Project description:Early and mature biofilm formation in the extremely halophilic euryarchaeon Halobacterium salinarum strain R1 was characterized by SWATH-LC/MS/MS. Using a simple surfactant-assisted protein solubilization protocol and one-dimensional ultrahigh performance nanoflow chromatography on the front end, 63.2% and 58.6% of the predicted Hbt. salinarum R1 proteome could be detected and quantified, respectively. Analysis of biophysical protein properties, functional analysis and pathway mapping indicate that we achieved a comprehensive characterization of the proteome. 60.8% of quantified proteins (or 34.5% of the predicted proteome) exhibited significant abundance changes between planktonic and biofilm states, demonstrating that haloarchaeal biofilm formation represents a profound “lifestyle change” on the molecular level. Taken together our results and analysis constitute the first comprehensive study to track the molecular changes from planktonic cells to initial and mature archaeal biofilms on the proteome level. Proteins exemplifying different protein expression level profiles were selected, and their corresponding gene transcripts targeted by qRT-PCR to test the feasibility of establishing rapid PCR-based assays for archaeal biofilm formation.
Project description:Transcriptional profiling of comparing wildtype strains with DR0199-deletion strains under normal growth conditions. One-condition experiment, wild type strains vs. DR0199-deletion strains. Three biological replicates were carried out.
Project description:Transcriptional profiling of comparing wildtype strains with DR1790-deletion strains under normal growth contidions. Keywords: Genetic modification One-condition experiment, wild type strains vs. DR1790-deletion strains. Two biological replicates were carried out.
Project description:To investigate the contribution of ribonucleases to post-transcriptional regulation of mRNA levels, we examined the fitness consequences and gene expression changes of ribonuclease mutants in the extreme halophilic archaeon Halobacterium salinarum NRC-1. H. salinarum NRC-1 is known to use a large repertoire of environment-specific transcriptional regulatory programs, which may be complemented by post-transcriptional regulatory mechanisms. Homology searches identified putative RNase genes in H. salinarum NRC-1 that include likely orthologs for RNases found in prokaryotic and eukaryotic lineages. The VNG2099C protein sequence is significantly similar (e = 2 x 10^-34) to the sequence of the rat liver perchloric acid-soluble protein (L-PSP), which has been shown to have endoribonuclease activity in vitro (Morishita et al 1999). The VNG2099C protein, like the archaeal Sulfolobus tokodaii YjgF/L-PSP protein for which a crystal structure has been solved (Miyakawa et al 2006), shares conservation of residues proposed to constitute the active site of the rat protein. The purpose of this gene expression study was to investigate the role of the putative endoribonuclease VNG2099C on gene regulation.
Project description:experiment is devided in 3 parts:<br> I. comparison H.sal. R1 wt vs H.sal. R1 TATA-box mutant<br> 3 microarrays belong to this objective<br> II. comparison H.sal. R1 wt vs H.sal. R1 deltaOE2375F<br> 2 microarrays belong to this objective<br> III. comparison H.sal. R1 wt vs H.sal. R1 6xHis-OE2375F<br> 1 microarray belongs to this objective
Project description:An inhibitory effect of novobiocin on bop transcription was reported for the NRC1 strain of Hbt. salinarum ([17] Yang and DasSarma, 1990, [18] Yang et al, 1996), but its influence in strain R1 has not beeen known yet. We were interested to see the genome wide influences of novobiocin on transcription in Hbt. salinarum. Therefore, a DNA microarray analysis of the transcripts from R1 was performed, comparing cells grown in the presence or absence of novobiocin.
