Project description:Nickel is an essential component of many eukaryotic and prokaryotic metallo-enzymes. Due to its employment in many industrial applications, wastewaters from industrial plants often contain millimolar concentrations of Ni2+ that are toxic and life-threatening for many organism. Several lines of preliminary evidence suggest that members of the genus Sphingobium are able to grow in the presence of high concentrations of metal ions. We have isolated a novel Sphingobium strain (sp. ba1) able to grow in the presence of high concentrations (up to 20 mM) of NiCl2. Sequencing of its genome allowed the identification of several genes coding for proteins potentially involved in efflux-mediated resistance mechanisms. Here we use the RNA-seq approach to analyze the response of the Sphingobium sp. ba1 strain to high concentrations (10 mM) of Ni ions. Transcriptomic data show the differential expression of about one-hundred and twenty genes, most of which are up-regulated and encode proteins such as membrane proteins and components of metal efflux systems, enzymes involved in oxidative stress responses (catalases, peroxidases) and signal transduction systems.
Project description:Clavibacter michiganensis subsp. michiganensis is an important Gram-positive phytopathogenic bacteria that causes bacterial wilt and canker in tomato. The genome of the type strain, NCPPB382, has been sequenced and annotated, however comparative genomics suggests that certain regions are under- or misannotated. In order to improve the genome annotation, we have undertaken a proteogenomic study of this important pathogen. Samples were grown in culture and the proteome of the pellet and supernatant were analyzed separately using shotgun HPLC-MS/MS. These proteomics datasets were analyzed and a number of missing gene were found and a number of existing gene calls were modified.
Project description:The project aims to to understand the response of the lin genes in Sphingobium indicum B90A under the stress of HCH isomers and the metabolites formed during degradation of hexachlorocyclohexane (HCH). Entire cell proteome from Sphingobium indicum B90A was extracted in presence of four HCH isomers. Quantitative proteomics confirmed the constitutive expression of the linA, linB and linC genes of the HCH degradation pathway crucial for the initiation of HCH isomers degradation. LinM and LinN were upregulated in the presence of β- and δ-isomers suggested the important role of ABC transporter system in the depletion of β- and δ-HCH. Besides this HCH isomers induced oxidative stress caused systemic changes in strain B90A proteome.
