A proteome analysis of the subcutaneous gel in avian hatchlings

A proteomic approach to identify seminal plasma proteins in roosters (Gallus gallus domesticus)

Considering the interest in avian semen processing and storage, the objective of this study was to identify the domestic fowl seminal plasma proteins using two-dimensional gel electrophoresis (2-DE) and mass spectrometry MS/MS. For three times in a 4-month period, seminal plasma was obtained from semen collected from four local male chickens (Gallus gallus domesticus) and prepared for two-dimensional polyacrylamide gel electrophoresis. A total of 83 spots were detected across all gels and analyzed by MALDI-TOF/TOF. Among these spots, 17 have been successfully identified. The most intensely stained spots were recognized as serum albumin, ovotransferrin, alpha-enolase, fatty acid binding protein, thioredoxin, trypsin inhibitor CITI-1 and gallinacin-9. From these proteins, two are characteristic of avian seminal plasma, the ovotransferrin and gallinacin-9, and one is specific of the Gallus species, the chicken trypsin inhibitor CITI-1.

Mapping the extracellular and membrane proteome associated with the vasculature and the stroma in the embryo

In order to map the extracellular or membrane proteome associated with the vasculature and the stroma in an embryonic organism in vivo, we developed a biotinylation technique for chicken embryo and combined it with mass spectrometry and bioinformatic analysis. We also applied this procedure to implanted tumors growing on the chorioallantoic membrane or after the induction of granulation tissue. Membrane and extracellular matrix proteins were the most abundant components identified. Relative quantitative analysis revealed differential protein expression patterns in several tissues. Through a bioinformatic approach, we determined endothelial cell protein expression signatures, which allowed us to identify several proteins not yet reported to be associated with endothelial cells or the vasculature. This is the first study reported so far that applies in vivo biotinylation, in combination with robust label-free quantitative proteomics approaches and bioinformatic analysis, to an embryonic organism. It also provides the first description of the vascular and matrix proteome of the embryo that might constitute the starting point for further developments.

Functional genomics of the chicken--a model organism

Since the sequencing of the genome and the development of high-throughput tools for the exploration of functional elements of the genome, the chicken has reached model organism status. Functional genomics focuses on understanding the function and regulation of genes and gene products on a global or genome-wide scale. Systems biology attempts to integrate functional information derived from multiple high-content data sets into a holistic view of all biological processes within a cell or organism. Generation of a large collection ( approximately 600K) of chicken expressed sequence tags, representing most tissues and developmental stages, has enabled the construction of high-density microarrays for transcriptional profiling. Comprehensive analysis of this large expressed sequence tag collection and a set of approximately 20K full-length cDNA sequences indicate that the transcriptome of the chicken represents approximately 20,000 genes. Furthermore, comparative analyses of these sequences have facilitated functional annotation of the genome and the creation of several bioinformatic resources for the chicken. Recently, about 20 papers have been published on transcriptional profiling with DNA microarrays in chicken tissues under various conditions. Proteomics is another powerful high-throughput tool currently used for examining the dynamics of protein expression in chicken tissues and fluids. Computational analyses of the chicken genome are providing new insight into the evolution of gene families in birds and other organisms. Abundant functional genomic resources now support large-scale analyses in the chicken and will facilitate identification of transcriptional mechanisms, gene networks, and metabolic or regulatory pathways that will ultimately determine the phenotype of the bird. New technologies such as marker-assisted selection, transgenics, and RNA interference offer the opportunity to modify the phenotype of the chicken to fit defined production goals. This review focuses on functional genomics in the chicken and provides a road map for large-scale exploration of the chicken genome.

Avian proteomics: advances, challenges and new technologies

Proteomics is defined as an analysis of the full complement of proteins of a cell or tissue under given conditions. Avian proteomics, or more specifically chicken proteomics, has focussed on the study of individual tissues and organs of interest to specific researchers. Researchers have looked at skeletal muscle and growth, and embryonic development and have performed initial studies in avian disease. Traditional proteomics involves identifying and cataloguing proteins in a cell and identifying relative changes in populations between two or more states, be that physiological or disease-induced states. Recent advances in proteomic technologies have included absolute quantification, proteome simplification and the ability to determine the turnover of individual proteins in a global context. This review discusses the current developments in this relatively new field, new technologies and how they may be applied to biological questions, and the challenges faced by researchers in this ever-expanding and exciting field.

Absolute multiplexed quantitative analysis of protein expression during muscle development using QconCAT

Stable isotope-labeled proteotypic peptides are used as surrogate standards for absolute quantification of proteins in proteomics. However, a stable isotope-labeled peptide has to be synthesized, at relatively high cost, for each protein to be quantified. To multiplex protein quantification, we developed a method in which gene design de novo is used to create and express artificial proteins (QconCATs) comprising a concatenation of proteotypic peptides. This permits absolute quantification of multiple proteins in a single experiment. This complete study was constructed to define the nature, sources of error, and statistical behavior of a QconCAT analysis. The QconCAT protein was designed to contain one tryptic peptide from 20 proteins present in the soluble fraction of chicken skeletal muscle. Optimized DNA sequences encoding these peptides were concatenated and inserted into a vector for high level expression in Escherichia coli. The protein was expressed in a minimal medium containing amino acids selectively labeled with stable isotopes, creating an equimolar series of uniformly labeled proteotypic peptides. The labeled QconCAT protein, purified by affinity chromatography and quantified, was added to a homogenized muscle preparation in a known amount prior to proteolytic digestion with trypsin. As anticipated, the QconCAT was completely digested at a rate far higher than the analyte proteins, confirming the applicability of such artificial proteins for multiplexed quantification. The nature of the technical variance was assessed and compared with the biological variance in a complete study. Alternative ionization and mass spectrometric approaches were investigated, particularly LC-ESI-TOF MS and MALDI-TOF MS, for analysis of proteins and tryptic peptides. QconCATs offer a new and efficient approach to precise and simultaneous absolute quantification of multiple proteins, subproteomes, or even entire proteomes.

Serum protein pattern during cow pregnancy: Acute-phase proteins increase in the peripartum period

Serum collected in a time-course mode during the pregnancy of a group of heifers was analyzed by 2-DE under various experimental conditions to optimize resolution of all protein spots. Changes in the levels of some components were detected during the last phase of pregnancy and early postpartum. These included a decrease of alpha2-HS-glycoprotein, an increase of alpha1-antichymotrypsin and, with a much larger and more abrupt variation, of orosomucoid and haptoglobin. These findings associate the weeks preceding calving with an acute-phase reaction. Analysis of individual animal's sera by 1-DE demonstrated a higher level of orosomucoid in the sera of cows developing postpartum endometritis during the 2 wk after calving (i.e., in the course of the infection) but a lower level during the 2 wk before calving. This observation could represent an important tool for the prepartum detection of animals prone to develop postpartum endometritis and lead to a more accurate peripartum management of those animals.

Proteome dynamics in complex organisms: Using stable isotopes to monitor individual protein turnover rates

The complete definition of changes in a proteome requires information about dynamics and specifically the rate at which the individual proteins are turned over intracellularly. Whilst this can be achieved in single-cell culture using stable isotope precursors, it is more challenging to develop methods for intact animals. In this study, we show how dietary administration of stable isotope-labelled amino acids can obtain information on the relative rates of synthesis and degradation of individual proteins in a proteome. The pattern of stable isotope-labelling in tryptic peptides can be deconstructed to yield a highly reliable measure of the isotope abundance of the precursor pool, a parameter that is often difficult to acquire. We demonstrate this approach using chickens fed a semisynthetic diet containing [(2)H(8)]valine at a calculated relative isotope abundance (RIA) of 0.5. When the labelling pattern of gel-resolved muscle proteins was analyzed, the intracellular precursor isotope abundance was 0.35, consistent with dilution of the amino acid precursor pool with unlabelled amino acids derived from degradation of pre-existing proteins. However, the RIA was stable over an extended labelling window, and permitted calculation of the rates of synthesis and degradation of individual proteins isolated by gel electrophoresis. For the first time, it is feasible to contemplate the analysis of turnover of individual proteins in intact animals.