Article (Scientific journals)
Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery.
Thiele, Ines; Fleming, Ronan MT; Bordbar, Aarash et al.
2010In Biophysical Journal, 98 (10), p. 2072-81
Peer Reviewed verified by ORBi
 

Files


Full Text
2010-Thiele - Functional Characterization of Alternate Optimal Solutions of Escherichia coli ’s Transcriptional and Translational Machinery.pdf
Publisher postprint (658.04 kB)
Request a copy

All documents in ORBilu are protected by a user license.

Send to



Details



Keywords :
Computational Biology; DNA, Bacterial/physiology; Endoribonucleases; Escherichia coli/genetics; Escherichia coli Proteins/biosynthesis/genetics; Gene Expression Profiling/methods; Gene Expression Regulation, Bacterial/genetics; Gene Regulatory Networks; Genes, Bacterial/genetics; Genetic Engineering; Genome, Bacterial/physiology; Genomics/methods/statistics & numerical data; Multienzyme Complexes; Oligonucleotide Array Sequence Analysis; Polyribonucleotide Nucleotidyltransferase; Protein Biosynthesis; RNA Helicases; RNA, Bacterial/biosynthesis; Ribosomes/metabolism/physiology; Solutions/chemistry
Abstract :
[en] The constraint-based reconstruction and analysis approach has recently been extended to describe Escherichia coli's transcriptional and translational machinery. Here, we introduce the concept of reaction coupling to represent the dependency between protein synthesis and utilization. These coupling constraints lead to a significant contraction of the feasible set of steady-state fluxes. The subset of alternate optimal solutions (AOS) consistent with maximal ribosome production was calculated. The majority of transcriptional and translational reactions were active for all of these AOS, showing that the network has a low degree of redundancy. Furthermore, all calculated AOS contained the qualitative expression of at least 92% of the known essential genes. Principal component analysis of AOS demonstrated that energy currencies (ATP, GTP, and phosphate) dominate the network's capability to produce ribosomes. Additionally, we identified regulatory control points of the network, which include the transcription reactions of sigma70 (RpoD) as well as that of a degradosome component (Rne) and of tRNA charging (ValS). These reactions contribute significant variance among AOS. These results show that constraint-based modeling can be applied to gain insight into the systemic properties of E. coli's transcriptional and translational machinery.
Disciplines :
Life sciences: Multidisciplinary, general & others
Author, co-author :
Thiele, Ines 
Fleming, Ronan MT 
Bordbar, Aarash
Schellenberger, Jan
Palsson, Bernhard O.
External co-authors :
yes
Language :
English
Title :
Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery.
Publication date :
2010
Journal title :
Biophysical Journal
ISSN :
1542-0086
Publisher :
Biophysical Society, United States - Maryland
Volume :
98
Issue :
10
Pages :
2072-81
Peer reviewed :
Peer Reviewed verified by ORBi
Commentary :
Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Available on ORBilu :
since 30 April 2014

Statistics


Number of views
104 (0 by Unilu)
Number of downloads
0 (0 by Unilu)

Scopus citations®
 
47
Scopus citations®
without self-citations
20
OpenCitations
 
49
WoS citations
 
37

Bibliography


Similar publications



Contact ORBilu