Sulfurimonas sp. HSL3-2
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PROVIDER: PRJNA1085840 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Expression profiles of Z. mobilis ZM1 strain and ZM4 strain during exponential growth phase.
2004-11-26 | E-MEXP-217 | biostudies-arrayexpress
Project description:Limited functional annotation of the Z. mobilis genome is a current barrier to both basic studies of Z. mobilis and its development as a synthetic-biology chassis. To gain insight, we collected sample-matched multiomics data including RNA-seq, transcription start site sequencing (TSS-seq), termination sequencing (term-seq), ribosome profiling, and label-free shotgun proteomic mass spectrometry across different growth conditions to improve annotation and assign functional sites in the Z. mobilis genome. Proteomics and ribosome profiling informed revisions of protein-coding genes, which included 44 start codon changes and 42 added proteins.
2020-07-10 | PXD016962 | Pride
Project description:Investigation of whole-genome gene expression level changes in RDM-4 strain of Zymomonas mobilis respiration-deficient mutant compared to the wild-type strain. The mutant strains were isolated from the antibiotics-resistant mutants of Z. mobilis ZM6. The RDM strains exhibited much higher ethanol fermentation abilities than the wild-type strain under aerobic conditions. The strains also gained thermotolerance and exhibited higher ethanol productivities at high temperature (39 ºC) under both non-aerobic and aerobic conditions compared with the wild-type strain. To evaluate the mechanisms of aerobic fermentation and thermotolerance of the RDM strain, we performed the microarray experiments.
2010-10-01 | GSE22355 | GEO
Project description:Investigation of whole-genome gene expression level changes in RDM-4 strain of Zymomonas mobilis respiration-deficient mutant compared to the wild-type strain. The mutant strains were isolated from the antibiotics-resistant mutants of Z. mobilis ZM6. The RDM strains exhibited much higher ethanol fermentation abilities than the wild-type strain under aerobic conditions. The strains also gained thermotolerance and exhibited higher ethanol productivities at high temperature (39 ºC) under both non-aerobic and aerobic conditions compared with the wild-type strain. To evaluate the mechanisms of aerobic fermentation and thermotolerance of the RDM strain, we performed the microarray experiments. A four-chip study using total RNA recovered from the shaking cultures of wt and RDM-4 strains grown at 30ºC, a non-aerobic culture of wt strain grown at 30ºC, and a non-aerobic culture of RDM-4 strain grown at 38ºC. Each chip measures the expression level of 1,998 genes from Z. mobilis.
2010-10-01 | E-GEOD-22355 | biostudies-arrayexpress
Project description:Zymomonas mobilis is an important bioenergy organism that has potential to produce biofuels, including ethanol, in high volumes. Here we examined the response of Zymomonas mobilis to various oxidative stresses using genome-scale transcriptomics data. We first examined the transcrpit abundance in WT aerobic growth compared to aerobic grown in paraquat, which forms superoxide. Under anaerobic growth conditions we compared WT Zymomonas mobilis with strains grown in media lacking iron as well as strains lacking iron that were treated with the iron chelator DIP before collection. Finally we examined transcript abundance in cells lacking ZMO_0422 (Rrf2 family transcription factor homolog) and ZMO_1411 (Fur homolog) grown under anaerobic conditions.
2025-11-20 | GSE304360 | GEO
Project description:Deletion of the IscR homolog ZMO_0422 was performed in Zymomonas mobilis to investigate the role of Fe-S cluster biogenesis in Zymomonas. Here we perform genome-wide transcirptomics study to examine transcript chagnes in delta-ZMO_0422 compared to WT Zymomonas mobilis under both aerobic and anaerobic growth conditions.
2025-11-20 | GSE304389 | GEO
Project description:We report the genome changes associated with a Zymomonas mobilis sodium acetate-tolerant mutant (AcR). We used comparative genomics, transcriptomics, and genetics to show nhaA over-expression conferred sodium acetate (NaAc) tolerance in Z. mobilis. We observed a synergistic effect for sodium and acetate ions that enhanced toxicity against the wild-type strain (ZM4), which was not observed for similar concentrations of potassium and ammonium acetate under controlled laboratory conditions. We extended our studies and demonstrated that Saccharomyces cerevisiae sodium-proton antiporter genes contribute to NaAc tolerance for this important ethanologen. The application of classical and systems biology tools is a paradigm for industrial strain improvement and combines benefits of few a priori assumptions with detailed, rapid, mechanistic studies. Finally, our studies reinforce the idea that one obtains what one selects for in mutant screens and that a genetic system is important for industrial strain development.
2010-05-05 | GSE18106 | GEO
Project description:We report the genome changes associated with a Zymomonas mobilis sodium acetate-tolerant mutant (AcR). We used comparative genomics, transcriptomics, and genetics to show nhaA over-expression conferred sodium acetate (NaAc) tolerance in Z. mobilis. We observed a synergistic effect for sodium and acetate ions that enhanced toxicity against the wild-type strain (ZM4), which was not observed for similar concentrations of potassium and ammonium acetate under controlled laboratory conditions. We extended our studies and demonstrated that Saccharomyces cerevisiae sodium-proton antiporter genes contribute to NaAc tolerance for this important ethanologen. The application of classical and systems biology tools is a paradigm for industrial strain improvement and combines benefits of few a priori assumptions with detailed, rapid, mechanistic studies. Finally, our studies reinforce the idea that one obtains what one selects for in mutant screens and that a genetic system is important for industrial strain development. ZM4_ACr_NaCl_NaAc_study. Whole-genome expression profiles of exponential and stationary phase cells were analyzed for the wild-type Zymomonas mobilis ZM4 and the acetate-tolerant mutant AcR under 12g/L sodium acetate and same molar concentration of sodium chloride (8.55g/L) control conditions.
2010-05-05 | E-GEOD-18106 | biostudies-arrayexpress
Project description:Zymomonas mobilis subsp. mobilis strain:NRRL B-1960 Genome sequencing
| PRJNA384222 | ENA
Project description:Zymomonas mobilis subsp. mobilis 2032 genome sequencing
| PRJNA391966 | ENA