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Comprehensive and quantitative proteomic analyses of zebrafish plasma reveals conserved protein profiles between genders and between zebrafish and human.

Li C, Tan XF, Lim TK, Lin Q, Gong Z - Sci Rep (2016)

Bottom Line: The types of plasma proteins based on IPA (Ingenuity Pathway Analysis) classification and tissue sources of production were also very similar.Furthermore, the zebrafish plasma proteome shares significant similarities with human plasma proteome, in particular in top abundant proteins including apolipoproteins and complements.Thus, the current study provided a valuable dataset for future evaluation of plasma proteins in zebrafish.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, National University of Singapore, Singapore 117543.

ABSTRACT
Omic approaches have been increasingly used in the zebrafish model for holistic understanding of molecular events and mechanisms of tissue functions. However, plasma is rarely used for omic profiling because of the technical challenges in collecting sufficient blood. In this study, we employed two mass spectrometric (MS) approaches for a comprehensive characterization of zebrafish plasma proteome, i.e. conventional shotgun liquid chromatography-tandem mass spectrometry (LC-MS/MS) for an overview study and quantitative SWATH (Sequential Window Acquisition of all THeoretical fragment-ion spectra) for comparison between genders. 959 proteins were identified in the shotgun profiling with estimated concentrations spanning almost five orders of magnitudes. Other than the presence of a few highly abundant female egg yolk precursor proteins (vitellogenins), the proteomic profiles of male and female plasmas were very similar in both number and abundance and there were basically no other highly gender-biased proteins. The types of plasma proteins based on IPA (Ingenuity Pathway Analysis) classification and tissue sources of production were also very similar. Furthermore, the zebrafish plasma proteome shares significant similarities with human plasma proteome, in particular in top abundant proteins including apolipoproteins and complements. Thus, the current study provided a valuable dataset for future evaluation of plasma proteins in zebrafish.

No MeSH data available.


Characteristics of plasma protein composition.(A–C) GO distribution of plasma proteins based on number of protein entries (left) and protein abundance (right) in both genders as indicated. GO annotation was retrieved for a total of 791 unique UniProt entries of zebrafish plasma proteins. Categories of GO are: Biological Process (A), Cellular Component (B) and Molecular Function (C). (D) Comparison of types of plasma proteins between the two genders as classified by IPA.
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f2: Characteristics of plasma protein composition.(A–C) GO distribution of plasma proteins based on number of protein entries (left) and protein abundance (right) in both genders as indicated. GO annotation was retrieved for a total of 791 unique UniProt entries of zebrafish plasma proteins. Categories of GO are: Biological Process (A), Cellular Component (B) and Molecular Function (C). (D) Comparison of types of plasma proteins between the two genders as classified by IPA.

Mentions: To obtain an overview of the biological functions of these plasma proteins, Gene ontology (GO) annotations were retrieved using software STRAP. Combining proteins detected in both genders, a total of 795 Uniprot IDs were obtained. GO distributions for Biological Process, Cellular Component and Molecular Function are presented in Fig. 2A–C. Female and male plasma shared very similar distribution patterns. Top terms in Biological Process were Regulation (~25%), Cellular process (~25%), Localization (~10%), Metabolic process (~10%) and Developmental process (~10%). However, in term of protein abundance, Localization (~30% in female and ~40% in male) and Metabolic process (~25% in female and ~35% in male) were the two largest categories. For Cellular Component, the top term was Extracellular (~30% in female and 40% in male). Interestingly, a significant portion of the proteins was found to be in the cytoplasm (~10%), nucleus (~10%), and plasma membrane (~7–8%), while a small portion was from mitochondria, chromosome, endoplamic reticulum and endosome (~0.8–2%). These indicate that zebrafish plasma contained many cellular proteins that probably leaked from different tissues. As expected, in term of protein abundance, Extracellular proteins are predominant in both females (~40%) and males (~60%). For Molecular Function, most plasma proteins fell in the categories of Binding (~45%) and Catalytic activity (~30%), with a small percentage of proteins in the category of Enzyme regulator activity (~7% in female and 8% in male), Molecular transducer activity (~2% in female and ~1% in male) and Antioxidant activity (~1% in female and 0.5% in male). If protein abundance is taken into consideration, higher protein contents were attributed to Binding for Molecular function (Fig. 2C).


Comprehensive and quantitative proteomic analyses of zebrafish plasma reveals conserved protein profiles between genders and between zebrafish and human.

Li C, Tan XF, Lim TK, Lin Q, Gong Z - Sci Rep (2016)

Characteristics of plasma protein composition.(A–C) GO distribution of plasma proteins based on number of protein entries (left) and protein abundance (right) in both genders as indicated. GO annotation was retrieved for a total of 791 unique UniProt entries of zebrafish plasma proteins. Categories of GO are: Biological Process (A), Cellular Component (B) and Molecular Function (C). (D) Comparison of types of plasma proteins between the two genders as classified by IPA.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4829857&req=5

f2: Characteristics of plasma protein composition.(A–C) GO distribution of plasma proteins based on number of protein entries (left) and protein abundance (right) in both genders as indicated. GO annotation was retrieved for a total of 791 unique UniProt entries of zebrafish plasma proteins. Categories of GO are: Biological Process (A), Cellular Component (B) and Molecular Function (C). (D) Comparison of types of plasma proteins between the two genders as classified by IPA.
Mentions: To obtain an overview of the biological functions of these plasma proteins, Gene ontology (GO) annotations were retrieved using software STRAP. Combining proteins detected in both genders, a total of 795 Uniprot IDs were obtained. GO distributions for Biological Process, Cellular Component and Molecular Function are presented in Fig. 2A–C. Female and male plasma shared very similar distribution patterns. Top terms in Biological Process were Regulation (~25%), Cellular process (~25%), Localization (~10%), Metabolic process (~10%) and Developmental process (~10%). However, in term of protein abundance, Localization (~30% in female and ~40% in male) and Metabolic process (~25% in female and ~35% in male) were the two largest categories. For Cellular Component, the top term was Extracellular (~30% in female and 40% in male). Interestingly, a significant portion of the proteins was found to be in the cytoplasm (~10%), nucleus (~10%), and plasma membrane (~7–8%), while a small portion was from mitochondria, chromosome, endoplamic reticulum and endosome (~0.8–2%). These indicate that zebrafish plasma contained many cellular proteins that probably leaked from different tissues. As expected, in term of protein abundance, Extracellular proteins are predominant in both females (~40%) and males (~60%). For Molecular Function, most plasma proteins fell in the categories of Binding (~45%) and Catalytic activity (~30%), with a small percentage of proteins in the category of Enzyme regulator activity (~7% in female and 8% in male), Molecular transducer activity (~2% in female and ~1% in male) and Antioxidant activity (~1% in female and 0.5% in male). If protein abundance is taken into consideration, higher protein contents were attributed to Binding for Molecular function (Fig. 2C).

Bottom Line: The types of plasma proteins based on IPA (Ingenuity Pathway Analysis) classification and tissue sources of production were also very similar.Furthermore, the zebrafish plasma proteome shares significant similarities with human plasma proteome, in particular in top abundant proteins including apolipoproteins and complements.Thus, the current study provided a valuable dataset for future evaluation of plasma proteins in zebrafish.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, National University of Singapore, Singapore 117543.

ABSTRACT
Omic approaches have been increasingly used in the zebrafish model for holistic understanding of molecular events and mechanisms of tissue functions. However, plasma is rarely used for omic profiling because of the technical challenges in collecting sufficient blood. In this study, we employed two mass spectrometric (MS) approaches for a comprehensive characterization of zebrafish plasma proteome, i.e. conventional shotgun liquid chromatography-tandem mass spectrometry (LC-MS/MS) for an overview study and quantitative SWATH (Sequential Window Acquisition of all THeoretical fragment-ion spectra) for comparison between genders. 959 proteins were identified in the shotgun profiling with estimated concentrations spanning almost five orders of magnitudes. Other than the presence of a few highly abundant female egg yolk precursor proteins (vitellogenins), the proteomic profiles of male and female plasmas were very similar in both number and abundance and there were basically no other highly gender-biased proteins. The types of plasma proteins based on IPA (Ingenuity Pathway Analysis) classification and tissue sources of production were also very similar. Furthermore, the zebrafish plasma proteome shares significant similarities with human plasma proteome, in particular in top abundant proteins including apolipoproteins and complements. Thus, the current study provided a valuable dataset for future evaluation of plasma proteins in zebrafish.

No MeSH data available.