Computer-Aided Resolution of an Experimental Paradox in Bacterial Chemotaxis

Abstract

Escherichia coli responds to its environment by means of a network of intracellular reactions which process signals from membrane-bound receptors and relay them to the flagellar motors. Although characterization of the reactions in the chemotaxis signaling pathway is sufficiently complete to construct computer simulations that predict the phenotypes of mutant strains with a high degree of accuracy, two previous experimental investigations of the activity remaining upon genetic deletion of multiple signaling components yielded several contradictory results (M. P. Conley, A. J. Wolfe, D. F. Blair, and H. C. Berg, J. Bacteriol. 171:5190–5193, 1989; J. D. Liu and J. S. Parkinson, Proc. Natl. Acad. Sci. USA 86:8703–8707, 1989). For example, “building up” the pathway by adding back CheA and CheY to a gutted strain lacking chemotaxis genes resulted in counterclockwise flagellar rotation whereas “breaking down” the pathway by deleting chemotaxis genes except cheA and cheY resulted in alternating episodes of clockwise and counterclockwise flagellar rotation. Our computer simulation predicts that trace amounts of CheZ expressed in the gutted strain could account for this difference. We tested this explanation experimentally by constructing a mutant containing a new deletion of the che genes that cannot express CheZ and verified that the behavior of strains built up from the new deletion does in fact conform to both the phenotypes observed for breakdown strains and computer-generated predictions. Our findings consolidate the present view of the chemotaxis signaling pathway and highlight the utility of molecularly based computer models in the analysis of complex biochemical networks.

Swimming bacteria power microspin cycles

“…While E. coli and B. subtilis cells tumble approximately every 3 s, individual E. coli cells are more likely to tumble than B. subtilis ( 17 ). We, therefore, examined the nontumbling, chemotaxis-gutted E. coli strain RBB1050 ( 25 ) and found that it still produced periodic fluid flows with a comparable period to the WT cells (half-period, T 1/2 = 4.6 ± 2 s) (fig. S4), thereby ruling out tumbling as a requirement for periodic flow.…”

Activation of CheY mutant D57N by phosphorylation at an alternative site, Ser‐56

“…E. coli ΔcheY6021 strain KO641 recA (Bourret et al ., 1990) and Δ( cheA‐cheZ )::Zeo R strain RBB1050 (Abouhamad et al ., 1998) have been described previously. The Δ(cheY‐cheZ)4313 strain RP5231 (Liu and Parkinson, 1989) was a gift from J. S. Parkinson (University of Utah).…”

Temperature Dependence of Switching of the Bacterial Flagellar Motor by the Protein CheY 13DK106YW

“…In cells in which the cytoplasm has been exchanged for buffer (Ravid and Eisenbach, 1984), or in which CheY (Liu and Parkinson, 1989) or CheY and other cytoplasmic chemotaxis proteins have been deleted (Wolfe et al, 1987;Abouhamad et al, 1998), motors spin exclusively CCW. In the former case, switching between CW and CCW states can be induced by the addition of fumarate, which stabilizes the CW state (Prasad et al, 1998).…”