Collagen gene construction and evolution

Convergent analysis of food products using molecular barcodes, based on LC-HRMS data

There are various analytical techniques available to address the growing interest in the composition of food products. LC-HRMS(/MS) is the most comprehensive technique, providing detailed information at the molecular level. However, given the vast number of different molecules encountered in food products, it is important to obtain a global overview of the dataset before focusing on similarities and differences. Therefore, a convergent strategy was employed, going from non-targeted to targeted analysis, with insightful data representations, most notably Molecular Barcode. Additionally an intermediate, semi-targeted analysis was defined, aimed at the specific detection of animal tissue in food products, using pG+ and related fragments after all ion fragmentation. The use of Molecular Barcode as a starting point to obtain relevant molecular data was also demonstrated. In conclusion, the convergent approach facilitates the design of suitable targeted methods, either to discriminate between samples or to find a generic target.

Identification of collagen 1α3 in teleost fish species and typical collision induced internal fragmentations

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Identification of collagen 1α3 in several fish species using LC-MS.

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Visualization of collagen (type) similarity on the nucleotide and amino acid level.

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Assessment of database collagen annotations.

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Further investigation of the formation of pG⁺ fragment ions.

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Detailed description of collagen-specific collision induced internal fragment ion series.

In contrast to collagens 1α1 and 1α2, the more obscure collagen 1α3 is sparsely mentioned in literature. In skin collagen type 1 of teleosts (bony fish), however, the chain occurs in a heterotrimer together with collagens 1α1 and 1α2, which makes it one of the most abundant proteins in teleosts. As teleost fish species and gelatin (hydrolysate) prepared from their skin are a major source for food products and nutraceuticals, the goal of the study was to selectively identify collagen 1α3 in several fish species. Fish skin extracts and fish skin gelatins were analyzed using LC-MS. Depending on the amount of available genetic information different approaches were used to identify collagen 1α3. Additionally, collagen-specific collision induced internal fragmentations are discussed, which are important to consider during data analysis. Ultimately the presence of collagen 1α3 could be confirmed using LC-MS in multiple fish species.

Significant differences in single-platelet biophysics exist across species but attenuate during clot formation

Human, canine, ovine, and porcine platelets exhibit disparate biophysical signatures, whereas human and murine platelets are similar. Multiple biophysical parameters integrate during clot formation, measured by bulk clot contraction, and attenuate biophysical differences.

Genome duplication and the origin of the vertebrate skeleton

During vertebrate embryonic development, tissue patterning and differentiation are regulated by members of multigene families. Evolutionary expansion of these families is thought to have played a role in the evolution of anatomical complexity, including the origins of new cell and tissue types. A defining feature of vertebrates is an endoskeleton, the primary components of which are cartilage and bone. The molecular control of skeletal patterning has been the subject of intensive investigation for over two decades. More recently, comparative studies of organisms at key phylogenetic positions have highlighted the importance of gene duplication in the evolutionary diversification of connective tissues. Understanding the natural histories of gene families involved in skeletogenesis is therefore central to the issue of vertebrate skeletal evolution.

Cell Adhesion, Polarity, and Epithelia in the Dawn of Metazoans

Transporting epithelia posed formidable conundrums right from the moment that Du Bois Raymond discovered their asymmetric behavior, a century and a half ago. It took a century and a half to start unraveling the mechanisms of occluding junctions and polarity, but we now face another puzzle: lest its cells died in minutes, the first high metazoa (i.e., higher than a sponge) needed a transporting epithelium, but a transporting epithelium is an incredibly improbable combination of occluding junctions and cell polarity. How could these coincide in the same individual organism and within minutes? We review occluding junctions (tight and septate) as well as the polarized distribution of Na+-K+-ATPase both at the molecular and the cell level. Junctions and polarity depend on hosts of molecular species and cellular processes, which are briefly reviewed whenever they are suspected to have played a role in the dawn of epithelia and metazoan. We come to the conclusion that most of the molecules needed were already present in early protozoan and discuss a few plausible alternatives to solve the riddle described above.

Origin of the metazoan bodyplan: characterization and functional testing of the promoter of the homeobox gene EmH-3 from the freshwater sponge Ephydatia muelleri in mouse 3T3 cells

Porifera [sponges] represent the lowest metazoan phylum, probably already existing prior to the 'Cambrian explosion'. Based on amino acid sequences deduced from cDNAs that code for structural proteins, the monophyly of Metazoa was established. Now we analyzed for the first time a promoter of a sponge gene for its activity in a heterologous cell system from higher Metazoa. The promoter of the homeobox gene EmH-3 was cloned and sequenced from a genomic library of the freshwater sponge Ephydatia muelleri. For the determination of functional promoter activity, transient transfection experiments in mouse NIH 3T3 cells were performed; the promoter was fused with the luciferase reporter gene. The data revealed that a 401 nt long promoter fragment, comprising several binding elements for metazoan transcription factors, showed the highest activity, while the 175 bp long promoter segment, comprising solely the TATA- and Cap boxes, showed only 25% of that activity. This result demonstrates that the sponge promoter is activated by factors present in mammalian cells and supports the view that Porifera, together with the other metazoan phyla, are of monophyletic origin.

The evolution of diversity in ancient ecosystems: a review

On a perfect planet, such as might be acceptable to a physicist, one might predict that from its origin the diversity of life would grow exponentially until the carrying capacity, however defined, was reached. The fossil record of the Earth, however, tells a very different story. One of the most striking aspects of this record is the apparent evolutionary longueur, marked by the Precambrian record of prokaryotes and primitive eukaryotes, although our estimates of microbial diversity may be seriously incomplete. Subsequently there were various dramatic increases in diversity, including the Cambrian ‘explosion’ and the radiation of Palaeozoic–style faunas in the Ordovician. The causes of these events are far from resolved. It has also long been appreciated that the history of diversity has been punctuated by important extinctions. The subtleties and nuances of extinction as well as the survival of particular clades have to date, however, received rather too little attention, and there is still a tendency towards blanket assertions rather than a dissection of these extraordinary events. In addition, some but perhaps not all mass extinctions are characterized by long lag–times of recovery, which may reflect the slowing waning of extrinsic forcing factors or alternatively the incoherence associated with biological reassembly of stable ecosystems. The intervening periods between the identified mass extinctions may be less stable and benign than popularly thought, and in particular the frequency of extraterrestrial impacts leads to predictions of recurrent disturbance on timescales significantly shorter than the intervals separating the largest extinction events. Even at times of quietude it is far from clear whether biological communities enjoy stability and interlocked stasis or are dynamically reconstituted at regular intervals. Finally, can we yet rely on the present depictions of the rise and falls in the levels of ancient diversity? Existing data is almost entirely based on Linnean taxa, and the application of phylogenetic systematics to this problem is still in its infancy. Not only that, but even more intriguingly the pronounced divergence in estimates of origination times of groups as diverse as angiosperms, diatoms and mammals in terms of the fossil record as against molecular data point to the possibilities of protracted intervals of geological time with a cryptic diversity. If this is correct, and there are alternative explanations, then some of the mystery of adaptive radiations may be dispelled, in as much as the assembly of key features in the stem groups could be placed in a gradualistic framework of local adaptive response punctuated by intervals of opportunity.

Defusing the Cambrian 'explosion'?

A recent molecular phylogenetic study argues against the orthodox view that metazoan phyla emerged abruptly during the Cambrian 'explosion', pointing instead to a protracted history for metazoans that arguably stretches back a billion years or more; the fossils, however, seem to tell a different story.

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.

Burgess Shale Faunas and the Cambrian Explosion

Soft-bodied marine faunas from the Lower and Middle Cambrian, exemplified by the Burgess Shale of British Columbia, are a key component in understanding the major adaptive radiations at the beginning of the Phanerozoic ("Cambrian explosion"). These faunas have a widespread distribution, and many taxa have pronounced longevity. Among the components appear to be survivors of the preceding Ediacaran assemblages and a suite of bizarre forms that give unexpected insights into morphological diversification. Microevolutionary processes, however, seem adequate to account for this radiation, and the macroevolutionary patterns that set the seal on Phanerozoic life are contingent on random extinctions. They weeded out the morphological spectrum and permitted rediversification among surviving clades. Although the predictability of which clades will play in successive acts of the Phanerozoic theater is low, at least the outlines of the underlying ecological plot are already clear from the opening of the drama.

Identification, synthesis and immunogenicity of cuticular collagens from the filarial nematodes Brugia malayi and Brugia pahangi

The major structural proteins of the cuticle of the filarial nematode parasites Brugia malayi and Brugia pahangi were identified by extrinsic iodination and sensitivity to clostridial collagenase. At least 16 acidic components were identified in adult worms by 2-dimensional electrophoresis, with molecular weights ranging from 35,000 to 160,000. These proteins appear to be cross-linked by disulphide bonds, and localised in the basal and inner cortical layers of the cuticle. The outer cortex, containing the epicuticle, is insoluble in 1% sodium dodecyl sulphate and 5% 2-mercaptoethanol, and can be isolated free of cellular material. Despite their inaccessibility to the immune system in intact worms, antibodies to the cuticular collagens are provoked in humans infected with a variety of filarial parasites. Immunological cross-reactivity was demonstrated between a 35 kDa component and human type IV (basement membrane) collagen. Autoantibodies to type IV collagen were detected in a number of individuals with lymphatic filariasis, although no correlation could be drawn with observed pathology. Synthesis of cuticular collagens is discontinuous, occurs at negligible levels in mature adult male worms, and does not appear to involve the production of small molecular weight precursors, in contrast to Caenorhabditis elegans. Hybridisation with a heterologous cDNA probe coding for the alpha 2 chain of chicken type 1 collagen suggests that they are encoded by a multigene family.

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.

Molecular phylogeny of the animal kingdom

A rapid sequencing method for ribosomal RNA was applied to the resolution of evolutionary relationships among Metazoa. Representatives of 22 classes in 10 animal phyla were used to infer phylogenetic relationships, based on evolutionary distances determined from pairwise comparisons of the 18S ribosomal RNA sequences. The classical Eumetazoa are divided into two groups. Cnidarians arose from a protist ancestry different from the second group, the Bilateria. Within the Bilateria, an early split gave rise to Platyhelminthes (flatworms) and the coelomate lineage. Coelomates are thus monophyletic, and they radiated rapidly into four groups: chordates, echinoderms, arthropods, and eucoelomate protostomes.