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Exploring the functional complexity of cellular proteins by protein knockout.

ABSTRACT: Comprehensive dissection of protein functions entails more complicated manipulations than simply eliminating the protein of interest. Established knockdown technologies, such as RNA interference, antisense oligodeoxynucleotides, or ribozymes, are limited for specific applications such as modulating protein levels or specific targeting of a posttranslationally modified subpopulation. Here we show that the engineered Skp1, Cullin 1, and F-box-containing betaTrCP substrate receptor ubiquitin-proteolytic system, designated protein knockout, could achieve not only total elimination but also rapid and systematic reduction of a given cellular protein. Stable expression of a single engineered betaTrCP demonstrated simultaneous and sustained degradation of the entire retinoblastoma family proteins. Furthermore, the engineered betaTrCP was capable of selecting hypo- but not hyperphosphorylated forms of retinoblastoma for degradation. The engineered betaTrCP has been extensively modified to increase its specificity in substrate selection. This optimized protein-knockout system offers a powerful and versatile proteomic tool to dissect diverse functional properties of cellular proteins in somatic cells.

SUBMITTER: Zhang J

PROVIDER: S-EPMC283557 | biostudies-literature | 2003 Nov

REPOSITORIES: biostudies-literature

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Exploring the functional complexity of cellular proteins by protein knockout.

Zhang Jianxuan J Zheng Ning N Zhou Pengbo P

Proceedings of the National Academy of Sciences of the United States of America 20031030 24

Comprehensive dissection of protein functions entails more complicated manipulations than simply eliminating the protein of interest. Established knockdown technologies, such as RNA interference, antisense oligodeoxynucleotides, or ribozymes, are limited for specific applications such as modulating protein levels or specific targeting of a posttranslationally modified subpopulation. Here we show that the engineered Skp1, Cullin 1, and F-box-containing betaTrCP substrate receptor ubiquitin-proteo ...[more]

PMID: 14593203

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Project description:Background:In both prokaryotic and eukaryotic proteins, repeated occurrence of a single or a group of few amino acids are found. These regions are termed as low complexity regions (LCRs). It has been observed that amino acid bias in LCR is directly linked to their uncontrolled expansion and amyloid formation. But a comparative analysis of the behavior of LCR based on their constituent amino acids and their association with amyloidogenic propensity is not available. Methods:Firstly we grouped all LCRs on the basis of their composition: homo-polymers, positively charged amino acids, negatively charged amino acids, polar amino acids and hydrophobic amino acids. We analyzed the compositional pattern of LCRs in each group and their propensity to form amyloids. The functional characteristics of proteins containing different groups of LCRs were explored using DAVID. In addition, we also analyzed the classes, pathways and functions of human proteins that form amyloids in LCRs. Results:Among homopolymeric LCRs, the most common was Gln repeats. LCRs composed of repeats of Met and aromatic amino acids were amongst the least occurring. The results revealed that LCRs composed of negatively charged and polar amino acids were more common in comparison to LCRs formed by positively charged and hydrophobic amino acids. We also noted that generally proteins with LCRs were involved in transcription but those with Gly repeats were associated to translational activities. Our analysis suggests that proteins in which LCR is composed of hydrophobic residues are more prone toward amyloid formation. We also found that the human proteins with amyloid forming LCRs were generally involved in binding and catalytic activity. Discussion:The presented analysis summarizes the most common and least occurring LCRs in proteins. Our results show that though repeats of Gln are the most abundant but Asn repeats make longest stretch of low complexity. The results showed that potential of LCRs to form amyloids varies with their amino acid composition.

Dataset Information

Exploring the functional complexity of cellular proteins by protein knockout.

Publications

Exploring the functional complexity of cellular proteins by protein knockout.

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