sampling-human-indigenous-saliva-peptidome-using-lollipop-like

Sampling Human Indigenous Saliva Peptidome Using a Lollipop-Like Ultrafiltration Probe: Simplify and Enhance Peptide Detection for Clinical Mass Spectrometry

Although human saliva proteome and peptidome have been revealed 1-2 they were majorly identified from tryptic digests of saliva proteins. Identification ...

Sanford-Burnham Medical Research Institute

The gamma-proteobacterium Shewanella oneidensis strain MR-1 is a metabolically versatile organism that can reduce a wide range of organic compounds, metal ions, and radionuclides. Similar to most other sequenced organisms, approximately 40% of the predicted ORFs in the S. oneidensis genome were annotated as uncharacterized "hypothetical" genes. We implemented an integrative approach by using experimental and computational analyses to provide more detailed insight into gene function. Global expression profiles were determined for cells after UV irradiation and under aerobic and suboxic growth conditions. Transcriptomic and proteomic analyses confidently identified 538 hypothetical genes as expressed in S. oneidensis cells both as mRNAs and proteins (33% of all predicted hypothetical proteins). Publicly available analysis tools and databases and the expression data were applied to improve the annotation of these genes. The annotation results were scored by using a seven-category schema that ranked both confidence and precision of the functional assignment. We were able to identify homologs for nearly all of these hypothetical proteins (97%), but could confidently assign exact biochemical functions for only 16 proteins (category 1; 3%). Altogether, computational and experimental evidence provided functional assignments or insights for 240 more genes (categories 2-5; 45%). These functional annotations advance our understanding of genes involved in vital cellular processes, including energy conversion, ion transport, secondary metabolism, and signal transduction. We propose that this integrative approach offers a valuable means to undertake the enormous challenge of characterizing the rapidly growing number of hypothetical proteins with each newly sequenced genome.

Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations.

Most known organisms encode proteases that are crucial for constitutive proteolytic events. In the present paper, we describe a method to define these events in proteomes from Escherichia coli to humans. The method takes advantage of specific N-terminal biotinylation of protein samples, followed by affinity enrichment and conventional LC (liquid chromatography)-MS/MS (tandem mass spectrometry) analysis. The method is simple, uses conventional and easily obtainable reagents, and is applicable to most proteomics facilities. As proof of principle, we demonstrate profiles of proteolytic events that reveal exquisite in vivo specificity of methionine aminopeptidase in E. coli and unexpected processing of mitochondrial transit peptides in yeast, mouse and human samples. Taken together, our results demonstrate how to rapidly distinguish real proteolysis that occurs in vivo from the predictions based on in vitro experiments.

Article	Year
Journal of chromatography. A\| PubMed ID: 12613842	2003
Electrophoresis\| PubMed ID: 12652583	2003
Proteomics\| PubMed ID: 12748955	2003
Journal of proteome research\| PubMed ID: 15253435	2004
Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 15684069	2005
Science (New York, N.Y.)\| PubMed ID: 15790858	2005
Electrophoresis\| PubMed ID: 16315175	2005
Proteomics\| PubMed ID: 16342140	2006
Biochimica et biophysica acta\| PubMed ID: 16797259	2006
Profiling constitutive proteolytic events in vivo. The Biochemical journal\| PubMed ID: 17650073	2007
Proteomics\| PubMed ID: 17994620	2007
Proteomics\| PubMed ID: 18022937	2007
Proteomics\| PubMed ID: 18651708	2008
The Biochemical journal\| PubMed ID: 19232058	2009
PloS one\| PubMed ID: 19352504	2009
Combinatorial chemistry & high throughput screening\| PubMed ID: 19519332	2009
Nature structural & molecular biology\| PubMed ID: 19767749	2009
Journal of biomedicine & biotechnology\| PubMed ID: 19911078	2010
Vaccine\| PubMed ID: 20189489	2010
The Journal of biological chemistry\| PubMed ID: 20605791	2010
The Journal of biological chemistry\| PubMed ID: 20837484	2010
Vaccine\| PubMed ID: 21354482	2011
Journal of proteome research\| PubMed ID: 21366352	2011
The FEBS journal\| PubMed ID: 21752195	2011
The Journal of biological chemistry\| PubMed ID: 22496445	2012

Wenhong Zhu

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