activation of col-7 or col-19. A 235 bp segment of col-19 5′ sequences is sufficient to direct the adult-specific expression of a col-19/lacZ reporter gene in hypodermal cells. These findings indicate that the heterochronic gene pathway regulates the timing of hypodermal cell terminal differentiation by regulating larval- and adult-specific gene expression, perhaps by the direct action of lin-29.

Characterization of a dense granule antigen of Toxoplasma gondii (GRA6) associated to the network of the parasitophorous vacuole

This work describes the molecular characterization of GRA6, a novel Toxoplasma gondii dense granule antigen of 32 kDa. cDNA clones encoding this protein were isolated using a rat serum directed against an HPLC fraction enriched in the protein GRA5. Cross-reactivity between GRA5 and GRA6 was demonstrated by production of sera against the recombinant GRA5 protein. A serum against a recombinant fragment of GRA6 which does not react with GRA5 allowed the localization of this antigen at the subcellular level. GRA6 is detected in the dense granules of tachyzoites, and in the parasitophorous vacuole, closely associated to the network. The gene encoding GRA6 and its flanking regions were completely sequenced from cDNA and genomic inserts. Primer extension experiments demonstrated that the cap site of the GRA6 gene was located 37 bp upstream of the 5' end of the longest cDNA insert (1600 bp). The GRA6 gene potentially encodes a 230-amino-acid polypeptide, does not contain any introns and seems to be present as a single copy in the genome of T. gondii. The deduced polypeptide contains two hydrophobic regions with the characteristics of transmembrane domains. The N-terminal domain does not fit the classical feature of a signal peptide. The central hydrophobic domain is flanked by two hydrophilic domains which contain four blocks of amino acids homologous to the GRA5 protein. The C-terminal hydrophilic region comprises 24% of glycine residues, which may indicate a structural role for GRA6 in the network.

Caenorhabditis elegans sqt-3 mutants have mutations in the col-1 collagen gene

sqt-3 mutants of Caenorhabditis elegans form dumpy larvae and adults and display allele-specific defects in locomotion, fertility, and viability. We have determined that the sqt-3 locus encodes COL-1 collagen. We physically mapped the col-1 gene to a cosmid on chromosome V whose position is consistent with the location of the sqt-3 gene. We also observed morphological defects in sqt-3 mutants at stages that correlate with the mRNA expression patterns of col-1. Sequence analysis of the col-1 gene in the three temperature-sensitive mutants revealed that each allele of sqt-3 has a unique missense mutation causing arginine or glutamic acid to replace glycine in a Gly-X-Y triple helical domain. These glycine substitutions may result in longer non-collagenous domains, which may decrease the thermal stability or impart additional flexibility to mutant trimers. In addition, we describe four corrections to the published sequence of col-1, including one fifteen nucleotide addition that completes a conserved domain in the amino terminal coding region.

In vitro mutagenesis of Caenorhabditis elegans cuticle collagens identifies a potential subtilisin-like protease cleavage site and demonstrates that carboxyl domain disulfide bonding is required for normal function but not assembly

The importance of conserved amino acids in the amino and carboxyl non-Gly-X-Y domains of Caenorhabditis elegans cuticle collagens was examined by analyzing site-directed mutations of the sqt-1 and rol-6 collagen genes in transgenic animals. Altered collagen genes on transgenic arrays were shown to produce appropriate phenotypes by injecting in vivo cloned mutant alleles. Equivalent alterations in sqt-1 and rol-6 generally produced the same phenotypes, indicating that conserved amino acids in these two collagens have similar functions. Serine substitutions for either of two conserved carboxyl domain cysteines produced LRol phenotypes. Substitution for both cysteines in sqt-1 also resulted in an LRol phenotype, demonstrating that disulfide bonding is important for normal function but not required for assembly. Arg-1 or Arg-4 to Cys mutations in homology block A (HBA; consensus, 1-RXRRQ-5; in the amino non-Gly-X-Y domain) caused RRol phenotypes, while the same alteration at Arg-3 had no effect, indicating that Arg-3 is functionally different from Arg-1 and Arg-4. Substitutions of Arg-4 with Ser, Leu, or Glu also produced the RRol phenotype, while Lys substitutions for Arg-1 or Arg-4 did not generate any abnormal phenotypes. His substitutions for Arg-1 or Arg-4 caused somewhat less severe RRol phenotypes. Therefore, strong positively charged residues, Arg or Lys, are required at positions 1 and 4 for normal function. The conserved pattern of arginines in HBA matches the cleavage sites of the subtilisin-like endoproteinases. HBA may be a cleavage site for a subtilisin-like protease, and cleavage may be important for cuticle collagen processing.

In vitro mutagenesis of Caenorhabditis elegans cuticle collagens identifies a potential subtilisin-like protease cleavage site and demonstrates that carboxyl domain disulfide bonding is required for normal function but not assembly

The importance of conserved amino acids in the amino and carboxyl non-Gly-X-Y domains of Caenorhabditis elegans cuticle collagens was examined by analyzing site-directed mutations of the sqt-1 and rol-6 collagen genes in transgenic animals. Altered collagen genes on transgenic arrays were shown to produce appropriate phenotypes by injecting in vivo cloned mutant alleles. Equivalent alterations in sqt-1 and rol-6 generally produced the same phenotypes, indicating that conserved amino acids in these two collagens have similar functions. Serine substitutions for either of two conserved carboxyl domain cysteines produced LRol phenotypes. Substitution for both cysteines in sqt-1 also resulted in an LRol phenotype, demonstrating that disulfide bonding is important for normal function but not required for assembly. Arg-1 or Arg-4 to Cys mutations in homology block A (HBA; consensus, 1-RXRRQ-5; in the amino non-Gly-X-Y domain) caused RRol phenotypes, while the same alteration at Arg-3 had no effect, indicating that Arg-3 is functionally different from Arg-1 and Arg-4. Substitutions of Arg-4 with Ser, Leu, or Glu also produced the RRol phenotype, while Lys substitutions for Arg-1 or Arg-4 did not generate any abnormal phenotypes. His substitutions for Arg-1 or Arg-4 caused somewhat less severe RRol phenotypes. Therefore, strong positively charged residues, Arg or Lys, are required at positions 1 and 4 for normal function. The conserved pattern of arginines in HBA matches the cleavage sites of the subtilisin-like endoproteinases. HBA may be a cleavage site for a subtilisin-like protease, and cleavage may be important for cuticle collagen processing.

The cuticle of the nematode Caenorhabditis elegans: a complex collagen structure

The cuticle of the nematode Caenorhabditis elegans forms the barrier between the animal and its environment. In addition to being a protective layer, it is an exoskeleton which is important in maintaining and defining the normal shape of the nematode. The cuticle is an extracellular matrix consisting predominantly of small collagen-like proteins that are extensively crosslinked. Although it also contains other protein and non-protein compounds that undoubtedly play a significant part in its function, the specific role of collagen in cuticle structure and morphology is considered here. The C. elegans genome contains between 50 and 150 collagen genes, most of which are believed to encode cuticular collagens. Mutations that result in cuticular defects and grossly altered body form have been identified in more than 40 genes. Six of these genes are now known to encode cuticular collagens, a finding that confirms the importance of this group of structural proteins to the formation of the cuticle and the role of the cuticle as an exoskeleton in shaping the worm. It is likely that many more of the genes identified by mutations giving altered body form, will be collagen genes. Mutations in the cuticular collagen genes provide a powerful tool for investigating the mechanisms by which this group of proteins interact to form the nematode cuticle.

Characterizations of sea urchin fibrillar collagen and its cDNA clone

Collagens were isolated from the adult test of the sea urchin species, Hemicentrotus pulcherrimus and Strongylocentrotus purpuratus, and their molecular properties were compared with those of Asthenosoma ijimai collagen. Collagens from H. pulcherrimus and S. purpuratus comprised two major alpha-chains (alpha 120 and alpha 90) and a minor chain (alpha 140), while collagen from A. ijimai contained four alpha-chains (alpha 1, alpha 2, alpha 3 and alpha 4). Based on their molecular and immunological properties, the alpha 90 chain of H. pulcherrimus and S. purpuratus, and the alpha 2 and alpha 4 chains of A. ijimai are grouped together, while the alpha 120 and alpha 140 chains of H. pulcherrimus and S. purpuratus, and the alpha 1 and alpha 3 chains of A. ijimai are classified into another group. It is likely that collagen molecules of sea urchins are heterotrimers composed of these two types of alpha-chains. A cDNA of collagen was cloned from the cDNA library prepared from mRNA of H. pulcherrimus test and denoted as Hpcol1. This clone contained sequences for uninterrupted triple helical domain (378 amino acids), carboxyl telopeptide (28 amino acids) and carboxyl propeptide (225 amino acids). This structure is characteristic for fibril-forming collagens and was shown to encode alpha 120 and alpha 140 chains of H. pulcherrimus collagen. Hpcol1-mRNA was expressed in embryos as early as the prism stage.

Identification, sequence and expression patterns of the Caenorhabditis elegans col-36 and col-40 collagen-encoding genes

The collagen (Col)-encoding gene family in the nematode, Caenorhabditis elegans, consists of 50-150 members. We have undertaken studies of these genes as part of the analysis of the assembly of the cuticle, the nematode's exoskeleton. We present here the complete nucleotide and deduced amino acid sequences of the col-36 and col-40 genes, both located on chromosome II and encoding cuticle Col. Both Col possess the structural properties found in the type of Col that form the cuticle, such as short Gly-Xaa-Yaa interruptions and Cys clusters at conserved sites. On the basis of identical patterns of conserved cysteines, col-36 and col-40 belong to the col-6 cuticle Col family. Semi-quantitative analysis using reverse transcription-PCR demonstrates that the col-36 transcript is present in L1 larvae and at the L1-L2 and L2d-dauer molts. The col-40 transcript is present in L1 larvae and at the L2d-dauer molt. Different members of the col-6 family are structurally related, but have different developmental expression patterns.

Molecular and genetic analyses of the Caenorhabditis elegans dpy-2 and dpy-10 collagen genes: a variety of molecular alterations affect organismal morphology

We have identified and cloned the Caenorhabditis elegans dpy-2 and dpy-10 genes and determined that they encode collagens. Genetic data suggested that these genes are important in morphogenesis and possibly other developmental events. These data include the morphologic phenotypes exhibited by mutants, unusual genetic interactions with the sqt-1 collagen gene, and suppression of mutations in the glp-1 and mup-1 genes. The proximity of the dpy-2 and dpy-10 genes (3.5 kilobase) and the structural similarity of their encoded proteins (41% amino acid identity) indicate that dpy-2 and dpy-10 are the result of a gene duplication event. The genes do not, however, appear to be functionally redundant, because a dpy-10 null mutant is not rescued by the dpy-2 gene. In addition, full complementation between dpy-2 and dpy-10 can be demonstrated with all recessive alleles tested in trans. Sequence analysis of several mutant alleles of each gene was performed to determine the nature of the molecular defects that can cause the morphologic phenotypes. Glycine substitutions within the Gly-X-Y portion of the collagens can result in dumpy (Dpy), dumpy, left roller (DLRol), or temperature-sensitive DLRol phenotypes. dpy-10(cn64), a dominant temperature-sensitive DLRol allele, creates an Arg-to-Cys substitution in the amino non-Gly-X-Y portion of the protein. Three dpy-10 alleles contain Tc1 insertions in the coding region of the gene. dpy-10(cg36) (DRLol) creates a nonsense codon near the end of the Gly-X-Y region. The nature of this mutation, combined with genetic data, indicates that DLRol is the null phenotype of dpy-10. The Dpy phenotype results from reduced function of the dpy-10 collagen gene. Our results indicate that a variety of molecular defects in these collagens can result in severe morphologic changes in C. elegans.

Characterization of an intronless collagen gene family in the marine sponge Microciona prolifera

Two independent clones from the genomic DNA of a marine sponge Microciona prolifera were isolated by hybridization to the Caenorhabditis elegans Col-1 gene and one clone was obtained from genomic DNA by PCR. They contain open reading frames (MpCol1, MpCol2, MpCol3, MpCol4) capable of coding for a family of collagens different from those previously found in sponges. Southern blotting of genomic DNA suggested the presence of several other homologous genes. cDNA clones covering most of the triple-helical coding domain and the 3' untranslated region of MpCol1 were isolated by specific primers and reverse PCR. Two cDNA clones end in the middle of an AATAAA sequence 170 bp downstream from the translation stop codon of MpCol1. The putative NH2-terminal noncollagenous peptide is composed of only seven amino acid residues. The 1074-bp triple-helical coding region is not interrupted by intervening sequences. It codes for a polypeptide of 120 Gly-Xaa-Yaa triplets with only one short interruption near the COOH terminus. A putative N-glycosylation sequence (Asn-Gly-Ser), three Arg-Gly-Asp triplets known as cell recognition peptides, frequent Lys residues in the Yaa position (which are templates for hydroxylation), several Lys-Gly-Asn/Xaa-Arg peptides known as the lysyl oxidase recognition site, and long stretches without imino acids could be found within the triple-helical domain. The short COOH-terminal noncollagenous domain closely resembles that of nematode cuticular collagens and vertebrate nonfibrillar collagens. Our results strongly support the idea that the diversity of collagen genes and gene families found in higher organisms already existed in sponge.

Identification of a previously unknown human collagen chain, alpha 1(XV), characterized by extensive interruptions in the triple-helical region

A previously unknown collagen cDNA clone, PF19, was isolated from a human placenta library. The 2.1-kilobase insert has a complete open reading frame of 709 amino acids that includes 12 amino acids of the NH2-terminal domain, a principally collagenous region of 577 residues, and 120 residues of the noncollagenous COOH terminus. The collagenous part of the sequence encoded by PF19 is characterized by 13 interruptions ranging in size from 2 to 45 amino acids. Within four interruptions are consensus sequences for attachment of serine-linked glycosaminoglycans and asparagine-linked oligosaccharides suggesting that this collagen may be extensively glycosylated. A synthetic decapeptide representing a sequence at the beginning of the COOH-terminal noncollagenous domain was used to prepare an antibody in rabbits. This antiserum detected a 125-kDa bacterial collagenase-sensitive protein in Western blots of HeLa cell lysate. Consistent with the size of the collagen chain, Northern blot hybridization revealed a major transcript of 5.3 kilobases and two minor ones of 4.7 and 4.4 kilobases that are present in cultured human fibroblasts but absent from umbilical vein endothelial cells. We propose that the previously unidentified polypeptide described in this report be designated the alpha 1 chain of type XV collagen.

Sequence comparison of the Caenorhabditis elegans dpy-13 and col-34 genes, and their deduced collagen products

A 2232-nucleotide sequence spanning the col-34 gene from the nematode, Caenorhabditis elegans, is presented. This gene, which encodes a collagen protein (Clg), is transcribed from right to left with respect to the genetic map, and convergently with the nearby dpy-13 gene which also encodes a Clg. Both col-34 and dpy-13 have 5'-flanking elements in common with each other and also with other nematode Clg-encoding genes (clg). One element, variants of which are shared by col-7, col-19 and dpy-13, is predicted to be a target for a number of regulatory molecules, possibly including the ceh-18 product, a nematode POU-domain protein. The deduced amino acid sequence of Col-34 has a high degree of homology with the Dpy-13 collagen, although there are significant differences. In particular, one region of Dpy-13, which is predicted to have secondary structure different from Col-34, is altered by the recessive dpy-13(e225) mutation.

Caenorhabditis elegans expressed sequence tags identify gene families and potential disease gene homologues

A database containing mapped partial cDNA sequences from Caenorhabditis elegans will provide a ready starting point for identifying nematode homologues of important human genes and determining their functions in C. elegans. A total of 720 expressed sequence tags (ESTs) have been generated from 585 clones randomly selected from a mixed-stage C. elegans cDNA library. Comparison of these ESTs with sequence databases identified 422 new C. elegans genes, of which 317 are not similar to any sequences in the database. Twenty-six new genes have been mapped by YAC clone hybridization. Members of several gene families, including cuticle collagens, GTP-binding proteins, and RNA helicases were discovered. Many of the new genes are similar to known or potential human disease genes, including CFTR and the LDL receptor.

Extracellular matrix (mesoglea) of Hydra vulgaris. I. Isolation and characterization

Hydrozoans such as Hydra vulgaris, as with all classes of Cnidaria, are characterized by having their body wall organized as an epithelial bilayer with an intervening acellular layer termed the mesoglea. The present study was undertaken to determine what extracellular matrix (ECM) components are associated with Hydra mesoglea. Using polyclonal antibodies generated from vertebrate ECM molecules, initial light and electron microscopic immunocytochemical studies indicated the presence of type IV collagen, laminin, heparan sulfate proteoglycan, and fibronectin immunoreactive components in Hydra mesoglea. These immunocytochemical observations were in part supported by biochemical analyses of isolated Hydra mesoglea which indicated the presence of fibronectin and laminin based on Western blot analysis. Amino acid analysis of total mesoglea and some of its isolated components confirmed the presence of collagen molecules in mesoglea. Additional studies indicated the presence of (1) a gelatin binding protein in Hydra which was immunoreactive with antibodies raised to human plasma fibronectin and (2) a noncollagen fragment extracted from mesoglea which was immunoreactive to antibodies raised to the NC1 domain (alpha 1 subunit) of bovine glomerular basement membrane type IV collagen. These observations indicate that Hydra mesoglea is evolutionarily a primitive basement membrane that has retained some properties of interstitial ECM.

Molecular characterization of cuticle and interstitial collagens from worms collected at deep sea hydrothermal vents

Two different collagens were isolated and characterized from the body walls of the vestimentiferan tube worm Riftia pachyptila and the annelid Alvinella pompejana, both living around hydrothermal vents at a depth of 2600 m. The acid-soluble cuticle collagens consisted of a long triple helix (2.4 microns for Alvinella, 1.5 microns for Riftia) terminating into a globular domain. Molecular masses of 2600 and 1700 kDa, respectively, were estimated from their dimensions. The two cuticle collagens were also quite different in amino acid composition, in agreement with their different supramolecular organizations within tissues. Interstitial collagens corresponding to cross-striated fibrils underneath the epidermal cells could be solubilized by digestion with pepsin and consisted of a single alpha-chain. They were similar in molecular mass (340 kDa) and length (280 nm) but differed in composition and banding patterns of segment-long-spacing fibrils. This implicates significant sequence differences also in comparison to fibril-forming vertebrate collagens, although all form typical quarter-staggered fibrils. The thermal stability of the worm collagens was, with one exception (interstitial collagen of Riftia), in the range of mammalian and bird collagens (37 to 46 degrees C), and thus distinctly above that of shallow sea water annelids. Yet, their 4-hydroxyproline contents were not directly correlated to this stability. About 20% of Riftia collagen alpha-chain sequence was elucidated by Edman degradation and showed typical Gly-X-Y repeats but only a limited homology (45 to 58% identity) to fibril-forming vertebrate collagens. A single triplet imperfection and the variable hydroxylation of proline in the X position were additional unique features. It suggests that this collagen represents an ancestral form of fibril-forming collagens not directly corresponding to an individual fibril-forming collagen type of vertebrates.

Isolation and partial sequence of a collagen gene from the human filarial parasite Brugia malayi

We report the isolation and sequence of a part of a gene encoding a collagen from the genome of the human filarial parasite Brugia malayi. The deduced amino acid sequence of the sequenced portion of this gene, which we have designated BmCol1, differs from the most catalogued nematode collagens in that it is composed predominantly of the glycine-X-Y motif, where either X or Y (or both) may be proline. The gene appears to be similar to two recently described Caenorhabditis elegans collagen genes whose deduced amino acid sequences resemble mammalian basement membrane collagens. BmCol1 is a single copy gene and appears to be present in several other parasitic nematodes examined.

cDNA analysis predicts a cornea-specific collagen

In the development of chicken corneal stroma, two or more collagens often interact, either as constituents of a single heterotypic fibril or as components of the fibril surface. The latter, fibril-associated collagens, may facilitate interactions between fibrils and the surrounding extracellular matrix or between fibrils themselves. In an effort to isolate putative nonfibrillar collagens that may have such a function, we screened a 13-day embryonic cornea cDNA library under reduced stringency conditions, using a cDNA probe for a collagenous domain of type XII collagen. We isolated a 4.2-kilobase (kb) cDNA that predicts a "collagenous" protein that has three unusual, if not unique, features. (i) The putative polypeptide encoded by this cDNA has a structural arrangement in which numerous stretches of Gly-Xaa-Yaa triplets, typical of collagens, are interrupted by non-Gly-Xaa-Yaa regions. One of the potential triple-helical domains is 246 amino acids long, but most are much smaller, consisting of 15-36 amino acids. Many are very rich in the helix-stabilizing imino acid proline. (ii) Northern blot analyses demonstrated strong cDNA hybridization to a 6.8-kb mRNA whose expression is restricted to the cornea. No hybridization was observed to mRNAs from the nine other tissues used in these analyses, even with extended exposure of the film. (iii) The cDNA contains a short (less than or equal to 425-base-pair) sequence in the 3' untranslated region of the 6.8-kb mRNA that hybridizes to a 7.8-kb mRNA that has a wide tissue distribution.

Nematode collagen genes

The collagen genes of nematodes encode proteins that have a diverse range of functions. Among their most abundant products are the cuticular collagens, which include about 80% of the proteins present in the nematode cuticle. The structures of these collagens have been found to be strikingly similar in the free-living and parasitic nematode species studied so far, and the genes that encode them appear to constitute a large multigene family whose expression is subject to developmental regulation. Collagen genes that may have a role in cell-cell interactions and collagen genes that correspond to the vertebrate type IV collagen genes have also been identified and studied in nematodes.

Nuclear pre-mRNA introns: analysis and comparison of intron sequences from Tetrahymena thermophila and other eukaryotes

We have sequenced 14 introns from the ciliate Tetrahymena thermophila and include these in an analysis of the 27 intron sequences available from seven T. thermophila protein-encoding genes. Consensus 5' and 3' splice junctions were determined and found to resemble the junctions of other nuclear pre-mRNA introns. Unique features are noted and discussed. Overall the introns have a mean A + T content of 85% (21% higher than neighbouring exons) with smaller introns tending towards a higher A + T content. Approximately half of the introns are less than 100 bp. Introns from other organisms (approximately 30 of each) were also examined. The introns of Dictyostelium discoideum, Caenorhabditis elegans and Drosophila melanogaster, like those of T. thermophila, have a much higher mean A + T content than their neighbouring exons (greater than 20%). Introns from plants, Neurospora crassa and Schizosaccharomyces pombe also have a significantly higher A + T content (10%-20%). Since a high A + T content is required for intron splicing in plants (58), the elevated A + T content in the introns of these other organisms may also be functionally significant. The introns of yeast (Saccharomyces cerevisiae) and mammals (humans) appear to lack this trait and thus in some aspects may be atypical. The polypyrimidine tract, so distinctive of vertebrate introns, is not a trait of the introns in the non-vertebrate organisms examined in this study.

Characterization of a fibrillar collagen gene in sponges reveals the early evolutionary appearance of two collagen gene families

We have characterized cDNA and genomic clones coding for a sponge collagen. The partial cDNA has an open reading frame encoding 547 amino acid residues. The conceptual translation product contains a probably incomplete triple-helical domain (307 amino acids) with one Gly-Xaa-Yaa-Zaa imperfection in the otherwise perfect Gly-Xaa-Yaa repeats and a carboxyl propeptide (240 amino acids) that includes 7 cysteine residues. Amino acid sequence comparisons indicate that this sponge collagen is homologous to vertebrate and sea urchin fibrillar collagens. Partial characterization of the corresponding gene reveals an intron-exon organization clearly related to the fibrillar collagen gene family. The exons coding for the triple-helical domain are 54 base pairs (bp) or multiples thereof, except for a 57-bp exon containing the Gly-Xaa-Yaa-Zaa coding sequence and for two unusual exons of 126 and 18 bp, respectively. This latter 18-bp exon marks the end of the triple-helical domain, contrary to the other known fibrillar collagen genes that contain exons coding for the junction between the triple-helical domain and the carboxyl propeptide. Compared to other fibrillar collagen genes, the introns are remarkably small. Hybridization to blotted RNAs established that the gene transcript is 4.9 kilobases. Together with previous results that showed the existence of a nonfibrillar collagen in the same species, these data demonstrate that at least two collagen gene families are represented in the most primitive metazoa.

Cloning and sequencing of a Porifera partial cDNA coding for a short-chain collagen

Collagen is present in Porifera, the lowest multicellular animals, but there is no information available on the primary structure of the collagen chains in this phylum. Developing fresh-water sponges have been used to extract total RNA in order to study in vitro translation products and to construct a cDNA library. Four translated proteins were collagenase-sensitive (200 kDa, 160 kDa, 81 kDa and 48 kDa). The cDNA library was screened with a human collagen probe and a clone, EmC4, covering 1.2 kb was isolated. Nucleotide sequencing of EmC4 revealed a conceptual open reading frame coding for 366 amino acids terminated by a stop codon TGA with 103 nucleotides downstream. The presumed translation product encoded contained several domains: a non-collagenous C-terminal domain of 156 amino acids with 9 cysteines, an uninterrupted collagenous domain of 171 amino acids, a non-collagenous domain of 16 amino acids with 3 cysteines and a probably incomplete N-terminal collagenous domain of 23 amino acids. Comparison with other sequences suggested that this collagen chain might belong to a non-fibrillar collagen family which evolved into several sub-families giving rise to nematode cuticular collagens, and type IV collagens.

Collagens as multidomain proteins

The number of proteins known to contain collagen-like triple helical domains is rapidly increasing. The functions of these domains are to provide molecular rods that separate spatially non-triple helical domains with varied properties and structures and to permit lateral interactions between molecules. Two-thirds of the amino acids of the triple helical domains have their side-chains at the surface of the protein. The triple helix is also a structure that is easily predictable from the primary structure. The structure of several recently discovered collagens are discussed in terms of domains and functions. The triple helical domains have sizes varying from 33 to over 1,000 amino acid residues. The longest uninterrupted triple helices are involved in the formation of the classical quarter-staggered fibrils. Other triple helical domains permit varied molecular aggregates. A very broad spectrum of non-triple helical or globular domains are interspersed by triple helices. Only those located at the extremities of the molecules are large in size, sometimes several hundred kDa, while the domains separating 2 triple helices are small (less than 50 amino acids) and provide the molecules with hinges, proteolytic cleavage sites or other specialized functions like a glycosaminoglycan attachment site. If the assembly of the 3 chains required for the triple helix formation can be controlled in vitro, collagen-like molecules offer an as yet unexploited potential for protein engineering.

Evolution of collagen IV genes from a 54-base pair exon: a role for introns in gene evolution

The exon structure of the collagen IV gene provides a striking example for collagen evolution and the role of introns in gene evolution. Collagen IV, a major component of basement membranes, differs from the fibrillar collagens in that it contains numerous interruptions in the triple helical Gly-X-Y repeat domain. We have characterized all 47 exons in the mouse alpha 2(IV) collagen gene and find two 36-, two 45-, and one 54-bp exons as well as one 99- and three 108-bp exons encoding the Gly-X-Y repeat sequence. All these exons sizes are also found in the fibrillar collagen genes. Strikingly, of the 24 interruption sequences present in the alpha 2-chain of mouse collagen IV, 11 are encoded at the exon/intron borders of the gene, part of one interruption sequence is encoded by an exon of its own, and the remaining interruptions are encoded within the body of exons. In such "fusion exons" the Gly-X-Y encoding domain is also derived from 36-, 45-, or 54-bp sequence elements. These data support the idea that collagen IV genes evolved from a primordial 54-bp coding unit. We furthermore interpret these data to suggest that the interruption sequences in collagen IV may have evolved from introns, presumably by inactivation of splice site signals, following which intronic sequences could have been recruited into exons. We speculated that this mechanism could provide a role for introns in gene evolution in general.

The Caenorhabditis elegans rol-6 gene, which interacts with the sqt-1 collagen gene to determine organismal morphology, encodes a collagen

The rol-6 gene is one of the more than 40 loci in Caenorhabditis elegans that primarily affect organismal morphology. Certain mutations in the rol-6 gene produce animals that have the right roller phenotype, i.e., they are twisted into a right-handed helix. The rol-6 gene interacts with another gene that affects morphology, sqt-1; a left roller allele of sqt-1 acts as a dominant suppressor of a right roller allele of rol-6. The sqt-1 gene has previously been shown to encode a collagen. We isolated and sequenced the rol-6 gene and found that it also encodes a collagen. The rol-6 gene was identified by physical mapping of overlapping chromosomal deficiencies that cover the gene and by identification of an allele-specific restriction site alteration. The amino acid sequence of the collagen encoded by rol-6 is more similar to that of the sqt-1 collagen than to any of the other ten C. elegans cuticle collagen sequences compared. The locations of cysteine residues flanking the Gly-X-Y repeat regions of rol-6 and sqt-1 are identical, but differ from those in the other collagens. The sequence similarities between rol-6 and sqt-1 indicate that they represent a new collagen subfamily in C. elegans. These findings suggest that these two collagens physically interact, possibly explaining the genetic interaction seen between the rol-6 and sqt-1 genes.

The Caenorhabditis elegans rol-6 gene, which interacts with the sqt-1 collagen gene to determine organismal morphology, encodes a collagen

The rol-6 gene is one of the more than 40 loci in Caenorhabditis elegans that primarily affect organismal morphology. Certain mutations in the rol-6 gene produce animals that have the right roller phenotype, i.e., they are twisted into a right-handed helix. The rol-6 gene interacts with another gene that affects morphology, sqt-1; a left roller allele of sqt-1 acts as a dominant suppressor of a right roller allele of rol-6. The sqt-1 gene has previously been shown to encode a collagen. We isolated and sequenced the rol-6 gene and found that it also encodes a collagen. The rol-6 gene was identified by physical mapping of overlapping chromosomal deficiencies that cover the gene and by identification of an allele-specific restriction site alteration. The amino acid sequence of the collagen encoded by rol-6 is more similar to that of the sqt-1 collagen than to any of the other ten C. elegans cuticle collagen sequences compared. The locations of cysteine residues flanking the Gly-X-Y repeat regions of rol-6 and sqt-1 are identical, but differ from those in the other collagens. The sequence similarities between rol-6 and sqt-1 indicate that they represent a new collagen subfamily in C. elegans. These findings suggest that these two collagens physically interact, possibly explaining the genetic interaction seen between the rol-6 and sqt-1 genes.

Information content of Caenorhabditis elegans splice site sequences varies with intron length

A database of sequences of 139 introns from the nematode Caenorhabditis elegans was analyzed using the information measure of Schneider et al. (1986) J. Mol. Biol. 128: 415-431. Statistically significant information is encoded by at least the first 30 nt and last 20 nt of C. elegans introns. Both the quantity and the distribution of information in the 5' splice site sequences differs between the typical short (length less than 75 nt) and rarer long (length greater than 75 nt) introns, with the 5 sites of long introns containing approximately one bit more information. 3' splice site sequences of long and short C. elegans introns differ significantly in the region between -20 and -10 nt.

Haemonchus contortus: evidence that the 3A3 collagen gene is a member of an evolutionarily conserved family of nematode cuticle collagens

Rabbit antisera were raised against an 18 amino acid-long peptide that corresponds to the predicted sequence of the carboxy-terminal, nontriple helical region of the Haemonchus contortus 3A3 collagen gene. This sequence is highly conserved and diagnostic for members of the col-l collagen family, which includes the 3A3 gene. We find that these antisera react predominantly with multiple, high molecular weight (greater than 68 kDa) proteins on Western blots of whole worm extracts. The number and molecular weights of the reacting proteins vary depending upon the developmental stage of the worms analyzed. All of the reacting proteins are collagenase sensitive. The reacting collagens copurify with cuticles and are released from cuticles by reducing agents. In indirect immunofluorescence assays the antisera react only with the broken edges of isolated cuticles, suggesting that the antisera are reacting with an internal cuticle layer. This layer appears to be circular and to extend throughout the length of the worm. The antisera react on Western blots with multiple, high molecular weight collagens of eight other nematodes examined, representing two classes and several orders. These data provide additional support for the notion that the 3A3 collagen gene, and other members of the col-l collagen family, encode cuticle collagens. Collagens with this peptide sequence, presumably other members of the col-l collagen family, appear to be widely distributed in the phylum Nematoda.

Tandemly duplicated Caenorhabditis elegans collagen genes differ in their modes of splicing

Caenorhabditis elegans contains 50 to 150 collagen genes dispersed throughout its genome. We have determined the complete nucleotide sequences of two collagen genes, col-12 and col-13, that are separated by only 1800 bases and are transcribed in the same direction. The 951 nucleotides of their coding regions differ by only five nucleotides (99.5% identity). The amino acid sequences are identical except for two conservative amino acid changes within the putative secretory signal sequences, so the mature forms of the col-12 and col-13 collagens would be identical. The position and sequence of the intron (52 base-pairs) within the coding region of each gene are perfectly conserved. In contrast to the coding regions and the introns, the 5' and 3' flanking regions show little sequence similarity, col-12 and col-13 are expressed at similar levels at the same developmental stages, and appear to utilize conserved TATA boxes and transcription start sites. The major differences between the genes is that, preceding the initiator ATG, col-12 has a cis-spliced intron, while col-13 is transspliced. Thus, col-12 and col-13 are essentially identical in all aspects except that the col-12 mRNA has a 26-nucleotide cis-spliced leader at the same place where the col-13 mRNA has a 22-nucleotide trans-spliced leader. These results suggest that col-12 and col-13 are derived from a gene duplication and that sequence homology in the coding regions, but not in the flanking regions, has been maintained by gene conversion. The fact that the only significant difference between the two genes is in their modes of splicing suggests that cis and trans-splicing can be interchanged during gene evolution.

Domain organization and intron positions in Caenorhabditis elegans collagen genes: the 54-bp module hypothesis revisited

The amino acid (aa) sequences of the polypeptides encoded by five collagen genes of the nematode Caenorhabditis elegans, col-6, col-7 (partial), col-8, col-14, and col-19, were determined. These collagen polypeptides, as well as those encoded by the previously sequenced C. elegans collagen genes col-1 and col-2, share a common organization into five domains: an amino-terminal leader, a short (30-33 aa) (Gly-X-Y)n domain, a non(Gly-X-Y) spacer, a long (127-132 aa) (Gly-X-Y)n domain, and a short carboxyl-terminal domain. The domain organizations and intron positions of these polypeptides were compared with those of the polypeptides encoded by Drosophila and Strongylocentrotus type IV, and vertebrate types I, II, III, IV, and IX collagen genes; the C. elegans collagen polypeptides are most similar to the vertebrate type IX collagens. It is suggested that the collagen gene family comprises two divergent subfamilies, one of which includes the vertebrate interstitial collagen genes, and the other of which includes the invertebrate collagen genes and the vertebrate type IV and type IX collagen genes. Only the vertebrate interstitial collagen genes display clear evidence of evolution via the tandem duplication of a 54-bp exon.