To gain molecular insight into the role of Rv2872 in increased vancomycin resistance, change of the intracellular amino acids content and cell wall structure, the transcriptome of Rv2872 overexpression M. smegmatis was assessed through RNA-Seq analysis. The transcriptome data showed that the transcription of four genes involved in peptidoglycan synthesis was significantly lower in the MS_Rv2872 overexpression strain . The decreased vancomycin targets might underlie the observed vancomycin resistance. Consistent with altered intracellular amino acids levels in the recombinant M. smegmatis MS_Rv2872, the transcription level of relevant genes was also altered. This is also seen in the altered fatty acids levels. The data showed that 38  fatty acid metabolism genes were down regulated, and 15 were up regulated in the recombinant M.smegmatis MS_Rv2872.  Overall design: mRNA profiles of M.smegmatis overexpression strains MS_Vec and MS_Rv2872 by deep sequencing, using Illumina Hiseq Xten.