scholarly journals Engineering of a Bacillus subtilis Strain with Adjustable Levels of Intracellular Biotin for Secretory Production of Functional Streptavidin

2002 ◽  
Vol 68 (3) ◽  
pp. 1102-1108 ◽  
Author(s):  
Sau-Ching Wu ◽  
Sui-Lam Wong
Keyword(s):  
Bacillus Subtilis ◽  
Binding Sites ◽  
Culture Medium ◽  
Regulatory Region ◽  
Subtilis Strain ◽  
Biotin Deficiency ◽  
Poor Growth ◽  
Biotin Binding

ABSTRACT Streptavidin is a biotin-binding protein which has been widely used in many in vitro and in vivo applications. Because of the ease of protein recovery and availability of protease-deficient strains, the Bacillus subtilis expression-secretion system is an attractive system for streptavidin production. However, attempts to produce streptavidin using B. subtilis face the problem that cells overproducing large amounts of streptavidin suffer poor growth, presumably because of biotin deficiency. This problem cannot be solved by supplementing biotin to the culture medium, as this will saturate the biotin binding sites in streptavidin. We addressed this dilemma by engineering a B. subtilis strain (WB800BIO) which overproduces intracellular biotin. The strategy involves replacing the natural regulatory region of the B. subtilis chromosomal biotin biosynthetic operon (bioWAFDBIorf2) with an engineered one consisting of the B. subtilis groE promoter and gluconate operator. Biotin production in WB800BIO is induced by gluconate, and the level of biotin produced can be adjusted by varying the gluconate dosage. A level of gluconate was selected to allow enhanced intracellular production of biotin without getting it released into the culture medium. WB800BIO, when used as a host for streptavidin production, grows healthily in a biotin-limited medium and produces large amounts (35 to 50 mg/liter) of streptavidin, with over 80% of its biotin binding sites available for future applications.

scholarly journals Genetic and Biochemical Analysis of CodY-Binding Sites in Bacillus subtilis

2007 ◽  
Vol 190 (4) ◽  
pp. 1224-1236 ◽  
Author(s):  
Boris R. Belitsky ◽  
Abraham L. Sonenshein
Keyword(s):  
Bacillus Subtilis ◽  
Lactococcus Lactis ◽  
Binding Sites ◽  
Biochemical Analysis ◽  
Transcriptional Regulator ◽  
Promoter Regions ◽  
Dnase I Footprinting ◽  
Target Dna

ABSTRACT CodY is a global transcriptional regulator that is known to control directly the expression of at least two dozen operons in Bacillus subtilis, but the rules that govern the binding of CodY to its target DNA have been unclear. Using DNase I footprinting experiments, we identified CodY-binding sites upstream of the B. subtilis ylmA and yurP genes. The protected regions overlapped versions of a previously proposed CodY-binding consensus motif, AATTTTCWGAAAATT. Multiple single mutations were introduced into the CodY-binding sites of the ylmA, yurP, dppA, and ilvB genes. The mutations affected both the affinity of CodY for its binding sites in vitro and the expression in vivo of lacZ fusions that carry these mutations in their promoter regions. Our results show that versions of the AATTTTCWGAAAATT motif, first identified for Lactococcus lactis CodY, with up to five mismatches play an important role in the interaction of B. subtilis CodY with DNA.

scholarly journals Methylation of Transcription Factor Binding Sites in the Epstein-Barr Virus Latent Cycle Promoter Wp Coincides with Promoter Down-Regulation during Virus-Induced B-Cell Transformation

2000 ◽  
Vol 74 (22) ◽  
pp. 10468-10479 ◽  
Author(s):  
R. J. Tierney ◽  
H. E. Kirby ◽  
J. K. Nagra ◽  
J. Desmond ◽  
A. I. Bell ◽  
...  
Keyword(s):  
B Cells ◽  
Binding Sites ◽  
Epstein Barr Virus ◽  
Regulatory Region ◽  
Nuclear Antigen ◽  
Regulatory Sequences ◽  
Barr Virus ◽  
Epstein Barr

ABSTRACT Two Epstein-Barr virus latent cycle promoters for nuclear antigen expression, Wp and Cp, are activated sequentially during virus-induced transformation of B cells to B lymphoblastoid cell lines (LCLs) in vitro. Previously published restriction enzyme studies have indicated hypomethylation of CpG dinucleotides in the Wp and Cp regions of the viral genome in established LCLs, whereas these same regions appeared to be hypermethylated in Burkitt's lymphoma cells, where Wp and Cp are inactive. Here, using the more sensitive technique of bisulfite genomic sequencing, we reexamined the situation in established LCLs with the typical pattern of dominant Cp usage; surprisingly, this showed substantial methylation in the 400-bp regulatory region upstream of the Wp start site. This was not an artifact of long-term in vitro passage, since, in cultures of recently infected B cells, we found progressive methylation of Wp (but not Cp) regulatory sequences occurring between 7 and 21 days postinfection, coincident with the period in which dominant nuclear antigen promoter usage switches from Wp to Cp. Furthermore, in the equivalent in vivo situation, i.e., in the circulating B cells of acute infectious mononucleosis patients undergoing primary EBV infection, we again frequently observed selective methylation of Wp but not Cp sequences. An effector role for methylation in Wp silencing was supported by methylation cassette assays of Wp reporter constructs and by bandshift assays, where the binding of two sets of transcription factors important for Wp activation in B cells, BSAP/Pax5 and CREB/ATF proteins, was shown to be blocked by methylation of their binding sites.

scholarly journals Bacillus Subtilis 29784 as a Feed Additive for Broilers Shifts the Intestinal Microbial Composition and Supports the Production of Hypoxanthine and Nicotinic Acid

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1335
Author(s):  
Pearl Choi ◽  
Lamya Rhayat ◽  
Eric Pinloche ◽  
Estelle Devillard ◽  
Ellen De Paepe ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Nicotinic Acid ◽  
16S Rrna Gene Sequencing ◽  
Intestinal Content ◽  
Feed Additive ◽  
Subtilis Strain ◽  
Rrna Gene ◽  
Microbial Composition

The probiotic Bacillus subtilis strain 29784 (Bs29784) has been shown to improve performance in broilers. In this study, we used a metabolomic and 16S rRNA gene sequencing approach to evaluate effects of Bs29874 in the broiler intestine. Nicotinic acid and hypoxanthine were key metabolites that were produced by the strain in vitro and were also found in vivo to be increased in small intestinal content of broilers fed Bs29784 as dietary additive. Both metabolites have well-described anti-inflammatory effects in the intestine. Furthermore, Bs29784 supplementation to the feed significantly altered the ileal microbiome of 13-day-old broilers, thereby increasing the abundance of genus Bacillus, while decreasing genera and OTUs belonging to the Lactobacillaceae and Enterobacteriacae families. Moreover, Bs29784 did not change the cecal microbial community structure, but specifically enriched members of the family Clostridiales VadinBB60, as well as the butyrate-producing families Ruminococcaceae and Lachnospiraceae. The abundance of various OTUs and genera belonging to these families was significantly associated with nicotinic acid levels in the cecum, suggesting a possible cross-feeding between B. subtilis strain 29784 and these beneficial microbes. Taken together, the data indicate that Bs29784 exerts its described probiotic effects through a combined action of its metabolites on both the host and its microbiome.

scholarly journals Regulation of therhaEWRBMAOperon Involved in l-Rhamnose Catabolism through Two Transcriptional Factors, RhaR and CcpA, in Bacillus subtilis

2015 ◽  
Vol 198 (5) ◽  
pp. 830-845 ◽  
Author(s):  
Kazutake Hirooka ◽  
Yusuke Kodoi ◽  
Takenori Satomura ◽  
Yasutaro Fujita
Keyword(s):  
Bacillus Subtilis ◽  
Plant Pathogens ◽  
Bacterial Species ◽  
Regulatory Region ◽  
Regulatory System ◽  
Direct Repeat ◽  
Plant Interactions ◽  
Content Type

ABSTRACTTheBacillus subtilisrhaEWRBMA(formerlyyuxG-yulBCDE) operon consists of four genes encoding enzymes forl-rhamnose catabolism and therhaRgene encoding a DeoR-type transcriptional regulator. DNase I footprinting analysis showed that the RhaR protein specifically binds to the regulatory region upstream of therhaEWgene, in which two imperfect direct repeats are included. Gel retardation analysis revealed that the direct repeat farther upstream is essential for the high-affinity binding of RhaR and that the DNA binding of RhaR was effectively inhibited byl-rhamnulose-1-phosphate, an intermediate ofl-rhamnose catabolism. Moreover, it was demonstrated that the CcpA/P-Ser-HPr complex, primarily governing the carbon catabolite control inB. subtilis, binds to the catabolite-responsive element, which overlaps the RhaR binding site.In vivoanalysis of therhaEWpromoter-lacZfusion in the background ofccpAdeletion showed that thel-rhamnose-responsive induction of therhaEWpromoter was negated by the disruption ofrhaAorrhaBbut notrhaEWorrhaM, whereasrhaRdisruption resulted in constitutiverhaEWpromoter activity. Thesein vitroandin vivoresults clearly indicate that RhaR represses the operon by binding to the operator site, which is detached byl-rhamnulose-1-phosphate formed froml-rhamnose through a sequence of isomerization by RhaA and phosphorylation by RhaB, leading to the derepression of the operon. In addition, thelacZreporter analysis using the strains with or without theccpAdeletion under the background ofrhaRdisruption supported the involvement of CcpA in the carbon catabolite repression of the operon.IMPORTANCESincel-rhamnose is a component of various plant-derived compounds, it is a potential carbon source for plant-associating bacteria. Moreover, it is suggested thatl-rhamnose catabolism plays a significant role in some bacteria-plant interactions, e.g., invasion of plant pathogens and nodulation of rhizobia. Despite the physiological importance ofl-rhamnose catabolism for various bacterial species, the transcriptional regulation of the relevant genes has been poorly understood, except for the regulatory system ofEscherichia coli. In this study, we show that, inBacillus subtilis, one of the plant growth-promoting rhizobacteria, therhaEWRBMAoperon forl-rhamnose catabolism is controlled by RhaR and CcpA. This regulatory system can be another standard model for better understanding the regulatory mechanisms ofl-rhamnose catabolism in other bacterial species.

scholarly journals Interaction of Bacillus subtilis Fur (Ferric Uptake Repressor) with the dhb Operator In Vitro and In Vivo

1999 ◽  
Vol 181 (14) ◽  
pp. 4299-4307 ◽  
Author(s):  
Nada Bsat ◽  
John D. Helmann
Keyword(s):  
Bacillus Subtilis ◽  
Dna Binding ◽  
Rna Polymerase ◽  
Metal Ion ◽  
Regulatory Region ◽  
Binding Activity ◽  
Dna Binding Activity ◽  
Metalloregulatory Proteins

ABSTRACT Bacillus subtilis contains three metalloregulatory proteins belonging to the ferric uptake repressor (Fur) family: Fur, Zur, and PerR. We have overproduced and purified Fur protein and analyzed its interaction with the operator region controlling the expression of the dihydroxybenzoate siderophore biosynthesis (dhb) operon. The purified protein binds with high affinity and selectivity to the dhb regulatory region. DNA binding does not require added iron, nor is binding reduced by dialysis of Fur against EDTA or treatment with Chelex. Fur selectively inhibits transcription from the dhb promoter by ςA RNA polymerase, even if Fur is added after RNA polymerase holoenzyme. Since neither DNA binding nor inhibition of transcription requires the addition of ferrous ion in vitro, the mechanism by which iron regulates Fur function in vivo is not obvious. Mutagenesis of the furgene reveals that in vivo repression of the dhb operon by iron requires His97, a residue thought to be involved in iron sensing in other Fur homologs. Moreover, we identify His96 as a second likely iron ligand, since a His96Ala mutant mediates repression at 50 μM but not at 5 μM iron. Our data lead us to suggest that Fur is able to bind DNA independently of bound iron and that the in vivo role of iron is to counteract the effect of an inhibitory factor, perhaps another metal ion, that antagonizes this DNA-binding activity.

scholarly journals Functional Interaction between the Fab-7 and Fab-8 Boundaries and the Upstream Promoter Region in the Drosophila Abd-B Gene

2008 ◽  
Vol 28 (12) ◽  
pp. 4188-4195 ◽  
Author(s):  
Olga Kyrchanova ◽  
Stepan Toshchakov ◽  
Yulia Podstreshnaya ◽  
Alexander Parshikov ◽  
Pavel Georgiev
Keyword(s):  
Binding Sites ◽  
Regulatory Region ◽  
Upstream Region ◽  
Functional Interaction ◽  
Long Distance ◽  
Functional Interactions ◽  
Upstream Promoter ◽  
Upstream Promoter Region

ABSTRACT Boundary elements have been found in the regulatory region of the Drosophila melanogaster Abdominal-B (Abd-B) gene, which is subdivided into a series of iab domains. The best-studied Fab-7 and Fab-8 boundaries flank the iab-7 enhancer and isolate it from the four promoters regulating Abd-B expression. Recently binding sites for the Drosophila homolog of the vertebrate insulator protein CTCF (dCTCF) were identified in the Fab-8 boundary and upstream of Abd-B promoter A, with no binding of CTCF to the Fab-7 boundary being detected either in vivo or in vitro. Taking into account the inability of the yeast GAL4 activator to stimulate the white promoter when its binding sites are separated by a 5-kb yellow gene, we have tested the functional interactions between the Fab-7 and Fab-8 boundaries and between these boundaries and the upstream promoter A region containing a dCTCF binding site. It has been found that dCTCF binding sites are essential for pairing between two Fab-8 insulators. However, a strong functional interaction between the Fab-7 and Fab-8 boundaries suggests that additional, as yet unidentified proteins are involved in long-distance interactions between them. We have also shown that Fab-7 and Fab-8 boundaries effectively interact with the upstream region of the Abd-B promoter.

In vivo and in vitro evaluation of antifungal activities from a halotolerant Bacillus subtilis strain J9

2012 ◽  
Vol 6 (19) ◽  
pp. 4073-4083 ◽  
Author(s):  
ESSGHAIER Badiaa ◽  
HEDI Abdeljabbar ◽  
Rabeh HAJLAOUI Mohamed ◽  
BOUDABOUS Abdellatif ◽  
SADFI-ZOUAOUI Najla
Keyword(s):  
Bacillus Subtilis ◽  
Subtilis Strain ◽  
In Vitro Evaluation ◽  
Antifungal Activities

scholarly journals Two ResD-Controlled Promoters RegulatectaA Expression in Bacillus subtilis

2001 ◽  
Vol 183 (10) ◽  
pp. 3237-3246 ◽  
Author(s):  
Salbi Paul ◽  
Xiaohui Zhang ◽  
F. Marion Hulett
Keyword(s):  
Bacillus Subtilis ◽  
Stationary Phase ◽  
Binding Site ◽  
Binding Sites ◽  
Promoter Activity ◽  
In Vitro Transcription ◽  
Promoter Deletion Analysis ◽  
Transcription Assays

ABSTRACT The Bacillus subtilis ResDE two-component system plays a positive role in global regulation of genes involved in aerobic and anaerobic respiration. ctaA is one of the several genes involved in aerobic respiration that requires ResD for in vivo expression. The ctaAB-divergent promoter regulatory region has three ResD binding sites; A1, A2, and A3. The A2 site is essential for in vivo promoter activity, while binding sites A2 and A3 are required for full ctaA promoter activity. In this study, we demonstrate the role of ResD∼P in the activation of thectaA promoter using an in vitro transcription system. The results indicate that the ctaA promoter (binding sites A2 and A3) has two transcriptional start sites. Binding site A2 was sufficient for weak transcription of the upstream promoter (Pv) by EςA, transcription which was enhanced approximately 1.5-fold by ResD and 5-fold by ResD∼P. The downstream promoter (Ps) required both binding sites A2 and A3 and was not transcribed by EςA with or without ResD∼P. RNA polymerase (RNAP) isolated from B. subtilis when cells were at the end of exponential growth (T0) or 3, 4, or 5 h into the stationary phase (T3, T4, or T 5, respectively) was used in in vitro transcription assays. Maximal transcription from Ps required T4 RNAP plus ResD∼P. RNAP isolated from a spo0A or a sigE mutant strain was not capable of Ps transcription. Comparison of the Ps promoter sequence with the SigE binding consensus suggests that thectaA Ps promoter may be a SigE promoter. The collective data from ResD footprinting, in vivo promoter deletion analysis, and in vitro transcription assays suggest that ctaA is transcribed during late exponential to early stationary phases of growth from the Pv promoter, which requires ResD binding site A2, EςA, and ResD∼P, and during later stationary phase from Ps, which requires binding sites A2 and A3, ResD∼P, and EςE or a sigma factor whose transcription is dependent on SigE.

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