Unexpected Abundance of Coenzyme F 420 -Dependent Enzymes in Mycobacterium tuberculosis and Other Actinobacteria

Abstract

ABSTRACT Regimens targeting Mycobacterium tuberculosis , the causative agent of tuberculosis (TB), require long courses of treatment and a combination of three or more drugs. An increase in drug-resistant strains of M. tuberculosis demonstrates the need for additional TB-specific drugs. A notable feature of M. tuberculosis is coenzyme F 420 , which is distributed sporadically and sparsely among prokaryotes. This distribution allows for comparative genomics-based investigations. Phylogenetic profiling (comparison of differential gene content) based on F 420 biosynthesis nominated many actinobacterial proteins as candidate F 420 -dependent enzymes. Three such families dominated the results: the luciferase-like monooxygenase (LLM), pyridoxamine 5′-phosphate oxidase (PPOX), and deazaflavin-dependent nitroreductase (DDN) families. The DDN family was determined to be limited to F 420 -producing species. The LLM and PPOX families were observed in F 420 -producing species as well as species lacking F 420 but were particularly numerous in many actinobacterial species, including M. tuberculosis . Partitioning the LLM and PPOX families based on an organism's ability to make F 420 allowed the application of the SIMBAL (sites inferred by metabolic background assertion labeling) profiling method to identify F 420 -correlated subsequences. These regions were found to correspond to flavonoid cofactor binding sites. Significantly, these results showed that M. tuberculosis carries at least 28 separate F 420 -dependent enzymes, most of unknown function, and a paucity of flavin mononucleotide (FMN)-dependent proteins in these families. While prevalent in mycobacteria, markers of F 420 biosynthesis appeared to be absent from the normal human gut flora. These findings suggest that M. tuberculosis relies heavily on coenzyme F 420 for its redox reactions. This dependence and the cofactor's rarity may make F 420 -related proteins promising drug targets.