Identification of transcription factors that promote pulmonary infection

The National Institute of Allergy and Infectious Diseases awarded The Trustees of Columbia University in the City of New York $452,375 on June 16, 2026, under the Allergy and Infectious Diseases Research program (CFDA 93.855) to identify transcription factors that promote pulmonary infection by opportunistic pathogens.

The recipient will conduct research to determine how the transcription factor RpoN responds to environmental signals in Pseudomonas aeruginosa and Klebsiella pneumoniae, and how RpoN regulation enables these pathogens to establish persistent pulmonary infection. The work will use IRG1-deficient mice and RpoN mutants in both bacterial species to assess whether host itaconate and other metabolites are sensed by RpoN and how this sensing directs pneumonia pathogenesis. The research will employ fluorescent promoter-fusion reporter constructs optimized for codon usage in each species to track RpoN activity in clinical isolates and laboratory strains, with the goal of identifying signals and transcription factors that enable pulmonary opportunists to successfully establish infection.

Performance will occur in New York, New York, with a period of performance from the award date through May 31, 2028. This is a Project Grant, a form of assistance funding that supports biomedical research and research training in infectious diseases and related areas.

Abstract

Opportunistic pathogens such as pseudomonas aeruginosa and klebsiella pneumoniae enjoy remarkable metabolic flexibility that enables them to rapidly adapt to diverse environmental niches including the human lung. P. Aeruginosa aspirated into the lung from contaminated water, for example, rapidly accommodates to a variety of potential carbon sources, from which IT optimizes its metabolic activity to secure a nidus of infection. We postulate that a few global regulators, such as the transcription factor rpon, respond to specific environmental signals. Rpon then either positively or negatively regulates cascades of gene expression to optimize the bacterial bioenergetic response and direct proliferation. By using IRG1-/- mice and rpon mutants in both species, we will determine if host itaconate, or other metabolites are sensed by rpon and how this directs the pathogenesis of pneumonia. We will establish how the ensuing up or down-regulation of rpon activity enables the selection of bacterial variants such as those producing biofilm, that are optimized for persistent pulmonary infection. K.pneumoniae occupy a similar environmental niche as p. Aeruginosa, with metabolic adaptation and the expression of extracellular polysaccharides under rpon control that are linked to protracted and often fatal infection. For both pathogens, we will use fluorescent promoter-fusion reporter constructs, optimized for codon usage in each species to follow rpon activity in both clinical isolates as well as laboratory strains. Our goal is to identify the signals and transcription factors that enable pulmonary opportunists to successfully establish infection.