Stochasticity in Protein Levels Drives Colinearity of Gene Order in Metabolic Operons of Escherichia coli
نویسندگان
چکیده
In bacterial genomes, gene order is not random. This is most evident when looking at operons, these often encoding enzymes involved in the same metabolic pathway or proteins from the same complex. Is gene order within operons nonrandom, however, and if so why? We examine this issue using metabolic operons as a case study. Using the metabolic network of Escherichia coli, we define the temporal order of reactions. We find a pronounced trend for genes to appear in operons in the same order as they are needed in metabolism (colinearity). This is paradoxical as, at steady state, enzymes abundance should be independent of order within the operon. We consider three extensions of the steady-state model that could potentially account for colinearity: (1) increased productivity associated with higher expression levels of the most 5' genes, (2) a faster metabolic processing immediately after up-regulation, and (3) metabolic stalling owing to stochastic protein loss. We establish the validity of these hypotheses by employing deterministic and stochastic models of enzyme kinetics. The stochastic stalling hypothesis correctly and uniquely predicts that colinearity is more pronounced both for lowly expressed operons and for genes that are not physically adjacent. The alternative models fail to find any support. These results support the view that stochasticity is a pervasive problem to a cell and that gene order evolution can be driven by the selective consequences of fluctuations in protein levels.
منابع مشابه
Detection of fim, pap, sfa and afa Adhesin-Encoding Operons in Escherichia coli Strains Isolated from Urinary Tract Infections
ABSTRACT Background and objectives: Urinary tract infections (UTIs) are one of the most common infectious diseases caused by bacteria. The primary etiologic agent of UTIs is Escherichia coli. Uropathogenic E.coli (UPEC) strains have a number of specific virulence factors, which can worsen UTIs. This study was performed to...
متن کاملSynthesis and Expression of Modified bFGF Gene in Escherichia coli Cells
A new strategy for construction of synthetic gene encoding human basic fibroblast growth factor comprising DNA annealing-ligation and augmentation by polymerase chain reaction was introduced. The sequence of the gene and corresponding amino acid chain were modified in order to increase stability of the protein. First, 300 bp and 160 bp fragments of the gene were assembled from 18 oligonucleotid...
متن کاملCloning and sequencing of ompf Salmonella typhi Salmonella ompf gene in Escherichia coli Origami
Background and Aim: Salmonella Typhi belongs to the family Enterobacteriaceae, gram-negative bacilli and causes gastrointestinal diseases such as typhoid. This bacterium has a special structure and various genes, including the ompf gene (outer membrane protein). Recent studies have shown the possibility of using ompf in the development of a diagnostic tuberculosis vaccine. Therefore, the aim of...
متن کاملDetermination of the optimal conditions of cloning Aerolysin gene from the common carp pathogen Aeromonas hydrophila in Escherichia coli BL21
Aeromonas hydrophila is a gram-negative bacterium which associated with gastrointestinal diseases and septicaemia. This pathogenic bacterium has several virulence factors ranging from pili to the excreted protein which called (Aerolysin) with minor and major effects, respectively. Additionally, Aeromonas hydrophila is a widely distributed bacterium that commonly causes ulcers in cyprinid fish s...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
- PLoS Biology
دوره 7 شماره
صفحات -
تاریخ انتشار 2009