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The NDST gene family in zebrafish: role of NDST1B in pharyngeal arch formation.

Filipek-Górniok B, Carlsson P, Haitina T, Habicher J, Ledin J, Kjellén L - PLoS ONE (2015)

Bottom Line: Interestingly, the single zebrafish orthologue ndst3, is equally similar to tetrapod Ndst3 and Ndst4.It is likely that a local duplication in the common ancestor of lobe-finned fish and tetrapods gave rise to these two genes.All zebrafish Ndst genes showed distinct but partially overlapping expression patterns during embryonic development.

View Article: PubMed Central - PubMed

Affiliation: Dept. of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Husargatan 3, PO Box 582, SE-751 23, Uppsala, Sweden.

ABSTRACT
Heparan sulfate (HS) proteoglycans are ubiquitous components of the extracellular matrix and plasma membrane of metazoans. The sulfation pattern of the HS glycosaminoglycan chain is characteristic for each tissue and changes during development. The glucosaminyl N-deacetylase/N-sulfotransferase (NDST) enzymes catalyze N-deacetylation and N-sulfation during HS biosynthesis and have a key role in designing the sulfation pattern. We here report on the presence of five NDST genes in zebrafish. Zebrafish ndst1a, ndst1b, ndst2a and ndst2b represent duplicated mammalian orthologues of NDST1 and NDST2 that arose through teleost specific genome duplication. Interestingly, the single zebrafish orthologue ndst3, is equally similar to tetrapod Ndst3 and Ndst4. It is likely that a local duplication in the common ancestor of lobe-finned fish and tetrapods gave rise to these two genes. All zebrafish Ndst genes showed distinct but partially overlapping expression patterns during embryonic development. Morpholino knockdown of ndst1b resulted in delayed development, craniofacial cartilage abnormalities, shortened body and pectoral fin length, resembling some of the features of the Ndst1 mouse knockout.

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Phylogenetic analysis of the NDST protein family.Based on sequence similarity and phylogenetic analysis, the NDST enzymes can be divided into three main branches: NDST1, NDST2 and a common branch for NDST3 and NDST4. Invertebrate genomes contain a single ndst. The consensus neighbor-joining tree was calculated with 1000 bootstrap replicates. Zebrafish Ndst enzymes are encircled. Species names are abbreviated as follows: hs, human; mm, mouse; gg, chicken; ga, stickleback; lc, coelacanth; dr, zebrafish; ci, sea squirt; dm, fruit fly; ce, C. elegans; nv, starlet sea anemone; ta, Trichoplax. The accession numbers are listed under Experimental procedures.
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pone.0119040.g001: Phylogenetic analysis of the NDST protein family.Based on sequence similarity and phylogenetic analysis, the NDST enzymes can be divided into three main branches: NDST1, NDST2 and a common branch for NDST3 and NDST4. Invertebrate genomes contain a single ndst. The consensus neighbor-joining tree was calculated with 1000 bootstrap replicates. Zebrafish Ndst enzymes are encircled. Species names are abbreviated as follows: hs, human; mm, mouse; gg, chicken; ga, stickleback; lc, coelacanth; dr, zebrafish; ci, sea squirt; dm, fruit fly; ce, C. elegans; nv, starlet sea anemone; ta, Trichoplax. The accession numbers are listed under Experimental procedures.

Mentions: By in silico search of the Ensembl database using mouse NDST sequences as templates, five putative zebrafish ndst orthologues were identified, cloned and sequenced. Based on amino acid sequence similarity and phylogenetic analysis, the zebrafish Ndst enzymes along with other known vertebrate NDST orthologues, form three main subgroups (Fig. 1), including the NDST1, the NDST2 and a common subtype for NDST3 and NDST4. In invertebrates, Ndsts are represented by a single member, sharing 35–56% amino acid identity with vertebrate NDST proteins (Fig. 1; S1 Table). Among the five zebrafish Ndsts, two of the proteins were found to be most similar to the NDST1s and were named Ndst1a and Ndst1b, while two of the others showed most similarity to the NDST2s and were named Ndst2a and Ndst2b. Comparing the amino acid sequences, zebrafish Ndst1b has slightly lower identity to other vertebrate NDST1 enzymes than Ndst1a (65–74% amino acid sequence identity compared to 73–81%). Similarly, zebrafish Ndst2b shares 73–79% identity to other NDST2 protein sequences compared to 76–86% for Ndst2a (S1 Table). The fifth zebrafish Ndst is found in the common NDST3/NDST4 subgroup (Fig. 1; S1 Table) and it shares 74–77% identity with tetrapod Ndst3 and Ndst4 amino acid sequences.


The NDST gene family in zebrafish: role of NDST1B in pharyngeal arch formation.

Filipek-Górniok B, Carlsson P, Haitina T, Habicher J, Ledin J, Kjellén L - PLoS ONE (2015)

Phylogenetic analysis of the NDST protein family.Based on sequence similarity and phylogenetic analysis, the NDST enzymes can be divided into three main branches: NDST1, NDST2 and a common branch for NDST3 and NDST4. Invertebrate genomes contain a single ndst. The consensus neighbor-joining tree was calculated with 1000 bootstrap replicates. Zebrafish Ndst enzymes are encircled. Species names are abbreviated as follows: hs, human; mm, mouse; gg, chicken; ga, stickleback; lc, coelacanth; dr, zebrafish; ci, sea squirt; dm, fruit fly; ce, C. elegans; nv, starlet sea anemone; ta, Trichoplax. The accession numbers are listed under Experimental procedures.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4359090&req=5

pone.0119040.g001: Phylogenetic analysis of the NDST protein family.Based on sequence similarity and phylogenetic analysis, the NDST enzymes can be divided into three main branches: NDST1, NDST2 and a common branch for NDST3 and NDST4. Invertebrate genomes contain a single ndst. The consensus neighbor-joining tree was calculated with 1000 bootstrap replicates. Zebrafish Ndst enzymes are encircled. Species names are abbreviated as follows: hs, human; mm, mouse; gg, chicken; ga, stickleback; lc, coelacanth; dr, zebrafish; ci, sea squirt; dm, fruit fly; ce, C. elegans; nv, starlet sea anemone; ta, Trichoplax. The accession numbers are listed under Experimental procedures.
Mentions: By in silico search of the Ensembl database using mouse NDST sequences as templates, five putative zebrafish ndst orthologues were identified, cloned and sequenced. Based on amino acid sequence similarity and phylogenetic analysis, the zebrafish Ndst enzymes along with other known vertebrate NDST orthologues, form three main subgroups (Fig. 1), including the NDST1, the NDST2 and a common subtype for NDST3 and NDST4. In invertebrates, Ndsts are represented by a single member, sharing 35–56% amino acid identity with vertebrate NDST proteins (Fig. 1; S1 Table). Among the five zebrafish Ndsts, two of the proteins were found to be most similar to the NDST1s and were named Ndst1a and Ndst1b, while two of the others showed most similarity to the NDST2s and were named Ndst2a and Ndst2b. Comparing the amino acid sequences, zebrafish Ndst1b has slightly lower identity to other vertebrate NDST1 enzymes than Ndst1a (65–74% amino acid sequence identity compared to 73–81%). Similarly, zebrafish Ndst2b shares 73–79% identity to other NDST2 protein sequences compared to 76–86% for Ndst2a (S1 Table). The fifth zebrafish Ndst is found in the common NDST3/NDST4 subgroup (Fig. 1; S1 Table) and it shares 74–77% identity with tetrapod Ndst3 and Ndst4 amino acid sequences.

Bottom Line: Interestingly, the single zebrafish orthologue ndst3, is equally similar to tetrapod Ndst3 and Ndst4.It is likely that a local duplication in the common ancestor of lobe-finned fish and tetrapods gave rise to these two genes.All zebrafish Ndst genes showed distinct but partially overlapping expression patterns during embryonic development.

View Article: PubMed Central - PubMed

Affiliation: Dept. of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Husargatan 3, PO Box 582, SE-751 23, Uppsala, Sweden.

ABSTRACT
Heparan sulfate (HS) proteoglycans are ubiquitous components of the extracellular matrix and plasma membrane of metazoans. The sulfation pattern of the HS glycosaminoglycan chain is characteristic for each tissue and changes during development. The glucosaminyl N-deacetylase/N-sulfotransferase (NDST) enzymes catalyze N-deacetylation and N-sulfation during HS biosynthesis and have a key role in designing the sulfation pattern. We here report on the presence of five NDST genes in zebrafish. Zebrafish ndst1a, ndst1b, ndst2a and ndst2b represent duplicated mammalian orthologues of NDST1 and NDST2 that arose through teleost specific genome duplication. Interestingly, the single zebrafish orthologue ndst3, is equally similar to tetrapod Ndst3 and Ndst4. It is likely that a local duplication in the common ancestor of lobe-finned fish and tetrapods gave rise to these two genes. All zebrafish Ndst genes showed distinct but partially overlapping expression patterns during embryonic development. Morpholino knockdown of ndst1b resulted in delayed development, craniofacial cartilage abnormalities, shortened body and pectoral fin length, resembling some of the features of the Ndst1 mouse knockout.

Show MeSH
Related in: MedlinePlus