Pressure cycling technology for challenging proteomic sample processing: application to barnacle adhesive.

AbstractSuccessful proteomic characterization of biological material depends on the development of robust sample processing methods. The acorn barnacle Amphibalanus amphitrite is a biofouling model for adhesive processes, but the identification of causative proteins involved has been hindered by their insoluble nature. Although effective, existing sample processing methods are labor and time intensive, slowing progress in this field. Here, a more efficient sample processing method is described which exploits pressure cycling technology (PCT) in combination with protein solvents. PCT aids in protein extraction and digestion for proteomics analysis. Barnacle adhesive proteins can be extracted and digested in the same tube using PCT, minimizing sample loss, increasing throughput to 16 concurrently processed samples, and decreasing sample processing time to under 8 hours. PCT methods produced similar proteomes in comparison to previous methods. Two solvents which were ineffective at extracting proteins from the adhesive at ambient pressure (urea and methanol) produced more protein identifications under pressure than highly polar hexafluoroisopropanol, leading to the identification and description of >40 novel proteins at the interface. Some of these have homology to proteins with elastomeric properties or domains involved with protein-protein interactions, while many have no sequence similarity to proteins in publicly available databases, highlighting the unique adherent processes evolved by barnacles. The methods described here can not only be used to further characterize barnacle adhesive to combat fouling, but may also be applied to other recalcitrant biological samples, including aggregative or fibrillar protein matrices produced during disease, where a lack of efficient sample processing methods has impeded advancement. Data are available via ProteomeXchange with identifier PXD012730

Molt-dependent transcriptomic analysis of cement proteins in the barnacle Amphibalanus amphitrite

Abstract Background A complete understanding of barnacle adhesion remains elusive as the process occurs within and beneath the confines of a rigid calcified shell. Barnacle cement is mainly proteinaceous and several individual proteins have been identified in the hardened cement at the barnacle-substrate interface. Little is known about the molt- and tissue-specific expression of cement protein genes but could offer valuable insight into the complex multi-step processes of barnacle growth and adhesion. Methods The main body and sub-mantle tissue of the barnacle Amphibalanus amphitrite (basionym Balanus amphitrite) were collected in pre- and post-molt stages. RNA-seq technology was used to analyze the transcriptome for differential gene expression at these two stages and liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) was used to analyze the protein content of barnacle secretions. Results We report on the transcriptomic analysis of barnacle cement gland tissue in pre- and post-molt growth stages and proteomic investigation of barnacle secretions. While no significant difference was found in the expression of cement proteins genes at pre- and post-molting stages, expression levels were highly elevated in the sub-mantle tissue (where the cement glands are located) compared to the main barnacle body. We report the discovery of a novel 114kD cement protein, which is identified in material secreted onto various surfaces by adult barnacles and with the encoding gene highly expressed in the sub-mantle tissue. Further differential gene expression analysis of the sub-mantle tissue samples reveals a limited number of genes highly expressed in pre-molt samples with a range of functions including cuticular development, biominerialization, and proteolytic activity. Conclusions The expression of cement protein genes appears to remain constant through the molt cycle and is largely confined to the sub-mantle tissue. Our results reveal a novel and potentially prominent protein to the mix of cement-related components in A. amphitrite. Despite the lack of a complete genome, sample collection allowed for extended transcriptomic analysis of pre- and post-molt barnacle samples and identified a number of highly-expressed genes. Our results highlight the complexities of this sessile marine organism as it grows via molt cycles and increases the area over which it exhibits robust adhesion to its substrate.http://deepblue.lib.umich.edu/bitstream/2027.42/115487/1/12864_2015_Article_2076.pd

Measuring the p<i>K</i>/p<i>I</i> of Biomolecules Using X‑ray Photoelectron Spectroscopy

Dissociation constants of GG–X–GG and X₅ peptides (X = G, D, H, or K), and bovine albumin (BSA) and fibronectin (FN) were measured by X-ray photoelectron spectroscopy (XPS) in ultrahigh vacuum at room temperature. The biomolecules were deposited on Au substrates by drying 2.0 μL drops of 1.0 μg μL^–1 stock solutions in 100 mM sodium phosphate buffers (pH 1–12) at room temperature. Because of the ∼+1.3 eV shift in binding energy (BE) of protonated amines, p<i>K</i> values of basic amino acids were calculated by plotting the fraction of protonated amines as a function of solution pH. Similarly, the BE of carboxyl groups shifted ∼−1.3 eV upon deprotonation. While C 1s spectra were convoluted by the multiple chemical states of carbon present in the samples, the ratio of the C 1s components centered at BE = 289.0 ± 0.4 and BE = 287.9 ± 0.3 proved to reliably assess deprotonation of carboxyl groups. The p<i>K</i> values for the Asp (3.1 and 2.4), His (6.7), and Lys (11.3 and 10.6) peptides, and the p<i>I</i> of BSA (4.8) and FN (5.7), were consistent with published values; thus, these methods could potentially be used to determine the dissociation constants of surface-bound biomolecules

Albumin Conformational Change and Aggregation Induced by Nanostructured Apatites

Biomaterials with nanostructured surfaces influence cellular response in a significantly different, and often beneficial, manner compared to materials with coarser features. Hydroxyapatite [HA, Ca10(PO4)6(OH)2] and strontium-apatite [Sr10(PO4)6(OH)2] microspheres that present nanotopographies similar to biological apatites were incubated in albumin solutions, at physiological conditions (40 mg ml-1; 37 °C), for up to 72 h. Electronic and vibrational circular dichroism spectroscopies revealed spectral signatures characteristic of stacked β-sheet regions in higher ordered structures (e.g., fibrils). The presence of stacked β-sheets was further evidenced by thioflavin T staining. The sequestration of interfacial Ca atoms by pyrophosphate ions (P2O7 4-), prior to albumin adsorption, prevented stacked β-sheet formation on hydroxyapatite. These results suggest that the charge and/or spatial arrangement of Ca atoms direct stacked β-sheet formation during bovine serum albumin adsorption. Stacked β-sheet spectral features were also observed after incubating HA in fetal bovine serum, highlighting that this phenomena could direct cellular response to these biomaterials in vivo

Surface-Induced Changes in the Conformation and Glucan Production of Glucosyltransferase Adsorbed on Saliva-Coated Hydroxyapatite

Glucosyltransferases (Gtfs) from S. mutans play critical roles in the development of virulent oral biofilms associated with dental caries disease. Gtfs adsorbed to the tooth surface produce glucans that promote local microbial colonization and provide an insoluble exopolysaccharides (EPS) matrix that facilitates biofilm initiation. Moreover, agents that inhibit the enzymatic activity of Gtfs in solution often have reduced or no effects on surface-adsorbed Gtfs. This study elucidated the mechanisms responsible for the differences in functionality that GtfB exhibits in solution vs surface-adsorbed. Upon adsorption to planar fused-quartz substrates, GtfB displayed a 37% loss of helices and 36% increase of β-sheets, as determined by circular dichroism (CD) spectroscopy, and surface-induced conformational changes were more severe on substrates modified with CH3- and NH2-terminated self-assembled monolayers. GtfB also underwent substantial conformation changes when adsorbing to hydroxyapatite (HA) microspheres, likely due to electrostatic interactions between negatively charged GtfB and positively charged HA crystal faces. Conformational changes were lessened when HA surfaces were coated with saliva (sHA) prior to GtfB adsorption. Furthermore, GtfB remained highly active on sHA, as determined by in situ attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy, producing glucans that were structurally different than GtfB in solution and known to increase the accumulation and virulence of biofilms. Our data provide the first insight into the structural underpinnings governing Gtf conformation and enzymatic function that occur on tooth surfaces in vivo, which may lead to designing potent new inhibitors and improved strategies to combat the formation of pathogenic oral biofilms

Supplemental File 3 from Proteomic comparison of the organic matrices from parietal and base plate of the acorn barnacle Amphibalanus amphitrite

Differential abundance analysis results tabulated for cement proteins

Supplemental File 5 from Proteomic comparison of the organic matrices from parietal and base plate of the acorn barnacle Amphibalanus amphitrite

Supplemental File 5.xls

Supplemental File 2 from Proteomic comparison of the organic matrices from parietal and base plate of the acorn barnacle Amphibalanus amphitrite

Inventory of protein abundance measurements, dataset-wide, as calculated by MaxQuant