Project description:Investigation of whole genome gene expression level changes in Lactococcus lactis KCTC 3769T,L. raffinolactis DSM 20443T, L. plantarum DSM 20686T, L. fujiensis JSM 16395T, L. garvieae KCTC 3772T, L. piscium DSM 6634T and L. chungangensis CAU 28T . This proves that transcriptional profiling can facilitate in elucidating the genetic distance between closely related strains.
Project description:The hydrothermal vent gammaproteobacterium Thiomicrospira crunogena inhabits an unstable environment and must endure dramatic sweeps in habitat chemistry. This sulfur chemolithoautotroph responds to changes in dissolved inorganic carbon (DIC; = CO2 + HCO3- + CO3-2) availability with a carbon concentrating mechanism (CCM), in which whole-cell affinity for DIC, as well as the intracellular DIC concentration, increase substantially under DIC-limitation. To determine whether this CCM is regulated at the level of transcription, cells cultivated under high-DIC conditions in chemostats were resuspended in growth medium with low concentrations of DIC, and CCM development was tracked in the presence and absence of RNA polymerase inhibitor rifampicin. The induction of the CCM, as measured by silicone oil centrifugation, was hindered in the presence of rifampicin. Similar results were observed for carboxysome gene transcription and assembly, as assayed by qRT-PCR and transmission electron microscopy, respectively. Genome-wide transcription patterns, assayed via microarrays, were compared for cells grown under DIC-limitation versus ammonia limitation. In addition to carboxysome genes, two novel genes (Tcr_1019 and Tcr_1315), present in other organisms including chemolithoautotrophs, but whose function(s) have not been elucidated in any organism, were found to be upregulated under low-DIC conditions. Likewise, under ammonia limitation, in addition to the expected enhancement of ammonia transporter and PII-gene transcription, the transcription of two novel genes was measurably enhanced (Tcr_0466 and Tcr_2018). Upregulation of all four genes was verified via qRT-PCR (Tcr_1019: 4-fold; Tcr_1315: ~7-fold; Tcr_0466: >200-fold; Tcr_2018: 7-fold), suggesting novel components are part of the response to nutrient limitation by this organism. In this study Thiomicrospira crunogena cells were grown under inorganic carbon limitation and ammonia limitation (high inorganic carbon concentrations) to examine genome wide transcription responses
Project description:Investigation of whole genome gene expression level changes in Lactococcus lactis KCTC 3769T,L. raffinolactis DSM 20443T, L. plantarum DSM 20686T, L. fujiensis JSM 16395T, L. garvieae KCTC 3772T, L. piscium DSM 6634T and L. chungangensis CAU 28T . This proves that transcriptional profiling can facilitate in elucidating the genetic distance between closely related strains. A one chip study using total RNA recovered from of L. raffinolactis DSM 20443T, L. plantarum DSM 20686T, L. fujiensis JSM 16395T, L. garvieae KCTC 3772T, L. piscium DSM 6634T and L. chungangensis CAU 28T . For the the transcriptome of of L. raffinolactis DSM 20443T, L. plantarum DSM 20686T, L. fujiensis JSM 16395T, L. garvieae KCTC 3772T, L. piscium DSM 6634T and L. chungangensis CAU 28T was analyzed using the Lactococcus lactis KCTC 3769T microarray platform
Project description:Experimentally mapped transcriptome structure of Pyrococcus furiosus DSM 3638 by hybridizing total RNA (including RNA species <200 nt) to genome-wide high-density tiling arrays (60 mer probes tiled every 16 nt).
