Project description:Ribosome profiling performed in Mycobacterium smegmatis MC2 155 wild-type cells versus cells with deletions of genes encoding small ORFs MSMEG_0945 and MSMEG_1916.
Project description:Mycobacterium smegmatis SigF is a group III sigma factor. Its ortholog in M. tuberculosis is reported to have role in regulation and function of cell wall components. In present study we have created an M. smegmatis ΔsigF mutant by allele exchange method. M. smegmatis sigF mutant shows non pigmented phenotype and is more sensitive to hydrogen peroxide generated oxidative stress. DNA microarray analysis of M. smegmatis wild type and ΔsigF mutant suggests that SigF in this species controls the expression of several energy and central intermediary metabolism genes along with regulation of carotenoid biosynthesis.
Project description:Investigation of whole genome gene expression level changes in a Mycobacterium smegmatis mc2 155 delta-MSMEG_0166 mutant, compared to the wild-type strain. MSMEG_0166 is a transcriptional regulator in the gntR family. Mutations in MSMEG_0166 result in hypersensitivity to the bactericidal ubiquitin peptide Ub2, as well as oxidative stress caused by either organic or inorganic agents A three chip study using total RNA recovered from three separate wild-type cultures of Mycobacterium smegmatis mc2 155 and three separate cultures of a MSMEG_0166 mutant strain, Mycobacterium smegmatis mc2 155 delta-MSMEG_0166, in which MSMEG_0166 is interupted by the insertion of a hygromycin resistance cassette. Each chip measures the expression level of 6,588 genes from Myobacterium smegmatis with five 60-mer probes per transcript and two replicates of each probe for a total of 65,880 experimental probes.
Project description:Transcriptional profiling of Mycobacterium smegmatis comparing strains undergoing I-SceI generated DNA damage at a single genomic locus Gene designations are the updated annotation
Project description:We employed a proteogenomics workflow to identify microproteins encoded by small Open Reading Frames (ORFs) in the genome of Mycobacterium smegmatis strain mc²155.
Project description:Transcriptional profiling of Mycobacterium smegmatis comparing the effects of wild type levels of CarD expression with CarD depletion. Transcriptional profile of the mgm1701 control strain was compared with that of mgm1703, a strain where CarD transcription is regulated by a Tet-On system. Both strains were grown in the absence of anhydrotetracline for 13 hours in nutrient rich broth to allow for depletion of CarD transcription in mgm1703.
Project description:Total transcriptome analyses were carried out to investigate changes in transcript patterns in the Mycobacterium smegmatis wild type strain SMR5 due to nitrogen starvation and to expand the knowledge about the role of the two transcriptional regulators of nitrogen metabolism, namely GlnR and AmtR, in these processes. A first experiment revealed enhanced transcript levels of 284 genes and reduced transcripts of 231 genes in the wild type under nitrogen starvation compared to nitrogen surplus. When glnR deletion strain MH1 was compared to the wild type under nitrogen starvation, decreased transcript levels of 125 genes were detected, indicating that these are activated by GlnR due to nitrogen limitation. Comparing amtR deletion strain YL1 to the wild type under nitrogen starvation, enhanced transcript levels of 2 genes were found, indicating that they are repressed by AmtR under nitrogen surplus. A comparison of YL1 and wild type under surplus, as well as a comparison of YL1 under nitrogen surplus and starvation and of MH1 under nitrogen surplus and starvation were carried out as additional control experiments. It can be concluded that GlnR is the master regulator of nitrogen control in M. smegmatis and that AmtR fulfills only a small, subordinate role in the regulation of an operon. This SuperSeries is composed of the following subset Series: GSE30033: Mycobacterium smegmatis - Comparison of glnR deletion strain MH1 under nitrogen surplus and starvation GSE30231: Mycobacterium smegmatis - Comparison of wild type SMR5 and amtR deletion strain YL1 under nitrogen starvation GSE30232: Mycobacterium smegmatis - Comparison of amtR deletion strain YL1 under nitrogen surplus and starvation GSE30233: Mycobacterium smegmatis - Comparison of wild type SMR5 under nitrogen surplus and starvation GSE30234: Mycobacterium smegmatis - Comparison of wild type SMR5 and glnR deletion strain MH1 under nitrogen starvation GSE30235: Mycobacterium smegmatis - Comparison of wild type SMR5 and amtR deletion strain YL1 under nitrogen surplus Refer to individual Series
Project description:We describe RNA polymerase and sigma A distribution in the genome of Mycobacterium smegmatis by ChIP-seq. The experiment was performed in exponential and stationary phase of growth.
