Probably less than one-tenth of the genes produce only the wild type protein without at least one additional protein isoform in some human cancer cell lines.

Rui Yan,Siqi Liu,Lucas Zellmer,Joshua D Liao,Ju Zhang,Ningzhi Xu,Di Wu,Lichan Chen

doi:10.18632/oncotarget.20015

Abstract

To estimate how many genes produce multiple protein isoforms, we electrophoresed proteins from MCF7 and MDA-MB231 (MB231) human breast cancer cells in SDS-PAGE and excised narrow stripes of the gel at the 48kD, 55kD and 72kD. Proteins in these stripes were identified using liquid chromatography and tandem mass spectrometry. A total of 765, 750 and 679 proteins from MB231 cells, as well as 470, 390 and 490 proteins from MCF7 cells, were identified from the 48kD, 55kD and 72kD stripes, respectively. We arbitrarily allowed a 10% technical variation from the proteins’ theoretical molecular mass (TMM) and considered those proteins with their TMMs within the 43-53 kD, 49-61 kD and 65-79 kD ranges as the wild type (WT) expected from the corresponding stripe, whereas those with a TMM above or below this range as a smaller- or larger-group, respectively. Only 263 (34.4%), 269 (35.9%) and 151 (22.2%) proteins from MB231 cells and 117 (24.9%), 135 (34.6%) and 130 (26.5%) proteins from MCF7 cells from the 48kD, 55kD and 72kD stripes, respectively, belonged to the WT, while the remaining majority belonged to the smaller- or larger-groups. Only about 3-16%, on average about 10% regardless of the stripe and cell line, of the proteins appeared in only one stripe and within the WT range, while the remaining preponderance appeared also in additional stripe(s) or had a larger or smaller TMM. We conclude that few (fewer than 10%) of the human genes produce only the WT protein without additional isoform(s).

Highlights

A large number of genes in the human genome undergo alternative initiation or termination of transcription to generate different RNA transcripts
Results from this sort of top-down approach of LC-MS/MS showed that only one-third to one-fourth of the proteins migrated in SDS-PAGE as anticipated from their theoretical molecular mass (TMM), while the vast rest of the proteins were those with a larger or a smaller TMM
We arbitrarily set a 10% divergence at the left or the right side of the TMM as the allowed variation, which is a lax criterion allowing those proteins with a TMM within the 43-53 kD, 49-61 kD and 65-79 kD ranges to be the wild type (WT), or the expected, in the 48kD, 55kD and 72kD stripes, respectively

Summary

Introduction

A large number of genes in the human genome undergo alternative initiation or termination of transcription to generate different RNA transcripts. One mRNA may be expressed to different protein isoforms via various mechanisms such as use of an alternative start codon or stop codon, as we recently reviewed [2]. Because of these and other mechanisms, in most cases one gene often produces multiple protein isoforms [3, 4], which provides the gene with multiple ways to diversify its functions and in turn allows the cell to be more flexible adapting to the environment. Many proteins appeared in both of the 26kD and 40kD stripes, including some having a much larger or smaller TMM than 26kD or 40kD, indicating that these genes have one or more additional isoforms besides the wild type (WT) protein, i.e. the protein with its TMM expected in the 26 kD or 40kD stripe [12]

Methods

Results

Discussion

Conclusion