Literature DB >> 18465893

Protein disorder is positively correlated with gene expression in Escherichia coli.

Oleg Paliy1, Shawn M Gargac, Yugong Cheng, Vladimir N Uversky, A Keith Dunker.   

Abstract

We considered, on a global scale, the relationship between the predicted fraction of protein disorder and the RNA and protein expression in Escherichia coli. Fraction of protein disorder correlated positively with both measured RNA expression levels of E. coli genes in three different growth media and with predicted abundance levels of E. coli proteins. Though weak, the correlation was highly significant. Correlation of protein disorder with RNA expression did not depend on the growth rate of E. coli cultures and was not caused by a small subset of genes showing exceptionally high concordance in their disorder and expression levels. Global analysis was complemented by detailed consideration of several groups of proteins.

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Year:  2008        PMID: 18465893      PMCID: PMC2754758          DOI: 10.1021/pr800055r

Source DB:  PubMed          Journal:  J Proteome Res        ISSN: 1535-3893            Impact factor:   4.466


  124 in total

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Journal:  Nat Struct Biol       Date:  1999-07

2.  Crystal structure of Skp, a prefoldin-like chaperone that protects soluble and membrane proteins from aggregation.

Authors:  Troy A Walton; Marcelo C Sousa
Journal:  Mol Cell       Date:  2004-08-13       Impact factor: 17.970

Review 3.  Flexible nets. The roles of intrinsic disorder in protein interaction networks.

Authors:  A Keith Dunker; Marc S Cortese; Pedro Romero; Lilia M Iakoucheva; Vladimir N Uversky
Journal:  FEBS J       Date:  2005-10       Impact factor: 5.542

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Authors:  J Adler; B Templeton
Journal:  J Gen Microbiol       Date:  1967-02

5.  Phosphoenolpyruvate-dependent protein kinase enzyme I of Streptococcus faecalis: purification and properties of the enzyme and characterization of its active center.

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Journal:  Biochemistry       Date:  1985-02-12       Impact factor: 3.162

6.  The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.

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Journal:  Nucleic Acids Res       Date:  1987-02-11       Impact factor: 16.971

7.  Sugar transport by the bacterial phosphotransferase system. Isolation and characterization of enzyme I from Salmonella typhimurium.

Authors:  N Weigel; E B Waygood; M A Kukuruzinska; A Nakazawa; S Roseman
Journal:  J Biol Chem       Date:  1982-12-10       Impact factor: 5.157

8.  Investigation of the local structure and dynamics of the H subunit of the mitochondrial glycine decarboxylase using heteronuclear NMR spectroscopy.

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Journal:  Biochemistry       Date:  1999-06-29       Impact factor: 3.162

9.  Acetyl CoA carboxylase: isolation and characterization of native biotin carboxyl carrier protein.

Authors:  R R Fall; A M Nervi; A W Alberts; P R Vagelos
Journal:  Proc Natl Acad Sci U S A       Date:  1971-07       Impact factor: 11.205

10.  Conformational studies of the interdomain linker peptides in the dihydrolipoyl acetyltransferase component of the pyruvate dehydrogenase multienzyme complex of Escherichia coli.

Authors:  J D Green; R N Perham; S J Ullrich; E Appella
Journal:  J Biol Chem       Date:  1992-11-25       Impact factor: 5.157

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  16 in total

Review 1.  Understanding protein non-folding.

Authors:  Vladimir N Uversky; A Keith Dunker
Journal:  Biochim Biophys Acta       Date:  2010-02-01

2.  Inactivation of the bacterial RNA polymerase due to acquisition of secondary structure by the ω subunit.

Authors:  Paramita Sarkar; Abhijit A Sardesai; Katsuhiko S Murakami; Dipankar Chatterji
Journal:  J Biol Chem       Date:  2013-07-10       Impact factor: 5.157

3.  Cross-linking measurements of in vivo protein complex topologies.

Authors:  Chunxiang Zheng; Li Yang; Michael R Hoopmann; Jimmy K Eng; Xiaoting Tang; Chad R Weisbrod; James E Bruce
Journal:  Mol Cell Proteomics       Date:  2011-06-22       Impact factor: 5.911

4.  Expanding the proteome: disordered and alternatively folded proteins.

Authors:  H Jane Dyson
Journal:  Q Rev Biophys       Date:  2011-07-01       Impact factor: 5.318

5.  Tyrosine phosphorylation-dependent localization of TmaR that controls activity of a major bacterial sugar regulator by polar sequestration.

Authors:  Tamar Szoke; Nitsan Albocher; Sutharsan Govindarajan; Anat Nussbaum-Shochat; Orna Amster-Choder
Journal:  Proc Natl Acad Sci U S A       Date:  2021-01-12       Impact factor: 11.205

Review 6.  Physicochemical properties of cells and their effects on intrinsically disordered proteins (IDPs).

Authors:  Francois-Xavier Theillet; Andres Binolfi; Tamara Frembgen-Kesner; Karan Hingorani; Mohona Sarkar; Ciara Kyne; Conggang Li; Peter B Crowley; Lila Gierasch; Gary J Pielak; Adrian H Elcock; Anne Gershenson; Philipp Selenko
Journal:  Chem Rev       Date:  2014-06-05       Impact factor: 60.622

7.  Comparative proteome analysis of Helicobacter pylori clinical strains by two-dimensional gel electrophoresis.

Authors:  Ya-nan Zhang; Shi-gang Ding; Liu-huan Huang; Jing Zhang; Yan-yan Shi; Li-jun Zhong
Journal:  J Zhejiang Univ Sci B       Date:  2011-10       Impact factor: 3.066

8.  Cellular proteomes have broad distributions of protein stability.

Authors:  Kingshuk Ghosh; Ken Dill
Journal:  Biophys J       Date:  2010-12-15       Impact factor: 4.033

9.  When a domain is not a domain, and why it is important to properly filter proteins in databases: conflicting definitions and fold classification systems for structural domains make filtering of such databases imperative.

Authors:  Clare-Louise Towse; Valerie Daggett
Journal:  Bioessays       Date:  2012-10-26       Impact factor: 4.345

10.  Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression data.

Authors:  Yvonne J K Edwards; Anna E Lobley; Melissa M Pentony; David T Jones
Journal:  Genome Biol       Date:  2009-05-11       Impact factor: 13.583

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