Transcriptional profiling analysis of Bacillus subtilis in response to high levels of iron (Fe3+)
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ABSTRACT:
ORGANISM(S): Bacillus subtilis Bacillus subtilis subsp. subtilis str. 168
PROVIDER: GSE71694 | GEO | 2015/08/05
SECONDARY ACCESSION(S): PRJNA291831
REPOSITORIES: GEO
Similar Datasets
Project description:Transcriptional profiling analysis was used to reveral the genetic changes of B.subtilis after addition of high levels of iron. This study is to reveal the effect of high levels of iron on B.subtilis' metabolism and identify the potential resistance mechanism to high levels of iron. 1_1 is the independent biological replicate of sample 2_1, while sample 1_2 is the independent biological replicate of sample 2_2. Bacteria collected from each B.subtilis culture at 0min were mixed and used as ch2 source for each sample. The ch1 sources of sample 1_1 and 2_1 are bacteria collected from cultures without addition of Fe3+ at 20min, while the ch1 sources of sample 2_1 and 2_2 are bacteria collected from cultures with addition of 4mM Fe3+ at 20min.
2015-08-05 | E-GEOD-71694 | biostudies-arrayexpress
Project description:Bacterial cells often modulate their transcriptional profiles in response to the changes in iron availability. Ferric uptake regulator (Fur), as a global iron biosensor, plays a central role in maintaining iron homeostasis in Bacillus subtilis. Here we utilized a high affinity Fe2+ efflux transporter, Listeria monocytogenes FrvA, as an inducible genetic tool to deplete intracellular iron. We then characterized the responses of the Fur, FsrA, and PerR regulons as cells transition from iron sufficiency to deficiency. Our results indicate that the Fur regulon is derepressed in three distinct waves. First, elemental iron uptake (ywbLMN), ferric citrate uptake (ymfCDEF-yhfQ), and petrobactin uptake (yclNOPQ) systems are induced to prevent iron deficiency. Second, B. subtilis synthesizes its own siderophore bacillibactin (dhbACEBF) and turns on bacillibactin uptake (feuABC-yusV) along with flavodoxin (ykuNOP) and hydroxamate siderophore uptake (fhuBCGD-yxeB) to scavenge iron from the environment. Third, as iron levels decline further, an iron sparing response (fsrA, fbpAB, and fbpC) is induced to block the translation of nonessential iron-using proteins and permit only essential iron-dependent enzymes to utilize the limited iron. ChIP experiments demonstrate that in vivo occupancy of Fur correlates with derepression of each operon, and the graded response observed here results, at least in part, from higher affinity binding of Fur to the late induced genes. These results provide insights into the distinct roles of Fur-regulated target genes as intracellular iron levels decline.
2017-06-30 | GSE100668 | GEO
Project description:Transcriptome analysis of B.subtilis in response to cyclic lipopeptide antibiotic (fusaricidin)
2015-07-15 | GSE70916 | GEO
Project description:Transcriptional profiling analysis of Bacillus subtilis in response to high levels of iron (Fe3+)
| PRJNA291831 | ENA
Project description:Comparison of expression of known 'iron' genes in liver, spleen and duodenum of C57BL/6J and SWR mouse strains which have low and high basal iron levels respectively.
2006-07-11 | E-MEXP-486 | biostudies-arrayexpress
Project description:Bacillus subtilis strain AG174 was grown in the presence and absence of benzoate (30 mM). Benzoate was used in order to equalize the external and internal pH. The cultures were grown at external pH 7.0, and the addition of benzoate did not change the external pH. Microarray analysis was performed on cDNA synthesized from bacterial RNA. Real-time PCR of highly up-regulated genes confirmed the results of the microarray. These data were compared to previous B.subtilis microarray results, where genes regulated by external pH were identified.
2009-12-01 | GSE12263 | GEO
Project description:Proteome analysis of Bacillus subtilis cells grown at low and high salinity revealed the induction of 16 protein spots and the repression of 2 protein spots, respectively. Most of these protein spots were identified by mass spectrometry. Four of the 16 high-salinity-induced proteins corresponded to DhbA, DhbB, DhbC, and DhbE, enzymes that are involved in the synthesis of 2,3-dihydroxybenzoate (DHB) and its modification and esterification to the iron siderophore bacillibactin. These proteins are encoded by the dhbACEBF operon, which is negatively controlled by the central iron regulatory protein Fur and is derepressed upon iron limitation. We found that iron limitation and high salinity derepressed dhb expression to a similar extent and that both led to the accumulation of comparable amounts of DHB in the culture supernatant. DHB production increased linearly with the degree of salinity of the growth medium but could still be reduced by an excess of iron. Such an excess of iron also partially reversed the growth defect exhibited by salt-stressed B. subtilis cultures. Taken together, these findings strongly suggest that B. subtilis cells grown at high salinity experience iron limitation. In support of this notion, we found that the expression of several genes and operons encoding putative iron uptake systems was increased upon salt stress. The unexpected finding that high-salinity stress has an iron limitation component might be of special ecophysiological importance for the growth of B. subtilis in natural settings, in which bioavailable iron is usually scarce.
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Project description:The aim of our study is to elucidate the gene expression changes in rice in response to colonization by a plant growth promoting rhizobacteria such as the Bacillus subtilis through microarray high throughput technology. In particular, the effect of B.subtilis on root exudation (secretion of phytochemicals through roots) will be analysed. For this rice plantlets were grown in hydroponics and treated with B.subtilis RR4 for 48 hrs. The root samples of the control and treated plants were then used for the microarray experiment. The data obtained through microarray revealed genes related to cell wall modification, phytohormone synthesis, defense response, root exudation, etc. to be differentially regulated in response to B.subtilis RR4. Real time PCR analysis of few chosen genes (OsMS, OsALMT, OsABC, OsSDH, etc) also confirmed the validity of the microarray data. The initial responses of a plant in response to colonization by the microbe will be changes in cell wall of the plant tissues and the secretion of phytochemicals to attract/repel the colonizing beneficial/pathogenic organism. From analysis of microarray data we found the cell wall related genes which aid in root colonization and the root exudate related genes (biosynthesis and transport) which play a role in providing nutrition for the bacterial growth to be differentially regulated significantly. Analysis of specific genes and their biosynthesis pathways indicated that rice plants responded positively to root colonization by B.subtilis RR4. Notable among the exudation related genes such as Malate synthase and ALMT were found to be upregulated which indicates the significant role played by organic acids particularly malate in recruiting the PGPR towards the plant roots. This recruitment will thereby facilitate plant growth. Subsequently, these genes can be engineered in crop plants to recruit beneficial bacteria which might further open new avenues for improved crop production.
2017-01-05 | GSE80800 | GEO
Project description:The sigma(B)-dependent general stress response in the common soil bacterium Bacillus subtilis can be elicited by a range of stress factors, such as starvation or an ethanol-, salt-, or heat-shock, via a complex upstream signaling cascade. Additionally, sigma(B) can be activated by blue light, via the phototropin homologue YtvA, a component of the environmental branch of the signaling cascade. The genome-wide transcriptomes of B. subtilis reported here show that sigma(B) can activated by blue as well as red light via RsbP/RspQ, the energy branch of sigma(B) upstream signaling cascade. A 16 chip genome-wide expression study using RNA recovered from B.subtilis strain PB565/pYtvA under light and dark conditions before and after induction with IPTG, and from B.subtilis strain PB565 under light and dark conditions. Each B.subtilis subsp. subtilis strain 168 NC_000964 chip measures the expression level of 4,104 genes in two-fold from with eight 60-mer probe pairs (PM/MM) per gene.
2010-05-16 | E-GEOD-19464 | biostudies-arrayexpress
Project description:Expression analysis of GFP+ and GFP- populations of B.subtilis strain DS901
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