Journal: Open Biology

Article Title: Comparative analysis of stalked and acorn barnacle adhesive proteomes

doi: 10.1098/rsob.210142

Figure Lengend Snippet: Comparison of the proteins identified via mass spectrometry in the adhesive of A. amphitrite and P. pollicipes . ( a ) Venn diagram indicating the number and percentage of the total identified proteins that do and do not share homology between the two species. Seventy-one A. amphitrite proteins align to 132 P. pollicipes proteins. ( b ) Number of proteins per protein category for each species, with the number of proteins with no homology to the other species in parenthesis. These broad categories are based on the annotation or conserved domains present in the protein sequences or homology to barnacle proteins identified in previous studies. The bulk proteins are either predicted to make up the bulk mass of the adhesive and may contribute to adhesion. Pheromones are either α-macroglobulins (settlement inducing or MULTIFUNCin pheromones) or have cupin domains (waterborne settlement pheromones). Enzymes cover a range of potential processes, including oxidation and protease (inhibition) activity. The homologous group includes the remaining proteins with homology to broader taxa. These numbers exclude highly likely intracellular proteins (35 P. pollicipes ; three A. amphitrite ), based on annotation and the lack of predicted signal peptides.

Article Snippet: The P. pollicipes cement protein MS files (E4801_PPCIM1, E4802_PPCIM2 and E4803_PPCIM3) [ ] were obtained from the Mendeley Data repository ( http://dx.doi.org/10.17632/pgkf3mtb4m.1 ), and the spectra from these Orbitrap raw files were matched to the Ppol_2 proteome, RefSeq GCF_011947565.2 (electronic supplementary material, file S5).

Techniques: Comparison, Mass Spectrometry, Adhesive, Inhibition, Activity Assay

Journal: Open Biology

Article Title: Comparative analysis of stalked and acorn barnacle adhesive proteomes

doi: 10.1098/rsob.210142

Figure Lengend Snippet: Heatmap of P. pollicipes bulk cement protein amino acid (AA) composition. Only glycine and leucine-enriched bulk cement proteins are included in this analysis. Clustering is based on row means and shows distinct grouping of proteins based on amino acid enrichment. The two leucine-rich groups (LrCP1 and LrCP2) glycine-rich proteins (GrCP1 and GrCP2) groups seen in A. amphitrite are apparent in this P. pollicipes analysis.

Article Snippet: The P. pollicipes cement protein MS files (E4801_PPCIM1, E4802_PPCIM2 and E4803_PPCIM3) [ ] were obtained from the Mendeley Data repository ( http://dx.doi.org/10.17632/pgkf3mtb4m.1 ), and the spectra from these Orbitrap raw files were matched to the Ppol_2 proteome, RefSeq GCF_011947565.2 (electronic supplementary material, file S5).

Techniques:

Journal: Open Biology

Article Title: Comparative analysis of stalked and acorn barnacle adhesive proteomes

doi: 10.1098/rsob.210142

Figure Lengend Snippet: Comparison of A. amphitrite and P. pollicipes bulk glycine (GrCP) and leucine (LrCP)-rich cement protein. ( a ) Venn diagrams showing overlap between the A. amphitrite and P. pollicipes GrCP and LrCP groups. The overlapping proteins do not contain the same number of proteins, as a single protein from one species can align significantly to multiple proteins of the other species; therefore, these dissimilar values are indicated by A. amphitrite (Aa) proteins = P. pollicipes (Pp) proteins. Colour key is that same as in b . ( b ) Principal component analysis (PCA) of individual proteins from both A. amphitrite (Aamp, circles) and P. pollicipes (Ppol, triangles) with GrCP and LrCP categories indicated by colour. ( c ) PCA variable plot of the amino acids driving protein separation seen in ( b ). Amino acid vectors are coloured by contribution score.

Article Snippet: The P. pollicipes cement protein MS files (E4801_PPCIM1, E4802_PPCIM2 and E4803_PPCIM3) [ ] were obtained from the Mendeley Data repository ( http://dx.doi.org/10.17632/pgkf3mtb4m.1 ), and the spectra from these Orbitrap raw files were matched to the Ppol_2 proteome, RefSeq GCF_011947565.2 (electronic supplementary material, file S5).

Techniques: Comparison

Journal: Open Biology

Article Title: Comparative analysis of stalked and acorn barnacle adhesive proteomes

doi: 10.1098/rsob.210142

Figure Lengend Snippet: Glycosylation site prediction of bulk cement proteins. ( a ) Total number of predicted N - and O -linked glycosylation sites for A. amphitrite (Aamp) and P. pollicipes (Ppol) bulk adhesive proteins. ( b ) Average number of N - and O -linked glycosylation sites for each amino acid group (glycine rich: GrCP1 and GrCP2; leucine rich: LrCP1 and LrCP2; cysteine rich: CrCP).

Article Snippet: The P. pollicipes cement protein MS files (E4801_PPCIM1, E4802_PPCIM2 and E4803_PPCIM3) [ ] were obtained from the Mendeley Data repository ( http://dx.doi.org/10.17632/pgkf3mtb4m.1 ), and the spectra from these Orbitrap raw files were matched to the Ppol_2 proteome, RefSeq GCF_011947565.2 (electronic supplementary material, file S5).

Techniques: Glycoproteomics, Adhesive

Journal: Open Biology

Article Title: Comparative analysis of stalked and acorn barnacle adhesive proteomes

doi: 10.1098/rsob.210142

Figure Lengend Snippet: Multiple sequence alignment of the α-macroglobulin and waterborne settlement pheromones identified in the adhesive. ( a ) A tree constructed from multiple sequence alignment data of the α-macroglobulin pheromones that contain an Isopren_C2_like domain shows clustering by family (Multi: MULTIFUNCin; SIPC: settlement inducing complex). Bolded accession numbers indicate sequences with predicted signal peptides. The conserved domains identified for each protein are shown to the right. A. amphitrite proteins are distinguished by a black backbone (KAF accessions) and P. pollicipes are distinguished by a grey backbone (XP accessions). One protein (KAF0294115.1) contains an Rnase_HI_RT_non_LTR (cd09276; indicated by a yellow and black striped box) that was likely inserted by a transposon. Dashed lines between families were added to improve visualization. ( b ) Multiple sequence alignment of all waterborne settlement pheromones (WSPs). The WSPs cluster by species rather than by family, as seen in the α-macroglobulin pheromones. Each of these proteins contains the domain cupin_RmlC-like super family (cl40423). Bolded accession numbers indicate sequences with predicted signal peptides. ( c ) The average number of predicted N - and O -linked glycosylation sites for the α-macroglobulin pheromones. The MULTIFUNCin familes (Multi-1 through 3) have been combined for analysis. AaMulti: A. amphitrite MULTIFUNCin; PpMulti: P. pollicipes MULTIFUNCin; AaSIPC: A. amphitrite settlement inducing complex; PpSIPC: P. pollicipes settlement inducing complex.

Article Snippet: The P. pollicipes cement protein MS files (E4801_PPCIM1, E4802_PPCIM2 and E4803_PPCIM3) [ ] were obtained from the Mendeley Data repository ( http://dx.doi.org/10.17632/pgkf3mtb4m.1 ), and the spectra from these Orbitrap raw files were matched to the Ppol_2 proteome, RefSeq GCF_011947565.2 (electronic supplementary material, file S5).

Techniques: Sequencing, Adhesive, Construct, Glycoproteomics

Journal: Open Biology

Article Title: Comparative analysis of stalked and acorn barnacle adhesive proteomes

doi: 10.1098/rsob.210142

Figure Lengend Snippet: Enzyme and protease inhibitor families identified in the adhesive proteomes of A. amphitrite and P. pollicipes .

Article Snippet: The P. pollicipes cement protein MS files (E4801_PPCIM1, E4802_PPCIM2 and E4803_PPCIM3) [ ] were obtained from the Mendeley Data repository ( http://dx.doi.org/10.17632/pgkf3mtb4m.1 ), and the spectra from these Orbitrap raw files were matched to the Ppol_2 proteome, RefSeq GCF_011947565.2 (electronic supplementary material, file S5).

Techniques: Protease Inhibitor, Adhesive, Histone Deacetylase Assay

Journal: Open Biology

Article Title: Comparative analysis of stalked and acorn barnacle adhesive proteomes

doi: 10.1098/rsob.210142

Figure Lengend Snippet: Homologous protein families identified in the adhesive proteomes of A. amphitrite and P. pollicipes .

Article Snippet: The P. pollicipes cement protein MS files (E4801_PPCIM1, E4802_PPCIM2 and E4803_PPCIM3) [ ] were obtained from the Mendeley Data repository ( http://dx.doi.org/10.17632/pgkf3mtb4m.1 ), and the spectra from these Orbitrap raw files were matched to the Ppol_2 proteome, RefSeq GCF_011947565.2 (electronic supplementary material, file S5).

Techniques: Adhesive, Binding Assay, Ligand Binding Assay