Similarities between Mycobacterium tuberculosis phoP-phoR mutants and the attenuated laboratory strain M. tuberculosis H37Ra in terms of morphological and cytochemical properties, lipid content, gene expression and virulence attenuation prompted us to analyze the functionality of this two-component regulator in the latter strain. Sequence analysis revealed a base substitution resulting in a one-amino-acid change in the likely DNA-binding region of PhoP in H37Ra relative to H37Rv. Using gel-shift assays, we show that this mutation abrogates the ability of the H37Ra PhoP protein to bind to a 40-bp segment of its own promoter. Consistent with this result, the phoP gene from H37Rv but not that from H37Ra was able to restore the synthesis of sulfolipids, diacyltrehaloses and polyacyltrehaloses in an isogenic phoP-phoR knock-out mutant of M. tuberculosis Moreover, complementation of H37Ra with phoP from H37Rv fully restored sulfolipid, diacyltrehalose and polyacyltrehalose synthesis, clearly indicating that the lack of production of these lipids in H37Ra is solely due to the point mutation in phoP. Using a pks2-3/4 knock-out mutant of M. tuberculosis H37Rv, evidence is further provided that the above-mentioned polyketide-derived acyltrehaloses do not significantly contribute to the virulence of the tubercle bacillus in a mouse model of infection. Reasons for the attenuation of H37Ra thus most likely stand in other virulence factors, many of which are expected to belong to the PhoP regulon and another of which, unrelated to PhoP, appears to be the lack of production of phthiocerol dimycocerosates in this strain.H37Rv and H37Ra are two variants of an Mycobacterium tuberculosis strain named H37 that was originally isolated from the sputum of a tuberculosis patient in 1905. Serial passaging of H37 through different media led to the dissociation of this isolate into two variants, a virulent one known as H37Rv and an avirulent one known as H37Ra, which also differ in their colonial morphology and cording properties (27,39). With the goal of identifying the molecular determinants underlying the virulence attenuation of H37Ra, numerous approaches including genetic complementation of H37Ra with H37Rv genomic DNA (29), gene expression profiling (15, 28, 32), subtractive RNA hybridization (22) and comparative genomics, proteomics and lipidomics (4,7,10,18,26) have been undertaken. Although these studies have led to the identification of a number of genes or gene products the expression of which differs between H37Rv and H37Ra, it is still at present unclear to what extent these products account for the virulence attenuation of H37Ra. Furthermore, as attempts to restore the virulence of the H37Ra strain through genetic complementation with H37Rv DNA have so far yielded negative results (4, 29), it has been concluded that the virulence attenuation of H37Ra was certainly the result of multiple mutations and/or rearrangements affecting multiple chromosomal loci.With the recent study by different groups of the two-component regulator...