Catarina Franco

Mass spectrometry and animal science: Protein identification strategies and particularities of farm animal species ☆

Proteomic approaches are gaining increasing importance in the context of all fields of animal and veterinary sciences, including physiology, productive characterization, and disease/parasite tolerance, among others. Proteomic studies mainly aim the proteome characterization of a certain organ, tissue, cell type or organism, either in a specific condition or comparing protein differential expression within two or more selected situations. Due to the high complexity of samples, usually total protein extracts, proteomics relies heavily on separation procedures, being 2D-electrophoresis and HPLC the most common, as well as on protein identification using mass spectrometry (MS) based methodologies. Despite the increasing importance of MS in the context of animal and veterinary science studies, the usefulness of such tools is still poorly perceived by the animal science community. This is primarily due to the limited knowledge on mass spectrometry by animal scientists. Additionally, confidence and success in protein identification is hindered by the lack of information in public databases for most of farm animal species and their pathogens, with the exception of cattle (Bos taurus), pig (Sus scrofa) and chicken (Gallus gallus). In this article, we will briefly summarize the main methodologies available for protein identification using mass spectrometry providing a case study of specific applications in the field of animal science. We will also address the difficulties inherent to protein identification using MS, with particular reference to experiments using animal species poorly described in public databases. Additionally, we will suggest strategies to increase the rate of successful identifications when working with farm animal species.

First Insights into the Biochemistry of Tube Foot Adhesive from the Sea Urchin Paracentrotus lividus (Echinoidea, Echinodermata)

Sea urchins are common inhabitants of wave-swept shores. To withstand the action of waves, they rely on highly specialized independent adhesive organs, the adoral tube feet. The latter are extremely well-designed for temporary adhesion being composed by two functional subunits: (1) an apical disc that produces an adhesive secretion to fasten the sea urchin to the substratum, as well as a deadhesive secretion to allow the animal to move and (2) a stem that bears the tensions placed on the animal by hydrodynamism. Despite their technological potential for the development of new biomimetic underwater adhesives, very little is known about the biochemical composition of sea urchin adhesives. A characterization of sea urchin adhesives is presented using footprints. The latter contain inorganic residues (45.5%), proteins (6.4%), neutral sugars (1.2%), and lipids (2.5%). Moreover, the amino acid composition of the soluble protein fraction revealed a bias toward six amino acids: glycine, alanine, valine, serine, threonine, and asparagine/aspartic acid, which comprise 56.8% of the total residues. In addition, it also presents higher levels of proline (6.8%) and half-cystine (2.6%) than average eukaryotic proteins. Footprint insolubility was partially overcome using strong denaturing and reducing buffers, enabling the visualization of 13 proteins by sodium dodecyl sulfate polyacrylamide gel electrophoresis. The conjugation of mass spectrometry with homology–database search allowed the identification of six proteins: alpha and beta tubulin, actin, and histones H2B, H3, H2A, and H4, whose location and function in the adhesive are discussed but require further investigation. For the remaining unidentified proteins, five de novo-generated peptide sequences were found that were not present in the available protein databases, suggesting that they might be novel or modified proteins.

Changes in mouse whole saliva soluble proteome induced by tannin-enriched diet

BackgroundPrevious studies suggested that dietary tannin ingestion may induce changes in mouse salivary proteins in addition to the primarily studied proline-rich proteins (PRPs). The aim of the present study was to determine the protein expression changes induced by condensed tannin intake on the fraction of mouse whole salivary proteins that are unable to form insoluble tannin-protein complexes. Two-dimensional polyacrylamide gel electrophoresis protein separation was used, followed by protein identification by mass spectrometry.ResultsFifty-seven protein spots were excised from control group gels, and 21 different proteins were identified. With tannin consumption, the expression levels of one α-amylase isoform and one unidentified protein increased, whereas acidic mammalian chitinase and Muc10 decreased. Additionally, two basic spots that stained pink with Coomassie Brilliant Blue R-250 were newly observed, suggesting that some induced PRPs may remain uncomplexed or form soluble complexes with tannins.ConclusionThis proteomic analysis provides evidence that other salivary proteins, in addition to tannin-precipitating proteins, are affected by tannin ingestion. Changes in the expression levels of the acidic mammalian chitinase precursor and in one of the 14 salivary α-amylase isoforms underscores the need to further investigate their role in tannin ingestion.

Exploring the proteome of an echinoderm nervous system: 2‐DE of the sea star radial nerve cord and the synaptosomal membranes subproteome

We describe the first proteomic characterization of the radial nerve cord (RNC) of an echinoderm, the sea star Marthasterias glacialis. The combination of 2‐DE with MS (MALDI‐TOF/TOF) resulted in the identification of 286 proteins in the RNC. Additionally, 158 proteins were identified in the synaptosomal membranes enriched fraction after 1‐DE separation. The 2‐DE RNC reference map is available via the WORLD‐2DPAGE Portal (http://www.expasy.ch/world‐2dpage/) along with the associated protein identification data which are also available in the PRIDE database. The identified proteins constitute the first high‐throughput evidence that seems to indicate that echinoderms nervous transmission relies primarily on chemical synapses which is similar to the synaptic activity in adult mammals spinal cord. Furthermore, several homologous proteins known to participate in the regeneration events of other organisms were also identified, and thus can be used as targets for future studies aiming to understand the poorly uncharacterized regeneration capability of echinoderms. This “echinoderm missing link” is also a contribution to unravel the mystery of deuterostomian CNS evolution.

Characterisation of Zea mays L. plastidial transglutaminase: interactions with thylakoid membrane proteins

Chloroplast transglutaminase (chlTGase) activity is considered to play a significant role in response to a light stimulus and photo-adaptation of plants, but its precise function in the chloroplast is unclear. The characterisation, at the proteomic level, of the chlTGase interaction with thylakoid proteins and demonstration of its association with photosystem II (PSII) protein complexes was accomplished with experiments using maize thylakoid protein extracts. By means of a specific antibody designed against the C-terminal sequence of the maize TGase gene product, different chlTGase forms were immunodetected in thylakoid membrane extracts from three different stages of maize chloroplast differentiation. These bands co-localised with those of lhcb 1, 2 and 3 antenna proteins. The most significant, a 58 kDa form present in mature chloroplasts, was characterised using biochemical and proteomic approaches. Sequential fractionation of thylakoid proteins from light-induced mature chloroplasts showed that the 58 kDa form was associated with the thylakoid membrane, behaving as a soluble or peripheral membrane protein. Two-dimensional gel electrophoresis discriminated, for the first time, the 58-kDa band in two different forms, probably corresponding to the two different TGase cDNAs previously cloned. Electrophoretic separation of thylakoid proteins in native gels, followed by LC-MS mass spectrometry identification of protein complexes indicated that maize chlTGase forms part of a specific PSII protein complex, which includes LHCII, ATPase and pSbS proteins. The results are discussed in relation to the interaction between these proteins and the suggested role of the enzyme in thylakoid membrane organisation and photoprotection.

Proteome characterization of sea star coelomocytes - The innate immune effector cells of echinoderms

Sea star coelomic fluid is in contact with all internal organs, carrying signaling molecules and a large population of circulating cells, the coelomocytes. These cells, also known as echinoderm blood cells, are responsible for the innate immune responses and are also known to have an important role in the first stage of regeneration, i.e. wound closure, necessary to prevent disruption of the body fluid balance and to limit the invasion of pathogens. This study focuses on the proteome characterization of these multifunctional cells. The identification of 358 proteins was achieved using a combination of two techniques for protein separation (1‐D SDS‐PAGE followed by nanoLC and 2‐D SDS‐PAGE) and MALDI‐TOF/TOF MS for protein identification. To our knowledge, the present report represents the first comprehensive list of sea star coelomocyte proteins, constituting an important database to validate many echinoderm‐predicted proteins. Evidence for new pathways in these particular echinoderm cells are also described, and thus representing a valuable resource to stimulate future studies aiming to unravel the homology with vertebrate immune cells and particularly the origins of the immune system itself.

Monitoring virus-like particle and viral protein production by intact cell MALDI-TOF mass spectrometry

A new application of intact cell MALDI-TOF MS (ICM-MS) methodology is described for monitoring the production of viral proteins and viral like particles using the baculovirus/insect cells expression system. Various MALDI matrices, cell preparation methods, cell/matrix volume ratio and MALDI target application procedures were tested in order to obtain the highest intensity and reproducibility of intact insect cell spectra. The web interface, SPECLUST (http://bioinfo.thep.lu.se/speclust.html), was used to construct dendograms based on MALDI-TOF MS data for evaluation of fingerprint changes. We demonstrate that insect cell mass spectrum fingerprints are characteristic of each viral protein/particle production. Their changes along the time for each production experiment correlate with the intracellular viral protein content determined by Western blot. This work shows that this simple, fast and low cost assay, which requires low sample volume, is a powerful analytical tool that complements the most common analytical methods used for monitoring bioprocesses and has potential application in the biotechnological industry namely, in the production of recombinant proteins.

Mapping sea urchins tube feet proteome--a unique hydraulic mechano-sensory adhesive organ.

Marine organisms secrete adhesives for substrate attachment that to be effective require functional assembly underwater and displacement of water, ions, and weakly bound polyions that are ubiquitous in seawater. Therefore, understanding the characteristics of these protein/carbohydrate-based marine adhesives is imperative to decipher marine adhesion and also, to accelerate the development of new biomimetic underwater adhesives and anti-fouling agents. The present study, aims at mapping the proteome of the sea urchin Paracentrotus lividus adhesive organs using a combination of complementary protein separation techniques (1-D-nanoLC and 2-DE), databases and search algorithms. This strategy resulted in the identification of 328 non-redundant proteins, constituting the first comprehensive list of sea urchin tube feet proteins. Given the known importance of phosphorylation and glycosylation in marine adhesion, the 2DE proteome was re-analyzed with specific fluorescent stains for these two PTMs, resulting in the identification of 69 non-redundant proteins. The obtained results demonstrate that tube feet are unique mechano-sensory adhesive organs and highlight putative adhesive proteins, that although requiring further confirmation, constitute a step forward in the quest to decipher sea urchins temporary adhesion.

Sodium dodecyl sulfate-capillary gel electrophoresis analysis of rotavirus-like particles

This work describes the application of a sodium dodecyl sulfate-capillary gel electrophoresis (SDS-CGE) method for the analysis of triple 2/6/7 and double-layered 2/6 rotavirus-like particles (RLPs), candidate vaccines against rotavirus infection. SDS-CGE analysis of RLPs resulted in peaks that could be attributed to the viral proteins (VP2, VP6 and VP7) according to their apparent molecular mass (MWapp). Samples containing the glycoprotein VP7 were analysed after deglycosylation with PNGase F. Upon deglycosylation, VP7 MWapp decreased 4-7kDa consistent with a degree of glycosylation of approximately 12-21%. VP2 was eventually detected in the form of more than one related proteins, despite the small areas due to the relative low mass proportion of this protein in the particle (16%). The effect of analytical parameters such as capillary temperature on method performance was evaluated. MWapp values estimated by SDS-CGE were compared with values obtained by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The method described in this work proved to be fast, consistent and reproducible, representing a feasible alternative to the laborious conventional electrophoresis for the characterization of RLPs.

Understanding regeneration through proteomics

Regeneration is a complex cellular process that, rather than simply forming a scar following injury, the animal forms a new functional tissue. Regeneration is a widespread process among metazoa, although not uniformly. Planaria, starfish, and some worms can regenerate most of their body, whereas many other species can only regenerate parts of specific tissues or fail to accomplish a functional regrowth, as is the case of mammals CNS. Research in regenerative medicine will possibly culminate in the regeneration of organs/tissues originally not prone to this process. Despite the complexity of the interactions and regulatory systems involved, the variety of tissues and organs these cells differentiate into has so far impaired the success of direct transplantation to restore damaged tissues. For this reason, a study, at the molecular level of the regeneration mechanisms developed by different animal models is likely to provide answers to why these processes are not readily activated in mammals. Proteomic‐based approaches are being recognized as extremely useful to study of regeneration events, also because there is a relevant contribution of posttranscriptional processes that involve frequently the occurrence of a broad range of PTMs. The present review focuses on the significant knowledge brought up by proteomics in diverse aspects of regeneration research on different animal models, tissues, and organs.