Genetic components that regulate arbuscular mycorrhizal (AM) interactions in hosts and non-hosts are not completely known. Comparative transcriptomic analysis was combined with phylogenetic studies to identify the factors that distinguish AM host from non-host. Mycorrhized host, non-mycorrhized host and non-host cultivars of tomato (Solanum lycopersicum) were subjected to RNA seq analysis. The top 10 differentially expressed genes were subjected to extensive in silico phylogenetic analysis along with 10 more candidate genes that have been previously reported for AM-plant interactions. Seven distantly related hosts and four non-hosts were selected to identify structural differences in selected gene/protein candidates. The screened genes/proteins were subjected to MEME, CODEML and DIVERGE analysis to identify evolutionary patterns that differentiate hosts from non-hosts. Based on the results, candidate genes were categorized as highly influenced (SYMRK and CCaMK), moderately influenced and minimally influenced by evolutionary constraints. We propose that the amino acid and nucleotide changes specific to non-hosts are likely to correspond to aberrations in functionality towards AM symbiosis. This study paves way for future research aimed at understanding innate differences in genetic make-up of AM hosts and non-hosts, in addition to the theory of gene losses from the “AM-symbiotic toolkit”.

A novel transcriptional regulator has been identified in the 400-bp upstream region of the guaA gene of Mycobacterium tuberculosis H37Rv that promotes the expression of lacZ gene in Mycobacterium smegmatis mc(2)155 and M. tuberculosis H37Rv but not in Escherichia coli DH5alpha. PCR-mediated deletion mutagenesis and cloning identified a 120-bp fragment upstream from the guaA gene to be the actual regulator. Primer extension analysis mapped the transcription start site to be the first 'G' residue of the translation start codon GTG of the guaA gene. Electrophoretic mobility shift assay showed strong binding of M. smegmatis RNA polymerase holoenzyme to the 400-bp fragment that expresses lacZ in mycobacterial species and a weak binding to the 280-bp fragment that expresses only in E. coli DH5alpha. Both promoter recombinants revealed varied response in the presence of purine nucleotides and exhibited down-regulation when subjected to amino acid starvation.

Isolation and analysis of strong and regulatable promoters of mycobacteria should be useful tools to aid the expression of cloned genes in mycobacteria. In the present study, we have mapped the transcriptional start site of the inducible acetamidase gene of Mycobacterium smegmatis and studied the mechanism of its regulation. Northern blot, reverse transcription-PCR and primer extension analysis studies were used to determine the position of the promoter.