Phenotype microarray analysis of Escherichia coli K-12 mutants with deletions of all two-component systems

Abstract

Two-component systems are the most common mechanism of transmembrane signal transduction in bacteria. A typical system consists of a histidine kinase and a partner response regulator. The histidine kinase senses an environmental signal, which it transmits to its partner response regulator via a series of autophosphorylation, phosphotransfer, and dephosphorylation reactions. Much work has been done on particular systems, including several systems with regulatory roles in cellular physiology, communication, development, and, in the case of bacterial pathogens, the expression of genes important for virulence. We used two methods to investigate two-component regulatory systems in Escherichia coli K-12. First, we systematically constructed mutants with deletions of all two-component systems by using a now-standard technique of gene disruption (K. A. Datsenko and B. L. Wanner, Proc. Natl. Acad. Sci. USA 97:6640-6645, 2000). We then analyzed these deletion mutants with a new technology called Phenotype MicroArrays, which permits assays of nearly 2,000 growth phenotypes simultaneously. In this study we tested 100 mutants, including mutants with individual deletions of all two-component systems and several related genes, including creBC-regulated genes (cbrA and cbrBC), phoBR-regulated genes (phoA, phoH, phnCDEFGHIJKLMNOP, psiE, and ugpBAECQ), csgD, luxS, and rpoS. The results of this battery of nearly 200,000 tests provided a wealth of new information concerning many of these systems. Of 37 different two-component mutants, 22 showed altered phenotypes. Many phenotypes were expected, and several new phenotypes were also revealed. The results are discussed in terms of the biological roles and other information concerning these systems, including DNA microarray data for a large number of the same mutants. Other mutational effects are also discussed.

FIG. 1.

Phenotypic changes in PM assays. Significant changes are enclosed in boxes and indicated by arrows. Yellow indicates that growth of the wild type and growth of the mutant were similar. Red indicates faster growth of the wild type. Green indicates faster growth of the mutant. The quantitative difference values are shown in Table 4. (A) Comparison of BW29134 (ΔphoBR) with BW25113. Well B6, d-2-phosphoglyceric acid; well B7, d-3-phosphoglyceric acid; well C7, 6-phosphogluconic acid; well D5, O-phospho-d-serine; well D7, O-phospho-l-threonine; well E4, phosphorylcholine; well E5, ο-phosphorylethanolamine. (B) Comparison of BW27880 (ΔntrBC) with BW25113.

FIG. 1.

Phenotypic changes in PM assays. Significant changes are enclosed in boxes and indicated by arrows. Yellow indicates that growth of the wild type and growth of the mutant were similar. Red indicates faster growth of the wild type. Green indicates faster growth of the mutant. The quantitative difference values are shown in Table 4. (A) Comparison of BW29134 (ΔphoBR) with BW25113. Well B6, d-2-phosphoglyceric acid; well B7, d-3-phosphoglyceric acid; well C7, 6-phosphogluconic acid; well D5, O-phospho-d-serine; well D7, O-phospho-l-threonine; well E4, phosphorylcholine; well E5, ο-phosphorylethanolamine. (B) Comparison of BW27880 (ΔntrBC) with BW25113.