| 1. |
- Pagels, Martin, et al.
(författare)
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Redox sensing by a Rex-family repressor is involved in the regulation of anaerobic gene expression in Staphylococcus aureus
- 2010
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Ingår i: Molecular Microbiology. - : Wiley. - 1365-2958 .- 0950-382X. ; 76:5, s. 1142-1161
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Tidskriftsartikel (refereegranskat)abstract
- P>An alignment of upstream regions of anaerobically induced genes in Staphylococcus aureus revealed the presence of an inverted repeat, corresponding to Rex binding sites in Streptomyces coelicolor. Gel shift experiments of selected upstream regions demonstrated that the redox-sensing regulator Rex of S. aureus binds to this inverted repeat. The binding sequence - TTGTGAAW(4)TTCACAA - is highly conserved in S. aureus. Rex binding to this sequence leads to the repression of genes located downstream. The binding activity of Rex is enhanced by NAD+ while NADH, which competes with NAD+ for Rex binding, decreases the activity of Rex. The impact of Rex on global protein synthesis and on the activity of fermentation pathways under aerobic and anaerobic conditions was analysed by using a rex-deficient strain. A direct regulatory effect of Rex on the expression of pathways that lead to anaerobic NAD+ regeneration, such as lactate, formate and ethanol formation, nitrate respiration, and ATP synthesis, is verified. Rex can be considered a central regulator of anaerobic metabolism in S. aureus. Since the activity of lactate dehydrogenase enables S. aureus to resist NO stress and thus the innate immune response, our data suggest that deactivation of Rex is a prerequisite for this phenomenon.
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| 2. |
- Aggarwal, Swati, et al.
(författare)
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A protocol for production of perdeuterated OmpF porin for neutron crystallography
- 2021
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Ingår i: Protein Expression and Purification. - : Elsevier BV. - 1046-5928. ; 188
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Tidskriftsartikel (refereegranskat)abstract
- Hydrogen atoms are at the limit of visibility in X-ray structures even at high resolution. Neutron macromolecular crystallography (NMX) is an unambiguous method to locate hydrogens and study the significance of hydrogen bonding interactions in biological systems. Since NMX requires very large crystals, very few neutron structures of proteins have been determined yet. In addition, the most common hydrogen isotope 1H gives rise to significant background due to its large incoherent scattering cross-section. Therefore, it is advantageous to substitute as many hydrogens as possible with the heavier isotope 2H (deuterium) to reduce the sample volume requirement. While the solvent exchangeable hydrogens can be substituted by dissolving the protein in heavy water, complete deuterium labelling – perdeuteration – requires the protein to be expressed in heavy water with a deuterated carbon source. In this work, we developed an optimized method for large scale production of deuterium-labelled bacterial outer membrane protein F (OmpF) for NMX. OmpF was produced using deuterated media with different carbon sources. Mass spectrometry verified the integrity and level of deuteration of purified OmpF. Perdeuterated OmpF crystals diffracted X-rays to a resolution of 1.9 Å. This work lays the foundation for structural studies of membrane protein by neutron diffraction in future.
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| 3. |
- Al-Eryani, Yusra, et al.
(författare)
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Exploring structure and interactions of the bacterial adaptor protein YjbH by crosslinking mass spectrometry
- 2016
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Ingår i: Proteins: Structure, Function and Genetics. - : Wiley. - 0887-3585. ; 84:9, s. 1234-1245
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Tidskriftsartikel (refereegranskat)abstract
- Adaptor proteins assist proteases in degrading specific proteins under appropriate conditions. The adaptor protein YjbH promotes the degradation of an important global transcriptional regulator Spx, which controls the expression of hundreds of genes and operons in response to thiol-specific oxidative stress in Bacillus subtilis. Under normal growth conditions, the transcription factor is bound to the adaptor protein and therefore degraded by the AAA+ protease ClpXP. If this binding is alleviated during stress, the transcription factor accumulates and turns on genes encoding stress-alleviating proteins. The adaptor protein YjbH is thus a key player involved in these interactions but its structure is unknown. To gain insight into its structure and interactions we have used chemical crosslinking mass spectrometry. Distance constraints obtained from the crosslinked monomer were used to select and validate a structure model of YjbH and then to probe its interactions with other proteins. The core structure of YjbH is reminiscent of DsbA family proteins. One lysine residue in YjbH (K177), located in one of the α-helices outside the thioredoxin fold, crosslinked to both Spx K99 and Spx K117, thereby suggesting one side of the YjbH for the interaction with Spx. Another lysine residue that crosslinked to Spx was YjbH K5, located in the long and presumably very flexible N-terminal arm of YjbH. Our crosslinking data lend support to a model proposed based on site-directed mutagenesis where the YjbH interaction with Spx can stabilize and present the C-terminal region of Spx for protease recognition and proteolysis. Proteins 2016; 84:1234–1245.
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| 4. |
- Alferov, Sergey, et al.
(författare)
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Electrical communication of cytochrome enriched Escherichia coli JM109 cells with graphite electrodes
- 2009
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Ingår i: Electrochimica Acta. - : Elsevier BV. - 0013-4686 .- 1873-3859. ; 54:22, s. 4979-4984
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Konferensbidrag (refereegranskat)abstract
- In the present study three different strains of Escherichia coli (JM 109 - a native "wild type" strain, JM 109/pBSD 1300 - a strain overproducing the membrane anchor domain of Bacillus subtilis succinate-quinone reductase, SQR, a protein that contains two transmembraneously arranged heme groups and JM109/pLUV 1900 - a strain overproducing cytochrome c(550) from B. subtilis, a protein where the cytochrome domain is anchored to the membrane with a transmembrane helix) were immobilised on the surface of a spectrographic graphite electrode and tested for electrical communication using mediators. Such compounds as ferricyanide, 2,6-dichlorophenolindophenol (DCPIP) and ubiquinone (Q(0)) were used as soluble mediators and two flexible osmium redox polymers; poly(1-vinylimidazole)(12)-[Os-(4,4'-dimethyl-2,2'-di'pyridyl)(2)Cl-2](2 +/+) (osmium redox polymer I) and poly(vinylpyridine)-[Os-(N,N'-methylated-2,2'-biimidazole)(3)](2+/3+) (osmium redox polymer II) were co-immobilised with the bacterial cells onto the electrode surface. The effects of applied potential, buffer pH and different substrates were compared for the different combinations bacterial strains - mediators. Through the introduction of the cytochromes in the bacterial membrane it was established that it had great effect on the ability of the bacterial cells to effectively communicate with artificial mediators. The introduction of the transmembraneously arranged heme groups of B. subtilis made it possible for this strain to communicate with the Os-polymers, whereas the introduction of the cytochrome c(550) had an effect especially increasing ability of Q(0) to act as an efficient e(-) acceptor. (C) 2009 Elsevier Ltd. All rights reserved.
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| 5. |
- Awad, Wael, et al.
(författare)
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Structural Basis for YjbH Adaptor-Mediated Recognition of Transcription Factor Spx
- 2019
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Ingår i: Structure. - : Elsevier BV. - 0969-2126. ; 27:6, s. 6-936
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Tidskriftsartikel (refereegranskat)abstract
- YjbH is a bacterial adaptor protein required for efficient proteolysis of the RNA polymerase-binding transcription factor Spx by the ClpXP protease. We report the structure of YjbH in complex with Spx. YjbH comprises a DsbA-like thioredoxin domain connected via a linker to a C-terminal domain reminiscent of the winged helix-turn-helix fold. The interaction between YjbH and Spx involves a large surface area. Binding to YjbH stabilizes the C-terminal ClpX recognition region of Spx. We show that mutation of critical YjbH contact residues abrogates Spx recognition. Small-angle X-ray scattering and hydrogen-deuterium exchange mass spectrometry analyses determined the existence of a stable heterodimeric complex in solution and provide evidence that binding of Spx to YjbH reduces the overall conformational flexibility of Spx. Our findings provide insights into the molecular basis for Spx recognition and suggest a model for how YjbH stabilizes Spx and displays the C terminus of Spx for engagement by ClpXP. Awad et al. determined the crystal structure of the ClpXP adaptor protein YjbH in complex with the transcription factor Spx. Structural dynamics of the complex were investigated by hydrogen-deuterium exchange mass spectrometry. The insights provided in this work add molecular details to the recognition of Spx by YjbH.
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| 6. |
- Azarkina, Natalia, et al.
(författare)
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A bb´-type quinol oxidase in Bacillus subtilis strain 168
- 1999
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Ingår i: Journal of Biological Chemistry. - : Elsevier BV. - 1083-351X .- 0021-9258. ; 274, s. 32810-32817
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Tidskriftsartikel (refereegranskat)abstract
- The aerobic respiratory system of Bacillus subtilis 168 is known to contain three terminal oxidases: cytochrome caa3, which is a cytochrome c oxidase, and cytochrome aa3 and bd, which are quinol oxidases. The presence of a possible fourth oxidase in the bacterium was investigated using a constructed mutant, LUH27, that lacks the aa3 and caa3 terminal oxidases and is also deficient in succinate:menaquinone oxidoreductase. The cytochrome bd content of LUH27 can be varied by using different growth conditions. LUH27 membranes virtually devoid of cytochrome bd respired with NADH or exogenous quinol as actively as preparations containing 0.4 nmol of cytochrome bd/mg of protein but were more sensitive to cyanide and aurachin D. The reduced minus oxidized difference spectra of the bd-deficient membranes as well as absorption changes induced by CO and cyanide indicated the presence of a 'cytochrome o'-like component; however, the membranes did not contain heme O. The results provide strong evidence for the presence of a terminal oxidase of the bb' type in B. subtilis. The enzyme does not pump protons and combines with CO much faster than typical heme-copper oxidases; in these respects, it resembles a cytochrome bd rather than members of the heme-copper oxidase superfamily. The genome sequence or B. subtilis 168 contains gene clusters for four respiratory oxidases. Two of these clusters, cta and qox, are deleted in LUH27. The remaining two, cydAB and ythAB, encode the identified cytochrome bd and a putative second cytochrome bd, respectively. Deletion of ythAB in strain LUH27 or the presence of the yth genes on plasmid did not affect the expression of the bb' oxidase. It is concluded that the novel bb'- type oxidase probably is cytochrome bd encoded by the cyd locus but with heme D being substituted by high spin heme B at the oxygen reactive site, i.e. cytochrome b558b595b'.
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| 7. |
- Belitsky, B R, et al.
(författare)
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An lrp-like gene of Bacillus subtilis involved in branched-chain amino acid transport
- 1997
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Ingår i: Journal of Bacteriology. - 0021-9193. ; 179:17, s. 5448-5457
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Tidskriftsartikel (refereegranskat)abstract
- The azlB locus of Bacillus subtilis was defined previously by a mutation conferring resistance to a leucine analog, 4-azaleucine (J. B. Ward, Jr., and S. A. Zahler, J. Bacteriol. 116:727-735, 1973). In this report, azlB is shown to be the first gene of an operon apparently involved in branched-chain amino acid transport. The product of the azlB gene is an Lrp-like protein that negatively regulates expression of the azlBCDEF operon. Resistance to 4-azaleucine in azlB mutants is due to overproduction of AzlC and AzlD, two novel hydrophobic proteins.
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| 8. |
- Bengtsson, Jenny, et al.
(författare)
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CtaG is required for formation of active cytochrome C oxidase in Bacillus subtilis
- 2004
-
Ingår i: Microbiology. - : Microbiology Society. - 1465-2080 .- 1350-0872. ; 150, s. 415-425
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Tidskriftsartikel (refereegranskat)abstract
- The Gram-positive bacterium Bacillus subtilis contains two respiratory oxidases of the haem-copper superfamily: cytochrome aa(3), which is a quinol oxidase, and cytochrome caa(3), which is a cytochrome c oxidase. Cytochrome c oxidase uniquely contains a di-copper centre, Cu-A. B. subtilis CtaG is a membrane protein encoded by the same gene cluster as that which encodes the subunits of cytochrome c oxidase. The role of B. subtilis CrtaG and orthologous proteins present in many other Gram-positive bacteria has remained unexplored. The sequence of CtaG is unrelated to that of CtaG/Cox11p, of proteobacteria and eukaryotic cells. This study shows that B. subtilis CtaG is essential for the formation of active cytochrome caa(3) but is not required for assembly of the core subunits I and II with haem in the membrane and it has no role in the synthesis of active cytochrome aa(3). B. subtilis YpmQ, a homologue to Sco1p of eukaryotic cells, is also a membrane-bound cytochrome c oxidase-specific assembly factor. Properties of CtaG- and YpmQ-deficient mutants were compared. Cells lacking YpmQ showed a low cytochrome c oxidase activity and this defect was suppressed by the supplementation of the growth medium with copper ions. It has previously been proposed that YpmQ/Sco1p is involved in synthesis of the Cu-A centre. The results of this study are consistent with this proposal but the exact role of YpmQ in assembly of cytochrome c oxidase remains to be elucidated.
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| 9. |
- Coman, Vasile, et al.
(författare)
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Electrical wiring of live, metabolically enhanced Bacillus subtilis cells with flexible osmium-redox polymers.
- 2009
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 131:44, s. 16171-16176
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Tidskriftsartikel (refereegranskat)abstract
- The present study explores genetic engineering of the respiratory chain and the application of two different flexible osmium redox polymers to achieve efficient electric communication between the gram-positive organism Bacillus subtilis and an electrode. Poly(1-vinylimidazole)(12)-[Os-(4,4'-dimethyl-2,2'-bipyridyl)(2)Cl(2)](+/2+) (osmium redox polymer I) and poly(vinylpyridine)-[Os-(N,N'-methylated-2,2'-biimidazole)(3)](2+/3+) (osmium redox polymer II) were investigated for efficient electrical "wiring" of viable gram-positive bacterial cells to electrodes. Using a B. subtilis strain that overproduces succinate/quinone oxidoreductase (respiratory complex II), we were able to improve the current response several fold using succinate as substrate, in both batch and flow analysis modes, and using gold and graphite electrodes. The efficiency of the osmium redox polymer, working as electron transfer mediator between the cells and the electrode, was compared with that of a soluble mediator (hexacyanoferrate). The results demonstrated that mediators did not have to pass the cytosolic membrane to bring about an efficient electronic communication between bacterial cells with a thick cell wall and electrodes.
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| 10. |
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| 11. |
- Engman, Jakob, et al.
(författare)
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Regulated protein aggregation, a mechanism to control the activity of the ClpXP adaptor protein YjbH.
- 2015
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Ingår i: Molecular Microbiology. - : Wiley. - 1365-2958 .- 0950-382X. ; 95:1, s. 51-63
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Tidskriftsartikel (refereegranskat)abstract
- Bacteria use stress response pathways to activate diverse target genes to react to a variety of stresses. The Bacillus subtilis Spx protein is a global transcriptional regulator that controls expression of more than 140 genes and operons in response to thiol-specific oxidative stress. Under non-stress conditions the concentration of Spx is kept low by proteolysis catalyzed by the ClpXP complex. Spx protein levels increase in response to disulfide stress, and decrease when the cells cope with the stress. The cytosolic adaptor protein YjbH is required to target Spx for efficient proteolysis by ClpXP. We demonstrate that YjbH aggregates in response to disulfide stress, that is, the YjbH protein is soluble under non-stressed conditions and destabilized during stress leading to aggregation. Stress conditions (heat and ethanol) that cause severe perturbations in protein stability/folding also induced aggregation of YjbH and led to induction of Spx. By heterologous expression of a less aggregation prone YjbH homolog Spx induction was abolished. Thus we show that moderation of YjbH solubility is an important mechanism of signal transduction and represents a new mechanism of controlling the activity of adaptor proteins.
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| 12. |
- Engman, Jakob, et al.
(författare)
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The YjbH adaptor protein enhances proteolysis of the transcriptional regulator Spx in Staphylococcus aureus.
- 2012
-
Ingår i: Journal of Bacteriology. - 0021-9193. ; 194:5, s. 1186-1194
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Tidskriftsartikel (refereegranskat)abstract
- Spx is a global regulator that is widespread among the low G+C Gram-positive bacteria. Spx has been extensively studied in Bacillus subtilis, where it acts as an activator and a repressor of transcription in response to disulfide stress. Under non-stress conditions, Spx is rapidly degraded by the ClpXP protease. This degradation is enhanced by the YjbH adaptor protein. Upon disulfide stress, the amount of Spx rapidly increases due to a decrease in degradation. In the opportunistic pathogen Staphylococcus aureus, Spx is a global regulator influencing growth, biofilm formation and general stress protection, and cells lacking the spx gene exhibit poor growth also under non-stress conditions. To investigate the mechanism by which the activity of Spx is regulated we identified a homolog in S. aureus of the B. subtilis yjbH gene. The gene encodes a protein that shows approximately 30% sequence identity to YjbH of B. subtilis. Heterologous expression of S. aureus yjbH in a B. subtilis yjbH mutant restored Spx to wild type levels both under non-stress conditions and under conditions of disulfide stress. From these studies we conclude that the two YjbH homologues have a conserved physiological function. Accordingly, inactivation of yjbH in S. aureus increased the level of Spx protein and transcription of the Spx-regulated gene trxB. Notably, the yjbH mutant exhibited reduced growth and increased pigmentation, and both phenotypes were reversed by complementation of the yjbH gene.
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| 13. |
- Fapyane, Deby, et al.
(författare)
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Gated electron transfer reactions of truncated hemoglobin from Bacillus subtilis differently orientated on SAM-modified electrodes
- 2015
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Ingår i: Physical Chemistry Chemical Physics. - : Royal Society of Chemistry (RSC). - 1463-9084 .- 1463-9076. ; 17:23, s. 15365-15374
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Tidskriftsartikel (refereegranskat)abstract
- Electron transfer (ET) reactions of truncated hemoglobin from Bacillus subtilis (trHb-Bs) are suggested to be implicated in biological redox signalling and actuating processes that may be used in artificial environment-sensing bioelectronic devices. Here, kinetics of ET in trHb-Bs covalently attached via its surface amino acid residues either to COOH- or NH2-terminated (CH2)(2-16) alkanethiol SAM assembled on gold are shown to depend on the alkanethiol length and functionalization, not being limited by electron tunnelling through the SAMs but gated by ET preceding reactions due to conformational changes in the heme active site/at the interface. ET gating was sensitive to the properties of SAMs that trHb-Bs interacted with. The ET rate constant k(s) for a 1e(-)/H+ reaction between the SAM-modified electrode and heme of trHb-Bs was 789 and 110 s(-1) after extrapolation to a zero length SAM, while the formal redox potential shifted 142 and 31 mV, for NH2- and COOH-terminated SAMs, respectively. Such domain-specific sensitivity and responsivity of redox reactions in trHb-Bs may be of immediate biological relevance and suggest the existence of bioelectronic regulative mechanisms of ET proceeding in vivo at the protein-protein charged interfaces that modulate the protein reactivity in biological redox signalling and actuating events.
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| 14. |
- Fernandez, Esther, et al.
(författare)
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Electron transfer reactions, cyanide and O-2 binding of truncated hemoglobin from Bacillus subtilis
- 2013
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Ingår i: Electrochimica Acta. - : Elsevier BV. - 0013-4686. ; 110, s. 86-93
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Tidskriftsartikel (refereegranskat)abstract
- The truncated hemoglobin from Bacillus subtilis (trHb-Bs) possesses a surprisingly high affinity for oxygen and resistance to (auto)oxidation; its physiological role in the bacterium is not understood and may be connected with its very special redox and ligand binding reactions. Electron transfer reactions of trHb-Bs were electrochemically studied in solution and at graphite electrodes. Spectrophotometrical potentiometric titration and direct electrochemical measurements gave a heme iron redox potential of -103 +/- 4 mV and -108 +/- 2 mV vs. NHE, at pH 7, respectively. The redox potential of the heme in trHb-Bs shifted -59 mV per pH unit at pH higher than 7, consistently with a 1e(-)/1H(+) - transfer reaction. The heterogeneous rate constant k(s), for a quasi-reversible 1e(-)-1H(+) - transfer reaction between graphite and trHb-Bs was 10.1 +/- 2.3 s(-1). Upon reversible cyanide binding the ks doubled, while the redox potential of heme shifted 21 mV negatively, presumably reflecting changes in redox activity and in vivo signaling functions of trHb-Bs associated with ligand binding Bioelectrocatalytic reduction of O-2 catalyzed by trHb-Bs was one of the most efficient hitherto reported for Hbs, with an apparent catalytic rate constant, k(cat), of 56 +/- 6s(-1). The results obtained are of particular interest for applications of trHb in environmental biosensing and toxicity screening. (C) 2013 Elsevier Ltd. All rights reserved.
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| 15. |
- Franza, Thierry, et al.
(författare)
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NAD+ pool depletion as a signal for the Rex regulon involved in Streptococcus agalactiae virulence
- 2021
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Ingår i: PLoS Pathogens. - : Public Library of Science (PLoS). - 1553-7366 .- 1553-7374. ; 17:8
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Tidskriftsartikel (refereegranskat)abstract
- In many Gram-positive bacteria, the redox-sensing transcriptional repressor Rex controls central carbon and energy metabolism by sensing the intra cellular balance between the reduced and oxidized forms of nicotinamide adenine dinucleotide; the NADH/NAD+ ratio. Here, we report high-resolution crystal structures and characterization of a Rex ortholog (Gbs1167) in the opportunistic pathogen, Streptococcus agalactiae, also known as group B streptococcus (GBS). We present structures of Rex bound to NAD+ and to a DNA operator which are the first structures of a Rex-family member from a pathogenic bacterium. The structures reveal the molecular basis of DNA binding and the conformation alterations between the free NAD+ complex and DNA-bound form of Rex. Transcriptomic analysis revealed that GBS Rex controls not only central metabolism, but also expression of the monocistronic rex gene as well as virulence gene expression. Rex enhances GBS virulence after disseminated infection in mice. Mechanistically, NAD+ stabilizes Rex as a repressor in the absence of NADH. However, GBS Rex is unique compared to Rex regulators previously characterized because of its sensing mechanism: we show that it primarily responds to NAD+ levels (or growth rate) rather than to the NADH/NAD+ ratio. These results indicate that Rex plays a key role in GBS pathogenicity by modulating virulence factor gene expression and carbon metabolism to harvest nutrients from the host.
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| 16. |
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| 17. |
- Glader, Pernilla, et al.
(författare)
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Cigarette smoke extract modulates respiratory defence mechanisms through effects on T-cells and airway epithelial cells.
- 2006
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Ingår i: Respiratory Medicine. - : Elsevier BV. - 1532-3064 .- 0954-6111. ; 100:5, s. 818-827
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Tidskriftsartikel (refereegranskat)abstract
- Chronic obstructive pulmonary disease (CCPD) is a disease primarily caused by cigarette smoking, which in turn has been shown to affect the susceptibility to and progression of airway infections. The question addressed in this study was how components from cigarette smoke could affect the defence mechanisms of T-cells and epithelial cells, and thereby contribute to the development of the COPD pathology. T-cells and monocytes were isolated from buffycoats from healthy donors and T-cell responses studied in response to cigarette smoke extract (CSE). Activation level (CD25 expression), proliferation (BrdU incorporation) and intracellular expression of the cytotoxic markers granzyme-b and TIA-1 were determined using flowcytometry. Normal human bronchial epithelial cells were obtained from Cambrex and differentiated in air-liquid interface cultures. After exposure to CSE barrier function (trans-epithelial electric resistance, TEER), MUC5AC and interleukin-8 production were measured. T-cell activation, proliferation and expression of the cytotoxic proteins granzyme-b and TIA-1 were significantly reduced in response to 0.5-1% of CSE. The epithelial cells were more resistant to CSE and responded at doses 20 times higher than T-cells. The expression of interteukin-8 and MUC5AC was significantly increased after exposure to 15% and 30% CSE and TEER was largely unaffected at 30% CSE but clearly reduced at 40% CSE. This study shows that mechanisms, in both T-cells and airway epithelial cells, involved in the defence against infectious agents are modulated by CSE. (c) 2005 Elsevier Ltd. All rights reserved.
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| 18. |
- Glader, Pernilla, et al.
(författare)
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Systemic CD4+ T-cell activation is correlated with FEV(1) in smokers.
- 2006
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Ingår i: Respiratory Medicine. - : Elsevier BV. - 1532-3064 .- 0954-6111. ; 100:6, s. 1088-1093
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Tidskriftsartikel (refereegranskat)abstract
- The inflammation of the lungs in chronic obstructive pulmonary disease (COPD) is characterised by increased numbers of macrophages, neutrophils and T-cells. Decline in lung function in these patients has been correlated to the number of CD8+ T-cells present in the lung as well as to a decline in the ratio of CD4+/CD8+ T-cells. Although systemic components are likely to be present, circulating lymphocyte populations in COPD patients have not been well characterised. This study aimed at correlating lung function to expression of five different T-cell activation markers on peripheral blood CD4+ and CD8+ T-cells in COPD patients and matched smokers. Furthermore, proportions of lymphocyte populations and degree of systemic T-cell activation in COPD patients were compared to that in smokers and never-smokers. Peripheral blood lymphocytes from six never-smokers, eight smokers and 17 smokers with COPD were analysed using flowcytometry. The number of lymphocytes per millilitre was higher in smokers than in never-smokers. No differences were found between the three groups in regard to proportions of lymphocyte populations, but the number of CD4+ T-cells in smokers was higher than in both never-smokers and COPD patients. The degree of T-cell activation was similar in all patient groups; however, a clear correlation between CD69 expression on CD4+ T-cells and lung function (FEV1% of predicted) was found when examining current smokers, with or without COPD. Elevated numbers of CD69+ CD4+ T-cells in blood thus seem to be protective against airway obstruction in smokers while still exposed to cigarette smoke, the main inducer of COPD.
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| 19. |
- Green, AJ, et al.
(författare)
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Expression, purification and characterisation of a Bacillus subtilis ferredoxin: a potential electron transfer donor to cytochrome P450 BioI
- 2003
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Ingår i: Journal of Inorganic Biochemistry. - 1873-3344. ; 93:1-2, s. 92-99
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Tidskriftsartikel (refereegranskat)abstract
- The fer gene from Bacillus subtilis has been subcloned and overexpressed in Escherichia coli and the protein (Fer) purified to homogeneity. N-Terminal sequencing and mass spectrometry indicate that the initiator methionine is removed from the protein and that the molecular mass is 8732 Da consistent with that deduced from the gene sequence. Amino-acid sequence comparisons indicate that Fer is a ferredoxin containing a 4Fe-4S cluster. The electron paramagnetic resonance spectrum of the reduced form of Fer is typical for a [4Fe-4S](+) cluster showing rhombic signals with g values of 2.07, 1.93 and 1.88. Reduced Fer also gives rise to a magnetic circular dichroism spectrum typical of a [4Fe-4S] + cluster. Potentiometric titrations indicate that Fer has a reduction potential of -385 +/- 10 MV for the [4Fe-4S](+) -[4Fe-4S](2+) redox couple, well within the normal range expected for such a ferredoxin. A proposed physiological role for Fer is as an electron donor to cytochrome P450 BioI. Studies on Fer binding to P450 BioI give rise to a K-d value of 0.87 +/- 0.10 muM. Anaerobic experiments using CO-saturated buffer indicate that Fer is indeed capable of transferring electrons to this cytochrome P450 albeit at a fairly low rate. (C) 2002 Elsevier Science Inc. All rights reserved.
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| 20. |
- Gustafsson, Mattias, et al.
(författare)
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A novel diffusible substance can overcome the apparent AbrB repression of the Bacillus subtilis fatR promoter
- 2001
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Ingår i: FEMS Microbiology Letters. - 1574-6968. ; 199:2, s. 197-202
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Tidskriftsartikel (refereegranskat)abstract
- In this work we present evidence for a novel diffusible extracellular factor that modulates gene expression in Bacillus subtilis. The factor was found when studying the regulation of the fatR-cyp102A3 operon. In a Spo0A(-) mutant expression of the fatR-cyp102A3 operon was almost abolished. The fatR-cyp102A3 expression defect of a Spo0A(-) mutant could be overcome either by a mutation in the abrB gene or by a diffusible substance excreted by wild-type, abrB mutant and abrB-spo0A double mutant strains.
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| 21. |
- Gustafsson, Mattias, et al.
(författare)
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Expression, purification, and characterization of Bacillus subtilis cytochromes P450CYP102A2 and CYP102A3: Flavocytochronie homologues of P450BM3 from Bacillus megaterium
- 2004
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Ingår i: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 43:18, s. 5474-5487
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Tidskriftsartikel (refereegranskat)abstract
- The cyp102A2 and cyp102A3 genes encoding the two Bacillus subtilis homologues (CYP102A2 and CYP102A3) of flavocytochrome P450 BM3 (CYP102A1) from Bacillus megaterium have been cloned, expressed in Escherichia coli, purified, and characterized spectroscopically and enzymologically. Both enzymes contain heme, flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) cofactors and bind a variety of fatty acid molecules, as demonstrated by conversion of the low-spin resting form of the heme iron to the high-spin form induced by substrate-binding. CYP102A2 and CYP102A3 catalyze the fatty acid-dependent oxidation of reduced nicotinamide adenine dinucleotide phosphate (NADPH) and reduction of artificial electron acceptors at high rates. Binding of carbon monoxide to the reduced forms of both enzymes results in the shift of the heme Soret band to 450 nm, confirming the P450 nature of the enzymes. Reverse-phase high-performance liquid chromatography (HPLC) of products from the reaction of the enzymes with myristic acid demonstrates that both catalyze the subterminal hydroxylation of this substrate, though with different regioselectivity and catalytic rate. Both P450s 102A2 and 102A3 show kinetic and binding, preferences for long-chain unsaturated and branched-chain fatty acids over saturated fatty acids, indicating that the former two molecule types may be the true substrates. P450s 102A2 and 102A3 exhibit differing substrate selectivity profiles from each other and from P450 BM3, indicating that they may fulfill subtly different cellular roles. Titration curves for binding and turnover kinetics of several fatty acid Substrates with P450s 102A2 and 102A3 are better described by sigmoidal (rather than hyperbolic) functions, suggesting binding of more than one molecule of substrate to the P450s, or possibly cooperativity in substrate binding. Comparison of the amino acid sequences of the three flavocytochromes shows that several important amino acids in P450 BM3 are not conserved in the B. subtilis homologues, pointing to differences in the binding modes for the substrates that may explain the unusual sigmoidal kinetic and titration properties.
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| 22. |
- Gustafsson, Mattias, et al.
(författare)
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Fatty-acid-displaced transcriptional repressor, a conserved regulator of cytochrome P450 102 transcription in Bacillus species
- 2001
-
Ingår i: Archives of Microbiology. - : Springer Science and Business Media LLC. - 0302-8933 .- 1432-072X. ; 176:6, s. 459-464
-
Tidskriftsartikel (refereegranskat)abstract
- Bacillus subtilis strain 168 encodes two flavocytochromes P450, Cyp102A2 and Cyp102A3. The cyp102A3 gene is preceded by, and organized in an operon with, a gene for a transcriptional regulator, encoded by fatR. The paralogous gene, cyp102A2, is most likely transcribed as a mono-cistronic message. We show that fatR encodes a protein that binds to an operator sequence that is present upstream of its own reading frame, thereby repressing the expression of the fatR-cyp102A3 operon. Unsaturated fatty acids and phytanic acid have the capacity to interact with FatR and to abrogate its binding to the operator sequence.
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| 23. |
- Hambraeus, Gustav, et al.
(författare)
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Genome-wide survey of mRNA half-lives in Bacillus subtilis identifies extremely stable mRNAs
- 2003
-
Ingår i: Molecular Genetics and Genomics. - : Springer Science and Business Media LLC. - 1617-4615 .- 1617-4623. ; 269:5, s. 706-714
-
Tidskriftsartikel (refereegranskat)abstract
- We have used DNA microarrays to survey rates of mRNA decay on a genomic scale in early stationary-phase cultures of Bacillus subtilis. The decay rates for mRNAs corresponding to about 1500 genes could be estimated. About 80% of these mRNAs had a half-life of less than 7 min. More than 30 mRNAs, including both mono- and polycistronic transcripts, were found to be extremely stable, i.e. to have a half-life of greater than or equal to15 min. Only two such transcripts were known previously in B. subtilis. The results provide the first overview of mRNA decay rates in a gram-positive bacterium and help to identify polycistronic operons. We could find no obvious correlation between the stability of an mRNA and the function of the encoded protein. We have also not found any general features in the 5' regions of mRNAs that distinguish stable from unstable transcripts. The identified set of extremely stable mRNAs may be useful in the construction of stable recombinant genes for the overproduction of biomolecules in Bacillus species.
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| 24. |
- Hansson, Mats, et al.
(författare)
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Heme b (protoheme IX) is a precursor of heme a and heme d in Bacillus subtilis
- 1993
-
Ingår i: FEMS Microbiology Letters. - : Oxford University Press (OUP). - 1574-6968 .- 0378-1097. ; 107:1, s. 121-126
-
Tidskriftsartikel (refereegranskat)abstract
- Bacillus subtilis can synthesise cytochromes containing a-, b-, c- and d-type heme. The biosynthetic pathways of these heme prosthetic groups were investigated by using strains blocked in uroporphyrinogen III synthesis from porphobilinogen or in heme b (protoheme IX) synthesis from uroporphyrinogen III. The results strongly suggest that heme a and heme d are both synthesised from heme b (protoheme IX). They also indicate that B. subtilis contains a novel ferrochelatase involved in the synthesis of siroheme
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| 25. |
- Hederstedt, Lars, et al.
(författare)
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Molecular biology of Bacillus subtilis cytochromes
- 1992
-
Ingår i: FEMS Microbiology Letters. - 1574-6968. ; , s. 91-100
-
Tidskriftsartikel (refereegranskat)abstract
- Bacillus subtilis cells must have cytochromes for growth and can synthesize cytochromes of a-, b-, c-, d-, and o-types. After a long lag, our knowledge of the structure, genetics and specific role for these cytochromes is now growing exponentially as the result of recent research. This progress is reviewed here and includes, for example, the discovery of two different cytochrome a systems and genes required for their biogenesis.
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| 26. |
- Hollestelle, Antoinette, et al.
(författare)
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No clinical utility of KRAS variant rs61764370 for ovarian or breast cancer
- 2016
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Ingår i: Gynecologic Oncology. - : Elsevier BV. - 0090-8258 .- 1095-6859. ; 141:2, s. 386-401
-
Tidskriftsartikel (refereegranskat)abstract
- Objective Clinical genetic testing is commercially available for rs61764370, an inherited variant residing in a KRAS 3′ UTR microRNA binding site, based on suggested associations with increased ovarian and breast cancer risk as well as with survival time. However, prior studies, emphasizing particular subgroups, were relatively small. Therefore, we comprehensively evaluated ovarian and breast cancer risks as well as clinical outcome associated with rs61764370. Methods Centralized genotyping and analysis were performed for 140,012 women enrolled in the Ovarian Cancer Association Consortium (15,357 ovarian cancer patients; 30,816 controls), the Breast Cancer Association Consortium (33,530 breast cancer patients; 37,640 controls), and the Consortium of Modifiers of BRCA1 and BRCA2 (14,765 BRCA1 and 7904 BRCA2 mutation carriers). Results We found no association with risk of ovarian cancer (OR = 0.99, 95% CI 0.94-1.04, p = 0.74) or breast cancer (OR = 0.98, 95% CI 0.94-1.01, p = 0.19) and results were consistent among mutation carriers (BRCA1, ovarian cancer HR = 1.09, 95% CI 0.97-1.23, p = 0.14, breast cancer HR = 1.04, 95% CI 0.97-1.12, p = 0.27; BRCA2, ovarian cancer HR = 0.89, 95% CI 0.71-1.13, p = 0.34, breast cancer HR = 1.06, 95% CI 0.94-1.19, p = 0.35). Null results were also obtained for associations with overall survival following ovarian cancer (HR = 0.94, 95% CI 0.83-1.07, p = 0.38), breast cancer (HR = 0.96, 95% CI 0.87-1.06, p = 0.38), and all other previously-reported associations. Conclusions rs61764370 is not associated with risk of ovarian or breast cancer nor with clinical outcome for patients with these cancers. Therefore, genotyping this variant has no clinical utility related to the prediction or management of these cancers.
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| 27. |
- Hägerhäll, Cecilia, et al.
(författare)
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Two hemes in Bacillus subtilis succinate:menaquinone oxidoreductase (Complex II)
- 1992
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Ingår i: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 31, s. 7411-7421
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Tidskriftsartikel (refereegranskat)abstract
- Succinate:menaquinone-7 oxidoreductase (complex II) of the Gram-positive bacterium B subtilis consists of equimolar amounts of three polypeptides; a 65-kDa FAD-containing polypeptide, a 28-kDa iron-sulfur cluster containing polypeptide, and a 23-kDa membrane-spanning cytochrome b558 polypeptide, The enzyme complex was overproduced 2-3-fold in membranes of B. subtilis cells containing the sdhCAB operon on a low copy number plasmid and was purified in the presence of detergent. The cytochrome b558 subunit alone was similarly overexpressed in a complex II deficient mutant and partially purified. Isolated complex II catalyzed the reduction of various quinones and also quinol oxidation. Both activities were efficiently albeit not completely blocked by 2-n-heptyl-4-hydroxyquinoline N-oxide. Chemical analysis demonstrated two protoheme IX per complex II. One heme component was found to have an E(m,7.4) of +65 mV and an EPR g(max) signal at 3.68, to be fully reducible by succinate, and showed a symmetrical alpha-band absorption peak at 555 nm at 77 K. The other heme component was found to have an E(m,7.4) of -95 mV and an EPR g(max) signal at 3.42, was not reducible by succinate under steady-state conditions, and showed in the reduced state an apparent split alpha-band absorption peak with maxima at 553 and 558 nm at 77 K. Potentiometric titrations of partially purified cytochrome b558 subunit demonstrated that the isolated cytochrome b558 also contains two hemes. Some of the properties, i.e., the alpha-band light absorption peak at 77 K, the line shapes of the EPR g(max) signals, and reactivity with carbon monoxide were observed to be different in B. subtilis cytochrome b558 isolated and in complex II. This suggests that the bound flavoprotein and iron-sulfur protein subunits protect or affect the heme environment in the assembled complex
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| 28. |
- Ilari, Andrea, et al.
(författare)
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Crystal structure and ligand binding properties of the truncated hemoglobin from Geobacillus stearothermophilus
- 2007
-
Ingår i: Archives of Biochemistry and Biophysics. - : Elsevier BV. - 0003-9861. ; 457:1, s. 85-94
-
Tidskriftsartikel (refereegranskat)abstract
- A novel truncated hemoglobin has been identified in the thermophilic bacterium Geobacillus stearothermophilus (Gs-trHb). The protein has been expressed in Escherichia coli, the 3D crystal structure (at 1.5 angstrom resolution) and the ligand binding properties have been determined. The distal heme pocket displays an array of hydrogen bonding donors to the iron-bound ligands, including Tyr-B10 on one side of the heme pocket and Trp-G8 indole nitrogen on the opposite side. At variance with the highly similar Bacillus subtilis hemoglobin, Gs-trHb is dimeric both in the crystal and in solution and displays several unique structural properties. In the crystal cell, the iron-bound ligand is not homogeneously distributed within each distal site such that oxygen and an acetate anion can be resolved with relative occupancies of 50% each. Accordingly, equilibrium titrations of the oxygenated derivative in solution with acetate anion yield a partially saturated ferric acetate adduct. Moreover, the asymmetric unit contains two subunits and sedimentation velocity ultracentrifugation data confirm that the protein is dimeric. (c) 2006 Elsevier Inc. All rights reserved.
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| 29. |
- Kelpšas, Vinardas, et al.
(författare)
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Enhancing protein perdeuteration by experimental evolution of Escherichia coli K-12 for rapid growth in deuterium-based media
- 2021
-
Ingår i: Protein Science. - : Wiley. - 0961-8368 .- 1469-896X. ; 30:12, s. 2457-2473
-
Tidskriftsartikel (refereegranskat)abstract
- Deuterium is a natural low abundance stable hydrogen isotope that in high concentrations negatively affects growth of cells. Here, we have studied growth of Escherichia coli MG1655, a wild-type laboratory strain of E. coli K-12, in deuterated glycerol minimal medium. The growth rate and final biomass in deuterated medium is substantially reduced compared to cells grown in ordinary medium. By using a multi-generation adaptive laboratory evolution-based approach, we have isolated strains that show increased fitness in deuterium-based growth media. Whole-genome sequencing identified the genomic changes in the obtained strains and show that there are multiple routes to genetic adaptation to growth in deuterium-based media. By screening a collection of single-gene knockouts of nonessential genes, no specific gene was found to be essential for growth in deuterated minimal medium. Deuteration of proteins is of importance for NMR spectroscopy, neutron protein crystallography, neutron reflectometry, and small angle neutron scattering. The laboratory evolved strains, with substantially improved growth rate, were adapted for recombinant protein production by T7 RNA polymerase overexpression systems and shown to be suitable for efficient production of perdeuterated soluble and membrane proteins for structural biology applications.
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| 30. |
- Kelpšas, Vinardas, et al.
(författare)
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Evolving escherichia coli host strains for efficient deuterium labeling of recombinant proteins using sodium pyruvate-d3
- 2021
-
Ingår i: International Journal of Molecular Sciences. - : MDPI AG. - 1661-6596 .- 1422-0067. ; 22:18
-
Tidskriftsartikel (refereegranskat)abstract
- Labeling of proteins with deuterium (2H) is often necessary for structural biology tech-niques, such as neutron crystallography, NMR spectroscopy, and small-angle neutron scattering. Perdeuteration in which all protium (1H) atoms are replaced by deuterium is a costly process. Typ-ically, expression hosts are grown in a defined medium with heavy water as the solvent, which is supplemented with a deuterated carbon source. Escherichia coli, which is the most widely used host for recombinant protein production, can utilize several compounds as a carbon source. Glycerol-d8 is often used as a carbon source for deuterium labelling due to its lower cost compered to glucose-d7 . In order to expand available options for recombinant protein deuteration, we investigated the possibility of producing a deuterated carbon source in-house. E. coli can utilize pyruvate as a carbon source and pyruvate-d3 can be made by a relatively simple procedure. To circumvent the very poor growth of E. coli in minimal media with pyruvate as sole carbon source, adaptive laboratory evolution for strain improvement was applied. E. coli strains with enhanced growth in minimal pyruvate medium was subjected to whole genome sequencing and the genetic changes were revealed. One of the evolved strains was adapted for the widely used T7 RNA polymerase overexpression systems. Using the improved strain E. coli DAP1(DE3) and in-house produced deuterated carbon source (pyru-vic acid-d4 and sodium pyruvate-d3 ), we produce deuterated (>90%) triose-phosphate isomerase, at quantities sufficient enough for large volume crystal production and subsequent analysis by neutron crystallography.
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| 31. |
- Kelpšas, Vinardas, et al.
(författare)
-
Neutron structures of Leishmania mexicana triosephosphate isomerase in complex with reaction-intermediate mimics shed light on the proton-shuttling steps
- 2021
-
Ingår i: IUCrJ. - 2052-2525. ; 8:Pt 4, s. 633-643
-
Tidskriftsartikel (refereegranskat)abstract
- Triosephosphate isomerase (TIM) is a key enzyme in glycolysis that catalyses the interconversion of glyceraldehyde 3-phosphate and dihydroxy-acetone phosphate. This simple reaction involves the shuttling of protons mediated by protolysable side chains. The catalytic power of TIM is thought to stem from its ability to facilitate the deprotonation of a carbon next to a carbonyl group to generate an enediolate intermediate. The enediolate intermediate is believed to be mimicked by the inhibitor 2-phosphoglycolate (PGA) and the subsequent enediol intermediate by phosphoglycolohydroxamate (PGH). Here, neutron structures of Leishmania mexicana TIM have been determined with both inhibitors, and joint neutron/X-ray refinement followed by quantum refinement has been performed. The structures show that in the PGA complex the postulated general base Glu167 is protonated, while in the PGH complex it remains deprotonated. The deuteron is clearly localized on Glu167 in the PGA-TIM structure, suggesting an asymmetric hydrogen bond instead of a low-barrier hydrogen bond. The full picture of the active-site protonation states allowed an investigation of the reaction mechanism using density-functional theory calculations.
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| 32. |
- Kelpšas, Vinardas, et al.
(författare)
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Perdeuteration, large crystal growth and neutron data collection of Leishmania mexicana triose-phosphate isomerase E65Q variant
- 2019
-
Ingår i: Acta crystallographica. Section F, Structural biology communications. - 2053-230X. ; 75:4, s. 260-269
-
Tidskriftsartikel (refereegranskat)abstract
- Triose-phosphate isomerase (TIM) catalyses the interconversion of dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. Two catalytic mechanisms have been proposed based on two reaction-intermediate analogues, 2-phosphoglycolate (2PG) and phosphoglycolohydroxamate (PGH), that have been used as mimics of the cis-enediol(ate) intermediate in several studies of TIM. The protonation states that are critical for the mechanistic interpretation of these structures are generally not visible in the X-ray structures. To resolve these questions, it is necessary to determine the hydrogen positions using neutron crystallography. Neutron crystallography requires large crystals and benefits from replacing all hydrogens with deuterium. Leishmania mexicana triose-phosphate isomerase was therefore perdeuterated and large crystals with 2PG and PGH were produced. Neutron diffraction data collected from two crystals with different volumes highlighted the importance of crystal volume, as smaller crystals required longer exposures and resulted in overall worse statistics.
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| 33. |
- Kelpšas, Vinardas, et al.
(författare)
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Strain improvement of Escherichia coli K-12 for recombinant production of deuterated proteins
- 2019
-
Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9:1
-
Tidskriftsartikel (refereegranskat)abstract
- Deuterium isotope labelling is important for structural biology methods such as neutron protein crystallography, nuclear magnetic resonance and small angle neutron scattering studies of proteins. Deuterium is a natural low abundance stable hydrogen isotope that in high concentrations negatively affect growth of cells. The generation time for Escherichia coli K-12 in deuterated medium is substantially increased compared to cells grown in hydrogenated (protiated) medium. By using a mutagenesis plasmid based approach we have isolated an E. coli strain derived from E. coli K-12 substrain MG1655 that show increased fitness in deuterium based growth media, without general adaptation to media components. By whole-genome sequencing we identified the genomic changes in the obtained strain and show that it can be used for recombinant production of perdeuterated proteins in amounts typically needed for structural biology studies.
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| 34. |
- Larsson, Jonas, et al.
(författare)
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Coordinated patterns of cytochrome bd and lactate dehydrogenase expression in Bacillus subtilis
- 2005
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Ingår i: Microbiology. - : Microbiology Society. - 1465-2080 .- 1350-0872. ; 151:10, s. 3323-3335
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Tidskriftsartikel (refereegranskat)abstract
- A variety of pathways for electron and carbon flow in the soil bacterium Bacillus subtilis are differentially expressed depending on whether oxygen is present in the cell environment. This study characterizes the regulation of the respiratory oxidase cytochrome bd and the NADH-linked fermentative lactate dehydrogenase, (LDH). Transcription of the cydABCD operon, encoding cytochrome bd, is highly regulated and only becomes activated at low oxygen availability. This induction is not dependent on the gene encoding the redox regulator Fnr or the genes encoding the ResDE two-component regulatory system. The DNA-binding protein YdiH was found to be a principal regulator that controls cydABCD expression. Transcription from the cyd promoter is stimulated 15-fold by a region located upstream of the core promoter. The upstream region may constitute a binding site for an unidentified transcription activator that is likely to influence the level of transcription but not its timing, which is negatively controlled by YdiH. This report provides evidence that YdiH also functions as a repressor of the ldh gene encoding LDH and of a gene, ywcJ, which encodes a putative formate-nitrite transporter. Based on the similarity between YdiH and the Rex protein of Streptomyces coelicolor, it is proposed that YdiH serves as a redox sensor, the activity of which is regulated by cellular differences in the free levels of NAD(+) and NADH. It is suggested that ydiH be renamed as rex.
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| 35. |
- Larsson, Jonas, et al.
(författare)
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YjbH is a novel negative effector of the disulphide stress regulator,Spx, in Bacillus subtilis.
- 2007
-
Ingår i: Molecular Microbiology. - : Wiley. - 1365-2958 .- 0950-382X. ; 66:3, s. 669-684
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Tidskriftsartikel (refereegranskat)abstract
- In the soil bacterium Bacillus subtilis Spx is a key regulator that controls expression, positively or negatively, of several genes in response to certain oxidative stresses that lead to the formation of unwanted disulphide bonds. Here we characterized the yjbH gene and show that it encodes a novel effector of Spx. The yjbH gene is part of the yjbIH operon that encodes a truncated haemoglobin (YjbI) and a predicted 34 kDa cytosolic protein of unknown function (YjbH). Deletion of yjbIH or yjbH has pleiotropic effects and affects growth, sporulation and competence development. Cells lacking yjbIH display a reduced sensitivity to the thiol oxidant diamide and show an apparent down- or upregulation of several transcripts that belong to the Spx regulon. Twenty-two suppressor mutations that bypass the defects conferred by yjbH were isolated. These mutations were identified as six deletions, three nonsense and 11 missense substitutions in the spx gene. Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis showed that mutations in yjbIH or yjbH do not affect the level of spx transcription. The combined data from the present work show that strains lacking yjbIH or yjbH overproduce Spx under unperturbed growth. The elevated Spx concentration cannot be attributed to an increased spx expression but is likely to result from control at the post-transcriptional level. YjbH is proposed to affect the cellular concentration of Spx by modulating proteolysis via the ClpXP protease.
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| 36. |
- Lawson, RJ, et al.
(författare)
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Expression and characterization of the two flavodoxin proteins of Bacillus subtilis, YkuN and YkuP: Biophysical properties and interactions with cytochrome p450 BioI
- 2004
-
Ingår i: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 43:39, s. 12390-12409
-
Tidskriftsartikel (refereegranskat)abstract
- The two flavodoxins (YkuN and YkuP) from Bacillus subtilis have been cloned, overexpressed in Escherichia coli and purified. DNA sequencing, mass spectrometry, and flavin-binding properties showed that both YkuN and YkuP were typical short-chain flavodoxins (158 and 151 amino acids, respectively) and that an error in the published B. subtilis genome sequence had resulted in an altered reading frame and misassignment of YkuP as a long-chain flavodoxin. YkuN and YkuP were expressed in their blue (neutral semiquinone) forms and reoxidized to the quinone form during purification. Potentiometry confirmed the strong stabilization of the semiquinone form by both YkuN and YkuP (midpoint reduction potential for oxidized/serniquinone couple = -105 mV/-105 mV) with respect to the hydroquinone (midpoint reduction potential for semiquinone/hydroquinone couple = -382 mV/-377 mV). Apoflavodoxin forms were generated by trichloroacetic acid treatment. Circular dichroism studies indicated that flavin mononucleotide (FMN) binding led to considerable structural rearrangement for YkuP but not for YkuN. Both apoflavodoxins bound FMN but not riboflavin avidly, as expected for short-chain flavodoxins. Structural stability studies with the chaotrope guanidinium chloride revealed that there is moderate destabilization of secondary and tertiary structure on FMN removal from YkuN, but that YkuP apoflavodoxin has similar (or slightly higher) stability compared to the holoprotein. Differential scanning calorimetry reveals further differences in structural stability. YkuP has a lower melting temperature than YkuN, and its endotherm is composed of a single transition, while that for YkuN is biphasic. Optical and fluorimetric titrations with oxidized flavodoxins revealed strong affinity (K-d values consistently < 5 muM) for their potential redox partner P450 Biol, YkuN showing tighter binding. Stopped-flow reduction studies indicated that the maximal electron-transfer rate (k(red)) to fatty acid-bound P450 Biol occurs from YkuN and YkuP at similar to2.5 s(-1), considerably faster than from E. coli flavodoxin. Steady-state turnover with YkuN or YkuP, fatty acid-bound P450 Biol, and E. coli NADPH-flavodoxin reductase indicated that both flavodoxins supported lipid hydroxylation by P450 Biol with turnover rates of up to similar to100 min(-1) with lauric acid as substrate. Interprotein electron transfer is a likely rate-limiting step. YkuN and YkuP supported monohydroxylation of lauric acid and myristic acid, but secondary oxygenation of the primary product was observed with both palmitic acid and palmitoleic acid as substrates.
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| 37. |
- Levin, Mattias, et al.
(författare)
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A folded and immunogenic IgE-hyporeactive variant of the major allergen Phl p 1 produced in Escherichia coli.
- 2015
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Ingår i: BMC Biotechnology. - : Springer Science and Business Media LLC. - 1472-6750. ; 15
-
Tidskriftsartikel (refereegranskat)abstract
- Group 1 grass pollen allergens are a major cause of allergic disease. Specific immunotherapy involving controlled administration of allergens can be used as a disease-modifying treatment for such disease. Recombinant allergen variants with reduced IgE binding capacity may be used as component in such vaccines, as they may induce fewer treatment side effects than materials currently in use. A mutated variant of the immunodominant C-terminal domain of the group 1 grass pollen allergen Phl p 1 was recently established through an approach that used a set of human monoclonal IgE as a guide to identify mutations that disturbed IgE-allergen interactions. Further analysis of this domain is required to establish its potential for use in treatment.
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| 38. |
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| 39. |
- Matavacas, Judith, et al.
(författare)
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Bacillus subtilis forms twisted cells with cell wall integrity defects upon removal of the molecular chaperones DnaK and trigger factor
- 2023
-
Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 13
-
Tidskriftsartikel (refereegranskat)abstract
- The protein homeostasis network ensures a proper balance between synthesis, folding, and degradation of all cellular proteins. DnaK and trigger factor (TF) are ubiquitous bacterial molecular chaperones that assist in protein folding, as well as preventing protein misfolding and aggregation. In Escherichia coli, DnaK and TF possess partially overlapping functions. Their combined depletion results in proteostasis collapse and is synthetically lethal at temperatures above 30°C. To increase our understanding on how proteostasis is maintained in Gram-positive bacteria, we have investigated the physiological effects of deleting dnaK and tig (encoding for DnaK and TF) in Bacillus subtilis. We show that combined deletion of dnaK and tig in B. subtilis is non-lethal, but causes a severe pleiotropic phenotype, including an aberrant twisted and filamentous cell morphology, as well as decreased tolerance to heat and to cell wall active antibiotics and hydrolytic enzymes, indicative of defects in cell wall integrity. In addition, cells lacking DnaK and TF have a much smaller colony size due to defects in motility. Despite these physiological changes, we observed no major compromises in important cellular processes such as cell growth, FtsZ localization and division and only moderate defects in spore formation. Finally, through suppressor analyses, we found that the wild-type cell shape can be partially restored by mutations in genes involved in metabolism or in other diverse cellular processes.
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| 40. |
- Matavacas, Judith, et al.
(författare)
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New insights into the disulfide stress response by the Bacillus subtilis Spx system at a single-cell level
- 2023
-
Ingår i: Molecular Microbiology. - 0950-382X. ; 120:1, s. 75-90
-
Tidskriftsartikel (refereegranskat)abstract
- Spx is a global transcriptional regulator that orchestrates the Bacillus subtilis response to disulfide stress. The YjbH (SpxH) protein adapts Spx for ClpXP-mediated degradation, playing a critical role in the regulation of the cellular Spx levels. Upon stress, YjbH forms aggregates by a yet unknown mechanism, resulting in increased Spx levels due to reduced proteolysis. Here, we studied how individual cells use the Spx-YjbH system to respond to disulfide stress. We show, using fluorescent reporters, a correlation between the Spx levels and the amount of YjbH, as well as a transient growth inhibition upon disulfide stress. The in vivo dynamics and inheritance of YjbH aggregates are characterized by a bipolar distribution over time and appear to be entropy-driven by nucleoid exclusion. Moreover, we reveal that the population following disulfide stress is highly heterogenous in terms of aggregate load and that the aggregate load has strong implications for cellular fitness. We propose that the observed heterogeneity could be a mechanism to ensure population survival during stress. Finally, we find that the two YjbH domains (DsbA-like domain and winged-helix domain) contribute to its aggregation function, and show that the aggregation of the DsbA-like domain is conserved among other studied orthologs, whereas important differences are observed for the winged-helix domain.
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| 41. |
- Matavacas, Judith, et al.
(författare)
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Update on the Protein Homeostasis Network in Bacillus subtilis
- 2022
-
Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 13
-
Forskningsöversikt (refereegranskat)abstract
- Protein homeostasis is fundamental to cell function and survival. It relies on an interconnected network of processes involving protein synthesis, folding, post-translational modification and degradation as well as regulators of these processes. Here we provide an update on the roles, regulation and subcellular localization of the protein homeostasis machinery in the Gram-positive model organism Bacillus subtilis. We discuss emerging ideas and current research gaps in the field that, if tackled, increase our understanding of how Gram-positive bacteria, including several human pathogens, maintain protein homeostasis and cope with stressful conditions that challenge their survival.
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| 42. |
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| 43. |
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| 44. |
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| 45. |
- Rogstam, Annika, et al.
(författare)
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Mechanisms of adaptation to nitrosative stress in Bacillus subtilis
- 2007
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Ingår i: Journal of Bacteriology. - 0021-9193. ; 189:8, s. 3063-3071
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Tidskriftsartikel (refereegranskat)abstract
- Bacteria use a number of mechanisms for coping with the toxic effects exerted by nitric oxide (NO) and its derivatives. Here we show that the flavohemoglobin encoded by the hmp gene has a vital role in an adaptive response to protect the soil bacterium Bacillus subtilis from nitrosative stress. We further show that nitrosative stress induced by the nitrosonium cation donor sodium nitroprusside (SNP) leads to deactivation of the transcriptional repressor NsrR, resulting in derepression of hmp. Nitrosative stress induces the sigma B-controlled general stress regulon. However, a sigB null mutant did not show increased sensitivity to SNP, suggesting that the sigma B-dependent stress proteins are involved in a nonspecific protection against stress whereas the Hmp flavohemoglobin plays a central role in detoxification. Mutations in the yjbIH operon, which encodes a truncated hemoglobin (YjbI) and a predicted 34-kDa cytosolic protein of unknown function (YjbH), rendered B. subtilis hypersensitive to SNP, suggesting roles in nitrosative stress management.
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| 46. |
- Schiött, Torbjörn, et al.
(författare)
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Identification and characterization of the ccdA gene, required for cytochrome c synthesis in Bacillus subtilis
- 1997
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Ingår i: Journal of Bacteriology. - : American Society for Microbiology. - 0021-9193 .- 1098-5530. ; 179:6, s. 1962-1973
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Tidskriftsartikel (refereegranskat)abstract
- The gram-positive, endospore-forming bacterium Bacillus subtilis contains several membrane-bound c-type cytochromes. We have isolated a mutant pleiotropically deficient in cytochromes c. The responsible mutation resides in a gene which we have named ccdA (cytochrome c defective). This gene is located at 173 degrees on the B. subtilis chromosome. The ccdA gene was found to be specifically required for synthesis of cytochromes of the c type. CcdA is a predicted 26-kDa integral membrane protein with no clear similarity to any known cytochrome c biogenesis protein but seems to be related to a part of Escherichia coli DipZ/DsbD. The ccdA gene is cotranscribed with two other genes. These genes encode a putative 13.5-kDa single-domain response regulator, similar to B. subtilis CheY and SpoOF, and a predicted 18-kDa hydrophobic protein with no similarity to any protein in databases, respectively. Inactivation of the three genes showed that only ccdA is required for cytochrome c synthesis. The results also demonstrated that cytochromes of the c type are not needed for growth of B. subtilis.
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| 47. |
- Sen, Beer Chakra, et al.
(författare)
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Specific amino acid substitutions in β strand S2 of FtsZ cause spiraling septation and impair assembly cooperativity in Streptomyces spp.
- 2019
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Ingår i: Molecular Microbiology. - : Wiley. - 0950-382X .- 1365-2958. ; 112:1, s. 184-198
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Tidskriftsartikel (refereegranskat)abstract
- Bacterial cell division is orchestrated by the Z ring, which is formed by single-stranded treadmilling protofilaments of FtsZ. In Streptomyces, during sporulation, multiple Z rings are assembled and lead to formation of septa that divide a filamentous hyphal cell into tens of prespore compartments. We describe here mutant alleles of ftsZ in Streptomyces coelicolor and Streptomyces venezuelae that perturb cell division in such a way that constriction is initiated along irregular spiral-shaped paths rather than as regular septa perpendicular to the cell length axis. This conspicuous phenotype is caused by amino acid substitutions F37I and F37R in β strand S2 of FtsZ. The F37I mutation leads, instead of regular Z rings, to formation of relatively stable spiral-shaped FtsZ structures that are capable of initiating cell constriction. Further, we show that the F37 mutations affect the polymerization properties and impair the cooperativity of FtsZ assembly in vitro. The results suggest that specific residues in β strand S2 of FtsZ affect the conformational switch in FtsZ that underlies assembly cooperativity and enable treadmilling of protofilaments, and that these features are required for formation of regular Z rings. However, the data also indicate FtsZ-directed cell constriction is not dependent on assembly cooperativity.
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| 48. |
- Sprenger, Janina, et al.
(författare)
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Crystal structures of Val58Ile tryptophan repressor in a domain-swapped array in the presence and absence of l-tryptophan Sprenger Janina
- 2021
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Ingår i: Acta Crystallographica Section F: Structural Biology Communications. - 2053-230X. ; 77, s. 215-225
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Tidskriftsartikel (refereegranskat)abstract
- The crystal structures of domain-swapped tryptophan repressor (TrpR) variant Val58Ile before and after soaking with the physiological ligand l-tryptophan (l-Trp) indicate that l-Trp occupies the same location in the domain-swapped form as in native dimeric TrpR and makes equivalent residue contacts. This result is unexpected because the ligand binding-site residues arise from three separate polypeptide chains in the domain-swapped form. This work represents the first published structure of a domain-swapped form of TrpR with l-Trp bound. The presented structures also show that the protein amino-terminus, whether or not it bears a disordered extension of about 20 residues, is accessible in the large solvent channels of the domain-swapped crystal form, as in the structures reported previously in this form for TrpR without N-terminal extensions. These findings inspire the exploration of l-Trp analogs and N-terminal modifications as labels to orient guest proteins that cannot otherwise be crystallized in the solvent channels of crystalline domain-swapped TrpR hosts for potential diffraction analysis.
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| 49. |
- Sprenger, Janina, et al.
(författare)
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Guest-protein incorporation into solvent channels of a protein host crystal (hostal)
- 2021
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Ingår i: Acta Crystallographica Section D: Structural Biology. - 2059-7983. ; 77, s. 471-485
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Tidskriftsartikel (refereegranskat)abstract
- Soaking small molecules into the solvent channels of protein crystals is the most common method of obtaining crystalline complexes with ligands such as substrates or inhibitors. The solvent channels of some protein crystals are large enough to allow the incorporation of macromolecules, but soaking of protein guests into protein crystals has not been reported. Such protein host crystals (here given the name hostals) incorporating guest proteins may be useful for a wide range of applications in biotechnology, for example as cargo systems or for diffraction studies analogous to the crystal sponge method. The present study takes advantage of crystals of the Escherichia coli tryptophan repressor protein (ds-TrpR) that are extensively domain-swapped and suitable for incorporating guest proteins by diffusion, as they are robust and have large solvent channels. Confocal fluorescence microscopy is used to follow the migration of cytochrome c and fluorophore-labeled calmodulin into the solvent channels of ds-TrpR crystals. The guest proteins become uniformly distributed in the crystal within weeks and enriched within the solvent channels. X-ray diffraction studies on host crystals with high concentrations of incorporated guests demonstrate that diffraction limits of ∼2.5 Å can still be achieved. Weak electron density is observed in the solvent channels, but the guest-protein structures could not be determined by conventional crystallographic methods. Additional approaches that increase the ordering of guests in the host crystal are discussed that may support protein structure determination using the hostal system in the future. This host system may also be useful for biotechnological applications where crystallographic order of the guest is not required.
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| 50. |
- van der Oost, John, et al.
(författare)
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Bacillus subtilis cytochrome oxidase mutants: biochemical analysis and genetic evidence for two aa3-type oxidases
- 1991
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Ingår i: Molecular Microbiology. - : Wiley. - 1365-2958 .- 0950-382X. ; 5:8, s. 2063-2072
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Tidskriftsartikel (refereegranskat)abstract
- The ctaBCDEF genes coding for cytochrome c oxidase were found to reside adjacent to a regulatory gene ctaA at 127-degrees on the Bacillus subtilis chromosome. The structural genes for subunits I and II, ctaD and ctaC, were deleted by gene-replacement using a phleomycin-resistance marker. The mutant was unable to oxidize N,N,N',N'-tetramethyl-p-phenylenediamine and oxidized cytochrome c at a significantly lower rate. Absorption spectra of the mutant and wild-type membranes confirmed the presence of two haem A-containing enzymes in B. subtilis. Another mutant, with a spontaneous deletion upstream from ctaC, was found to express neither of these enzymes. Radioactive haem-labelling was used to identify subunit 11, which contains a haem C, and cytochrome c-550 among the membrane-bound c-type cytochromes of B. subtilis.
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