Dolmatov IY et al. (2021), Matrix Metalloproteinases and Tissue Inhibitors...

ECB-ART-48943

Cells 2021 Sep 06;109:. doi: 10.3390/cells10092331.

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Matrix Metalloproteinases and Tissue Inhibitors of Metalloproteinases in Echinoderms: Structure and Possible Functions.

Dolmatov IY , Nizhnichenko VA , Dolmatova LS .

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Echinoderms are one of the most ancient groups of invertebrates. The study of their genomes has made it possible to conclude that these animals have a wide variety of matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs). The phylogenetic analysis shows that the MMPs and TIMPs underwent repeated duplication and active divergence after the separation of Ambulacraria (Echinodermata+Hemichordata) from the Chordata. In this regard the homology of the proteinases and their inhibitors between these groups of animals cannot be established. However, the MMPs of echinoderms and vertebrates have a similar domain structure. Echinoderm proteinases can be structurally divided into three groups-archetypal MMPs, matrilysins, and furin-activatable MMPs. Gelatinases homologous to those of vertebrates were not found in genomes of studied species and are probably absent in echinoderms. The MMPs of echinoderms possess lytic activity toward collagen type I and gelatin and play an important role in the mechanisms of development, asexual reproduction and regeneration. Echinoderms have a large number of genes encoding TIMPs and TIMP-like proteins. TIMPs of these animals, with a few exceptions, have a structure typical for this class of proteins. They contain an NTR domain and 10-12 conservatively located cysteine residues. Repeated duplication and divergence of TIMP genes of echinoderms was probably associated with an increase in the functional importance of the proteins encoded by them in the physiology of the animals.

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	Figure 1. Phylogenetic tree showing the relationship of echinoderms to other animal groups.
	Figure 2. MUSCLE (MegaX) alignment of cysteine switch sequences (boxed area) of some MMPs of echinoderms.
	Figure 3. Scheme of structure of the matrix metalloproteinases of echinoderms. The domain structure was revealed using the Pfam (http://pfam.xfam.org/, accessed on 15 March 2021), Blast NCBI, and Smart (http://smart.embl-heidelberg.de/#, accessed on 15 March 2021) programs. In addition, SignalP-5.0 Server (http://www.cbs.dtu.dk/services/SignalP, accessed on 15 March 2021) and Phobius (https://phobius.sbc.su.se/index.html, accessed on 15 March 2021) were used to more accurately determine the presence of a signal peptide and transmembrane domains in a protein molecule.
	Figure 4. MUSCLE (MegaX) alignment of amino acid sequences of MMPs with a posterior transmembrane domain of echinoderms and vertebrates. (a) Catalytic domain with MT-Loop; (b) C-terminus of MMPs.
	Figure 5. Phylogenetic tree showing the relationships of MMPs of vertebrates, hemichordates, and echinoderms. Crinoids (Anneissia japonica)—pink color, asteroids (Patiria miniata)—blue color, echinoids (Strongylocentrotus purpuratus)—green color, holothurians (Apostichopus japonicus)—red color, hemichordates (Saccoglossus kowalevskii)—deep-blue color, vertebrates—black color. Determination of conserved regions of the putative amino acid sequences was carried out using the Gblock program. Construction of the phylogenetic tree was done using the MrBayes/Maximum Likelihood algorithm and the online service CIPRES (http://www.phylo.org, accessed on 15 March 2021). The nucleotide and amino acid sequences were analyzed using the Partitionfinder 2.1.1 [101,102]. The trees were visualized in the FigTree program.
	Figure 6. Phylogenetic tree showing the relationships of MMPs of echinoderms. Crinoids (Anneissia japonica)—pink color, asteroids (Patiria miniata)—blue color, echinoids (Strongylocentrotus purpuratus)—green color, holothurians (Apostichopus japonicus)—red color. Determination of conserved regions of the putative amino acid sequences was carried out using the Gblock program. Construction of the phylogenetic tree was done using the MrBayes/Maximum Likelihood algorithm and the online service CIPRES (http://www.phylo.org, accessed on 15 March 2021). The nucleotide and amino acid sequences were analyzed using the Partitionfinder 2.1.1 [101,102]. The trees were visualized in the FigTree program.
	Figure 7. MUSCLE (MegaX) alignment of N-terminus of amino acid sequences of some TIMPs of echinoderms and human.
	Figure 8. Phylogenetic tree showing the relationships of TIMPs of echinoderms. Crinoids (Anneissia japonica)—pink color, asteroids (Patiria miniata)—blue color, echinoids (Strongylocentrotus purpuratus)—green color, holothurians (Apostichopus japonicus)—red color, red asterisk—tensilin, blue asterisks—TIMP-like proteins that lack cysteines at the N-terminus of the molecule and/or the HPQ binding site. Construction of the phylogenetic tree was done using the MrBayes/Maximum Likelihood algorithm and the online service CIPRES (http://www.phylo.org, accessed on 15 March 2021). The nucleotide and amino acid sequences were analyzed using the Partitionfinder 2.1.1 [101,102]. The trees were visualized in the FigTree program.

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