Differential regulation of the two ferrochelatase paralogues in Shewanella loihica PV-4 in response to environmental stresses
Ontology highlight
ABSTRACT:
ORGANISM(S): Shewanella loihica PV-4
PROVIDER: GSE81743 | GEO | 2016/07/21
SECONDARY ACCESSION(S): PRJNA322557
REPOSITORIES: GEO
Similar Datasets
Project description:The microarray experiment compare the transcriptome of PV-4 wild type versus the deltahemH1 mutant, a PPIX accumulating strain. Only part of the data is used in the manuscript and we are working on this dataset for future manuscripts The wild type and deltahemH1 cell were revived and then cultured into late log-phase for collection, when significant PPIX accumulation occurred. Three biological replicates for wild type and deltahemH1
2016-07-21 | E-GEOD-81743 | biostudies-arrayexpress
Project description:5' RNASeq of mRNA from Shewanella loihica PV-4 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium
2013-03-21 | GSE45316 | GEO
Project description:UnlabelledDetermining the function and regulation of paralogues is important in understanding microbial functional genomics and environmental adaptation. Heme homeostasis is crucial for the survival of environmental microorganisms. Most Shewanella species encode two paralogues of ferrochelatase, the terminal enzyme in the heme biosynthesis pathway. The function and transcriptional regulation of two ferrochelatase genes, hemH1 and hemH2, were investigated in Shewanella loihica PV-4. The disruption of hemH1 but not hemH2 resulted in a significant accumulation of extracellular protoporphyrin IX (PPIX), the precursor to heme, and decreased intracellular heme levels. hemH1 was constitutively expressed, and the expression of hemH2 increased when hemH1 was disrupted. The transcription of hemH1 was regulated by the housekeeping sigma factor RpoD and potentially regulated by OxyR, while hemH2 appeared to be regulated by the oxidative stress-associated sigma factor RpoE2. When an oxidative stress condition was mimicked by adding H2O2 to the medium or exposing the culture to light, PPIX accumulation was suppressed in the ΔhemH1 mutant. Consistently, transcriptome analysis indicated enhanced iron uptake and suppressed heme synthesis in the ΔhemH1 mutant. These data indicate that the two paralogues are functional in the heme synthesis pathway but regulated by environmental conditions, providing insights into the understanding of bacterial response to environmental stresses and a great potential to commercially produce porphyrin compounds.ImportanceShewanella is capable of utilizing a variety of electron acceptors for anaerobic respiration because of the existence of multiple c-type cytochromes in which heme is an essential component. The cytochrome-mediated electron transfer across cellular membranes could potentially be used for biotechnological purposes, such as electricity generation in microbial fuel cells and dye decolorization. However, the mechanism underlying the regulation of biosynthesis of heme and cytochromes is poorly understood. Our study has demonstrated that two ferrochelatase genes involved in heme biosynthesis are differentially regulated in response to environmental stresses, including light and reactive oxygen species. This is an excellent example showing how bacteria have evolved to maintain cellular heme homeostasis. More interestingly, the high yields of extracellular protoporphyrin IX by the Shewanella loihica PV-4 mutants could be utilized for commercial production of this valuable chemical via bacterial fermentation.
| S-EPMC4988212 | biostudies-literature
Project description:5' RNASeq of mRNA from Shewanella loihica PV-4 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium 5'-end mRNA profiles of mid-log phase bacterial cells growing in LB or lactate medium were generated by next-generation sequencing.
2013-03-21 | E-GEOD-45316 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE9640: Transcriptome Profiling of Xanthomonas oryzae pv. oryzae and Xanthomonas oryzae pv. oryzicola on two different medias GSE9643: Transcriptome Profiling of Xanthomonas oryzae pv. oryzae knockout mutants at different hybridization conditions and PMTs Keywords: SuperSeries Refer to individual Series
2010-05-26 | E-GEOD-9658 | biostudies-arrayexpress
Project description:To define the molecular abnormalities at the stem cell level in polycythemia vera (PV), we examined global gene expression in circulating CD34+ cells from 19 JAK2 V617F-positive PV patients and 6 normal individuals using Affymetrix oligonucleotide microarray technology. We observed that CD34+ cell gene expression not only differed between the PV patients and the normal controls but also between men and women PV patients. Based on these gender-specific differences in gene expression, we were able to identify 102 genes differentially regulated concordantly by both men and women, which likely represent a core set of genes whose dysregulation is involved in the pathogenesis of PV. Gene expression was verified by Q-PCR of patient CD34+ cell RNA. Using the 102 gene set and unsupervised hierarchical clustering, the 19 PV patients could be separated in two groups that differed significantly with respect to hemoglobin level, thrombosis frequency, splenomegaly, splenectomy or chemotherapy exposure, leukemic transformation and overall survival. These results were confirmed using top scoring pairs, which identified a different set of 29 genes that independently segregated the 19 patients into the same two clinical groups: those with an aggressive form of the disease (7 patients), and those with an indolent form (12 patients).
2014-08-29 | GSE47018 | GEO
Project description:Aim was to identify novel targets of protoporphyrin-IX (PpIX) after silencing Ferrochelatase (FECH) enzyme. PpIX is a light sensitive metabolite of heme synthesis. Generation of PpIX is increased if FECH activity is suppressed. Here, silencing of FECH leads to down-regulation of PpIX, measured by a decrease of PpIX-specific fluorescence. PpIX is a photosensitizer used for photodynamic treatment of various carcinomas. Increasing PpIX leads to apoptosis of tumor cells.
2019-08-15 | GSE135845 | GEO
Project description:Shewanella loihica PV-4 Transposon Mutagenesis Sequencing
| PRJNA234434 | ENA
Project description:Transcript structures in Shewanella loihica PV-4
| PRJNA193551 | ENA
Project description:To define the molecular abnormalities at the stem cell level in polycythemia vera (PV), we examined global gene expression in circulating CD34+ cells from 19 JAK2 V617F-positive PV patients and 6 normal individuals using Affymetrix oligonucleotide microarray technology. We observed that CD34+ cell gene expression not only differed between the PV patients and the normal controls but also between men and women PV patients. Based on these gender-specific differences in gene expression, we were able to identify 102 genes differentially regulated concordantly by both men and women, which likely represent a core set of genes whose dysregulation is involved in the pathogenesis of PV. Gene expression was verified by Q-PCR of patient CD34+ cell RNA. Using the 102 gene set and unsupervised hierarchical clustering, the 19 PV patients could be separated in two groups that differed significantly with respect to hemoglobin level, thrombosis frequency, splenomegaly, splenectomy or chemotherapy exposure, leukemic transformation and overall survival. These results were confirmed using top scoring pairs, which identified a different set of 29 genes that independently segregated the 19 patients into the same two clinical groups: those with an aggressive form of the disease (7 patients), and those with an indolent form (12 patients). Samples from 19 PV patients (8 men and 11 women) and 6 normal controls (3 men and 3 women) were analyzed using Affymetrix oligonucleotide microarray U133A.
2014-08-29 | E-GEOD-47018 | biostudies-arrayexpress