Evidence for the existence of hypothetical proteins in human bronchial epithelial, fibroblast, amnion, lymphocyte, mesothelial and kidney cell lines

Abstract

The human genome maybe limited to about 30000 genes whereas the human proteome may be represented by a rough estimate of one million proteins. A legion of proteins have been described and information about these structures are readily available in data banks. There remains, however, a large series of unknown or hypothetical proteins (HPs). Many of them have been predicted from nucleic acid sequences only and are therefore named predicted or HPs. Carrying out "protein hunting" by generating large maps of human cell lines, we aimed to find and identify HPs and provide an analytical tool thereof. Cell lysates from human bronchial epithelial, fibroblast, amnion, lymphocyte, mesothelial and kidney cell lines were prepared and proteins run on two-dimensional gel-electrophoresis (2DE) with in-gel digestion and mass spectrometrical analysis using the MALDI-TOF principle.16 HPs were found in these cell lines and some show cell-specific expressional patterns. HPs belong to several protein classes including structural, signaling, transcriptional/translational, chaperone-related and others. We furthermore provide analytical data i.e. pIs that were often different from predicted values in data banks.A list of HPs has been shown to really exist in several human cell lines thus contributing to knowledge on protein machineries and cascades. Observed and predicted pI values are given representing an analytical tool along with unambiguous identification of protein spots by mass spectrometry independent of antibody availability and specificity thus complementing established methods.

From Nanotechnology to Nanomedicine: Applications to Cancer Research

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Metabolomics in Cardiovascular Disease: Towards Clinical Application

“…Only 2766 metabolites are estimated to be derived from man [Duarte et al, 2007], compared with 31896 genes [http://eugenes.org] and 10 6 different proteins estimated from gene expression, alternative splicing and post-translational modifications [Oh 2004, Goodacre 2007] makes the metabolome relatively simple.…”

Proteomics in renal research

“…Protein maps for the human proximal tubule cell line (HK-2) have been established by 2DE for chaperone proteins (79). In the same cell line, highabundance hypothetical proteins for amino acid transport, cell cycle regulation (MAD1-homolog), cell cycle arrest/proliferation (p38 -2g4 homolog), inorganic phosphatase, and oxidoreductase were identified by 2DE (1,85).…”