Progress in the field of mycobacterial research has been hindered by the inability to readily generate defined mutant strains of the slow-growing mycobacteria to investigate the function of specific genes. An efficient method is described that has been used to generate several mutants, including the first double unmarked deletion strain of Mycobacterium tuberculosis. Four mutants were constructed : a marked deletion of the plcABC cluster, which encodes three phospholipases C ; separate unmarked deletions in plcABC and tlyA (encoding a haemolysin) ; and a double unmarked mutant tlyA∆ plcABC∆. To accomplish this, two series of vectors were designed, the first of which, named pNIL, allows manipulation of the target gene sequence at a variety of convenient restriction sites. The second series, named pGOAL, contains marker cassettes flanked by PacI restriction enzyme sites. The final suicide plasmid vectors were then obtained by cloning a marker cassette from a pGOAL vector into the single PacI site of the pNIL vector with the modified gene of interest. Finally, a two-step strategy was employed whereby single cross-over events were first selected, then screening for the second cross-over was carried out to yield the mutant strains. This technique will now allow the construction of potential vaccine strains without the inclusion of antibiotic resistance markers, the ability to make multiple defined mutations and the possibility of making more subtle defined mutations, such as point mutations.

SummaryThe Mycobacterium tuberculosis TetR-type regulator Rv3574 has been implicated in pathogenesis as it is induced in vivo, and genome-wide essentiality studies show it is required for infection. As the gene is highly conserved in the mycobacteria, we deleted the Rv3574 orthologue in Mycobacterium smegmatis (MSMEG_6042) and used real-time quantitative polymerase chain reaction and microarray analyses to show that it represses the transcription both of itself and of a large number of genes involved in lipid metabolism. We identified a conserved motif within its own promoter (TnnAACnnGTTnnA) and showed that it binds as a dimer to 29 bp probes containing the motif. We found 16 and 31 other instances of the motif in intergenic regions of M. tuberculosis and M. smegmatis respectively. Combining the results of the microarray studies with the motif analyses, we predict that Rv3574 directly controls the expression of 83 genes in M. smegmatis, and 74 in M. tuberculosis. Many of these genes are known to be induced by growth on cholesterol in rhodococci, and palmitate in M. tuberculosis. We conclude that this regulator, designated elsewhere as kstR, controls the expression of genes used for utilizing diverse lipids as energy sources, possibly imported through the mce4 system.

BackgroundTranscriptional profiling using microarrays provides a unique opportunity to decipher host pathogen cross-talk on the global level. Here, for the first time, we have been able to investigate gene expression changes in both Mycobacterium tuberculosis, a major human pathogen, and its human host cells, macrophages and dendritic cells.Methodology/Principal FindingsIn addition to common responses, we could identify eukaryotic and microbial transcriptional signatures that are specific to the cell type involved in the infection process. In particular M. tuberculosis shows a marked stress response when inside dendritic cells, which is in accordance with the low permissivity of these specialized phagocytes to the tubercle bacillus and to other pathogens. In contrast, the mycobacterial transcriptome inside macrophages reflects that of replicating bacteria. On the host cell side, differential responses to infection in macrophages and dendritic cells were identified in genes involved in oxidative stress, intracellular vesicle trafficking and phagosome acidification.Conclusions/SignificanceThis study provides the proof of principle that probing the host and the microbe transcriptomes simultaneously is a valuable means to accessing unique information on host pathogen interactions. Our results also underline the extraordinary plasticity of host cell and pathogen responses to infection, and provide a solid framework to further understand the complex mechanisms involved in immunity to M. tuberculosis and in mycobacterial adaptation to different intracellular environments.

Two-component regulatory signal transduction systems are widely distributed among bacteria and enable the organisms to make coordinated changes in gene expression in response to a variety of environmental stimuli. The genome sequence of Mycobacterium tuberculosis contains 11 complete two-component systems, four isolated homologous regulators, and three isolated homologous sensors. We have constructed defined mutations in six of these genes and measured virulence in a SCID mouse model. Mice infected with four of the mutants (deletions of devR, tcrXY, trcS, and kdpDE) died more rapidly than those infected with wild-type bacteria. The other two mutants (narL and Rv3220c) showed no change compared to the wild-type H37Rv strain. The most hypervirulent mutant (devR⌬) also grew more rapidly in the acute stage of infection in immunocompetent mice and in gamma interferon-activated macrophages. These results define a novel class of genes in this pathogen whose presence slows down its multiplication in vivo or increases its susceptibility to host killing mechanisms. Thus, M. tuberculosis actively maintains a balance between its own survival and that of the host.Mycobacterium tuberculosis is an extraordinarily successful pathogen that currently infects approximately one-third of the global population and causes 8 million new cases of tuberculosis annually (41). The tubercle bacillus functions within several hostile environments in order to survive within the human host and cause disease. For instance, the bacteria must be able to gain entry into macrophages, multiply intracellularly, survive within the lung granuloma for years, and disperse to a new host via aerosols (9). It is therefore likely that the expression of different sets of genes by M. tuberculosis at various stages of infection is crucial to its survival. Two-component regulatory systems (2CRs) are widely distributed among bacteria and plants and enable the organisms to respond to many different external stimuli (20,37,38). These systems form a large family of related proteins that consist of a membrane-bound sensor protein that activates an effector protein, generally a transcriptional regulator, by phosphorylation. 2CRs have been shown to play a crucial role in the controlled expression of virulence genes in other bacteria (11). For example, in Salmonella enterica serovar Typhimurium, the membrane-bound sensor protein PhoQ is activated by changing levels of magnesium, and this activates the PhoP response regulator. PhoP is a DNA-binding protein that binds in a sequence-specific manner to selected promoters, thereby inducing or repressing their transcription, and S. enterica serovar Typhimurium phoP mutants are highly attenuated (14, 17).The genome of M. tuberculosis contains 11 paired 2CRs, four isolated regulators, and three isolated sensors (6). Mutants in two of these, phoP and mprA are highly attenuated in a murine model (31, 43), while a prrA mutant grows more slowly in macrophages (12), indicating that these regulators control genes which are important f...