201
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Lee BD, Apel WA, Sheridan PP, DeVeaux LC. Glycoside hydrolase gene transcription by Alicyclobacillus acidocaldarius during growth on wheat arabinoxylan and monosaccharides: a proposed xylan hydrolysis mechanism. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:110. [PMID: 29686728 PMCID: PMC5901876 DOI: 10.1186/s13068-018-1110-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 04/06/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND Metabolism of carbon bound in wheat arabinoxylan (WAX) polysaccharides by bacteria requires a number of glycoside hydrolases active toward different bonds between sugars and other molecules. Alicyclobacillus acidocaldarius is a Gram-positive thermoacidophilic bacterium capable of growth on a variety of mono-, di-, oligo-, and polysaccharides. Nineteen proposed glycoside hydrolases have been annotated in the A. acidocaldarius Type Strain ATCC27009/DSM 446 genome. Experiments were performed to understand the effect of monosaccharides on gene expression during growth on the polysaccharide, WAX. RESULTS Molecular analysis using high-density oligonucleotide microarrays was performed on A. acidocaldarius strain ATCC27009 when growing on WAX. When a culture growing exponentially at the expense of arabinoxylan saccharides was challenged with glucose or xylose, most glycoside hydrolases were downregulated. Interestingly, regulation was more intense when xylose was added to the culture than when glucose was added, showing a clear departure from classical carbon catabolite repression demonstrated by many Gram-positive bacteria. In silico analyses of the regulated glycoside hydrolases, along with the results from the microarray analyses, yielded a potential mechanism for arabinoxylan metabolism by A. acidocaldarius. Glycoside hydrolases expressed by this strain may have broad substrate specificity, and initial hydrolysis is catalyzed by an extracellular xylanase, while subsequent steps are likely performed inside the growing cell. CONCLUSIONS Glycoside hydrolases, for the most part, appear to be found in clusters, throughout the A. acidocaldarius genome. Not all of the glycoside hydrolase genes found at loci within these clusters were regulated during the experiment, indicating that a specific subset of the 19 glycoside hydrolase genes found in A. acidocaldarius were used during metabolism of WAX. While specific functions of the glycoside hydrolases were not tested as part of the research discussed, many of the glycoside hydrolases found in the A. acidocaldarius Type Strain appear to have a broader substrate range than that represented by the glycoside hydrolase family in which the enzymes were categorized.
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Affiliation(s)
- Brady D. Lee
- Biological Systems Department, Idaho National Laboratory, P. O. Box 1625, Idaho Falls, ID 83415 USA
- Department of Biological Sciences, Idaho State University, Campus Box 8007, Pocatello, ID 83209 USA
- Present Address: Pacific Northwest National Laboratory, Energy and Environment Directorate, Richland, WA USA
| | - William A. Apel
- Biological Systems Department, Idaho National Laboratory, P. O. Box 1625, Idaho Falls, ID 83415 USA
| | - Peter P. Sheridan
- Department of Biological Sciences, Idaho State University, Campus Box 8007, Pocatello, ID 83209 USA
| | - Linda C. DeVeaux
- Department of Biology, New Mexico Institute of Mining and Technology, 801 Leroy Pl, Socorro, NM 87801 USA
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202
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Neira JL, Hornos F, Cozza C, Cámara-Artigas A, Abián O, Velázquez-Campoy A. The histidine phosphocarrier protein, HPr, binds to the highly thermostable regulator of sigma D protein, Rsd, and its isolated helical fragments. Arch Biochem Biophys 2017; 639:26-37. [PMID: 29288053 DOI: 10.1016/j.abb.2017.12.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 02/06/2023]
Abstract
The phosphotransferase system (PTS) controls the preferential use of sugars in bacteria and it is also involved in other processes, such as chemotaxis. It is formed by a protein cascade in which the first two proteins are general (namely, EI and HPr) and the others are sugar-specific permeases. The Rsd protein binds specifically to the RNA polymerase (RNAP) σ70 factor. We first characterized the conformational stability of Escherichia coli Rsd. And second, we delineated the binding regions of Streptomyces coelicolor, HPrsc, and E. coli Rsd, by using fragments derived from each protein. To that end, we used several biophysical probes, namely, fluorescence, CD, NMR, ITC and BLI. Rsd had a free energy of unfolding of 15 kcal mol-1 at 25 °C, and a thermal denaturation midpoint of 103 °C at pH 6.5. The affinity between Rsd and HPrsc was 2 μM. Interestingly enough, the isolated helical-peptides, comprising the third (RsdH3) and fourth (RsdH4) Rsd helices, also interacted with HPrsc in a specific manner, and with affinities similar to that of the whole Rsd. Moreover, the isolated peptide of HPrsc, HPr9-30, comprising the active site, His15, also was bound to intact Rsd with similar affinity. Therefore, binding between Rsd and HPrsc was modulated by the two helices H3 and H4 of Rsd, and the regions around the active site of HPrsc. This implies that specific fragments of Rsd and HPrsc can be used to interfere with other protein-protein interactions (PPIs) of each other protein.
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Affiliation(s)
- José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Spain.
| | - Felipe Hornos
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain
| | - Concetta Cozza
- Molecular Biophysics Laboratory, Department of Physics, University of Calabria, Rende, Italy
| | - Ana Cámara-Artigas
- Department of Chemistry and Physics, Research Centre CIAIMBITAL, University of Almería- ceiA3, Almería, Spain
| | - Olga Abián
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Spain; Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain; Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Spain; Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain; Fundación ARAID, Diputación General de Aragón, Zaragoza, Spain.
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203
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Magnus N, Weise T, Piechulla B. Carbon Catabolite Repression Regulates the Production of the Unique Volatile Sodorifen of Serratia plymuthica 4Rx13. Front Microbiol 2017; 8:2522. [PMID: 29312220 PMCID: PMC5742105 DOI: 10.3389/fmicb.2017.02522] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/05/2017] [Indexed: 11/13/2022] Open
Abstract
Microorganisms are capable of synthesizing a plethora of secondary metabolites including the long-overlooked volatile organic compounds. Little knowledge has been accumulated regarding the regulation of the biosynthesis of such mVOCs. The emission of the unique compound sodorifen of Serratia plymuthica isolates was significantly reduced in minimal medium with glucose, while succinate elevated sodorifen release. The hypothesis of carbon catabolite repression (CCR) acting as a major control entity on the synthesis of mVOCs was proven by genetic evidence. Central components of the typical CCR of Gram-negative bacteria such as the adenylate cyclase (CYA), the cAMP binding receptor protein (CRP), and the catabolite responsive element (CRE) were removed by insertional mutagenesis. CYA, CRP, CRE1 mutants revealed a lower sodorifen release. Moreover, the emission potential of other S. plymuthica isolates was also evaluated.
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Affiliation(s)
- Nancy Magnus
- Institute for Biological Sciences, University of Rostock, Rostock, Germany
| | - Teresa Weise
- EuroImmun, Medizinische Labordiagnostik AG, Lübeck, Germany
| | - Birgit Piechulla
- Institute for Biological Sciences, University of Rostock, Rostock, Germany
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204
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Kasai T, Kouzuma A, Watanabe K. CpdA is involved in amino acid metabolism in Shewanella oneidensis MR-1. Biosci Biotechnol Biochem 2017; 82:166-172. [PMID: 29235426 DOI: 10.1080/09168451.2017.1413326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cyclic 3',5'-adenosine monophosphate (cAMP) phosphodiesterase (CPD) is an enzyme that catalyzes the hydrolysis of cAMP, a signaling molecule affecting diverse cellular and metabolic processes in bacteria. Some CPDs are also known to function in cAMP-independent manners, while their physiological roles remain largely unknown. Here, we investigated physiological roles of CPD in Shewanella oneidensis MR-1, a model environmental bacterium, and report that CPD is involved in amino-acid metabolism. We found that a CPD-deficient mutant of MR-1 (ΔcpdA) showed decreased expression of genes for the synthesis of methionine, S-adenosylmethionine, and histidine and required these three compounds to grow in minimal media. Interestingly, deletion of adenylate cyclases in ΔcpdA did not restore the ability to grow in minimal media, indicating that the amino acid requirements were not due to the accumulation of cAMP. These results suggest that CPD is involved in the regulation of amino acid metabolism in MR-1 in a cAMP-independent manner.
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Affiliation(s)
- Takuya Kasai
- a School of Life Sciences , Tokyo University of Pharmacy and Life Sciences , Tokyo , Japan
| | - Atsushi Kouzuma
- a School of Life Sciences , Tokyo University of Pharmacy and Life Sciences , Tokyo , Japan
| | - Kazuya Watanabe
- a School of Life Sciences , Tokyo University of Pharmacy and Life Sciences , Tokyo , Japan
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205
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Reuß DR, Rath H, Thürmer A, Benda M, Daniel R, Völker U, Mäder U, Commichau FM, Stülke J. Changes of DNA topology affect the global transcription landscape and allow rapid growth of a Bacillus subtilis mutant lacking carbon catabolite repression. Metab Eng 2017; 45:171-179. [PMID: 29242163 DOI: 10.1016/j.ymben.2017.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 12/04/2017] [Accepted: 12/06/2017] [Indexed: 12/27/2022]
Abstract
Bacteria are able to prioritize preferred carbon sources from complex mixtures. This is achieved by the regulatory phenomenon of carbon catabolite repression. To allow the simultaneous utilization of multiple carbon sources and to prevent the time-consuming adaptation to each individual nutrient in biotechnological applications, mutants lacking carbon catabolite repression can be used. However, such mutants often exhibit pleiotropic growth defects. We have isolated and characterized mutations that overcome the growth defect of Bacillus subtilis ccpA mutants lacking the major regulator of catabolite repression, in particular their glutamate auxotrophy. Here we show, that distinct mutations affecting the essential DNA topoisomerase I (TopA) cause glutamate prototrophy of the ccpA mutant. These suppressing variants of the TopA enzyme exhibit increased activity resulting in enhanced relaxation of the DNA. Reduced DNA supercoiling results in enhanced expression of the gltAB operon encoding the biosynthetic glutamate synthase. This is achieved by a significant re-organization of the global transcription network accompanied by re-routing of metabolism, which results in inactivation of the glutamate dehydrogenase. Our results provide a link between DNA topology, the global transcriptional network, and glutamate metabolism and suggest that specific topA mutants may be well suited for biotechnological purposes.
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Affiliation(s)
- Daniel R Reuß
- Department of General Microbiology, Georg-August-University Göttingen, Göttingen, Germany
| | - Hermann Rath
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Andrea Thürmer
- Department of Genomic and Applied Microbiology, Georg-August-University Göttingen, Göttingen, Germany
| | - Martin Benda
- Department of General Microbiology, Georg-August-University Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Georg-August-University Göttingen, Göttingen, Germany; Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Göttingen, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Ulrike Mäder
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Fabian M Commichau
- Department of General Microbiology, Georg-August-University Göttingen, Göttingen, Germany; Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Göttingen, Germany
| | - Jörg Stülke
- Department of General Microbiology, Georg-August-University Göttingen, Göttingen, Germany; Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Göttingen, Germany.
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206
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Pérez-Ramos A, Werning ML, Prieto A, Russo P, Spano G, Mohedano ML, López P. Characterization of the Sorbitol Utilization Cluster of the Probiotic Pediococcus parvulus 2.6: Genetic, Functional and Complementation Studies in Heterologous Hosts. Front Microbiol 2017; 8:2393. [PMID: 29259592 PMCID: PMC5723342 DOI: 10.3389/fmicb.2017.02393] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/20/2017] [Indexed: 02/02/2023] Open
Abstract
Pediococcus parvulus 2.6 secretes a 2-substituted (1,3)-β-D-glucan with prebiotic and immunomodulatory properties. It is synthesized by the GTF glycosyltransferase using UDP-glucose as substrate. Analysis of the P. parvulus 2.6 draft genome revealed the existence of a sorbitol utilization cluster of six genes (gutFRMCBA), whose products should be involved in sorbitol utilization and could generate substrates for UDP-glucose synthesis. Southern blot hybridization analysis showed that the cluster is located in a plasmid. Analysis of metabolic fluxes and production of the exopolysaccharide revealed that: (i) P. parvulus 2.6 is able to metabolize sorbitol, (ii) sorbitol utilization is repressed in the presence of glucose and (iii) sorbitol supports the synthesis of 2-substituted (1,3)-β-D-glucan. The sorbitol cluster encodes two putative regulators, GutR and GutM, in addition to a phosphoenolpyruvate-dependent phosphotransferase transport system and sorbitol-6-phosphate dehydrogenase. Therefore, we investigated the involvement of GutR and GutM in the expression of gutFRMCBA. The promoter-probe vector pRCR based on the mrfp gene, which encodes the fluorescence protein mCherry, was used to test the potential promoter of the cluster (P gut ) and the genes encoding the regulators. This was performed by transferring by electrotransformation the recombinant plasmids into two hosts, which metabolize sorbitol: Lactobacillus plantarum and Lactobacillus casei. Upon growth in the presence of sorbitol, but not of glucose, only the presence of P gut was required to support expression of mrfp in L. plantarum. In L. casei the presence of sorbitol in the growth medium and the pediococcal gutR or gutR plus gutM in the genome was required for P gut functionality. This demonstrates that: (i) P gut is required for expression of the gut cluster, (ii) P gut is subjected to catabolic repression in lactobacilli, (iii) GutR is an activator, and (iv) in the presence of sorbitol, trans-complementation for activation of P gut exists in L. plantarum but not in L. casei.
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Affiliation(s)
- Adrian Pérez-Ramos
- Biological Research Center (CIB), Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Maria L. Werning
- Biological Research Center (CIB), Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Center of Research and Transfer of Catamarca (CITCA), Consejo Nacional de Investigaciones Científicas y Técnicas, Catamarca, Argentina
| | - Alicia Prieto
- Biological Research Center (CIB), Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Pasquale Russo
- Department of Agricultural, Food and Environmental Sciences, University of Foggia, Foggia, Italy
| | - Giuseppe Spano
- Department of Agricultural, Food and Environmental Sciences, University of Foggia, Foggia, Italy
| | - Mari L. Mohedano
- Biological Research Center (CIB), Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Paloma López
- Biological Research Center (CIB), Consejo Superior de Investigaciones Científicas, Madrid, Spain
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207
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Um J, Kim DG, Jung MY, Saratale GD, Oh MK. Metabolic engineering of Enterobacter aerogenes for 2,3-butanediol production from sugarcane bagasse hydrolysate. BIORESOURCE TECHNOLOGY 2017; 245:1567-1574. [PMID: 28596073 DOI: 10.1016/j.biortech.2017.05.166] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/25/2017] [Accepted: 05/26/2017] [Indexed: 06/07/2023]
Abstract
The pathway engineering of Enterobacter aerogenes was attempted to improve its production capability of 2,3-butanediol from lignocellulosic biomass. In the medium containing glucose and xylose mixture as carbon sources, the gene deletion of pflB improved 2,3-butanediol carbon yield by 40%, while the deletion of ptsG increased xylose consumption rate significantly, improving the productivity at 12 hr by 70%. The constructed strain, EMY-22-galP, overexpressing glucose transporter (galP) in the triple gene knockout E. aerogenes, ldhA, pflB, and ptsG, provided the highest 2,3-butanediol titer and yield at 12 hr flask cultivation. Sugarcane bagasse was pretreated with green liquor, a solution containing Na2CO3 and Na2SO3 and was hydrolyzed by enzymes. The resulting hydrolysate was used as a carbon source for 2,3-butanediol production. After 72 hr in fermentation, the yield of 0.395g/g sugar was achieved, suggesting an economic production of 2,3-butanediol was possible from lignocellulosic biomass with the metabolically engineered strain.
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Affiliation(s)
- Jaeyong Um
- Department of Chemical and Biological Engineering, Korea University, Seongbuk-gu, Seoul 02841, South Korea
| | - Duck Gyun Kim
- Department of Chemical and Biological Engineering, Korea University, Seongbuk-gu, Seoul 02841, South Korea
| | - Moo-Young Jung
- CJ Research Institute of Biotechnology, Suwon, Gyeonggi 16495, South Korea
| | - Ganesh D Saratale
- Department of Food Science and Biotechnology, Dongguk University, Goyang, Gyeonggi 10326, South Korea
| | - Min-Kyu Oh
- Department of Chemical and Biological Engineering, Korea University, Seongbuk-gu, Seoul 02841, South Korea.
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208
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Park JH, Choi MA, Kim YJ, Kim YC, Chang YK, Jeong KJ. Engineering of Klebsiella oxytoca for production of 2,3-butanediol via simultaneous utilization of sugars from a Golenkinia sp. hydrolysate. BIORESOURCE TECHNOLOGY 2017; 245:1386-1392. [PMID: 28601394 DOI: 10.1016/j.biortech.2017.05.111] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/17/2017] [Accepted: 05/18/2017] [Indexed: 06/07/2023]
Abstract
The Klebsiella oxytoca was engineered to produce 2,3-butanediol (2,3-BDO) simultaneously utilizing glucose and galactose obtained from a Golenkinia sp. hydrolysate. For efficient uptake of galactose at a high concentration of glucose, Escherichia coli galactose permease (GalP) was introduced, and the expression of galP under a weak-strength promoter resulted in simultaneous consumption of galactose and glucose. Next, to improve the sugar consumption, a gene encoding methylglyoxal synthase (MgsA) known as an inhibitor of multisugar metabolism was deleted, and the mgsA-null mutant showed much faster consumption of both sugars than the wild-type strain did. Finally, we demonstrated that the engineered K. oxytoca could utilize sugar extracts from a Golenkinia sp. hydrolysate and successfully produces 2,3-BDO.
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Affiliation(s)
- Jong Hyun Park
- Department of Chemical and Biomolecular Engineering, BK21 Plus Program, KAIST, 291 Daehak-ro Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Min Ah Choi
- Department of Chemical and Biomolecular Engineering, BK21 Plus Program, KAIST, 291 Daehak-ro Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yong Jae Kim
- Department of Chemical and Biomolecular Engineering, BK21 Plus Program, KAIST, 291 Daehak-ro Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yeu-Chun Kim
- Department of Chemical and Biomolecular Engineering, BK21 Plus Program, KAIST, 291 Daehak-ro Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yong Keun Chang
- Department of Chemical and Biomolecular Engineering, BK21 Plus Program, KAIST, 291 Daehak-ro Yuseong-gu, Daejeon 34141, Republic of Korea; Advanced Biomass R&D Center (ABC), 291 Daehak-ro Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Ki Jun Jeong
- Department of Chemical and Biomolecular Engineering, BK21 Plus Program, KAIST, 291 Daehak-ro Yuseong-gu, Daejeon 34141, Republic of Korea; Advanced Biomass R&D Center (ABC), 291 Daehak-ro Yuseong-gu, Daejeon 34141, Republic of Korea; Institutes for the BioCentury (KIB), KAIST, 291 Daehak-ro Yuseong-gu, Daejeon 34141, Republic of Korea.
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209
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Wirebrand L, Madhushani AWK, Irie Y, Shingler V. Multiple Hfq-Crc target sites are required to impose catabolite repression on (methyl)phenol metabolism in Pseudomonas putida CF600. Environ Microbiol 2017; 20:186-199. [PMID: 29076626 DOI: 10.1111/1462-2920.13966] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/17/2017] [Accepted: 10/19/2017] [Indexed: 12/11/2022]
Abstract
The dmp-system encoded on the IncP-2 pVI150 plasmid of Pseudomonas putida CF600 confers the ability to assimilate (methyl)phenols. Regulation of the dmp-genes is subject to sophisticated control, which includes global regulatory input to subvert expression of the pathway in the presence of preferred carbon sources. Previously we have shown that in P. putida, translational inhibition exerted by the carbon repression control protein Crc operates hand-in-hand with the RNA chaperon protein Hfq to reduce translation of the DmpR regulator of the Dmp-pathway. Here, we show that Crc and Hfq co-target four additional sites to form riboprotein complexes within the proximity of the translational initiation sites of genes encoding the first two steps of the Dmp-pathway to mediate two-layered control in the face of selection of preferred substrates. Furthermore, we present evidence that Crc plays a hitherto unsuspected role in maintaining the pVI150 plasmid within a bacterial population, which has implications for (methyl)phenol degradation and a wide variety of other physiological processes encoded by the IncP-2 group of Pseudomonas-specific mega-plasmids.
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Affiliation(s)
- Lisa Wirebrand
- Department of Molecular Biology, Umeå University, Umeå SE 90187, Sweden
| | | | - Yasuhiko Irie
- Department of Molecular Biology, Umeå University, Umeå SE 90187, Sweden
| | - Victoria Shingler
- Department of Molecular Biology, Umeå University, Umeå SE 90187, Sweden
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210
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Blötz C, Stülke J. Glycerol metabolism and its implication in virulence in Mycoplasma. FEMS Microbiol Rev 2017; 41:640-652. [PMID: 28961963 DOI: 10.1093/femsre/fux033] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/09/2017] [Indexed: 12/11/2022] Open
Abstract
Glycerol and glycerol-containing compounds such as lipids belong to the most abundant organic compounds that may serve as nutrient for many bacteria. For the cell wall-less bacteria of the genus Mycoplasma, glycerol derived from phospholipids of their human or animal hosts is the major source of carbon and energy. The lipids are first degraded by lipases, and the resulting glycerophosphodiesters are transported into the cell and cleaved to release glycerol-3-phosphate. Alternatively, free glycerol can be transported, and then become phosphorylated. The oxidation of glycerol-3-phosphate in Mycoplasma spp. as well as in related firmicutes involves a hydrogen peroxide-generating glycerol-3-phosphate oxidase. This enzyme is a key player in the virulence of Mycoplasma spp. as the produced hydrogen peroxide is one of the major virulence factors of these bacteria. In this review, the different components involved in the utilization of lipids and glycerol in Mycoplasma pneumoniae and related bacteria are discussed.
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Affiliation(s)
- Cedric Blötz
- Department for General Microbiology, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Jörg Stülke
- Department for General Microbiology, Georg-August-University Göttingen, 37077 Göttingen, Germany
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211
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Davis R, Écija-Conesa A, Gallego-Jara J, de Diego T, Filippova EV, Kuffel G, Anderson WF, Gibson BW, Schilling B, Canovas M, Wolfe AJ. An acetylatable lysine controls CRP function in E. coli. Mol Microbiol 2017; 107:116-131. [PMID: 29105190 DOI: 10.1111/mmi.13874] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 10/27/2017] [Accepted: 10/31/2017] [Indexed: 01/02/2023]
Abstract
Transcriptional regulation is the key to ensuring that proteins are expressed at the proper time and the proper amount. In Escherichia coli, the transcription factor cAMP receptor protein (CRP) is responsible for much of this regulation. Questions remain, however, regarding the regulation of CRP activity itself. Here, we demonstrate that a lysine (K100) on the surface of CRP has a dual function: to promote CRP activity at Class II promoters, and to ensure proper CRP steady state levels. Both functions require the lysine's positive charge; intriguingly, the positive charge of K100 can be neutralized by acetylation using the central metabolite acetyl phosphate as the acetyl donor. We propose that CRP K100 acetylation could be a mechanism by which the cell downwardly tunes CRP-dependent Class II promoter activity, whilst elevating CRP steady state levels, thus indirectly increasing Class I promoter activity. This mechanism would operate under conditions that favor acetate fermentation, such as during growth on glucose as the sole carbon source or when carbon flux exceeds the capacity of the central metabolic pathways.
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Affiliation(s)
- Robert Davis
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Ana Écija-Conesa
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ''Campus Mare Nostrum'', Murcia, E-30100, Spain
| | - Julia Gallego-Jara
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ''Campus Mare Nostrum'', Murcia, E-30100, Spain
| | - Teresa de Diego
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ''Campus Mare Nostrum'', Murcia, E-30100, Spain
| | - Ekaterina V Filippova
- Department of Biochemistry and Molecular Genetics, Center for Structural Genomics of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Gina Kuffel
- Loyola Genomics Facility, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Wayne F Anderson
- Department of Biochemistry and Molecular Genetics, Center for Structural Genomics of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | | | | | - Manuel Canovas
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ''Campus Mare Nostrum'', Murcia, E-30100, Spain
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, IL, 60153, USA
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212
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Frank SA. Receptor uptake arrays for vitamin B 12, siderophores, and glycans shape bacterial communities. Ecol Evol 2017; 7:10175-10195. [PMID: 29238546 PMCID: PMC5723603 DOI: 10.1002/ece3.3544] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/20/2017] [Accepted: 09/28/2017] [Indexed: 01/15/2023] Open
Abstract
Molecular variants of vitamin B12, siderophores, and glycans occur. To take up variant forms, bacteria may express an array of receptors. The gut microbe Bacteroides thetaiotaomicron has three different receptors to take up variants of vitamin B12 and 88 receptors to take up various glycans. The design of receptor arrays reflects key processes that shape cellular evolution. Competition may focus each species on a subset of the available nutrient diversity. Some gut bacteria can take up only a narrow range of carbohydrates, whereas species such as B. thetaiotaomicron can digest many different complex glycans. Comparison of different nutrients, habitats, and genomes provides opportunity to test hypotheses about the breadth of receptor arrays. Another important process concerns fluctuations in nutrient availability. Such fluctuations enhance the value of cellular sensors, which gain information about environmental availability and adjust receptor deployment. Bacteria often adjust receptor expression in response to fluctuations of particular carbohydrate food sources. Some species may adjust expression of uptake receptors for specific siderophores. How do cells use sensor information to control the response to fluctuations? This question about regulatory wiring relates to problems that arise in control theory and artificial intelligence. Control theory clarifies how to analyze environmental fluctuations in relation to the design of sensors and response systems. Recent advances in deep learning studies of artificial intelligence focus on the architecture of regulatory wiring and the ways in which complex control networks represent and classify environmental states. I emphasize the similar design problems that arise in cellular evolution, control theory, and artificial intelligence. I connect those broad conceptual aspects to many testable hypotheses for bacterial uptake of vitamin B12, siderophores, and glycans.
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Affiliation(s)
- Steven A. Frank
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaIrvineCAUSA
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213
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Liao X, Yang F, Wang R, He X, Li H, Kao RYT, Xia W, Sun H. Identification of catabolite control protein A from Staphylococcus aureus as a target of silver ions. Chem Sci 2017; 8:8061-8066. [PMID: 29568454 PMCID: PMC5855135 DOI: 10.1039/c7sc02251d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 09/23/2017] [Indexed: 01/24/2023] Open
Abstract
Staphylococcus aureus is one of the most common pathogenic bacteria that causes human infectious diseases. The emergence of antibiotic-resistant strains of S. aureus promotes the development of new anti-bacterial strategies. Silver ions (Ag+) have attracted profound attention due to their broad-spectrum antimicrobial activities. Although the antibacterial properties of silver have been well known for many centuries, its mechanism of action remains unclear and its protein targets are rarely reported. Herein, we identify the catabolite control protein A (CcpA) of S. aureus as a putative target for Ag+. CcpA binds 2 molar equivalents of Ag+via its two cysteine residues (Cys216 and Cys242). Importantly, Ag+ binding induces CcpA oligomerization and abolishes its DNA binding capability, which further attenuates S. aureus growth and suppresses α-hemolysin toxicity. This study extends our understanding of the bactericidal effects of silver.
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Affiliation(s)
- Xiangwen Liao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry , School of Chemistry , Sun Yat-sen University , Guangzhou , 510275 , China . .,Hunan Provincial Key Laboratory for Ethnic Dong Medicine Research , Hunan University of Medicine , Huaihua , 418000 , China
| | - Fang Yang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry , School of Chemistry , Sun Yat-sen University , Guangzhou , 510275 , China .
| | - Runming Wang
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , P. R. China . .,Department of Microbiology , State Key Laboratory for Emerging Infectious Diseases , The University of Hong Kong , Hong Kong , P. R. China
| | - Xiaojun He
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry , School of Chemistry , Sun Yat-sen University , Guangzhou , 510275 , China .
| | - Hongyan Li
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , P. R. China .
| | - Richard Y T Kao
- Department of Microbiology , State Key Laboratory for Emerging Infectious Diseases , The University of Hong Kong , Hong Kong , P. R. China
| | - Wei Xia
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry , School of Chemistry , Sun Yat-sen University , Guangzhou , 510275 , China .
| | - Hongzhe Sun
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry , School of Chemistry , Sun Yat-sen University , Guangzhou , 510275 , China . .,Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , P. R. China .
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214
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Transcriptional Modulation of Transport- and Metabolism-Associated Gene Clusters Leading to Utilization of Benzoate in Preference to Glucose in Pseudomonas putida CSV86. Appl Environ Microbiol 2017; 83:AEM.01280-17. [PMID: 28733285 DOI: 10.1128/aem.01280-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 07/16/2017] [Indexed: 11/20/2022] Open
Abstract
The effective elimination of xenobiotic pollutants from the environment can be achieved by efficient degradation by microorganisms even in the presence of sugars or organic acids. Soil isolate Pseudomonas putida CSV86 displays a unique ability to utilize aromatic compounds prior to glucose. The draft genome and transcription analyses revealed that glucose uptake and benzoate transport and metabolism genes are clustered at the glc and ben loci, respectively, as two distinct operons. When grown on glucose plus benzoate, CSV86 displayed significantly higher expression of the ben locus in the first log phase and of the glc locus in the second log phase. Kinetics of substrate uptake and metabolism matched the transcription profiles. The inability of succinate to suppress benzoate transport and metabolism resulted in coutilization of succinate and benzoate. When challenged with succinate or benzoate, glucose-grown cells showed rapid reduction in glc locus transcription, glucose transport, and metabolic activity, with succinate being more effective at the functional level. Benzoate and succinate failed to interact with or inhibit the activities of glucose transport components or metabolic enzymes. The data suggest that succinate and benzoate suppress glucose transport and metabolism at the transcription level, enabling P. putida CSV86 to preferentially metabolize benzoate. This strain thus has the potential to be an ideal host to engineer diverse metabolic pathways for efficient bioremediation.IMPORTANCEPseudomonas strains play an important role in carbon cycling in the environment and display a hierarchy in carbon utilization: organic acids first, followed by glucose, and aromatic substrates last. This limits their exploitation for bioremediation. This study demonstrates the substrate-dependent modulation of ben and glc operons in Pseudomonas putida CSV86, wherein benzoate suppresses glucose transport and metabolism at the transcription level, leading to preferential utilization of benzoate over glucose. Interestingly, succinate and benzoate are cometabolized. These properties are unique to this strain compared to other pseudomonads and open up avenues to unravel novel regulatory processes. Strain CSV86 can serve as an ideal host to engineer and facilitate efficient removal of recalcitrant pollutants even in the presence of simpler carbon sources.
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215
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Yoshikawa M, Zhang M, Toyota K. Biodegradation of Volatile Organic Compounds and Their Effects on Biodegradability under Co-Existing Conditions. Microbes Environ 2017; 32:188-200. [PMID: 28904262 PMCID: PMC5606688 DOI: 10.1264/jsme2.me16188] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Volatile organic compounds (VOCs) are major pollutants that are found in contaminated sites, particularly in developed countries such as Japan. Various microorganisms that degrade individual VOCs have been reported, and genomic information related to their phylogenetic classification and VOC-degrading enzymes is available. However, the biodegradation of multiple VOCs remains a challenging issue. Practical sites, such as chemical factories, research facilities, and illegal dumping sites, are often contaminated with multiple VOCs. In order to investigate the potential of biodegrading multiple VOCs, we initially reviewed the biodegradation of individual VOCs. VOCs include chlorinated ethenes (tetrachloroethene, trichloroethene, dichloroethene, and vinyl chloride), BTEX (benzene, toluene, ethylbenzene, and xylene), and chlorinated methanes (carbon tetrachloride, chloroform, and dichloromethane). We also summarized essential information on the biodegradation of each kind of VOC under aerobic and anaerobic conditions, together with the microorganisms that are involved in VOC-degrading pathways. Interactions among multiple VOCs were then discussed based on concrete examples. Under conditions in which multiple VOCs co-exist, the biodegradation of a VOC may be constrained, enhanced, and/or unaffected by other compounds. Co-metabolism may enhance the degradation of other VOCs. In contrast, constraints are imposed by the toxicity of co-existing VOCs and their by-products, catabolite repression, or competition between VOC-degrading enzymes. This review provides fundamental, but systematic information for designing strategies for the bioremediation of multiple VOCs, as well as information on the role of key microorganisms that degrade VOCs.
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Affiliation(s)
- Miho Yoshikawa
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST).,Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology
| | - Ming Zhang
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Koki Toyota
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology
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216
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Gerritsen J, Hornung B, Renckens B, van Hijum SA, Martins dos Santos VA, Rijkers GT, Schaap PJ, de Vos WM, Smidt H. Genomic and functional analysis of Romboutsia ilealis CRIB T reveals adaptation to the small intestine. PeerJ 2017; 5:e3698. [PMID: 28924494 PMCID: PMC5598433 DOI: 10.7717/peerj.3698] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 07/26/2017] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates to survive in a complex and highly competitive ecosystem. Understanding how these communities function requires elucidating the role of its key players, the interactions among them and with their environment/host. METHODS The genome of the gut bacterium Romboutsia ilealis CRIBT was sequenced with multiple technologies (Illumina paired-end, mate-pair and PacBio). The transcriptome was sequenced (Illumina HiSeq) after growth on three different carbohydrate sources, and short chain fatty acids were measured via HPLC. RESULTS We present the complete genome of Romboutsia ilealis CRIBT, a natural inhabitant and key player of the small intestine of rats. R. ilealis CRIBT possesses a circular chromosome of 2,581,778 bp and a plasmid of 6,145 bp, carrying 2,351 and eight predicted protein coding sequences, respectively. Analysis of the genome revealed limited capacity to synthesize amino acids and vitamins, whereas multiple and partially redundant pathways for the utilization of different relatively simple carbohydrates are present. Transcriptome analysis allowed identification of the key components in the degradation of glucose, L-fucose and fructo-oligosaccharides. DISCUSSION This revealed that R. ilealis CRIBT is adapted to a nutrient-rich environment where carbohydrates, amino acids and vitamins are abundantly available.
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Affiliation(s)
- Jacoline Gerritsen
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Winclove Probiotics, Amsterdam, The Netherlands
| | - Bastian Hornung
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Bernadette Renckens
- Nijmegen Centre for Molecular Life Sciences, CMBI, Radboud UMC, Nijmegen, The Netherlands
| | - Sacha A.F.T. van Hijum
- Nijmegen Centre for Molecular Life Sciences, CMBI, Radboud UMC, Nijmegen, The Netherlands
- NIZO, Ede, The Netherlands
| | - Vitor A.P. Martins dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
- LifeGlimmer GmbH, Berlin, Germany
| | - Ger T. Rijkers
- Laboratory for Medical Microbiology and Immunology, St. Antonius Hospital, Nieuwegein, The Netherlands
- Department of Science, University College Roosevelt, Middelburg, The Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Departments of Microbiology and Immunology and Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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217
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Liu Y, Yoo BB, Hwang CA, Suo Y, Sheen S, Khosravi P, Huang L. LMOf2365_0442 Encoding for a Fructose Specific PTS Permease IIA May Be Required for Virulence in L. monocytogenes Strain F2365. Front Microbiol 2017; 8:1611. [PMID: 28900418 PMCID: PMC5581801 DOI: 10.3389/fmicb.2017.01611] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/07/2017] [Indexed: 02/06/2023] Open
Abstract
Listeria monocytogenes is a foodborne pathogen that causes listeriosis, which is a major public health concern due to the high fatality rate. LMOf2365_0442, 0443, and 0444 encode for fructose-specific EIIABC components of phosphotransferase transport system (PTS) permease that is responsible for sugar transport. In previous studies, in-frame deletion mutants of a putative fructose-specific PTS permease (LMOf2365_0442, 0443, and 0444) were constructed and analyzed. However, the virulence potential of these deletion mutants has not been studied. In this study, two in vitro methods were used to analyze the virulence potential of these L. monocytogenes deletion mutants. First, invasion assays were used to measure the invasion efficiencies to host cells using the human HT-29 cell line. Second, plaque forming assays were used to measure cell-to-cell spread in host cells. Our results showed that the deletion mutant ΔLMOf2365_0442 had reduced invasion and cell-to-cell spread efficiencies in human cell line compared to the parental strain LMOf2365, indicating that LMOf2365_0442 encoding for a fructose specific PTS permease IIA may be required for virulence in L. monocytogenes strain F2365. In addition, the gene expression levels of 15 virulence and stress-related genes were analyzed in the stationary phase cells of the deletion mutants using RT-PCR assays. Virulence-related gene expression levels were elevated in the deletion mutants ΔLMOf2365_0442-0444 compared to the wild type parental strain LMOf2365, indicating the down-regulation of virulence genes by this PTS permease in L. monocytogenes. Finally, stress-related gene clpC expression levels were also increased in all of the deletion mutants, suggesting the involvement of this PTS permease in stress response. Furthermore, these deletion mutants displayed the same pressure tolerance and the same capacity for biofilm formation compared to the wild-type parental strain LMOf2365. In summary, our findings suggest that the LMOf2365_0442 gene can be used as a potential target to develop inhibitors for new therapeutic and pathogen control strategies for public health.
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Affiliation(s)
- Yanhong Liu
- Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, WyndmoorPA, United States
| | - Brian B Yoo
- Clinical and Environmental Microbiology Branch, Division of Healthcare Quality and Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, AtlantaGA, United States
| | - Cheng-An Hwang
- Residue Chemistry and Predictive Microbiology Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, WyndmoorPA, United States
| | - Yujuan Suo
- Institute for Agri-Food Standards and Testing Technology, Shanghai Academy of Agricultural SciencesShanghai, China
| | - Shiowshuh Sheen
- Food Safety Intervention Technologies Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, WyndmoorPA, United States
| | - Parvaneh Khosravi
- Food Safety Intervention Technologies Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, WyndmoorPA, United States
| | - Lihan Huang
- Residue Chemistry and Predictive Microbiology Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, WyndmoorPA, United States
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218
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Beckmann A, Hüttel S, Schmitt V, Müller R, Stadler M. Optimization of the biotechnological production of a novel class of anti-MRSA antibiotics from Chitinophaga sancti. Microb Cell Fact 2017; 16:143. [PMID: 28818083 PMCID: PMC5561589 DOI: 10.1186/s12934-017-0756-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 08/08/2017] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Recently, the discovery of the elansolids, a group of macrolides, was reported. The molecules show activity against methicillin-resistant Staphylococcus aureus as well as other gram-positive organisms. This fact renders those substances a promising starting point for future chemical development. The active atropisomers A1/A2 are formed by macrolactonization of the biosynthesis product A3 but are prone to ring opening and subsequent formation of several unwanted side products. Recently it could be shown that addition of different nucleophiles to culture extracts of Chitinophaga sancti enable the formation of new stable elansolid derivatives. Furthermore, addition of such a nucleophile directly into the culture led exclusively to formation of a single active elansolid derivative. Due to low product yields, methods for production of gram amounts of these molecules have to be established to enable further development of this promising compound class. RESULTS Production of elansolid A2 by C. sancti was enabled using a synthetic medium with sucrose as carbon source to a final concentration of 18.9 mg L-1. A fed-batch fermentation was ensued that resulted in an elansolid A2 concentration of 55.3 mg L-1. When using glucose as carbon source in a fed-batch fermentation only 34.4 mg L-1 elansolid A2 but 223.1 mg L-1 elansolid C1 were produced. This finding was not unexpected since elansolids A1/A2 and A3 have been reported to easily react with nucleophiles like anthranilic acid, a precursor of tryptophan biosynthesis. Due to the fact that nucleophiles can be incorporated in vivo, a fed-batch cultivation under identical conditions, with addition of anthranilic acid was carried out and lead to almost exclusive formation of elansolid C1 (257.5 mg L-1). CONCLUSION Reproducible elansolid A2 and C1 production is feasible in different synthetic media at relatively high concentrations that will allow further investigation and semi-synthetic optimization. The feeding of anthranilic acid enables the exclusive production of the stable elansolid derivative C1, which reduces product loss by unspecific reactions and eases downstream processing. This derivative shows activity in the same range as the elansolids A1/A2. Hence, the method can possibly serve as a model-process for incorporation of other nucleophiles and biotechnological production of specifically designed molecules.
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Affiliation(s)
- Amelie Beckmann
- Department of Microbial Drugs, Helmholtz Centre for Infection Research, Brunswick, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Brunswick, Germany
| | - Stephan Hüttel
- Department of Microbial Drugs, Helmholtz Centre for Infection Research, Brunswick, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Brunswick, Germany
| | - Viktoria Schmitt
- Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Dept. Pharmaceutical Biotechnology of Saarland University, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Brunswick, Germany
| | - Rolf Müller
- Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Dept. Pharmaceutical Biotechnology of Saarland University, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Brunswick, Germany
| | - Marc Stadler
- Department of Microbial Drugs, Helmholtz Centre for Infection Research, Brunswick, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Brunswick, Germany
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219
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Zhu X, Zhao D, Qiu H, Fan F, Man S, Bi C, Zhang X. The CRISPR/Cas9-facilitated multiplex pathway optimization (CFPO) technique and its application to improve the Escherichia coli xylose utilization pathway. Metab Eng 2017; 43:37-45. [PMID: 28800965 DOI: 10.1016/j.ymben.2017.08.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/04/2017] [Accepted: 08/03/2017] [Indexed: 01/09/2023]
Abstract
One of the most important research subjects of metabolic engineering is the pursuit of balanced metabolic pathways, which requires the modulation of expression of many genes. However, simultaneously modulating multiple genes on the chromosome remains challenging in prokaryotic organisms, including the industrial workhorse - Escherichia coli. In this work, the CRISPR/Cas9-facilitated multiplex pathway optimization (CFPO) technique was developed to simultaneously modulate the expression of multiple genes on the chromosome. To implement it, two plasmids were employed to target Cas9 to regulatory sequences of pathway genes, and a donor DNA plasmid library was constructed containing a regulator pool to modulate the expression of these genes. A modularized plasmid construction strategy was used to enable the assembly of a complex donor DNA plasmid library. After genome editing using this technique, a combinatorial library was obtained with variably expressed pathway genes. As a demonstration, the CFPO technique was applied to the xylose metabolic pathway genes in E. coli to improve xylose utilization. Three transcriptional units containing a total of four genes were modulated simultaneously with 70% efficiency, and improved strains were selected from the resulting combinatorial library by growth enrichment. The best strain, HQ304, displayed a 3-fold increase of the xylose-utilization rate. Finally, the xylose-utilization pathway of HQ304 was analyzed enzymologically to determine the optimal combination of enzyme activities.
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Affiliation(s)
- Xinna Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Tianjin 300308, China
| | - Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Tianjin 300308, China
| | - Huanna Qiu
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Tianjin 300308, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Feiyu Fan
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Tianjin 300308, China
| | - Shuli Man
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Tianjin 300308, China.
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Tianjin 300308, China.
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220
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Lee BD, Apel WA, DeVeaux LC, Sheridan PP. Concurrent metabolism of pentose and hexose sugars by the polyextremophile Alicyclobacillus acidocaldarius. J Ind Microbiol Biotechnol 2017; 44:1443-1458. [PMID: 28776272 DOI: 10.1007/s10295-017-1968-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 07/18/2017] [Indexed: 11/24/2022]
Abstract
Alicyclobacillus acidocaldarius is a thermoacidophilic bacterium capable of growth on sugars from plant biomass. Carbon catabolite repression (CCR) allows bacteria to focus cellular resources on a sugar that provides efficient growth, but also allows sequential, rather than simultaneous use when more than one sugar is present. The A. acidocaldarius genome encodes all components of CCR, but transporters encoded are multifacilitator superfamily and ATP-binding cassette-type transporters, uncommon for CCR. Therefore, global transcriptome analysis of A. acidocaldarius grown on xylose or fructose was performed in chemostats, followed by attempted induction of CCR with glucose or arabinose. Alicyclobacillus acidocaldarius grew while simultaneously metabolizing xylose and glucose, xylose and arabinose, and fructose and glucose, indicating that CCR did not control carbon metabolism. Microarrays showed down-regulation of genes during growth on one sugar compared to two, and occurred primarily in genes encoding: (1) regulators; (2) enzymes for cell wall synthesis; and (3) sugar transporters.
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Affiliation(s)
- Brady D Lee
- Idaho National Laboratory, Biological Systems Department, Idaho Falls, ID, USA. .,Department of Biological Sciences, Idaho State University, Pocatello, ID, USA. .,Pacific Northwest National Laboratory, Energy and Environment Directorate, Richland, WA, USA.
| | - William A Apel
- Idaho National Laboratory, Biological Systems Department, Idaho Falls, ID, USA.,Aspenglow Associates, LLC, P. O. Box 12692, Jackson, WY, 83002, USA
| | - Linda C DeVeaux
- Department of Chemistry and Applied Biological Sciences, South Dakota School of Mines and Technology, Rapid City, SD, USA
| | - Peter P Sheridan
- Department of Biological Sciences, Idaho State University, Pocatello, ID, USA
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221
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Yu Q, Fein JB. Controls on Bacterial Cell Envelope Sulfhydryl Site Concentrations: The Effect of Glucose Concentration During Growth. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:7395-7402. [PMID: 28603975 DOI: 10.1021/acs.est.7b01047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Bacterial sulfhydryl sites can form strong complexes with chalcophilic metals such as Hg and Cd, thereby affecting the fate, transport, and bioavailability of these metals in both natural and engineered systems. In this study, five bacterial species were cultured in M9 minimal media containing a range of glucose concentrations as carbon source and in a high-nutrient TSB medium enriched with 50 g/L of glucose, and the sulfhydryl site concentrations of the obtained biomass samples were determined through selective sulfhydryl site-blocking, potentiometric titrations, and surface complexation modeling. The experimental results show that the glucose concentration in the M9 minimal media strongly affects the concentration of sulfhydryl sites that are present on the bacteria, with higher glucose concentrations yielding higher bacterial sulfhydryl site concentrations for each species studied. In contrast, although adding 50 g/L of glucose to the TSB medium significantly increases the sulfhydryl site concentrations for the three Bacillus species studied, the elevated glucose concentration does not significantly affect sulfhydryl site concentrations for S. oneidensis and P. putida samples when grown in the TSB medium. Our results suggest that bacterial sulfhydryl site concentrations in natural systems are likely affected by the composition of the bacterial community and by the available nutrients, and that these factors must be considered in order to determine and model the effects of bacterial cells on metal cycling and metal bioavailability in the environment.
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Affiliation(s)
- Qiang Yu
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Jeremy B Fein
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame , Notre Dame, Indiana 46556, United States
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222
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Liu Y, Gokhale CS, Rainey PB, Zhang XX. Unravelling the complexity and redundancy of carbon catabolic repression in Pseudomonas fluorescens SBW25. Mol Microbiol 2017; 105:589-605. [PMID: 28557013 DOI: 10.1111/mmi.13720] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2017] [Indexed: 12/11/2022]
Abstract
The two-component system CbrAB is the principal regulator for cellular metabolic balance in Pseudomonas fluorescens SBW25 and is necessary for growth on many substrates including xylose. To understand the regulatory linkage between CbrAB and genes for xylose utilization (xut), we performed transposon mutagenesis of ΔcbrB to select for Xut+ suppressors. This led to identification of crc and hfq. Subsequent genetic and biochemical analysis showed that Crc and Hfq are key mediators of succinate-provoked carbon catabolite repression (CCR). Specifically, Crc/Hfq sequentially bind to mRNAs of both the transcriptional activator and structural genes involved in xylose catabolism. However, in the absence of succinate, repression is relieved through competitive binding by two ncRNAs, CrcY and CrcZ, whose expression is activated by CbrAB. These findings provoke a model for CCR in which it is assumed that crc and hfq are functionally complementary, whereas crcY and crcZ are genetically redundant. Inactivation of either crcY or crcZ produced no effects on bacterial fitness in laboratory media, however, results of mathematical modelling predict that the co-existence of crcY and crcZ requires separate functional identity. Finally, we provide empirical evidence that CCR is advantageous in nutrient-complex environments where preferred carbon sources are present at high concentrations but fluctuate in their availability.
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Affiliation(s)
- Yunhao Liu
- Institute of Natural and Mathematical Sciences, Massey University at Albany, Auckland, 0745, New Zealand.,New Zealand Institute for Advanced Study, Massey University at Albany, Auckland, 0745, New Zealand
| | - Chaitanya S Gokhale
- New Zealand Institute for Advanced Study, Massey University at Albany, Auckland, 0745, New Zealand.,Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Paul B Rainey
- New Zealand Institute for Advanced Study, Massey University at Albany, Auckland, 0745, New Zealand.,Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany.,Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI ParisTech), CNRS UMR 8231, PSL Research University, 75231 Paris Cedex 05, France
| | - Xue-Xian Zhang
- Institute of Natural and Mathematical Sciences, Massey University at Albany, Auckland, 0745, New Zealand
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223
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Soberón-Chávez G, Alcaraz LD, Morales E, Ponce-Soto GY, Servín-González L. The Transcriptional Regulators of the CRP Family Regulate Different Essential Bacterial Functions and Can Be Inherited Vertically and Horizontally. Front Microbiol 2017; 8:959. [PMID: 28620358 PMCID: PMC5449483 DOI: 10.3389/fmicb.2017.00959] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 05/12/2017] [Indexed: 12/03/2022] Open
Abstract
One of the best-studied transcriptional regulatory proteins in bacteria is the Escherichia coli catabolite repressor protein (CRP) that when complexed with 3′-5′-cyclic AMP (cAMP) changes its conformation and interacts with specific DNA-sequences. CRP DNA-binding can result in positive or negative regulation of gene expression depending on the position of its interaction with respect to RNA polymerase binding site. The aim of this work is to review the biological role and phylogenetic relations that some members of the CRP family of transcriptional regulators (also known as cAMP receptor protein family) have in different bacterial species. This work is not intended to give an exhaustive revision of bacterial CRP-orthologs, but to provide examples of the role that these proteins play in the expression of genes that are fundamental for the life style of some bacterial species. We highlight the conservation of their structural characteristics and of their binding to conserved-DNA sequences, in contrast to their very diverse repertoire of gene activation. CRP activates a wide variety of fundamental genes for the biological characteristic of each bacterial species, which in several instances form part of their core-genome (defined as the gene sequences present in all members of a bacterial species). We present evidence that support the fact that some of the transcriptional regulators that belong to the CRP family in different bacterial species, and some of the genes that are regulated by them, can be inherited by horizontal gene transfer. These data are discussed in the framework of bacterial evolution models.
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Affiliation(s)
- Gloria Soberón-Chávez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad UniversitariaMexico City, Mexico
| | - Luis D Alcaraz
- Laboratorio de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad UniversitariaMexico City, Mexico
| | - Estefanía Morales
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad UniversitariaMexico City, Mexico
| | - Gabriel Y Ponce-Soto
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad UniversitariaMexico City, Mexico
| | - Luis Servín-González
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad UniversitariaMexico City, Mexico
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224
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Escherichia coli expressing endoglucanase gene from Thai higher termite bacteria for enzymatic and microbial hydrolysis of cellulosic materials. ELECTRON J BIOTECHN 2017. [DOI: 10.1016/j.ejbt.2017.03.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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225
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CcpA and CodY Coordinate Acetate Metabolism in Streptococcus mutans. Appl Environ Microbiol 2017; 83:AEM.03274-16. [PMID: 28130304 DOI: 10.1128/aem.03274-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/23/2017] [Indexed: 11/20/2022] Open
Abstract
In the dental caries pathogen Streptococcus mutans, phosphotransacetylase (Pta) and acetate kinase (Ack) convert pyruvate into acetate with the concomitant generation of ATP. The genes for this pathway are tightly regulated by multiple environmental and intracellular inputs, but the basis for differential expression of the genes for Pta and Ack in S. mutans had not been investigated. Here, we show that inactivation in S. mutans of ccpA or codY reduced the activity of the ackA promoter, whereas a ccpA mutant displayed elevated pta promoter activity. The interactions of CcpA with the promoter regions of both genes were observed using electrophoretic mobility shift and DNase protection assays. CodY bound to the ackA promoter region but only in the presence of branched-chain amino acids (BCAAs). DNase footprinting revealed that the upstream region of both genes contains two catabolite-responsive elements (cre1 and cre2) that can be bound by CcpA. Notably, the cre2 site of ackA overlaps with a CodY-binding site. The CcpA- and CodY-binding sites in the promoter region of both genes were further defined by site-directed mutagenesis. Some differences between the reported consensus CodY binding site and the region protected by S. mutans CodY were noted. Transcription of the pta and ackA genes in the ccpA mutant strain was markedly different at low pH relative to transcription at neutral pH. Thus, CcpA and CodY are direct regulators of transcription of ackA and pta in S. mutans that optimize acetate metabolism in response to carbohydrate, amino acid availability, and environmental pH.IMPORTANCE The human dental caries pathogen Streptococcus mutans is remarkably adept at coping with extended periods of carbohydrate limitation during fasting periods. The phosphotransacetylase-acetate kinase (Pta-Ack) pathway in S. mutans modulates carbohydrate flux and fine-tunes the ability of the organisms to cope with stressors that are commonly encountered in the oral cavity. Here, we show that CcpA controls transcription of the pta and ackA genes via direct interaction with the promoter regions of both genes and that branched-chain amino acids (BCAAs), particularly isoleucine, enhance the ability of CodY to bind to the promoter region of the ackA gene. A working model is proposed to explain how regulation of pta and ackA genes by these allosterically controlled regulatory proteins facilitates proper carbon flow and energy production, which are essential functions during infection and pathogenesis as carbohydrate and amino acid availability continually fluctuate.
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226
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Theodosiou E, Breisch M, Julsing MK, Falcioni F, Bühler B, Schmid A. An artificial TCA cycle selects for efficient α-ketoglutarate dependent hydroxylase catalysis in engineered Escherichia coli. Biotechnol Bioeng 2017; 114:1511-1520. [PMID: 28266022 DOI: 10.1002/bit.26281] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/13/2017] [Accepted: 03/01/2017] [Indexed: 01/24/2023]
Abstract
Amino acid hydroxylases depend directly on the cellular TCA cycle via their cosubstrate α-ketoglutarate (α-KG) and are highly useful for the selective biocatalytic oxyfunctionalization of amino acids. This study evaluates TCA cycle engineering strategies to force and increase α-KG flux through proline-4-hydroxylase (P4H). The genes sucA (α-KG dehydrogenase E1 subunit) and sucC (succinyl-CoA synthetase β subunit) were alternately deleted together with aceA (isocitrate lyase) in proline degradation-deficient Escherichia coli strains (ΔputA) expressing the p4h gene. Whereas, the ΔsucCΔaceAΔputA strain grew in minimal medium in the absence of P4H, relying on the activity of fumarate reductase, growth of the ΔsucAΔaceAΔputA strictly depended on P4H activity, thus coupling growth to proline hydroxylation. P4H restored growth, even when proline was not externally added. However, the reduced succinyl-CoA pool caused a 27% decrease of the average cell size compared to the wildtype strain. Medium supplementation partially restored the morphology and, in some cases, enhanced proline hydroxylation activity. The specific proline hydroxylation rate doubled when putP, encoding the Na+ /l-proline transporter, was overexpressed in the ΔsucAΔaceAΔputA strain. This is in contrast to wildtype and ΔputA single-knock out strains, in which α-KG availability obviously limited proline hydroxylation. Such α-KG limitation was relieved in the ΔsucAΔaceAΔputA strain. Furthermore, the ΔsucAΔaceAΔputA strain was used to demonstrate an agar plate-based method for the identification and selection of active α-KG dependent hydroxylases. This together with the possibility to waive selection pressure and overcome α-KG limitation in respective hydroxylation processes based on living cells emphasizes the potential of TCA cycle engineering for the productive application of α-KG dependent hydroxylases. Biotechnol. Bioeng. 2017;114: 1511-1520. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Eleni Theodosiou
- Department of Solar Materials, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, Leipzig 04318, Germany
| | - Marina Breisch
- Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | - Mattijs K Julsing
- Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | - Francesco Falcioni
- Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | - Bruno Bühler
- Department of Solar Materials, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, Leipzig 04318, Germany
| | - Andreas Schmid
- Department of Solar Materials, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, Leipzig 04318, Germany
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227
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Galinier A, Deutscher J. Sophisticated Regulation of Transcriptional Factors by the Bacterial Phosphoenolpyruvate: Sugar Phosphotransferase System. J Mol Biol 2017; 429:773-789. [PMID: 28202392 DOI: 10.1016/j.jmb.2017.02.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/01/2017] [Accepted: 02/04/2017] [Indexed: 11/16/2022]
Abstract
The phosphoenolpyruvate:sugar phosphotransferase system (PTS) is a carbohydrate transport and phosphorylation system present in bacteria of all different phyla and in archaea. It is usually composed of three proteins or protein complexes, enzyme I, HPr, and enzyme II, which are phosphorylated at histidine or cysteine residues. However, in many bacteria, HPr can also be phosphorylated at a serine residue. The PTS not only functions as a carbohydrate transporter but also regulates numerous cellular processes either by phosphorylating its target proteins or by interacting with them in a phosphorylation-dependent manner. The target proteins can be catabolic enzymes, transporters, and signal transduction proteins but are most frequently transcriptional regulators. In this review, we will describe how PTS components interact with or phosphorylate proteins to regulate directly or indirectly the activity of transcriptional repressors, activators, or antiterminators. We will briefly summarize the well-studied mechanism of carbon catabolite repression in firmicutes, where the transcriptional regulator catabolite control protein A needs to interact with seryl-phosphorylated HPr in order to be functional. We will present new results related to transcriptional activators and antiterminators containing specific PTS regulation domains, which are the phosphorylation targets for three different types of PTS components. Moreover, we will discuss how the phosphorylation level of the PTS components precisely regulates the activity of target transcriptional regulators or antiterminators, with or without PTS regulation domain, and how the availability of PTS substrates and thus the metabolic status of the cell are connected with various cellular processes, such as biofilm formation or virulence of certain pathogens.
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Affiliation(s)
- Anne Galinier
- Laboratoire de Chimie Bactérienne, UPR 9043, CNRS, Aix Marseille Université, IMM, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France.
| | - Josef Deutscher
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; Centre National de la Recherche Scientifique, UMR8261 (affiliated with the Univ. Paris Diderot, Sorbonne, Paris Cité), Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, 75005 Paris, France.
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228
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Ou Q, Fan J, Duan D, Xu L, Wang J, Zhou D, Yang H, Li B. Involvement of cAMP receptor protein in biofilm formation, fimbria production, capsular polysaccharide biosynthesis and lethality in mouse of Klebsiella pneumoniae serotype K1 causing pyogenic liver abscess. J Med Microbiol 2017; 66:1-7. [PMID: 27902401 DOI: 10.1099/jmm.0.000391] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The global regulator cAMP receptor protein (CRP) has been shown to be required for the full virulence and/or for the expression of virulence determinants in a wide set of bacterial pathogens. In this work, the crp mutant as well as the complemented mutant was constructed from a wild-type Klebsiella pneumoniae capsular serotype K1 strain causing the primary pyogenic liver abscess. The phenotypes of wild-type strain, crp mutant and complemented mutant were characterized systematically. It was disclosed that K. pneumoniae CRP was required for the in vitro growth, fimbria production, biofilm formation and lethality in mouse, but it inhibited the capsular polysaccharide biosynthesis. These indicated the important roles of CRP in regulating the expression of virulence and biofilm genes in K. pneumoniae.
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Affiliation(s)
- Qin Ou
- School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei 442000, PR China
| | - Jinming Fan
- School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei 442000, PR China
| | - Dejian Duan
- Department of Dermatology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, PR China
| | - Li Xu
- School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei 442000, PR China
| | - Jie Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, PR China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, PR China
| | - Huiying Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, PR China
| | - Bei Li
- Department of Dermatology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, PR China.,School of Basic Medicine, Hubei University of Medicine, Shiyan, Hubei 442000, PR China
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229
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Chu D. Limited by sensing - A minimal stochastic model of the lag-phase during diauxic growth. J Theor Biol 2017; 414:137-146. [DOI: 10.1016/j.jtbi.2016.10.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 10/03/2016] [Accepted: 10/28/2016] [Indexed: 11/30/2022]
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230
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Bacterial Responses to Glyoxal and Methylglyoxal: Reactive Electrophilic Species. Int J Mol Sci 2017; 18:ijms18010169. [PMID: 28106725 PMCID: PMC5297802 DOI: 10.3390/ijms18010169] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 11/29/2022] Open
Abstract
Glyoxal (GO) and methylglyoxal (MG), belonging to α-oxoaldehydes, are produced by organisms from bacteria to humans by glucose oxidation, lipid peroxidation, and DNA oxidation. Since glyoxals contain two adjacent reactive carbonyl groups, they are referred to as reactive electrophilic species (RES), and are damaging to proteins and nucleotides. Therefore, glyoxals cause various diseases in humans, such as diabetes and neurodegenerative diseases, from which all living organisms need to be protected. Although the glyoxalase system has been known for some time, details on how glyoxals are sensed and detoxified in the cell have not been fully elucidated, and are only beginning to be uncovered. In this review, we will summarize the current knowledge on bacterial responses to glyoxal, and specifically focus on the glyoxal-associated regulators YqhC and NemR, as well as their detoxification mediated by glutathione (GSH)-dependent/independent glyoxalases and NAD(P)H-dependent reductases. Furthermore, we will address questions and future directions.
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231
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Establishing a synergetic carbon utilization mechanism for non-catabolic use of glucose in microbial synthesis of trehalose. Metab Eng 2017; 39:1-8. [DOI: 10.1016/j.ymben.2016.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/30/2016] [Accepted: 11/01/2016] [Indexed: 11/20/2022]
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232
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Sugar Allocation to Metabolic Pathways is Tightly Regulated and Affects the Virulence of Streptococcus mutans. Genes (Basel) 2016; 8:genes8010011. [PMID: 28036052 PMCID: PMC5295006 DOI: 10.3390/genes8010011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 12/14/2016] [Accepted: 12/21/2016] [Indexed: 02/03/2023] Open
Abstract
Bacteria take up and metabolize sugar as a carbohydrate source for survival. Most bacteria can utilize many sugars, including glucose, sucrose, and galactose, as well as amino sugars, such as glucosamine and N-acetylglucosamine. After entering the cytoplasm, the sugars are mainly allocated to the glycolysis pathway (energy production) and to various bacterial component biosynthesis pathways, including the cell wall, nucleic acids and amino acids. Sugars are also utilized to produce several virulence factors, such as capsule and lipoteichoic acid. Glutamine-fructose-6-phosphate aminotransferase (GlmS) and glucosamine-6-phosphate deaminase (NagB) have crucial roles in sugar distribution to the glycolysis pathway and to cell wall biosynthesis. In Streptococcus mutans, a cariogenic pathogen, the expression levels of glmS and nagB are coordinately regulated in response to the presence or absence of amino sugars. In addition, the disruption of this regulation affects the virulence of S. mutans. The expression of nagB and glmS is regulated by NagR in S. mutans, but the precise mechanism underlying glmS regulation is not clear. In Staphylococcus aureus and Bacillus subtilis, the mRNA of glmS has ribozyme activity and undergoes self-degradation at the mRNA level. However, there is no ribozyme activity region on glmS mRNA in S. mutans. In this review article, we summarize the sugar distribution, particularly the coordinated regulation of GlmS and NagB expression, and its relationship with the virulence of S. mutans.
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233
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Fisunov GY, Garanina IA, Evsyutina DV, Semashko TA, Nikitina AS, Govorun VM. Reconstruction of Transcription Control Networks in Mollicutes by High-Throughput Identification of Promoters. Front Microbiol 2016; 7:1977. [PMID: 27999573 PMCID: PMC5138195 DOI: 10.3389/fmicb.2016.01977] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/25/2016] [Indexed: 01/05/2023] Open
Abstract
Bacteria of the class Mollicutes have significantly reduced genomes and gene expression control systems. They are also efficient pathogens that can colonize a broad range of hosts including plants and animals. Despite their simplicity, Mollicutes demonstrate complex transcriptional responses to various conditions, which contradicts their reduction in gene expression regulation mechanisms. We analyzed the conservation and distribution of transcription regulators across the 50 Mollicutes species. The majority of the transcription factors regulate transport and metabolism, and there are four transcription factors that demonstrate significant conservation across the analyzed bacteria. These factors include repressors of chaperone HrcA, cell cycle regulator MraZ and two regulators with unclear function from the WhiA and YebC/PmpR families. We then used three representative species of the major clades of Mollicutes (Acholeplasma laidlawii, Spiroplasma melliferum, and Mycoplasma gallisepticum) to perform promoter mapping and activity quantitation. We revealed that Mollicutes evolved towards a promoter architecture simplification that correlates with a diminishing role of transcription regulation and an increase in transcriptional noise. Using the identified operons structure and a comparative genomics approach, we reconstructed the transcription control networks for these three species. The organization of the networks reflects the adaptation of bacteria to specific conditions and hosts.
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Affiliation(s)
- Gleb Y Fisunov
- Federal Research and Clinical Centre of Physical-Chemical Medicine Moscow, Russia
| | - Irina A Garanina
- Federal Research and Clinical Centre of Physical-Chemical MedicineMoscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of SciencesMoscow, Russia
| | - Daria V Evsyutina
- Federal Research and Clinical Centre of Physical-Chemical Medicine Moscow, Russia
| | - Tatiana A Semashko
- Federal Research and Clinical Centre of Physical-Chemical Medicine Moscow, Russia
| | - Anastasia S Nikitina
- Federal Research and Clinical Centre of Physical-Chemical MedicineMoscow, Russia; Moscow Institute of Physics and TechnologyMoscow, Russia
| | - Vadim M Govorun
- Federal Research and Clinical Centre of Physical-Chemical MedicineMoscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of SciencesMoscow, Russia; Moscow Institute of Physics and TechnologyMoscow, Russia
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234
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Hunt KA, Jennings RD, Inskeep WP, Carlson RP. Stoichiometric modelling of assimilatory and dissimilatory biomass utilisation in a microbial community. Environ Microbiol 2016; 18:4946-4960. [PMID: 27387069 PMCID: PMC5629010 DOI: 10.1111/1462-2920.13444] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 06/30/2016] [Indexed: 11/26/2022]
Abstract
Assimilatory and dissimilatory utilisation of autotroph biomass by heterotrophs is a fundamental mechanism for the transfer of nutrients and energy across trophic levels. Metagenome data from a tractable, thermoacidophilic microbial community in Yellowstone National Park was used to build an in silico model to study heterotrophic utilisation of autotroph biomass using elementary flux mode analysis and flux balance analysis. Assimilatory and dissimilatory biomass utilisation was investigated using 29 forms of biomass-derived dissolved organic carbon (DOC) including individual monomer pools, individual macromolecular pools and aggregate biomass. The simulations identified ecologically competitive strategies for utilizing DOC under conditions of varying electron donor, electron acceptor or enzyme limitation. The simulated growth environment affected which form of DOC was the most competitive use of nutrients; for instance, oxygen limitation favoured utilisation of less reduced and fermentable DOC while carbon-limited environments favoured more reduced DOC. Additionally, metabolism was studied considering two encompassing metabolic strategies: simultaneous versus sequential use of DOC. Results of this study bound the transfer of nutrients and energy through microbial food webs, providing a quantitative foundation relevant to most microbial ecosystems.
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Affiliation(s)
- Kristopher A. Hunt
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
- Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Ryan deM. Jennings
- Thermal Biology Institute, Montana State University, Bozeman, MT, USA
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| | - William P. Inskeep
- Thermal Biology Institute, Montana State University, Bozeman, MT, USA
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| | - Ross P. Carlson
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
- Thermal Biology Institute, Montana State University, Bozeman, MT, USA
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235
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Saejung C, Thammaratana T. Biomass recovery during municipal wastewater treatment using photosynthetic bacteria and prospect of production of single cell protein for feedstuff. ENVIRONMENTAL TECHNOLOGY 2016; 37:3055-3061. [PMID: 27070497 DOI: 10.1080/09593330.2016.1175512] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Utilization of photosynthetic bacteria (PSB) for wastewater treatment and production of biomass for economical single cell protein production is a feasible option. In this study, Rhodopseudomonas sp. CSK01 was used for municipal wastewater treatment and the effect of initial pH, light intensity and additional carbon source was investigated. Optimum chemical oxygen demand (COD) removal and biomass production were achieved when the initial pH and light intensity were 7 and 4000 lux, respectively. The specific growth rate, biomass yield and biomass productivity were found to be 0.4/d, 3.2 g/g COD and 2.1 g/L/d, respectively, which were improved by 100%, 167% and 200% relative to the original condition. Under the optimal conditions, COD removal reached 85% and maximum biomass was 6.2 g/L accomplished within three days of cultivation. The biomass had a relatively high protein content (60.1%) consisting of all essential amino acids. The contents of histidine, lysine, phenylalanine and leucine were superior to those of the previously described PSB. Results showed that COD removal was not improved in the presence of additional carbon sources (glucose, sucrose and malic acid). The addition of malic acid significantly increased the biomass accumulation by 279% relative to the original condition, whereas COD removal was declined due to carbon catabolite repression. In this study, PSB biomass recovery and catabolite repression are proposed in municipal wastewater treatment by Rhodopseudomonas sp.
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Affiliation(s)
- Chewapat Saejung
- a Department of Microbiology, Faculty of Science , Khon Kaen University , Khon Kaen , Thailand
- b Applied Taxonomic Research Center, Faculty of Science , Khon Kaen University , Khon Kaen , Thailand
| | - Thani Thammaratana
- a Department of Microbiology, Faculty of Science , Khon Kaen University , Khon Kaen , Thailand
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236
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Cibrario A, Peanne C, Lailheugue M, Campbell-Sills H, Dols-Lafargue M. Carbohydrate metabolism in Oenococcus oeni: a genomic insight. BMC Genomics 2016; 17:984. [PMID: 27905883 PMCID: PMC5131533 DOI: 10.1186/s12864-016-3338-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 11/23/2016] [Indexed: 11/10/2022] Open
Abstract
Background Oenococcus oeni is the bacterial species that drives malolactic fermentation in most wines. Several studies have described a high intraspecific diversity regarding carbohydrate degradation abilities but the link between the phenotypes and the genes and metabolic pathways has been poorly described. Results A collection of 41 strains whose genomic sequences were available and representative of the species genomic diversity was analyzed for growth on 18 carbohydrates relevant in wine. The most frequently used substrates (more than 75% of the strains) were glucose, trehalose, ribose, cellobiose, mannose and melibiose. Fructose and L-arabinose were used by about half the strains studied, sucrose, maltose, xylose, galactose and raffinose were used by less than 25% of the strains and lactose, L-sorbose, L-rhamnose, sorbitol and mannitol were not used by any of the studied strains. To identify genes and pathways associated with carbohydrate catabolic abilities, gene-trait matching and a careful analysis of gene mutations and putative complementation phenomena were performed. Conclusions For most consumed sugars, we were able to propose putatively associated metabolic pathways. Most associated genes belong to the core genome. O. oeni appears as a highly specialized species, ideally suited to fermented fruit juice and more specifically to wine for a subgroup of strains. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3338-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alice Cibrario
- University of Bordeaux, ISVV, EA 4577, Oenologie, F-33140, Villenave d'Ornon, France
| | - Claire Peanne
- University of Bordeaux, ISVV, EA 4577, Oenologie, F-33140, Villenave d'Ornon, France
| | - Marine Lailheugue
- Bordeaux INP, ISVV, EA 4577, Oenologie, F-33140, Villenave d'Ornon, France
| | - Hugo Campbell-Sills
- University of Bordeaux, ISVV, EA 4577, Oenologie, F-33140, Villenave d'Ornon, France
| | - Marguerite Dols-Lafargue
- University of Bordeaux, ISVV, EA 4577, Oenologie, F-33140, Villenave d'Ornon, France. .,Bordeaux INP, ISVV, EA 4577, Oenologie, F-33140, Villenave d'Ornon, France.
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237
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Wei P, Lin M, Wang Z, Fu H, Yang H, Jiang W, Yang ST. Metabolic engineering of Propionibacterium freudenreichii subsp. shermanii for xylose fermentation. BIORESOURCE TECHNOLOGY 2016; 219:91-97. [PMID: 27479799 DOI: 10.1016/j.biortech.2016.07.056] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 07/10/2016] [Accepted: 07/12/2016] [Indexed: 05/12/2023]
Abstract
Propionibacterium freudenreichii cannot use xylose, the second most abundant sugar in lignocellulosic biomass. Although Propionibacterium acidipropionici can use xylose as a carbon source, it is difficult to genetically modify, impeding further improvement through metabolic engineering. This study identified three xylose catabolic pathway genes encoding for xylose isomerase (xylA), xylose transporter (xylT), and xylulokinase (xylB) in P. acidipropionici and overexpressed them in P. freudenreichii subsp. shermanii via an expression plasmid pKHEM01, enabling the mutant to utilize xylose efficiently even in the presence of glucose without glucose-induced carbon catabolite repression. The mutant showed similar fermentation kinetics with glucose, xylose, and the mixture of glucose and xylose, respectively, as carbon source, and with or without the addition of antibiotic for selection pressure. The engineered P. shermanii thus can provide a novel cell factory for industrial production of propionic acid and other value-added products from lignocellulosic biomass.
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Affiliation(s)
- Peilian Wei
- School of Biological and Chemical Engineering, Zhejiang University of Science & Technology, Hangzhou, Zhejiang 310023, China; William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Ave., Columbus, OH 43210, USA
| | - Meng Lin
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Ave., Columbus, OH 43210, USA; Bioprocessing Innovative Company, 4734 Bridle Path Ct., Dublin, OH 43017, USA
| | - Zhongqiang Wang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Ave., Columbus, OH 43210, USA
| | - Hongxin Fu
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Ave., Columbus, OH 43210, USA
| | - Hopen Yang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Ave., Columbus, OH 43210, USA
| | - Wenyan Jiang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Ave., Columbus, OH 43210, USA
| | - Shang-Tian Yang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 West Woodruff Ave., Columbus, OH 43210, USA.
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238
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Simultaneous Saccharification and Fermentation of Sugar Beet Pulp with Mixed Bacterial Cultures for Lactic Acid and Propylene Glycol Production. Molecules 2016; 21:molecules21101380. [PMID: 27763527 PMCID: PMC6272889 DOI: 10.3390/molecules21101380] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/07/2016] [Accepted: 10/12/2016] [Indexed: 12/05/2022] Open
Abstract
Research into fermentative production of lactic acid from agricultural by-products has recently concentrated on the direct conversion of biomass, whereby pure sugars are replaced with inexpensive feedstock in the process of lactic acid production. In our studies, for the first time, the source of carbon used is sugar beet pulp, generated as a by-product of industrial sugar production. In this paper, we focus on the simultaneous saccharification of lignocellulosic biomass and fermentation of lactic acid, using mixed cultures with complementary assimilation profiles. Lactic acid is one of the primary platform chemicals, and can be used to synthesize a wide variety of useful products, including green propylene glycol. A series of controlled batch fermentations was conducted under various conditions, including pretreatment with enzymatic hydrolysis. Inoculation was performed in two sequential stages, to avoid carbon catabolite repression. Biologically-synthesized lactic acid was catalytically reduced to propylene glycol over 5% Ru/C. The highest lactic acid yield was obtained with mixed cultures. The yield of propylene glycol from the biological lactic acid was similar to that obtained with a water solution of pure lactic acid. Our results show that simultaneous saccharification and fermentation enables generation of lactic acid, suitable for further chemical transformations, from agricultural residues.
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239
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Hung CS, Zingarelli S, Nadeau LJ, Biffinger JC, Drake CA, Crouch AL, Barlow DE, Russell JN, Crookes-Goodson WJ. Carbon Catabolite Repression and Impranil Polyurethane Degradation in Pseudomonas protegens Strain Pf-5. Appl Environ Microbiol 2016; 82:6080-6090. [PMID: 27496773 PMCID: PMC5068165 DOI: 10.1128/aem.01448-16] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 07/28/2016] [Indexed: 01/03/2023] Open
Abstract
Polyester polyurethane (PU) coatings are widely used to help protect underlying structural surfaces but are susceptible to biological degradation. PUs are susceptible to degradation by Pseudomonas species, due in part to the degradative activity of secreted hydrolytic enzymes. Microorganisms often respond to environmental cues by secreting enzymes or secondary metabolites to benefit their survival. This study investigated the impact of exposing several Pseudomonas strains to select carbon sources on the degradation of the colloidal polyester polyurethane Impranil DLN (Impranil). The prototypic Pseudomonas protegens strain Pf-5 exhibited Impranil-degrading activities when grown in sodium citrate but not in glucose-containing medium. Glucose also inhibited the induction of Impranil-degrading activity by citrate-fed Pf-5 in a dose-dependent manner. Biochemical and mutational analyses identified two extracellular lipases present in the Pf-5 culture supernatant (PueA and PueB) that were involved in degradation of Impranil. Deletion of the pueA gene reduced Impranil-clearing activities, while pueB deletion exhibited little effect. Removal of both genes was necessary to stop degradation of the polyurethane. Bioinformatic analysis showed that putative Cbr/Hfq/Crc-mediated regulatory elements were present in the intergenic sequences upstream of both pueA and pueB genes. Our results confirmed that both PueA and PueB extracellular enzymes act in concert to degrade Impranil. Furthermore, our data showed that carbon sources in the growth medium directly affected the levels of Impranil-degrading activity but that carbon source effects varied among Pseudomonas strains. This study uncovered an intricate and complicated regulation of P. protegens PU degradation activity controlled by carbon catabolite repression. IMPORTANCE Polyurethane (PU) coatings are commonly used to protect metals from corrosion. Microbiologically induced PU degradation might pose a substantial problem for the integrity of these coatings. Microorganisms from diverse genera, including pseudomonads, possess the ability to degrade PUs via various means. This work identified two extracellular lipases, PueA and PueB, secreted by P. protegens strain Pf-5, to be responsible for the degradation of a colloidal polyester PU, Impranil. This study also revealed that the expression of the degradative activity by strain Pf-5 is controlled by glucose carbon catabolite repression. Furthermore, this study showed that the Impranil-degrading activity of many other Pseudomonas strains could be influenced by different carbon sources. This work shed light on the carbon source regulation of PU degradation activity among pseudomonads and identified the polyurethane lipases in P. protegens.
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Affiliation(s)
- Chia-Suei Hung
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio, USA UES, Inc., Dayton, Ohio, USA
| | - Sandra Zingarelli
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio, USA UES, Inc., Dayton, Ohio, USA
| | - Lloyd J Nadeau
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio, USA
| | | | - Carrie A Drake
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio, USA UES, Inc., Dayton, Ohio, USA
| | - Audra L Crouch
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio, USA UES, Inc., Dayton, Ohio, USA
| | - Daniel E Barlow
- Chemistry Division, U.S. Naval Research Laboratory, Washington, DC, USA
| | - John N Russell
- Chemistry Division, U.S. Naval Research Laboratory, Washington, DC, USA
| | - Wendy J Crookes-Goodson
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio, USA
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Use of a Bacterial Luciferase Monitoring System To Estimate Real-Time Dynamics of Intracellular Metabolism in Escherichia coli. Appl Environ Microbiol 2016; 82:5960-8. [PMID: 27474708 DOI: 10.1128/aem.01400-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/20/2016] [Indexed: 01/10/2023] Open
Abstract
UNLABELLED Regulation of central carbon metabolism has long been an important research subject in every organism. While the dynamics of metabolic flows during changes in available carbon sources have been estimated based on changes in metabolism-related gene expression, as well as on changes in the metabolome, the flux change itself has scarcely been measured because of technical difficulty, which has made conclusions elusive in many cases. Here, we used a monitoring system employing Vibrio fischeri luciferase to probe the intracellular metabolic condition in Escherichia coli Using a batch culture provided with a limited amount of glucose, we performed a time course analysis, where the predominant carbon source shifts from glucose to acetate, and identified a series of sequential peaks in the luciferase activity (peaks 1 to 4). Two major peaks, peaks 1 and 3, were considered to correspond to the glucose and acetate consuming phases, respectively, based on the glucose, acetate, and dissolved oxygen concentrations in the medium. The pattern of these peaks was changed by the addition of a different carbon source or by an increasing concentration of glucose, which was consistent with the present model. Genetically, mutations involved in glycolysis or the tricarboxylic acid (TCA) cycle/gluconeogenesis specifically affected peak 1 or peak 3, respectively, as expected from the corresponding metabolic phase. Intriguingly, mutants for the acetate excretion pathway showed a phenotype of extended peak 2 and delayed transition to the TCA cycle/gluconeogenesis phase, which suggests that peak 2 represents the metabolic transition phase. These results indicate that the bacterial luciferase monitoring system is useful to understand the real-time dynamics of metabolism in living bacterial cells. IMPORTANCE Intracellular metabolic flows dynamically change during shifts in available carbon sources. However, because of technical difficulty, the flux change has scarcely been measured in living cells. Here, we used a Vibrio fischeri luciferase monitoring system to probe the intracellular metabolic condition in Escherichia coli Using a limited amount of glucose batch culture, a series of sequential peaks (peaks 1 to 4) in the luciferase activity was observed. Changes in the pattern of these peaks by the addition of extra carbon sources and in mutant strains involved in glycolysis or the TCA cycle/gluconeogenesis gene assigned the metabolic phase corresponding to peak 1 as the glycolysis phase and peak 3 as the TCA cycle/gluconeogenesis phase. Intriguingly, the acetate excretion pathway engaged in peak 2 represents the metabolic transition phase. These results indicate that the bacterial luciferase monitoring system is useful to understand the real-time dynamics of metabolism in living bacterial cells.
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241
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Kentache T, Milohanic E, Cao TN, Mokhtari A, Aké FM, Ma Pham QM, Joyet P, Deutscher J. Transport and Catabolism of Pentitols by Listeria monocytogenes. J Mol Microbiol Biotechnol 2016; 26:369-380. [PMID: 27553222 DOI: 10.1159/000447774] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/22/2016] [Indexed: 11/19/2022] Open
Abstract
Transposon insertion into Listeria monocytogenes lmo2665, which encodes an EIIC of the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS), was found to prevent D-arabitol utilization. We confirm this result with a deletion mutant and show that Lmo2665 is also required for D-xylitol utilization. We therefore called this protein EIICAxl. Both pentitols are probably catabolized via the pentose phosphate pathway (PPP) because lmo2665 belongs to an operon, which encodes the three PTSAxl components, two sugar-P dehydrogenases, and most PPP enzymes. The two dehydrogenases oxidize the pentitol-phosphates produced during PTS-catalyzed transport to the PPP intermediate xylulose-5-P. L. monocytogenes contains another PTS, which exhibits significant sequence identity to PTSAxl. Its genes are also part of an operon encoding PPP enzymes. Deletion of the EIIC-encoding gene (lmo0508) affected neither D-arabitol nor D-xylitol utilization, although D-arabitol induces the expression of this operon. Both operons are controlled by MtlR/LicR-type transcription activators (Lmo2668 and Lmo0501, respectively). Phosphorylation of Lmo0501 by the soluble PTSAxl components probably explains why D-arabitol also induces the second pentitol operon. Listerial virulence genes are submitted to strong repression by PTS sugars, such as glucose. However, D-arabitol inhibited virulence gene expression only at high concentrations, probably owing to its less efficient utilization compared to glucose.
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Affiliation(s)
- Takfarinas Kentache
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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242
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Transcription of Sialic Acid Catabolism Genes in Corynebacterium glutamicum Is Subject to Catabolite Repression and Control by the Transcriptional Repressor NanR. J Bacteriol 2016; 198:2204-18. [PMID: 27274030 DOI: 10.1128/jb.00820-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 05/18/2016] [Indexed: 12/31/2022] Open
Abstract
UNLABELLED Corynebacterium glutamicum metabolizes sialic acid (Neu5Ac) to fructose-6-phosphate (fructose-6P) via the consecutive activity of the sialic acid importer SiaEFGI, N-acetylneuraminic acid lyase (NanA), N-acetylmannosamine kinase (NanK), N-acetylmannosamine-6P epimerase (NanE), N-acetylglucosamine-6P deacetylase (NagA), and glucosamine-6P deaminase (NagB). Within the cluster of the three operons nagAB, nanAKE, and siaEFGI for Neu5Ac utilization a fourth operon is present, which comprises cg2936, encoding a GntR-type transcriptional regulator, here named NanR. Microarray studies and reporter gene assays showed that nagAB, nanAKE, siaEFGI, and nanR are repressed in wild-type (WT) C. glutamicum but highly induced in a ΔnanR C. glutamicum mutant. Purified NanR was found to specifically bind to the nucleotide motifs A[AC]G[CT][AC]TGATGTC[AT][TG]ATGT[AC]TA located within the nagA-nanA and nanR-sialA intergenic regions. Binding of NanR to promoter regions was abolished in the presence of the Neu5Ac metabolism intermediates GlcNAc-6P and N-acetylmannosamine-6-phosphate (ManNAc-6P). We observed consecutive utilization of glucose and Neu5Ac as well as fructose and Neu5Ac by WT C. glutamicum, whereas the deletion mutant C. glutamicum ΔnanR simultaneously consumed these sugars. Increased reporter gene activities for nagAB, nanAKE, and nanR were observed in cultivations of WT C. glutamicum with Neu5Ac as the sole substrate compared to cultivations when fructose was present. Taken together, our findings show that Neu5Ac metabolism in C. glutamicum is subject to catabolite repression, which involves control by the repressor NanR. IMPORTANCE Neu5Ac utilization is currently regarded as a common trait of both pathogenic and commensal bacteria. Interestingly, the nonpathogenic soil bacterium C. glutamicum efficiently utilizes Neu5Ac as a substrate for growth. Expression of genes for Neu5Ac utilization in C. glutamicum is here shown to depend on the transcriptional regulator NanR, which is the first GntR-type regulator of Neu5Ac metabolism not to use Neu5Ac as effector but relies instead on the inducers GlcNAc-6P and ManNAc-6P. The identification of conserved NanR-binding sites in intergenic regions within the operons for Neu5Ac utilization in pathogenic Corynebacterium species indicates that the mechanism for the control of Neu5Ac catabolism in C. glutamicum by NanR as described in this work is probably conserved within this genus.
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243
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Kumar B. N. V, Guo S, Bocklitz T, Rösch P, Popp J. Demonstration of Carbon Catabolite Repression in Naphthalene Degrading Soil Bacteria via Raman Spectroscopy Based Stable Isotope Probing. Anal Chem 2016; 88:7574-82. [DOI: 10.1021/acs.analchem.6b01046] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Vinay Kumar B. N.
- Institute
of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University of Jena, Helmholtzweg 4, D-07743 Jena, Germany
- InfectoGnostics, Forschungscampus Jena, Philosophenweg
7, D-07743 Jena, Germany
| | - Shuxia Guo
- Institute
of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University of Jena, Helmholtzweg 4, D-07743 Jena, Germany
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, D-07745 Jena, Germany
| | - Thomas Bocklitz
- Institute
of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University of Jena, Helmholtzweg 4, D-07743 Jena, Germany
- InfectoGnostics, Forschungscampus Jena, Philosophenweg
7, D-07743 Jena, Germany
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, D-07745 Jena, Germany
| | - Petra Rösch
- Institute
of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University of Jena, Helmholtzweg 4, D-07743 Jena, Germany
- InfectoGnostics, Forschungscampus Jena, Philosophenweg
7, D-07743 Jena, Germany
| | - Jürgen Popp
- Institute
of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University of Jena, Helmholtzweg 4, D-07743 Jena, Germany
- InfectoGnostics, Forschungscampus Jena, Philosophenweg
7, D-07743 Jena, Germany
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, D-07745 Jena, Germany
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244
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Ceapa C, Davids M, Ritari J, Lambert J, Wels M, Douillard FP, Smokvina T, de Vos WM, Knol J, Kleerebezem M. The Variable Regions of Lactobacillus rhamnosus Genomes Reveal the Dynamic Evolution of Metabolic and Host-Adaptation Repertoires. Genome Biol Evol 2016; 8:1889-905. [PMID: 27358423 PMCID: PMC4943194 DOI: 10.1093/gbe/evw123] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Lactobacillus rhamnosus is a diverse Gram-positive species with strains isolated from different ecological niches. Here, we report the genome sequence analysis of 40 diverse strains of L. rhamnosus and their genomic comparison, with a focus on the variable genome. Genomic comparison of 40 L. rhamnosus strains discriminated the conserved genes (core genome) and regions of plasticity involving frequent rearrangements and horizontal transfer (variome). The L. rhamnosus core genome encompasses 2,164 genes, out of 4,711 genes in total (the pan-genome). The accessory genome is dominated by genes encoding carbohydrate transport and metabolism, extracellular polysaccharides (EPS) biosynthesis, bacteriocin production, pili production, the cas system, and the associated clustered regularly interspaced short palindromic repeat (CRISPR) loci, and more than 100 transporter functions and mobile genetic elements like phages, plasmid genes, and transposons. A clade distribution based on amino acid differences between core (shared) proteins matched with the clade distribution obtained from the presence–absence of variable genes. The phylogenetic and variome tree overlap indicated that frequent events of gene acquisition and loss dominated the evolutionary segregation of the strains within this species, which is paralleled by evolutionary diversification of core gene functions. The CRISPR-Cas system could have contributed to this evolutionary segregation. Lactobacillus rhamnosus strains contain the genetic and metabolic machinery with strain-specific gene functions required to adapt to a large range of environments. A remarkable congruency of the evolutionary relatedness of the strains’ core and variome functions, possibly favoring interspecies genetic exchanges, underlines the importance of gene-acquisition and loss within the L. rhamnosus strain diversification.
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Affiliation(s)
- Corina Ceapa
- Gut Biology & Microbiology Platform, Nutricia Research Centre, Utrecht, the Netherlands Laboratory of Microbiology, Wageningen University, the Netherlands
| | - Mark Davids
- Laboratory of Systems and Synthetic Biology, Wageningen University, the Netherlands
| | - Jarmo Ritari
- RPU Immunobiology, Department of Bacteriology and Immunology, University of Helsinki, Finland
| | - Jolanda Lambert
- Gut Biology & Microbiology Platform, Nutricia Research Centre, Utrecht, the Netherlands
| | | | | | | | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, the Netherlands RPU Immunobiology, Department of Bacteriology and Immunology, University of Helsinki, Finland Department of Veterinary Biosciences, University of Helsinki, Finland
| | - Jan Knol
- Gut Biology & Microbiology Platform, Nutricia Research Centre, Utrecht, the Netherlands Laboratory of Microbiology, Wageningen University, the Netherlands
| | - Michiel Kleerebezem
- Host-Microbe Interactomics Group, Department of Animal Sciences, Wageningen University and Research Centre, Wageningen, the Netherlands
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The lag-phase during diauxic growth is a trade-off between fast adaptation and high growth rate. Sci Rep 2016; 6:25191. [PMID: 27125900 PMCID: PMC4850433 DOI: 10.1038/srep25191] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 04/11/2016] [Indexed: 01/23/2023] Open
Abstract
Bi-phasic or diauxic growth is often observed when microbes are grown in a chemically defined medium containing two sugars (for example glucose and lactose). Typically, the two growth stages are separated by an often lengthy phase of arrested growth, the so-called lag-phase. Diauxic growth is usually interpreted as an adaptation to maximise population growth in multi-nutrient environments. However, the lag-phase implies a substantial loss of growth during the switch-over. It therefore remains unexplained why the lag-phase is adaptive. Here we show by means of a stochastic simulation model based on the bacterial PTS system that it is not possible to shorten the lag-phase without incurring a permanent growth-penalty. Mechanistically, this is due to the inherent and well established limitations of biological sensors to operate efficiently at a given resource cost. Hence, there is a trade-off between lost growth during the diauxic switch and the long-term growth potential of the cell. Using simulated evolution we predict that the lag-phase will evolve depending on the distribution of conditions experienced during adaptation. In environments where switching is less frequently required, the lag-phase will evolve to be longer whereas, in frequently changing environments, the lag-phase will evolve to be shorter.
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246
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Abstract
Borrelia burgdorferi, the spirochetal agent of Lyme disease, is a zoonotic pathogen that is maintained in a natural cycle that typically involves mammalian reservoir hosts and a tick vector of the Ixodes species. During each stage of the enzootic cycle, B. burgdorferi is exposed to environments that differ in temperature, pH, small molecules, and most important, nutrient sources. B. burgdorferi has a highly restricted metabolic capacity because it does not contain a tricarboxylic acid cycle, oxidative phosphorylation, or any pathways for de novo biosynthesis of carbohydrates, amino acids, or lipids. Thus, B. burgdorferi relies solely on glycolysis for ATP production and is completely dependent on the transport of nutrients and cofactors from extracellular sources. Herein, pathways for carbohydrate uptake and utilization in B. burgdorferi are described. Regulation of these pathways during the different phases of the enzootic cycle is discussed. In addition, a model for differential control of nutrient flux through the glycolytic pathway as the spirochete transits through the enzootic cycle is presented.
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247
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Lee STM, Davy SK, Tang SL, Kench PS. Mucus Sugar Content Shapes the Bacterial Community Structure in Thermally Stressed Acropora muricata. Front Microbiol 2016; 7:371. [PMID: 27047481 PMCID: PMC4805648 DOI: 10.3389/fmicb.2016.00371] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/07/2016] [Indexed: 11/13/2022] Open
Abstract
It has been proposed that the chemical composition of a coral's mucus can influence the associated bacterial community. However, information on this topic is rare, and non-existent for corals that are under thermal stress. This study therefore compared the carbohydrate composition of mucus in the coral Acropora muricata when subjected to increasing thermal stress from 26 to 31°C, and determined whether this composition correlated with any changes in the bacterial community. Results showed that, at lower temperatures, the main components of mucus were N-acetyl glucosamine and C6 sugars, but these constituted a significantly lower proportion of the mucus in thermally stressed corals. The change in the mucus composition coincided with a shift from a γ-Proteobacteria- to a Verrucomicrobiae- and α-Proteobacteria-dominated community in the coral mucus. Bacteria in the class Cyanobacteria also started to become prominent in the mucus when the coral was thermally stressed. The increase in the relative abundance of the Verrucomicrobiae at higher temperature was strongly associated with a change in the proportion of fucose, glucose, and mannose in the mucus. Increase in the relative abundance of α-Proteobacteria were associated with GalNAc and glucose, while the drop in relative abundance of γ-Proteobacteria at high temperature coincided with changes in fucose and mannose. Cyanobacteria were highly associated with arabinose and xylose. Changes in mucus composition and the bacterial community in the mucus layer occurred at 29°C, which were prior to visual signs of coral bleaching at 31°C. A compositional change in the coral mucus, induced by thermal stress could therefore be a key factor leading to a shift in the associated bacterial community. This, in turn, has the potential to impact the physiological function of the coral holobiont.
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Affiliation(s)
- Sonny T M Lee
- School of Environment, The University of Auckland Auckland, New Zealand
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington Wellington, New Zealand
| | - Sen-Lin Tang
- Microbial Lab, Biodiversity Research Center, Academia Sinica Taipei, Taiwan
| | - Paul S Kench
- School of Environment, The University of Auckland Auckland, New Zealand
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Derkaoui M, Antunes A, Poncet S, Nait Abdallah J, Joyet P, Mazé A, Henry C, Taha MK, Deutscher J, Deghmane AE. The phosphocarrier protein HPr of Neisseria meningitidis interacts with the transcription regulator CrgA and its deletion affects capsule production, cell adhesion, and virulence. Mol Microbiol 2016; 100:788-807. [PMID: 26858137 DOI: 10.1111/mmi.13349] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2016] [Indexed: 01/08/2023]
Abstract
The bacterial phosphotransferase system (PTS) transports and phosphorylates sugars, but also carries out numerous regulatory functions. The β-proteobacterium Neisseria meningitidis possesses an incomplete PTS unable to transport carbon sources because it lacks a membrane component. Nevertheless, the residual phosphorylation cascade is functional and the meningococcal PTS was therefore expected to carry out regulatory roles. Interestingly, a ΔptsH mutant (lacks the PTS protein HPr) exhibited reduced virulence in mice and after intraperitoneal challenge it was rapidly cleared from the bloodstream of BALB/c mice. The rapid clearance correlates with lower capsular polysaccharide production by the ΔptsH mutant, which is probably also responsible for its increased adhesion to Hec-1-B epithelial cells. In addition, compared to the wild-type strain more apoptotic cells were detected when Hec-1-B cells were infected with the ΔptsH strain. Coimmunoprecipitation revealed an interaction of HPr and P-Ser-HPr with the LysR type transcription regulator CrgA, which among others controls its own expression. Moreover, ptsH deletion caused increased expression of a ΦcrgA-lacZ fusion. Finally, the presence of HPr or phospho-HPr's during electrophoretic mobility shift assays enhanced the affinity of CrgA for its target sites preceding crgA and pilE, but HPr did not promote CrgA binding to the sia and pilC1 promoter regions.
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Affiliation(s)
- Meriem Derkaoui
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Institut Pasteur, Unité des Infections Bactériennes Invasives, 75000, Paris Cedex, France
| | - Ana Antunes
- Institut Pasteur, Unité des Infections Bactériennes Invasives, 75000, Paris Cedex, France
| | - Sandrine Poncet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Jamila Nait Abdallah
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Institut Pasteur, Unité des Infections Bactériennes Invasives, 75000, Paris Cedex, France
| | - Philippe Joyet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Alain Mazé
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Céline Henry
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Muhamed-Kheir Taha
- Institut Pasteur, Unité des Infections Bactériennes Invasives, 75000, Paris Cedex, France
| | - Josef Deutscher
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Centre National de la Recherche Scientifique, UMR8261, Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, 75005, Paris, France
| | - Ala-Eddine Deghmane
- Institut Pasteur, Unité des Infections Bactériennes Invasives, 75000, Paris Cedex, France
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Olive AJ, Sassetti CM. Metabolic crosstalk between host and pathogen: sensing, adapting and competing. Nat Rev Microbiol 2016; 14:221-34. [PMID: 26949049 DOI: 10.1038/nrmicro.2016.12] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Our understanding of bacterial pathogenesis is dominated by the cell biology of the host-pathogen interaction. However, the majority of metabolites that are used in prokaryotic and eukaryotic physiology and signalling are chemically similar or identical. Therefore, the metabolic crosstalk between pathogens and host cells may be as important as the interactions between bacterial effector proteins and their host targets. In this Review we focus on host-pathogen interactions at the metabolic level: chemical signalling events that enable pathogens to sense anatomical location and the local physiology of the host; microbial metabolic pathways that are dedicated to circumvent host immune mechanisms; and a few metabolites as central points of competition between the host and bacterial pathogens.
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Affiliation(s)
- Andrew J Olive
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
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Chen S, Thompson KM, Francis MS. Environmental Regulation of Yersinia Pathophysiology. Front Cell Infect Microbiol 2016; 6:25. [PMID: 26973818 PMCID: PMC4773443 DOI: 10.3389/fcimb.2016.00025] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/15/2016] [Indexed: 12/26/2022] Open
Abstract
Hallmarks of Yersinia pathogenesis include the ability to form biofilms on surfaces, the ability to establish close contact with eukaryotic target cells and the ability to hijack eukaryotic cell signaling and take over control of strategic cellular processes. Many of these virulence traits are already well-described. However, of equal importance is knowledge of both confined and global regulatory networks that collaborate together to dictate spatial and temporal control of virulence gene expression. This review has the purpose to incorporate historical observations with new discoveries to provide molecular insight into how some of these regulatory mechanisms respond rapidly to environmental flux to govern tight control of virulence gene expression by pathogenic Yersinia.
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Affiliation(s)
- Shiyun Chen
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan, China
| | - Karl M Thompson
- Department of Microbiology, College of Medicine, Howard University Washington, DC, USA
| | - Matthew S Francis
- Umeå Centre for Microbial Research, Umeå UniversityUmeå, Sweden; Department of Molecular Biology, Umeå UniversityUmeå, Sweden
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