Collagen IV and basement membrane at the evolutionary dawn of metazoan tissues

  • Fidler A
  • Darris C
  • Chetyrkin S
  • et al.
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Abstract

The role of the cellular microenvironment in enabling metazoan tissue genesis remains obscure. Ctenophora has recently emerged as one of the earliest-branching extant animal phyla, providing a unique opportunity to explore the evolutionary role of the cellular microenvironment in tissue genesis. Here, we characterized the extracellular matrix (ECM), with a focus on collagen IV and its variant, spongin short-chain collagens, of non-bilaterian animal phyla. We identified basement membrane (BM) and collagen IV in Ctenophora, and show that the structural and genomic features of collagen IV are homologous to those of non-bilaterian animal phyla and Bilateria. Yet, ctenophore features are more diverse and distinct, expressing up to twenty genes compared to six in vertebrates. Moreover, collagen IV is absent in unicellular sister-groups. Collectively, we conclude that collagen IV and its variant, spongin, are primordial components of the extracellular microenvironment, and as a component of BM, collagen IV enabled the assembly of a fundamental architectural unit for multicellular tissue genesis.The emergence of the diversity of multicellular animals involved cells joining together to form tissues and organs. The ‘glue’ that enabled the cells to work together is made of rope-like molecules called collagen, which assemble into scaffolds. These smart scaffolds tether proteins forming basement membranes that connect cells, provide strength to tissues, and transmit information that influences how the cells behave.How did collagen evolve over millions of years to enable the ever-increasing complexity, size and diversity of animals? To investigate, Fidler, Darris, Chetyrkin et al. explored the tissues of the most ancient of currently living animals – the comb jellies and sponges. This revealed that among all the collagens that make up the human body, a type called collagen IV was a key innovation that enabled single celled organisms to evolve into multicellular animals. Collagen IV, as molecular glue, enabled the formation of a fundamental architectural unit of basement membrane and cells that allowed multicellular tissues and organs to evolve.The findings presented by Fidler, Darris, Chetyrkin et al. pose questions about how collagen IV glues cells together, and how information is stored in the rope-like scaffolds to influence cell behavior. Understanding these processes could ultimately lead to the development of new treatments for diseases in which the collagen smart scaffolds play a key role, such as in kidney diseases and cancer.

Figures

  • Figure 1. Extracellular matrix of the non-bilaterian animal phyla. (A) The transition from single-cell organisms to complex multicellular animals was enabled by an extracellular matrix. (B) Electron microscopy (EM) and immunohistochemistry (IHC) of the Ctenophora species, Mnemiopsis (IHC: 20X magnification), Pleurobrachia (IHC: 20X magnification), and Beroe (IHC: 40X magnification) and ECM components of Ctenophora. (C) Electron microscopy (EM) and immunohistochemistry (IHC) of the non-bilaterian animal phyla, Cnidaria (Nematostella; 20X magnification), Placozoa (Trichoplax), and Porifera (Homoscleromorpha and Demosponges) and ECM components of Porifera, Placozoa, and Cnidaria. Demosponge EM reproduced from Figure 1E of Adams, et al., Freshwater Sponges Have Functional, Sealing Epithelia with High Transepithelial Resistance and Negative Transepithelial Potential, PLoS ONE, 2010, volume 5; Homoscleromorph EM reproduced from Figure 3B, Leys et al., Epithelia and integration in sponges, Integrative and Comparative Biology, 2009, volume 49 with permission from Oxford University Press; Homoscleromorph IHC reproduced from Boute et al., Type IV collagen in sponges, the missing link in basement membrane ubiquity, Biology of the Cell, 1996, volume 88 with permission from Wiley; Trichoplax EM reproduced from Ruthmann et al., The ventral epithelium of Trichoplax adhaerens (Placozoa): Cytoskeletal structures, cell contacts and endocytosis, Zoomorphology, 1986, volume 106 with permission from Springer. (D) ECM components in choanoflagellates, the unicellular sister-group to metazoa. All scale bars 500 nm, unless otherwise noted. DOI: 10.7554/eLife.24176.003
  • Figure 2. Extracellular matrix gene content across bilaterian, non-bilaterian animal, and unicellular protist phyla. Protein BLAST searches using the human ortholog of each protein as bait was conducted for ECM gene content analysis. Where possible (with exception of ctenophore species), we performed a search by protein name across each database. The databases used were Ensembl (http://protists.ensembl.org), NeuroBase (http://neurobase.rc. ufl.edu), AmoebaDB (http://amoebadb.org) and NCBI’s Blast (https://blast.ncbi.nlm.nih.gov/Blast.cgi). Complete hits are denoted in green, while partial protein or domain sequences are denoted in orange. White boxes indicate absence of that protein/domain. DOI: 10.7554/eLife.24176.004
  • Figure 3. Mnemiopsis reveals multiple duplications of collagen IV genes, and non-bilaterian animal phyla collagen IV organization is similar to Bilateria. (A) Collagen IV Gene Orientation. Mnemiopsis collagen IV genes were separated into two groups base on genomic orientation. Group I genes are found on the same scaffold (colored in blue). Group II genes (colored in orange) are spread across four different scaffolds and do not have head-tohead orientation. (B) Transcriptome analysis of Mnemiopsis confirmed a total of 11 collagen IV genes and one NC1 proto-domain gene (colored in grey). (C) Human COL4A1 spans 150 kb, contains 52 exons and has an intron composition of 95%. Mnemiopsis collagen IV genes are approximately one sixth the length of human collagen IV genes ranging in length from 1 to 23 kb with an intronic composition of 50–82%. (D) In Nematostella and Trichoplax, two collagen IV genes are located in head-to-head orientation on one genomic scaffold (Nematostella, scaffold 14; Trichoplax, scaffold 235), which indicates that they share one chromosome. The arrows at the top of each species indicate gene orientation: either minus or plus strands. The search for conserved domains revealed multiple collagens repeats (PF01391, light blue boxes) and C4 domains (PF01413, dark blue) further support that these genes belongs to collagen IV gene family. Pfam domains were identified using HMM against the genomic sequence. Mapping RNAseq reads to the genome strongly supports the proposed collagen IV genes model. DOI: 10.7554/eLife.24176.005 The following source data and figure supplements are available for figure 3:
  • Figure 4. Collagen IV in Ctenophora underwent numerous gene duplication events resulting in an unprecedented diversity. (A) Collagen IV chain distribution across non-bilaterian animal phyla and Bilateria. Two collagen IV chains are found across invertebrates, and six chains in chordate/ vertebrate lineages. The poriferan class of Demosponges lacks collagen IV and BM. (B) Ctenophora collagen IV chains range from four to twenty distinct chains across species, indicating a variable number of gene duplication events. Ctenophora chains can be split into Group I, Group II, and NC1/ C4 subgroupings. All ctenophore species contain Group I, II, and NC1 genes except for the two Beroe species, which lack Group I chains. (C) NC1 genes identified across Ctenophora were analyzed for signal peptide presence to determine whether sequences were truncated, or represented standalone NC1 proteins. Putative signal peptides were detected in at least three ctenophore NC1 genes, Mnemiopsis (ml047918a), Pleurobrachia pileus (pp_COL4_i), and Pleurobrachia bachei (PBNC1_1) based on SignalP prediction (http://www.cbs.dtu.dk/services/SignalP/). DOI: 10.7554/eLife.24176.011
  • Figure 5. Collagen IV structural features are conserved across metazoa, and Ctenophora exhibits novel domains. Signature features of collagen IV are found in each of the identified in Mnemiopsis chains. The collagenous region (yellow) of each chain contains characteristic interruptions (black lines) of the Gly-X-Y motif repeats. Group II chains also possess a NC2 domain (blue), which interrupts the collagenous region, and a cysteine loop (green) that is an extension of canonical NC1 domain (red). The NC1 domain of each chain is composed of two C4 domains. Group II chains possess the chloridebinding motif (purple) within the NC1 domain. While conservation of most Mnemiopsis collagen IV features can be found throughout metazoan species the NC2 domain and cysteine loop are structural innovations restricted to Ctenophora. DOI: 10.7554/eLife.24176.012 The following figure supplements are available for figure 5:
  • Figure 6. Collagen IV in Ctenophora and the non-bilaterian animal phyla are structurally homologous to bilateria. Representative collagen IV sequences from human (UniProt entries P02462, P08572, Q01955, P53420, P29400, Q14031), Drosophila (UniProt entries P08120, O18407), C. elegans (UniProt entries P17139, P17140), Nematostella, Trichoplax, and Mnemiopsis genomes. The following regions are depicted: (based on prediction from http:// www.cbs.dtu.dk/services/SignalP/; shown as orange arrow), NC3 domain (black box), uninterrupted triple helical segments with at least three GXY repeats (yellow boxes), NC2 domain (blue box), cysteine loop (green box), C4 domains (based on conserved domain search at http://www.ncbi.nlm.nih. gov/Structure/cdd/wrpsb.cgi; shown as red boxes). DOI: 10.7554/eLife.24176.019
  • Figure 7. Ctenophora exhibits a novel collagen IV cross-linking mechanism. (A) Gel filtration chromatography elution profile of Mnemiopsis collagenase digest (black) and native, purified placental basement membrane NC1 hexamer (dashed) run successively. Three ctenophore species were digested with bacterial collagenase to solubilize NC1 hexamer for analysis of collagen IV crosslinking. (B) Western blot of gel filtration fractions encompassing elution of NC1 hexamer (12 mL to 16.4 mL) from Mnemiopsis, Pleurobrachia, and Beroe, developed with NC1-specific monoclonal antibodies. HMW=high-molecular-weight complex. (C) Western blot of ctenophore NC1 hexamer separated by SDS-PAGE under reducing (+) and non-reducing (-) conditions (5% bmercaptoethanol). (D) Reduction of the high-molecular-weight complex from Beroe (first lane, >250 kDa) following by alkylation results in formation of dimers at low DTT concentration, and complete reduction to monomers at high DTT concentration. (E) Structure of Ctenophora collagen IV group II chain, highlighting cysteine-loop region of the NC1, and multiple-sequence alignment of cysteine-loop region of Group II chains of Mnemiopsis (NC1 domain is partial sequence). DOI: 10.7554/eLife.24176.020
  • Figure 8. Evolutionary relationships of collagen IV and spongin NC1 domains across metazoa compared to Ctenophora. Metazoan collagen IV chains feature a sulfilimine bond cross-linked collagen IV network, with the exception of the cnidarian, Hydra, and the non-bilaterian animal phyla Porifera and Placozoa. However, the structural domains across bilaterians and the non-bilaterian animal phyla are homologous; however, Ctenophora also contains novel domains. Unrooted maximum likelihood tree of collagen IV NC1 domains in human, mouse, zebrafish, Trichoplax (Placozoa), Pseudocorticium jarrei (Porifera), and Oscarella sp. (Porifera), in comparison with 10 ctenophore species. All analyses were based off amino acid sequence alignments of the NC1 domain, omitting the cysteine-loop region of Ctenophora NC1 domains. DOI: 10.7554/eLife.24176.021

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Fidler, A. L., Darris, C. E., Chetyrkin, S. V., Pedchenko, V. K., Boudko, S. P., Brown, K. L., … Hudson, B. G. (2017). Collagen IV and basement membrane at the evolutionary dawn of metazoan tissues. ELife, 6. https://doi.org/10.7554/elife.24176

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