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Korza G, Goulet M, DeMarco A, Wicander J, Setlow P. Role of Bacillus subtilis Spore Core Water Content and pH in the Accumulation and Utilization of Spores' Large 3-Phosphoglyceric Acid Depot, and the Crucial Role of This Depot in Generating ATP Early during Spore Germination. Microorganisms 2023; 11:microorganisms11010195. [PMID: 36677488 PMCID: PMC9864370 DOI: 10.3390/microorganisms11010195] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/03/2023] [Accepted: 01/10/2023] [Indexed: 01/13/2023] Open
Abstract
The development of Bacillus spore cores involves the accumulation of 3-phosphoglycerate (3PGA) during sporulation, following core acidification to ~6.4, and before decreases in core water content occur due to Ca-dipicolinc acid (CaDPA) uptake. This core acidification inhibits phosphoglycerate mutase (PGM) at pH 6.4, allowing 3PGA accumulation, although PGM is active at pH 7.4. Spores’ 3PGA is stable for months at 4 °C and weeks at 37 °C. However, in wild-type spore germination, increases in core pH to 7.5−8 and in core water content upon CaDPA release and cortex peptidoglycan hydrolysis allow for rapid 3PGA catabolism, generating ATP; indeed, the earliest ATP generated following germination is from 3PGA catabolism. The current work found no 3PGA in those Bacillus subtilis spores that do not accumulate CaDPA during sporulation and have a core pH of ~7.4. The ATP production in the germination of 3PGA-less spores in a poor medium was minimal, and the germinated spores were >99% dead. However, the 3PGA-replete spores that germinated in the poor medium accumulated >30 times more ATP, and >70% of the germinated spores were found to be alive. These findings indicate why 3PGA accumulation during sporulation (and utilization during germination) in all the Firmicute spores studied can be crucial for spore revival due to the generation of essential ATP. The latter finding further suggests that targeting PGM activity during germination could be a novel way to minimize the damaging effects of spores.
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Mechanisms and Applications of Bacterial Sporulation and Germination in the Intestine. Int J Mol Sci 2022; 23:ijms23063405. [PMID: 35328823 PMCID: PMC8953710 DOI: 10.3390/ijms23063405] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
Recent studies have suggested a major role for endospore forming bacteria within the gut microbiota, not only as pathogens but also as commensal and beneficial members contributing to gut homeostasis. In this review the sporulation processes, spore properties, and germination processes will be explained within the scope of the human gut. Within the gut, spore-forming bacteria are known to interact with the host’s immune system, both in vegetative cell and spore form. Together with the resistant nature of the spore, these characteristics offer potential for spores’ use as delivery vehicles for therapeutics. In the last part of the review, the therapeutic potential of spores as probiotics, vaccine vehicles, and drug delivery systems will be discussed.
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Abstract
Despite being resistant to a variety of environmental insults, the bacterial endospore can sense the presence of small molecules and respond by germinating, losing the specialized structures of the dormant spore, and resuming active metabolism, before outgrowing into vegetative cells. Our current level of understanding of the spore germination process in bacilli and clostridia is reviewed, with particular emphasis on the germinant receptors characterized in Bacillus subtilis, Bacillus cereus, and Bacillus anthracis. The recent evidence for a local clustering of receptors in a "germinosome" would begin to explain how signals from different receptors could be integrated. The SpoVA proteins, involved in the uptake of Ca2+-dipicolinic acid into the forespore during sporulation, are also responsible for its release during germination. Lytic enzymes SleB and CwlJ, found in bacilli and some clostridia, hydrolyze the spore cortex: other clostridia use SleC for this purpose. With genome sequencing has come the appreciation that there is considerable diversity in the setting for the germination machinery between bacilli and clostridia.
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Berisio R, Squeglia F, Ruggiero A, Petraccone L, Stellato MI, Del Vecchio P. Differential thermodynamic behaviours of the extra-cellular regions of two Ser/Thr PrkC kinases revealed by calorimetric studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:402-9. [PMID: 25668224 DOI: 10.1016/j.bbapap.2015.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 01/13/2015] [Accepted: 02/03/2015] [Indexed: 10/24/2022]
Abstract
Eukaryotic-type Ser/Thr protein-kinases are critical mediators of developmental changes and host pathogen interactions in bacteria. Although with lower abundance compared to their homologues from eukaryotes, Ser/Thr protein-kinases (STPK) are widespread in gram positive bacteria, where they regulate several cellular functions. STPKs belong to the protein kinase family named as one-component signal transduction systems, which combine both sensing and regulating properties. Thermodynamic investigations of sensing extra-cellular portions of two important Ser-Thr kinases, PrkC, from Staphylococcus aureus and Bacillus subtilis were conducted by differential scanning calorimetry (DSC) and circular dichroism (CD) melting measurements, coupled with modelling studies. The study of thermodynamic properties of the two domains is challenging since they share a modular domain organization. Consistently, DSC and CD data show that they present similar thermodynamic behaviours and that folding/unfolding transitions do not fit a two-state folding model. However, the thermal unfolding of the two proteins is differentially sensitive to pH. In particular, their unfolding is characteristic of modular structures at the neutral pH, with independent contributions of individual domains to folding. Differently, a cooperative unfolding is evidenced at acidic pH for the B. subtilis member, suggesting that a significant interaction between domains becomes valuable.
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Affiliation(s)
- Rita Berisio
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone 16, Napoli, Italy.
| | - Flavia Squeglia
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone 16, Napoli, Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, CNR, via Mezzocannone 16, Napoli, Italy
| | - Luigi Petraccone
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 80126 Napoli, Italy
| | - Marco Ignazio Stellato
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 80126 Napoli, Italy
| | - Pompea Del Vecchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 80126 Napoli, Italy.
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Roychowdhury A, Kundu A, Bose M, Gujar A, Mukherjee S, Das AK. Complete catalytic cycle of cofactor-independent phosphoglycerate mutase involves a spring-loaded mechanism. FEBS J 2015; 282:1097-110. [DOI: 10.1111/febs.13205] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 01/13/2015] [Accepted: 01/16/2015] [Indexed: 11/27/2022]
Affiliation(s)
- Amlan Roychowdhury
- Department of Biotechnology; Indian Institute of Technology; Kharagpur India
| | - Anirban Kundu
- Department of Biotechnology; Indian Institute of Technology; Kharagpur India
| | - Madhuparna Bose
- Department of Biotechnology; Indian Institute of Technology; Kharagpur India
| | - Akanksha Gujar
- Department of Biotechnology; Indian Institute of Technology; Kharagpur India
| | - Somnath Mukherjee
- Department of Biotechnology; Indian Institute of Technology; Kharagpur India
| | - Amit Kumar Das
- Department of Biotechnology; Indian Institute of Technology; Kharagpur India
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Roychowdhury A, Kundu A, Gujar A, Bose M, Das AK. Expression, purification, crystallization and preliminary X-ray diffraction studies of phosphoglycerate mutase from Staphylococcus aureus NCTC8325. Acta Crystallogr F Struct Biol Commun 2014; 70:53-6. [PMID: 24419617 PMCID: PMC3943096 DOI: 10.1107/s2053230x13031476] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 11/18/2013] [Indexed: 11/11/2022] Open
Abstract
Phosphoglycerate mutase (PGM) is a key enzyme in carbohydrate metabolism. It takes part in both glycolysis and gluconeogenesis. PGM from pathogenic Staphylococcus aureus (NCTC8325) was cloned in pQE30 expression vector overexpressed in Escherichia coli M15 (pREP4) cells and purified to homogeneity. The protein was crystallized from two different conditions, (i) 0.1 M HEPES pH 7.5, 20%(w/v) polyethylene glycol 10,000 and (ii) 0.2 M NaCl, 0.1 M bis-tris pH 6.5, 25%(w/v) polyethylene glycol 3350, at 25°C by the sitting-drop vapour-diffusion method. Crystals grown at pH 7.5 diffracted to 2.5 Å resolution and belonged to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 77.0, b = 86.11, c = 94.07 Å. Crystals from the second condition at pH 6.5 diffracted to 2.00 Å resolution. These crystals belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 73.21, b = 81.75, c = 89.18 Å. X-ray diffraction data have been collected and processed to the maximum resolution to determine the structure of PGM. The structure has been solved by molecular replacement and structure refinement is now in progress.
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Affiliation(s)
- Amlan Roychowdhury
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721 302, India
| | - Anirban Kundu
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721 302, India
| | - Akanksha Gujar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721 302, India
| | - Madhuparna Bose
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721 302, India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721 302, India
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van Beilen JWA, Brul S. Compartment-specific pH monitoring in Bacillus subtilis using fluorescent sensor proteins: a tool to analyze the antibacterial effect of weak organic acids. Front Microbiol 2013; 4:157. [PMID: 23785365 PMCID: PMC3685010 DOI: 10.3389/fmicb.2013.00157] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 05/30/2013] [Indexed: 11/25/2022] Open
Abstract
The internal pH (pHi) of a living cell is one of its most important physiological parameters. To monitor the pH inside Bacillus subtilis during various stages of its life cycle, we constructed an improved version (IpHluorin) of the ratiometric, pH-sensitive fluorescent protein pHluorin by extending it at the 5′ end with the first 24 bp of comGA. The new version, which showed an approximate 40% increase in fluorescence intensity, was expressed from developmental phase-specific, native promoters of B. subtilis that are specifically active during vegetative growth on glucose (PptsG) or during sporulation (PspoIIA, PspoIIID, and PsspE). Our results show strong, compartment-specific expression of IpHluorin that allowed accurate pHi measurements of live cultures during exponential growth, early and late sporulation, spore germination, and during subsequent spore outgrowth. Dormant spores were characterized by an pHi of 6.0 ± 0.3. Upon full germination the pHi rose dependent on the medium to 7.0–7.4. The presence of sorbic acid in the germination medium inhibited a rise in the intracellular pH of germinating spores and inhibited germination. Such effects were absent when acetic was added at identical concentrations.
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Affiliation(s)
- Johan W A van Beilen
- Department of Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam Amsterdam, Netherlands
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Siegumfeldt H, Arneborg N. Assessment of survival of food-borne microorganisms in the food chain by fluorescence ratio imaging microscopy. Trends Food Sci Technol 2011. [DOI: 10.1016/j.tifs.2011.01.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Abstract
CodY is a global transcriptional regulator that is activated by branched-chain amino acids. A palindromic 15-bp sequence motif, AATTTTCNGAAAATT, is associated with CodY DNA binding. A gel mobility shift assay was used to examine the effect of pH on the binding of Bacillus subtilis CodY to the hutPp and ureAp(3) promoters. CodY at pH 6.0 has higher affinity for DNA, more enhanced activation by isoleucine, and a lower propensity for nonspecific DNA binding than CodY at pH 8.0. DNase I footprinting was used to identify the CodY-protected regions in the hutPp and ureAp(3) promoters. The CodY-protected sequences for both promoters were found to contain multiple copies of the 15-bp motif with 6-bp overlaps. Mutational analysis of the hutPp regulatory region revealed that two overlapping sequence motifs were required for CodY-mediated regulation. The presence of overlapping sequence motifs in the regulatory regions of many B. subtilis CodY-regulated genes suggests that CodY binds to native operators that contain overlapping binding sites.
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Slonczewski JL, Fujisawa M, Dopson M, Krulwich TA. Cytoplasmic pH measurement and homeostasis in bacteria and archaea. Adv Microb Physiol 2009; 55:1-79, 317. [PMID: 19573695 DOI: 10.1016/s0065-2911(09)05501-5] [Citation(s) in RCA: 293] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Of all the molecular determinants for growth, the hydronium and hydroxide ions are found naturally in the widest concentration range, from acid mine drainage below pH 0 to soda lakes above pH 13. Most bacteria and archaea have mechanisms that maintain their internal, cytoplasmic pH within a narrower range than the pH outside the cell, termed "pH homeostasis." Some mechanisms of pH homeostasis are specific to particular species or groups of microorganisms while some common principles apply across the pH spectrum. The measurement of internal pH of microbes presents challenges, which are addressed by a range of techniques under varying growth conditions. This review compares and contrasts cytoplasmic pH homeostasis in acidophilic, neutralophilic, and alkaliphilic bacteria and archaea under conditions of growth, non-growth survival, and biofilms. We present diverse mechanisms of pH homeostasis including cell buffering, adaptations of membrane structure, active ion transport, and metabolic consumption of acids and bases.
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Strauch MA, Bobay BG, Cavanagh J, Yao F, Wilson A, Le Breton Y. Abh and AbrB control of Bacillus subtilis antimicrobial gene expression. J Bacteriol 2007; 189:7720-32. [PMID: 17720793 PMCID: PMC2168746 DOI: 10.1128/jb.01081-07] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Accepted: 08/10/2007] [Indexed: 11/20/2022] Open
Abstract
The Bacillus subtilis abh gene encodes a protein whose N-terminal domain has 74% identity to the DNA-binding domain of the global regulatory protein AbrB. Strains with a mutation in abh showed alterations in the production of antimicrobial compounds directed against some other Bacillus species and gram-positive microbes. Relative to its wild-type parental strain, the abh mutant was found deficient, enhanced, or unaffected for the production of antimicrobial activity. Using lacZ fusions, we examined the effects of abh upon the expression of 10 promoters known to be regulated by AbrB, including five that transcribe well-characterized antimicrobial functions (SdpC, SkfA, TasA, sublancin, and subtilosin). For an otherwise wild-type background, the results show that Abh plays a negative regulatory role in the expression of four of the promoters, a positive role for the expression of three, and no apparent regulatory role in the expression of the other three promoters. Binding of AbrB and Abh to the promoter regions was examined using DNase I footprinting, and the results revealed significant differences. The transcription of abh is not autoregulated, but it is subject to a degree of AbrB-afforded negative regulation. The results indicate that Abh is part of the complex interconnected regulatory system that controls gene expression during the transition from active growth to stationary phase.
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Affiliation(s)
- Mark A Strauch
- Department of Biomedical Sciences, Dental School, University of Maryland, Baltimore, 650 W. Baltimore Street, Baltimore, MD 21201, USA.
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Raverdy S, Zhang Y, Foster J, Carlow CKS. Molecular and biochemical characterization of nematode cofactor independent phosphoglycerate mutases. Mol Biochem Parasitol 2007; 156:210-6. [PMID: 17897734 DOI: 10.1016/j.molbiopara.2007.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2007] [Revised: 08/10/2007] [Accepted: 08/13/2007] [Indexed: 11/20/2022]
Abstract
Phosphoglycerate mutase (PGM, EC 5.4.2.1) catalyzes the isomerization of 3-phosphoglycerate and 2-phosphoglycerate in glycolysis and gluconeogenesis. Two distinct types of PGM exist in nature, one that requires 2,3-bisphosphoglycerate as a cofactor (dPGM) and another that does not (iPGM). The two enzymes are structurally distinct and possess different mechanisms of action. In any particular organism, one form may exist or both. Nematodes possess the iPGM form whereas mammals have dPGM. In the present study, we have cloned and expressed iPGM from Onchocerca volvulus and described the catalytic properties of O. volvulus, Brugia malayi and Caenorhabditis elegans iPGM enzymes. Temperature and pH optima were determined for each enzyme. Like other iPGM enzymes, the activities of the nematode iPGM enzymes were dependent on the presence of divalent ions. Inactivation by EDTA could be restored most effectively by magnesium and manganese ions. Kinetic parameters and specific activities of the various recombinant enzymes were determined. The high similarity in catalytic properties among the enzymes indicates that a single enzyme inhibitor would likely be effective against all nematode enzymes. Inhibition of iPGM activity in vivo may lead to lethality as indicated by RNAi studies in C. elegans. Our results support the development of iPGM as a promising drug target in parasitic nematodes.
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Affiliation(s)
- Sylvine Raverdy
- New England Biolabs, Division of Parasitology, 240 County Road, Ipswich, MA 01938, USA
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Kobayashi H, Akitomi J, Fujii N, Kobayashi K, Altaf-Ul-Amin M, Kurokawa K, Ogasawara N, Kanaya S. The entire organization of transcription units on the Bacillus subtilis genome. BMC Genomics 2007; 8:197. [PMID: 17598888 PMCID: PMC1925097 DOI: 10.1186/1471-2164-8-197] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Accepted: 06/28/2007] [Indexed: 11/17/2022] Open
Abstract
Background In the post-genomic era, comprehension of cellular processes and systems requires global and non-targeted approaches to handle vast amounts of biological information. Results The present study predicts transcription units (TUs) in Bacillus subtilis, based on an integrated approach involving DNA sequence and transcriptome analyses. First, co-expressed gene clusters are predicted by calculating the Pearson correlation coefficients of adjacent genes for all the genes in a series that are transcribed in the same direction with no intervening gene transcribed in the opposite direction. Transcription factor (TF) binding sites are then predicted by detecting statistically significant TF binding sequences on the genome using a position weight matrix. This matrix is a convenient way to identify sites that are more highly conserved than others in the entire genome because any sequence that differs from a consensus sequence has a lower score. We identify genes regulated by each of the TFs by comparing gene expression between wild-type and TF mutants using a one-sided test. By applying the integrated approach to 11 σ factors and 17 TFs of B. subtilis, we are able to identify fewer candidates for genes regulated by the TFs than were identified using any single approach, and also detect the known TUs efficiently. Conclusion This integrated approach is, therefore, an efficient tool for narrowing searches for candidate genes regulated by TFs, identifying TUs, and estimating roles of the σ factors and TFs in cellular processes and functions of genes composing the TUs.
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Affiliation(s)
- Hirokazu Kobayashi
- Department of Bioinformatics and Genomes, Graduate School of Information Sciences, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Joe Akitomi
- Department of Bioinformatics and Genomes, Graduate School of Information Sciences, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Nobuyuki Fujii
- Department of Bioinformatics and Genomes, Graduate School of Information Sciences, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Kazuo Kobayashi
- Department of Bioinformatics and Genomes, Graduate School of Information Sciences, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Md Altaf-Ul-Amin
- Department of Bioinformatics and Genomes, Graduate School of Information Sciences, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Ken Kurokawa
- Department of Bioinformatics and Genomes, Graduate School of Information Sciences, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Naotake Ogasawara
- Department of Bioinformatics and Genomes, Graduate School of Information Sciences, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
| | - Shigehiko Kanaya
- Department of Bioinformatics and Genomes, Graduate School of Information Sciences, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
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Bumbaca D, Kosman J, Setlow P, Henderson RK, Jedrzejas MJ. Crystallization and preliminary X-ray analysis of the complex between a Bacillus subtilis alpha/beta-type small acid-soluble spore protein and DNA. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:503-6. [PMID: 17554173 PMCID: PMC2335083 DOI: 10.1107/s1744309107022750] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Accepted: 05/08/2007] [Indexed: 11/10/2022]
Abstract
An engineered variant of an alpha/beta-type small acid-soluble spore protein (SASP) from Bacillus subtilis was crystallized in a complex with a ten-base-pair double-stranded DNA by the hanging-drop vapor-diffusion method using ammonium sulfate as a precipitating agent. Crystals grew at 281 K using sodium cacodylate buffer pH 5.5 and these crystals diffracted X-rays to beyond 2.4 A resolution using synchrotron radiation. The crystallized complex contains two or three SASP molecules bound to one DNA molecule. The crystals belong to the hexagonal space group P6(1)22 or P6(5)22, with unit-cell parameters a = b = 87.0, c = 145.4 A, alpha = beta = 90.0, gamma = 120.0 degrees. Diffraction data were 96.6% complete to 2.4 A resolution, with an R(sym) of 8.5%. Structure solution by the multiwavelength/single-wavelength anomalous dispersion method using isomorphous crystals of selenomethionine-labeled protein is in progress.
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Affiliation(s)
- Daniela Bumbaca
- Children’s Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | - Jeffrey Kosman
- Department of Molecular, Microbial and Structural Biology, University of Connecticut Health Center, Farmington, CT 06032, USA
| | - Peter Setlow
- Department of Molecular, Microbial and Structural Biology, University of Connecticut Health Center, Farmington, CT 06032, USA
| | - R. Keith Henderson
- Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mark J. Jedrzejas
- Children’s Hospital Oakland Research Institute, Oakland, CA 94609, USA
- Correspondence e-mail:
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15
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Nukui M, Mello LV, Littlejohn JE, Setlow B, Setlow P, Kim K, Leighton T, Jedrzejas MJ. Structure and molecular mechanism of Bacillus anthracis cofactor-independent phosphoglycerate mutase: a crucial enzyme for spores and growing cells of Bacillus species. Biophys J 2006; 92:977-88. [PMID: 17085493 PMCID: PMC1779985 DOI: 10.1529/biophysj.106.093872] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phosphoglycerate mutases (PGMs) catalyze the isomerization of 2- and 3-phosphoglycerates and are essential for glucose metabolism in most organisms. This study reports the production, structure, and molecular dynamics analysis of Bacillus anthracis cofactor-independent PGM (iPGM). The three-dimensional structure of B. anthracis PGM is composed of two structural and functional domains, the phosphatase and transferase. The structural relationship between these two domains is different than in the B. stearothermophilus iPGM structure determined previously. However, the structures of the two domains of B. anthracis iPGM show a high degree of similarity to those in B. stearothermophilus iPGM. The novel domain arrangement in B. anthracis iPGM and the dynamic property of these domains is directly linked to the mechanism of enzyme catalysis, in which substrate binding is proposed to result in close association of the two domains. The structure of B. anthracis iPGM and the molecular dynamics of this structure provide unique insight into the mechanism of iPGM catalysis, in particular the roles of changes in coordination geometry of the enzyme's two bivalent metal ions and the regulation of this enzyme's activity by changes in intracellular pH during spore formation and germination in Bacillus species.
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Affiliation(s)
- Masatoshi Nukui
- Children's Hospital Oakland Research Institute, Oakland, California 94609, USA, and Northwest Institute for Bio-Health Informatics/University of Liverpool, UK
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Cortezzo DE, Setlow P. Analysis of factors that influence the sensitivity of spores of Bacillus subtilis to DNA damaging chemicals. J Appl Microbiol 2005; 98:606-17. [PMID: 15715863 DOI: 10.1111/j.1365-2672.2004.02495.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
AIMS To elucidate factors influencing the sensitivity of Bacillus subtilis spores to DNA damaging chemicals. METHODS AND RESULTS Wild-type spores of B. subtilis made at lower temperatures were more sensitive to the DNA damaging chemicals formaldehyde and nitrous acid than were spores made at higher temperatures, but this was not the case with the DNA alkylating agents ethylmethanesulphonate and methylmethanesulphonate. Spores lacking most DNA protective alpha/beta-type small, acid-soluble proteins (termed alpha-beta- spores) made at lower temperatures were also more sensitive to killing through DNA damage by hydrogen peroxide than were alpha-beta- spores made at higher temperatures. The spore coat, whose composition varies significantly with sporulation temperature, played only a minor role in spore resistance to these DNA damaging agents. Spores made at lower temperatures exhibited higher permeability to the methylamine and germinated more rapidly with the surfactant dodecylamine than did spores made at higher temperatures. Treatment of spores with the oxidizing agent cumene hydroperoxide sensitized the surviving spores to all these DNA damaging agents. The fatty acid composition of the inner membrane of spores made at different temperatures differed significantly, but levels of unsaturated fatty acids in the inner membrane did not influence spore resistance to DNA damaging agents or the sensitization to such agents by prior treatment with cumene hydroperoxide. CONCLUSIONS The higher rates of methylamine permeation across the inner membrane of spores made at lower temperatures and the greater sensitivity of wild-type spores made at lower temperatures to formaldehyde and nitrous acid and of alpha-beta- spores made at lower temperatures to hydrogen peroxide, all agents that must pass through the spore's inner membrane to damage DNA in the spore core, suggest that the permeability of the inner membrane is a significant factor influencing spore sensitivity to these agents. The sensitization of spores to DNA damaging chemicals by pretreatment with an oxidizing agent, a treatment that increases the permeability of the spore's inner membrane, and the more rapid dodecylamine germination of spores made at lower temperatures are consistent with this suggestion. SIGNIFICANCE AND IMPACT OF THE STUDY The results in this communication provide new insight into the factors that influence the resistance of spores of Bacillus species to chemicals that kill spores by damaging spore DNA.
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Affiliation(s)
- D E Cortezzo
- Department of Molecular, Microbial and Structural Biology, University of Connecticut Health Center, Farmington, CT 06032, USA
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Cortezzo DE, Koziol-Dube K, Setlow B, Setlow P. Treatment with oxidizing agents damages the inner membrane of spores of Bacillus subtilis and sensitizes spores to subsequent stress. J Appl Microbiol 2004; 97:838-52. [PMID: 15357734 DOI: 10.1111/j.1365-2672.2004.02370.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
AIMS To determine if treatment of Bacillus subtilis spores with a variety of oxidizing agents causes damage to the spore's inner membrane. METHODS AND RESULTS Spores of B. subtilis were killed 80-99% with wet heat or a variety of oxidizing agents, including betadine, chlorine dioxide, cumene hydroperoxide, hydrogen peroxide, Oxone, ozone, sodium hypochlorite and t-butylhydroperoxide, and the agents neutralized and/or removed. Survivors of spores pretreated with oxidizing agents exhibited increased sensitivity to killing by a normally minimal lethal heat treatment, while spores pretreated with wet heat did not. In addition, spores treated with wet heat or the oxidizing agents, except sodium hypochlorite, were more sensitive to high NaCl in plating media than were untreated spores. The core region of spores treated with at least two oxidizing agents was also penetrated much more readily by methylamine than was the core of untreated spores, and spores treated with oxidizing agents but not wet heat germinated faster with dodecylamine than did untreated spores. Spores of strains with very different levels of unsaturated fatty acids in their inner membrane exhibited essentially identical resistance to oxidizing agents. CONCLUSIONS Treatment of spores with oxidizing agents has been suggested to cause damage to the spore's inner membrane, a membrane whose integrity is essential for spore viability. The sensitization of spores to killing by heat and to high salt after pretreatment with oxidizing agents is consistent with and supports this suggestion. Presumably mild pretreatment with oxidizing agents causes some damage to the spore's inner membrane. While this damage may not be lethal under normal conditions, the damaged inner membrane may be less able to maintain its integrity, when dormant spores are exposed to high temperature or when germinated spores are faced with osmotic stress. Triggering of spore germination by dodecylamine likely involves action by this agent on the spore's inner membrane allowing release of the spore core's depot of dipicolinic acid. Presumably dodecylamine more readily alters the permeability of a damaged inner membrane and thus more readily triggers germination of spores pretreated with oxidizing agents. Damage to the inner spore membrane by oxidizing agents is also consistent with the more rapid penetration of methylamine into the core of treated spores, as the inner membrane is likely the crucial permeability barrier to methylamine entry into the spore core. As spores of strains with very different levels of unsaturated fatty acids in their inner membrane exhibited essentially identical resistance to oxidizing agents, it is not through oxidation of unsaturated fatty acids that oxidizing agents kill and/or damage spores. Perhaps these agents work by causing oxidative damage to key proteins in the spore's inner membrane. SIGNIFICANCE AND IMPACT OF THE STUDY The more rapid heat killing and germination with dodecylamine, the greater permeability of the spore core and the osmotic stress sensitivity in outgrowth of spores pretreated with oxidizing agents is consistent with such agents causing damage to the spore's inner membrane, even if this damage is not lethal under normal conditions. It may be possible to take advantage of this phenomenon to devise improved, less costly regimens for spore inactivation.
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Affiliation(s)
- D E Cortezzo
- Department of Molecular, Microbial and Structural Biology, University of Connecticut Health Center, Farmington, CT 06032, USA
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18
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Guerra DG, Vertommen D, Fothergill-Gilmore LA, Opperdoes FR, Michels PAM. Characterization of the cofactor-independent phosphoglycerate mutase from Leishmania mexicana mexicana. Histidines that coordinate the two metal ions in the active site show different susceptibilities to irreversible chemical modification. ACTA ACUST UNITED AC 2004; 271:1798-810. [PMID: 15096219 DOI: 10.1111/j.1432-1033.2004.04097.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phosphoglycerate mutase (PGAM) activity in promastigotes of the protozoan parasite Leishmania mexicana is found only in the cytosol. It corresponds to a cofactor-independent PGAM as it is not stimulated by 2,3-bisphosphoglycerate and is susceptible to EDTA and resistant to vanadate. We have cloned and sequenced the gene and developed a convenient bacterial expression system and a high-yield purification protocol. Kinetic properties of the bacterially produced protein have been determined (3-phosphoglycerate: K(m) = 0.27 +/- 0.02 mm, k(cat) = 434 +/- 54 s(-1); 2-phosphoglycerate: K(m) = 0.11 +/- 0.03 mm, k(cat) = 199 +/- 24 s(-1)). The activity is inhibited by phosphate but is resistant to Cl(-) and SO(4) (2-). Inactivation by EDTA is almost fully reversed by incubation with CoCl(2) but not with MnCl(2), FeSO(4), CuSO(4), NiCl(2) or ZnCl(2). Alkylation by diethyl pyrocarbonate resulted in irreversible inhibition, but saturating concentrations of substrate provided full protection. Kinetics of the inhibitory reaction showed the modification of a new group of essential residues only after removal of metal ions by EDTA. The modified residues were identified by MS analysis of peptides generated by trypsin digestion. Two substrate-protected histidines in the proximity of the active site were identified (His136, His467) and, unexpectedly, also a distant one (His160), suggesting a conformational change in its environment. Partial protection of His467 was observed by the addition of 25 micro m CoCl(2) to the EDTA treated enzyme but not of 125 micro m MnCl(2), suggesting that the latter metal ion cannot be accommodated in the active site of Leishmania PGAM.
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Affiliation(s)
- Daniel G Guerra
- Research Unit for Tropical Diseases,Universite, Catholique de Louvain, Brussels, Belgium
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19
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Kosman J, Setlow P. Effects of carboxy-terminal modifications and pH on binding of a Bacillus subtilis small, acid-soluble spore protein to DNA. J Bacteriol 2003; 185:6095-103. [PMID: 14526021 PMCID: PMC225040 DOI: 10.1128/jb.185.20.6095-6103.2003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Variants of the wild-type Bacillus subtilis alpha/beta-type small, acid-soluble spore protein (SASP) SspC(wt) were designed to evaluate the contribution of C-terminal residues to these proteins' affinity for DNA. SspC variants lacking one to three C-terminal residues were similar to SspC(wt) in DNA binding, but removal of six C-terminal residues greatly decreased DNA binding. In contrast, a C-terminal extension of three residues increased SspC's affinity for DNA 5- to 10-fold. C-terminal and N-terminal changes that independently caused large increases in SspC-DNA binding affinity were combined and produced an additive effect on DNA binding; the affinity of the resulting variant, SspC(DeltaN11-D13K-C3), for DNA was increased >/==" BORDER="0">20-fold over that of SspC(wt). For most of the SspC variants tested, lowering the pH from 7 to 6 improved DNA binding two- to sixfold, although the opposite effect was observed with variants having additional C-terminal basic residues. In vitro, the binding of SspC(DeltaN11-D13K-C3) to DNA suppressed the formation of cyclobutane-type thymine dimers and promoted the formation of the spore photoproduct upon UV irradiation to the same degree as the binding of SspC(wt). However, B. subtilis spores lacking major alpha/beta-type SASP and overexpressing SspC(DeltaN11-D13K-C3) had a 10-fold-lower viability and far less UV and heat resistance than spores overexpressing SspC(wt). This apparent lack of DNA protection by SspC(DeltaN11-D13K-C3) in vivo is likely due to the twofold-lower level of this protein in spores compared to the level of SspC(wt), perhaps because of effects of SspC(DeltaN11-D13K-C3) on gene expression in the forespore during sporulation. The latter results indicate that only moderately strong binding of alpha/beta-type SASP to DNA is important to balance the potentially conflicting requirements for these proteins in DNA transcription and DNA protection during spore formation, spore dormancy, and spore germination and outgrowth.
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Affiliation(s)
- Jeffrey Kosman
- Department of Biochemistry, University of Connecticut Health Center, Farmington, Connecticut 06032, USA
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20
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Webb CD, Resnekov O. Use of green fluorescent protein for visualization for cell-specific gene expression and subcellular protein localization in Bacillus subtilis. Methods Enzymol 2003; 302:136-53. [PMID: 12876768 DOI: 10.1016/s0076-6879(99)02015-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Affiliation(s)
- C D Webb
- Information Technology Office, Defense Advanced Research Projects Agency, Arlington, Virginia 22203-1714, USA
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21
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Jedrzejas MJ, Setlow P. Comparison of the binuclear metalloenzymes diphosphoglycerate-independent phosphoglycerate mutase and alkaline phosphatase: their mechanism of catalysis via a phosphoserine intermediate. Chem Rev 2001; 101:607-18. [PMID: 11712498 DOI: 10.1021/cr000253a] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M J Jedrzejas
- Department of Microbiology, University of Alabama at Birmingham, 933 19th Street South, CHSB-19 Room 545, Birmingham, Alabama 35294, USA.
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22
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Jedrzejas MJ. Structure, function, and evolution of phosphoglycerate mutases: comparison with fructose-2,6-bisphosphatase, acid phosphatase, and alkaline phosphatase. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2001; 73:263-87. [PMID: 10958932 DOI: 10.1016/s0079-6107(00)00007-9] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- M J Jedrzejas
- Department of Microbiology, University of Alabama at Birmingham, 933 19th Street South, CHSB-19 room 545, Birmingham, AL 35-294-2041, USA.
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23
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Jedrzejas MJ, Chander M, Setlow P, Krishnasamy G. Mechanism of catalysis of the cofactor-independent phosphoglycerate mutase from Bacillus stearothermophilus. Crystal structure of the complex with 2-phosphoglycerate. J Biol Chem 2000; 275:23146-53. [PMID: 10764795 DOI: 10.1074/jbc.m002544200] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The structure of the complex between the 2, 3-diphosphoglycerate-independent phosphoglycerate mutase (iPGM) from Bacillus stearothermophilus and its 3-phosphoglycerate substrate has recently been solved, and analysis of this structure allowed formulation of a mechanism for iPGM catalysis. In order to obtain further evidence for this mechanism, we have solved the structure of this iPGM complexed with 2-phosphoglycerate and two Mn(2+) ions at 1. 7-A resolution. The structure consists of two different domains connected by two loops and interacting through a network of hydrogen bonds. This structure is consistent with the proposed mechanism for iPGM catalysis, with the two main steps in catalysis being a phosphatase reaction removing the phosphate from 2- or 3-phosphoglycerate, generating an enzyme-bound phosphoserine intermediate, followed by a phosphotransferase reaction as the phosphate is transferred from the enzyme back to the glycerate moiety. The structure also allowed the assignment of the function of the two domains of the enzyme, one of which participates in the phosphatase reaction and formation of the phosphoserine enzyme intermediate, with the other involved in the phosphotransferase reaction regenerating phosphoglycerate. Significant structural similarity has also been found between the active site of the iPGM domain catalyzing the phosphatase reaction and Escherichia coli alkaline phosphatase.
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Affiliation(s)
- M J Jedrzejas
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA.
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24
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Siegumfeldt H, Björn Rechinger K, Jakobsen M. Dynamic changes of intracellular pH in individual lactic acid bacterium cells in response to a rapid drop in extracellular pH. Appl Environ Microbiol 2000; 66:2330-5. [PMID: 10831407 PMCID: PMC110524 DOI: 10.1128/aem.66.6.2330-2335.2000] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/1999] [Accepted: 03/08/2000] [Indexed: 11/20/2022] Open
Abstract
We describe the dynamics of changes in the intracellular pH (pH(i)) values of a number of lactic acid bacteria in response to a rapid drop in the extracellular pH (pH(ex)). Strains of Lactobacillus delbrueckii subsp. bulgaricus, Streptococcus thermophilus, and Lactococcus lactis were investigated. Listeria innocua, a gram-positive, non-lactic acid bacterium, was included for comparison. The method which we used was based on fluorescence ratio imaging of single cells, and it was therefore possible to describe variations in pH(i) within a population. The bacteria were immobilized on a membrane filter, placed in a closed perfusion chamber, and analyzed during a rapid decrease in the pH(ex) from 7.0 to 5.0. Under these conditions, the pH(i) of L. innocua remained neutral (between 7 and 8). In contrast, the pH(i) values of all of the strains of lactic acid bacteria investigated decreased to approximately 5.5 as the pH(ex) was decreased. No pronounced differences were observed between cells of the same strain harvested from the exponential and stationary phases. Small differences between species were observed with regard to the initial pH(i) at pH(ex) 7.0, while different kinetics of pH(i) regulation were observed in different species and also in different strains of S. thermophilus.
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Affiliation(s)
- H Siegumfeldt
- Department of Dairy and Food Science, Food Microbiology, The Royal Veterinary and Agricultural University, 1958 Frederiksberg C, Denmark.
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25
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Jedrzejas MJ, Chander M, Setlow P, Krishnasamy G. Structure and mechanism of action of a novel phosphoglycerate mutase from Bacillus stearothermophilus. EMBO J 2000; 19:1419-31. [PMID: 10747010 PMCID: PMC313928 DOI: 10.1093/emboj/19.7.1419] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bacillus stearothermophilus phosphoglycerate mutase (PGM), which interconverts 2- and 3-phosphoglyceric acid (PGA), does not require 2,3-diphosphoglyceric acid for activity. However, this enzyme does have an absolute and specific requirement for Mn(2+) ions for catalysis. Here we report the crystal structure of this enzyme complexed with 3PGA and manganese ions to 1.9 A resolution; this is the first crystal structure of a diphosphoglycerate-independent PGM to be determined. This information, plus the location of the two bound Mn(2+) ions and the 3PGA have allowed formulation of a possible catalytic mechanism for this PGM. In this mechanism Mn(2+) ions facilitate the transfer of the substrate's phosphate group to Ser62 to form a phosphoserine intermediate. In the subsequent phosphotransferase part of the reaction, the phosphate group is transferred from Ser62 to the O2 or O3 positions of the reoriented glycerate to yield the PGA product. Site-directed mutagenesis studies were used to confirm our mechanism and the involvement of specific enzyme residues in Mn(2+) binding and catalysis.
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Affiliation(s)
- M J Jedrzejas
- Department of Microbiology, University of Alabama at Birmingham, 933 19th Street South, Birmingham, AL 35294, USA.
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26
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Ross MA, Setlow P. The Bacillus subtilis HBsu protein modifies the effects of alpha/beta-type, small acid-soluble spore proteins on DNA. J Bacteriol 2000; 182:1942-8. [PMID: 10715001 PMCID: PMC101886 DOI: 10.1128/jb.182.7.1942-1948.2000] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HBsu, the Bacillus subtilis homolog of the Escherichia coli HU proteins and the major chromosomal protein in vegetative cells of B. subtilis, is present at similar levels in vegetative cells and spores ( approximately 5 x 10(4) monomers/genome). The level of HBsu in spores was unaffected by the presence or absence of the alpha/beta-type, small acid-soluble proteins (SASP), which are the major chromosomal proteins in spores. In developing forespores, HBsu colocalized with alpha/beta-type SASP on the nucleoid, suggesting that HBsu could modulate alpha/beta-type SASP-mediated properties of spore DNA. Indeed, in vitro studies showed that HBsu altered alpha/beta-type SASP protection of pUC19 from DNase digestion, induced negative DNA supercoiling opposing alpha/beta-type SASP-mediated positive supercoiling, and greatly ameliorated the alpha/beta-type SASP-mediated increase in DNA persistence length. However, HBsu did not significantly interfere with the alpha/beta-type SASP-mediated changes in the UV photochemistry of DNA that explain the heightened resistance of spores to UV radiation. These data strongly support a role for HBsu in modulating the effects of alpha/beta-type SASP on the properties of DNA in the developing and dormant spore.
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MESH Headings
- Bacillus subtilis/genetics
- Bacillus subtilis/growth & development
- Bacillus subtilis/metabolism
- Bacillus subtilis/physiology
- Bacterial Proteins/metabolism
- DNA Topoisomerases, Type I/metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- DNA, Bacterial/radiation effects
- DNA, Superhelical/chemistry
- DNA, Superhelical/genetics
- DNA, Superhelical/metabolism
- DNA, Superhelical/radiation effects
- DNA-Binding Proteins/metabolism
- Deoxyribonucleases/metabolism
- Dimerization
- Fluorescent Antibody Technique
- Molecular Weight
- Photochemistry
- Plasmids/chemistry
- Plasmids/genetics
- Plasmids/metabolism
- Plasmids/radiation effects
- Pyrimidine Dimers/genetics
- Pyrimidine Dimers/metabolism
- Pyrimidine Dimers/radiation effects
- Sigma Factor
- Spores, Bacterial/genetics
- Spores, Bacterial/growth & development
- Spores, Bacterial/metabolism
- Spores, Bacterial/radiation effects
- Transcription Factors
- Ultraviolet Rays
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Affiliation(s)
- M A Ross
- Department of Biochemistry, University of Connecticut Health Center, Farmington, Connecticut 06032, USA
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27
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Chander M, Setlow P, Lamani E, Jedrzejas MJ. Structural studies on a 2,3-diphosphoglycerate independent phosphoglycerate mutase from Bacillus stearothermophilus. J Struct Biol 1999; 126:156-65. [PMID: 10388626 DOI: 10.1006/jsbi.1999.4112] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Phosphoglycerate mutase (PGM), an important enzyme in the glycolytic pathway, catalyzes the transfer of a phosphate group between the 2 and the 3 positions of glyceric acid. The gene coding for the 2, 3-diphosphoglycerate independent monomeric PGM from Bacillus stearothermophilus (57 kDa), whose activity is extremely pH sensitive and has an absolute and specific requirement for Mn2+, has been cloned and the enzyme overexpressed and purified to homogeneity. Circular dichroism studies showed at most only small secondary structure changes in the enzyme upon binding to Mn2+ or its 3-phosphoglycerate substrate, but thermal unfolding analyses revealed that Mn2+ but not 3-phosphoglycerate caused a large increase in the enzyme's stability. Diffraction-quality crystals of the enzyme were obtained at neutral pH in the presence of 3-phosphoglyceric acid with ammonium sulfate as the precipitating agent; these crystals diffract X rays to beyond 2.5-A resolution and belong to the orthorhombic space group C2221 with unit cell dimensions, a = 58.42, b = 206.08, c = 124.87 A, and alpha = beta = gamma = 90.0 degrees. The selenomethionyl version of the B. stearothermophilus protein has also been overexpressed, purified, and crystallized. Employing these crystals, the determination of the three-dimensional structure of this PGM by the multiwavelength anomalous dispersion method is in progress.
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Affiliation(s)
- M Chander
- Department of Biochemistry, University of Connecticut Health Center, Farmington, Connecticut 06032, USA
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28
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Hayes CS, Setlow P. Analysis of deamidation of small, acid-soluble spore proteins from Bacillus subtilis in vitro and in vivo. J Bacteriol 1997; 179:6020-7. [PMID: 9324247 PMCID: PMC179503 DOI: 10.1128/jb.179.19.6020-6027.1997] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Deamidation of one specific asparagine residue in an alpha/beta-type small, acid-soluble spore protein (SASP) of Bacillus subtilis took place readily in vitro (time for 50% deamidation [t(1/2)], approximately 1 h at 70 degrees C), and the deamidated SASP no longer bound to DNA effectively. However, DNA binding protected against this deamidation in vitro. A mutant alpha/beta-type SASP in which the reactive asparagine was changed to aspartate also failed to bind to DNA in vitro, and this protein did not restore UV radiation and heat resistance to spores lacking the majority of their alpha/beta-type SASP. When expressed in Escherichia coli, where it is bound to DNA, the alpha/beta-type SASP deamidated with a t(1/2) of 2 to 3 h at 95 degrees C. However, the alpha/beta-type SASP was extremely resistant to deamidation within spores (t(1/2), >50 h at 95 degrees C). A gamma-type SASP of B. subtilis also deamidated readily in vitro (t(1/2) for one net deamidation, approximately 1 h at 70 degrees C), but this protein (which is not associated with DNA) deamidated fairly readily in spores (t(1/2), approximately 1 h at 95 degrees C). Total spore core protein also deamidated in vivo, although the rate was two- to threefold slower than that of deamidation of total protein in heated vegetative cells. These data indicate that protein deamidation is slowed significantly in spores, presumably due to the spore's environment. However, alpha/beta-type SASP are even more strongly protected against deamidation in vivo, presumably by their binding to spore DNA. Thus, not only do alpha/beta-type SASP protect spore DNA from damage; DNA also protects alpha/beta-type SASP.
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Affiliation(s)
- C S Hayes
- Department of Biochemistry, University of Connecticut Health Center, Farmington 06030, USA
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