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Keeping track of the growing number of biological functions of chitin and its interaction partners in biomedical research.

Koch BE, Stougaard J, Spaink HP - Glycobiology (2015)

Bottom Line: In many studies, these proteins have been found to be involved in immune regulation and in mediating the degradation of chitinous external protective structures of invading pathogens.Finally, we examine the existing literature on zebrafish chitinases, and propose the use of zebrafish as a versatile model to complement the existing murine models.This could especially be of benefit to the exploration of the function of chitinases in infectious diseases using high-throughput approaches and pharmaceutical interventions.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark Leiden University, Institute of Biology, Leiden, The Netherlands.

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Phylogenetic tree of GH18 domains from three fish species, with selected human and mice genes. The overall phylogeny is characterized by one CHID1 and CTBS gene per species, and an expanded group of chitinase/CLP-encoding genes. Most of the zebrafish genes, CHIA.2 to CHIA.6, are placed in the CHIA superclade of the chitinase/CLP phylum. As also suggested by Hussain and Wilson (2013), it seems that, if indeed any zebrafish members of the CHIT1 superclade within the chitinase/CLP phylum exist, CHIA.1 seems the most likely candidate. Sequences with mutations in the active DxxDxDxE motif are indicated with an asterisk. Method: Nucleotide sequences encoding the GH18 domain of each of the genes were aligned by ClustalW. The best substitution model, as measured by the lowest Bayesian information criterion score, was found to be the general time reversible with five discrete gamma distributions and assuming the presence of invariable sites. The phylogeny was inferred by maximum likelihood, and 500 bootstrap replications were applied to test the phylogeny. The percentage bootstrap values are given next to each branchpoint. The evolutionary analysis was performed using MEGA6 (Tamura et al. 2013).
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CWV005F4: Phylogenetic tree of GH18 domains from three fish species, with selected human and mice genes. The overall phylogeny is characterized by one CHID1 and CTBS gene per species, and an expanded group of chitinase/CLP-encoding genes. Most of the zebrafish genes, CHIA.2 to CHIA.6, are placed in the CHIA superclade of the chitinase/CLP phylum. As also suggested by Hussain and Wilson (2013), it seems that, if indeed any zebrafish members of the CHIT1 superclade within the chitinase/CLP phylum exist, CHIA.1 seems the most likely candidate. Sequences with mutations in the active DxxDxDxE motif are indicated with an asterisk. Method: Nucleotide sequences encoding the GH18 domain of each of the genes were aligned by ClustalW. The best substitution model, as measured by the lowest Bayesian information criterion score, was found to be the general time reversible with five discrete gamma distributions and assuming the presence of invariable sites. The phylogeny was inferred by maximum likelihood, and 500 bootstrap replications were applied to test the phylogeny. The percentage bootstrap values are given next to each branchpoint. The evolutionary analysis was performed using MEGA6 (Tamura et al. 2013).

Mentions: The three major clades of GH18 proteins can be recognized in all vertebrates. However, the expansion of the chitinase/CLP group makes it harder to assign one-to-one orthologs between more distantly related species (see Figure 4). In fish genomes, there is a general propensity to encode a higher number of proteins that, by virtue of conserved active amino acid motifs and retention of chitin-binding domains, are predicted to encode active chitinases. The zebrafish genome, for example, encodes five predicted active chitinases and one predicted CLP. The emergence of the high number of genes has been attributed to a whole-genome duplication (WGD) specific to teleost fish (Hussain and Wilson 2013). However, mining the genome of the spotted gar (Lepisosteus oculatus), which branched off the teleost linage before the WGD (Amores et al. 2011), we have identified five genes encoding predicted active chitinases and one predicted to encode a CLP, the same number of predicted active chitinases in the chitinase/CLP group as in zebrafish (see Table I). This indicates that the number of genes has normalized itself after the WGD event.Table I.


Keeping track of the growing number of biological functions of chitin and its interaction partners in biomedical research.

Koch BE, Stougaard J, Spaink HP - Glycobiology (2015)

Phylogenetic tree of GH18 domains from three fish species, with selected human and mice genes. The overall phylogeny is characterized by one CHID1 and CTBS gene per species, and an expanded group of chitinase/CLP-encoding genes. Most of the zebrafish genes, CHIA.2 to CHIA.6, are placed in the CHIA superclade of the chitinase/CLP phylum. As also suggested by Hussain and Wilson (2013), it seems that, if indeed any zebrafish members of the CHIT1 superclade within the chitinase/CLP phylum exist, CHIA.1 seems the most likely candidate. Sequences with mutations in the active DxxDxDxE motif are indicated with an asterisk. Method: Nucleotide sequences encoding the GH18 domain of each of the genes were aligned by ClustalW. The best substitution model, as measured by the lowest Bayesian information criterion score, was found to be the general time reversible with five discrete gamma distributions and assuming the presence of invariable sites. The phylogeny was inferred by maximum likelihood, and 500 bootstrap replications were applied to test the phylogeny. The percentage bootstrap values are given next to each branchpoint. The evolutionary analysis was performed using MEGA6 (Tamura et al. 2013).
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Related In: Results  -  Collection

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CWV005F4: Phylogenetic tree of GH18 domains from three fish species, with selected human and mice genes. The overall phylogeny is characterized by one CHID1 and CTBS gene per species, and an expanded group of chitinase/CLP-encoding genes. Most of the zebrafish genes, CHIA.2 to CHIA.6, are placed in the CHIA superclade of the chitinase/CLP phylum. As also suggested by Hussain and Wilson (2013), it seems that, if indeed any zebrafish members of the CHIT1 superclade within the chitinase/CLP phylum exist, CHIA.1 seems the most likely candidate. Sequences with mutations in the active DxxDxDxE motif are indicated with an asterisk. Method: Nucleotide sequences encoding the GH18 domain of each of the genes were aligned by ClustalW. The best substitution model, as measured by the lowest Bayesian information criterion score, was found to be the general time reversible with five discrete gamma distributions and assuming the presence of invariable sites. The phylogeny was inferred by maximum likelihood, and 500 bootstrap replications were applied to test the phylogeny. The percentage bootstrap values are given next to each branchpoint. The evolutionary analysis was performed using MEGA6 (Tamura et al. 2013).
Mentions: The three major clades of GH18 proteins can be recognized in all vertebrates. However, the expansion of the chitinase/CLP group makes it harder to assign one-to-one orthologs between more distantly related species (see Figure 4). In fish genomes, there is a general propensity to encode a higher number of proteins that, by virtue of conserved active amino acid motifs and retention of chitin-binding domains, are predicted to encode active chitinases. The zebrafish genome, for example, encodes five predicted active chitinases and one predicted CLP. The emergence of the high number of genes has been attributed to a whole-genome duplication (WGD) specific to teleost fish (Hussain and Wilson 2013). However, mining the genome of the spotted gar (Lepisosteus oculatus), which branched off the teleost linage before the WGD (Amores et al. 2011), we have identified five genes encoding predicted active chitinases and one predicted to encode a CLP, the same number of predicted active chitinases in the chitinase/CLP group as in zebrafish (see Table I). This indicates that the number of genes has normalized itself after the WGD event.Table I.

Bottom Line: In many studies, these proteins have been found to be involved in immune regulation and in mediating the degradation of chitinous external protective structures of invading pathogens.Finally, we examine the existing literature on zebrafish chitinases, and propose the use of zebrafish as a versatile model to complement the existing murine models.This could especially be of benefit to the exploration of the function of chitinases in infectious diseases using high-throughput approaches and pharmaceutical interventions.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark Leiden University, Institute of Biology, Leiden, The Netherlands.

Show MeSH
Related in: MedlinePlus