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Fan Q, Neubauer P, Gimpel M. Production of soluble regulatory hydrogenase from Ralstonia eutropha in Escherichia coli using a fed-batch-based autoinduction system. Microb Cell Fact 2021; 20:201. [PMID: 34663324 PMCID: PMC8522226 DOI: 10.1186/s12934-021-01690-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/27/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Autoinduction systems can regulate protein production in Escherichia coli without the need to monitor cell growth or add inducer at the proper time following culture growth. Compared to classical IPTG induction, autoinduction provides a simple and fast way to obtain high protein yields. In the present study, we report on the optimization process for the enhanced heterologous production of the Ralstonia eutropha regulatory hydrogenase (RH) in E. coli using autoinduction. These autoinduction methods were combined with the EnPresso B fed-batch like growth system, which applies slow in situ enzymatic glucose release from a polymer to control cell growth and protein synthesis rate. RESULTS We were able to produce 125 mg L-1 RH corresponding to a productivity averaged over the whole process time of 3 mg (L h)-1 in shake flasks using classic single-shot IPTG induction. IPTG autoinduction resulted in a comparable volumetric RH yield of 112 mg L-1 and due to the shorter overall process time in a 1.6-fold higher productivity of 5 mg (L h)-1. In contrast, lactose autoinduction increased the volumetric yield more than 2.5-fold and the space time yield fourfold reaching 280 mg L-1 and 11.5 mg (L h)-1, respectively. Furthermore, repeated addition of booster increased RH production to 370 mg L-1, which to our knowledge is the highest RH concentration produced in E. coli to date. CONCLUSIONS The findings of this study confirm the general feasibility of the developed fed-batch based autoinduction system and provide an alternative to conventional induction systems for efficient recombinant protein production. We believe that the fed-batch based autoinduction system developed herein will favor the heterologous production of larger quantities of difficult-to-express complex enzymes to enable economical production of these kinds of proteins.
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Affiliation(s)
- Qin Fan
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Matthias Gimpel
- Chair of Bioprocess Engineering, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.
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202
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Activity of CcpA-Regulated GH18 Family Glycosyl Hydrolases That Contributes to Nutrient Acquisition and Fitness in Enterococcus faecalis. Infect Immun 2021; 89:e0034321. [PMID: 34424752 DOI: 10.1128/iai.00343-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The ability of Enterococcus faecalis to colonize host anatomical sites is dependent on its adaptive response to host conditions. Three glycosyl hydrolase gene clusters, each belonging to glycosyl hydrolase family 18 (GH18) (ef0114, ef0361, and ef2863), in E. faecalis were previously found to be upregulated under glucose-limiting conditions. The GH18 catalytic domain is present in proteins that are classified as either chitinases or β-1,4 endo-β-N-acetylglucosaminidases (ENGases) based on their β-1,4 endo-N-acetyl-β-d-glucosaminidase activity, and ENGase activity is commonly associated with cleaving N-linked glycoprotein, an abundant glycan structure on host epithelial surfaces. Here, we show that all three hydrolases are negatively regulated by the transcriptional regulator carbon catabolite protein A (CcpA). Additionally, we demonstrate that a constitutively active CcpA variant represses the expression of CcpA-regulated genes irrespective of glucose availability. Previous studies showed that the GH18 catalytic domains of EndoE (EF0114) and EfEndo18A (EF2863) were capable of deglycosylating RNase B, a model high-mannose-type glycoprotein. However, it remained uncertain which glycosidase is primarily responsible for the deglycosylation of high-mannose-type glycoproteins. In this study, we show by mutation analysis as well as a dose-dependent analysis of recombinant protein expression that EfEndo18A is primarily responsible for deglycosylating high-mannose glycoproteins and that the glycans removed by EfEndo18A support growth under nutrient-limiting conditions in vitro. In contrast, IgG is representative of a complex-type glycoprotein, and we demonstrate that the GH18 domain of EndoE is primarily responsible for the removal of this glycan decoration. Finally, our data highlight the combined contribution of glycosidases to the virulence of E. faecalis in vivo.
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203
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Adams AND, Azam MS, Costliow ZA, Ma X, Degnan PH, Vanderpool CK. A Novel Family of RNA-Binding Proteins Regulate Polysaccharide Metabolism in Bacteroides thetaiotaomicron. J Bacteriol 2021; 203:e0021721. [PMID: 34251866 PMCID: PMC8508124 DOI: 10.1128/jb.00217-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/08/2021] [Indexed: 11/20/2022] Open
Abstract
Human gut microbiome composition is constantly changing, and diet is a major driver of these changes. Gut microbial species that persist in mammalian hosts for long periods of time must possess mechanisms for sensing and adapting to nutrient shifts to avoid being outcompeted. Global regulatory mechanisms mediated by RNA-binding proteins (RBPs) that govern responses to nutrient shifts have been characterized in Proteobacteria and Firmicutes but remain undiscovered in the Bacteroidetes. Here, we report the identification of RBPs that are broadly distributed across the Bacteroidetes, with many genomes encoding multiple copies. Genes encoding these RBPs are highly expressed in many Bacteroides species. A purified RBP, RbpB, from Bacteroides thetaiotaomicron binds to single-stranded RNA in vitro with an affinity similar to other characterized regulatory RBPs. B. thetaiotaomicron mutants lacking RBPs show dramatic shifts in expression of polysaccharide utilization and capsular polysaccharide loci, suggesting that these RBPs may act as global regulators of polysaccharide metabolism. A B. thetaiotaomicron ΔrbpB mutant shows a growth defect on dietary sugars belonging to the raffinose family of oligosaccharides (RFOs). The ΔrbpB mutant had reduced expression of BT1871, encoding a predicted RFO-degrading melibiase, compared to the wild-type strain. Mutation of BT1871 confirmed that the enzyme it encodes is essential for growth on melibiose and promotes growth on the RFOs raffinose and stachyose. Our data reveal that RbpB is required for optimal expression of BT1871 and other polysaccharide-related genes, suggesting that we have identified an important new family of global regulatory proteins in the Bacteroidetes. IMPORTANCE The human colon houses hundreds of bacterial species, including many belonging to the genus Bacteroides, that aid in breaking down our food to keep us healthy. Bacteroides have many genes responsible for breaking down different dietary carbohydrates, and complex regulatory mechanisms ensure that specific genes are only expressed when the right carbohydrates are available. In this study, we discovered that Bacteroides use a family of RNA-binding proteins as global regulators to coordinate expression of carbohydrate utilization genes. The ability to turn different carbohydrate utilization genes on and off in response to changing nutrient conditions is critical for Bacteroides to live successfully in the gut, and thus the new regulators we have identified may be important for life in the host.
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Affiliation(s)
- Amanda N. D. Adams
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Muhammad S. Azam
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Zachary A. Costliow
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Xiangqian Ma
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Patrick H. Degnan
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, California, USA
| | - Carin K. Vanderpool
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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204
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Culture media based on effluent derived from soy protein concentrate production for Lacticaseibacillus paracasei 90 biomass production: statistical optimisation, mineral characterization, and metabolic activities. Antonie van Leeuwenhoek 2021; 114:2047-2063. [PMID: 34609626 DOI: 10.1007/s10482-021-01660-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 09/11/2021] [Indexed: 10/20/2022]
Abstract
The waste and by-products of the soybean industry could be an economic source of nutrients to satisfy the high nutritional demands for the cultivation of lactic acid bacteria. The aims of this work were to maximize the biomass production of Lacticaseibacillus paracasei 90 (L90) in three culture media formulated from an effluent derived from soy protein concentrate production and to assess the effects these media have on the enzymatic activity of L90, together with their influence on its fermentation profile in milk. The presence of essential minerals and fermentable carbohydrates (sucrose, raffinose, and stachyose) in the effluent was verified. L90 reached high levels of microbiological counts (∼ 9 log cfu mL-1) and dry weight (> 1 g L-1) on the three optimized media. Enzymatic activities (lactate dehydrogenase and β-galactosidase) of L90, and its metabolism of lactose and citric acid, as well as lactic acid and pyruvic acid production in milk, were modified depending on the growth media. The ability of the L90 to produce the key flavour compounds (diacetyl and acetoin) was maintained or improved by growing in the optimized media in comparison with MRS.
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205
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Residual Helicity at the Active Site of the Histidine Phosphocarrier, HPr, Modulates Binding Affinity to Its Natural Partners. Int J Mol Sci 2021; 22:ijms221910805. [PMID: 34639146 PMCID: PMC8509676 DOI: 10.3390/ijms221910805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/01/2021] [Accepted: 10/02/2021] [Indexed: 11/16/2022] Open
Abstract
The phosphoenolpyruvate-dependent phosphotransferase system (PTS) modulates the preferential use of sugars in bacteria. The first proteins in the cascade are common to all organisms (EI and HPr). The active site of HPr involves a histidine (His15) located immediately before the beginning of the first α-helix. The regulator of sigma D (Rsd) protein also binds to HPr. The region of HPr comprising residues Gly9-Ala30 (HPr9–30), involving the first α-helix (Ala16-Thr27) and the preceding active site loop, binds to both the N-terminal region of EI and intact Rsd. HPr9–30 is mainly disordered. We attempted to improve the affinity of HPr9–30 to both proteins by mutating its sequence to increase its helicity. We designed peptides that led to a marginally larger population in solution of the helical structure of HPr9–30. Molecular simulations also suggested a modest increment in the helical population of mutants, when compared to the wild-type. The mutants, however, were bound with a less favorable affinity than the wild-type to both the N-terminal of EI (EIN) or Rsd, as tested by isothermal titration calorimetry and fluorescence. Furthermore, mutants showed lower antibacterial properties against Staphylococcus aureus than the wild-type peptide. Therefore, we concluded that in HPr, a compromise between binding to its partners and residual structure at the active site must exist to carry out its function.
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206
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Venkat K, Hoyos M, Haycocks JR, Cassidy L, Engelmann B, Rolle-Kampczyk U, von Bergen M, Tholey A, Grainger DC, Papenfort K. A dual-function RNA balances carbon uptake and central metabolism in Vibrio cholerae. EMBO J 2021; 40:e108542. [PMID: 34612526 PMCID: PMC8672173 DOI: 10.15252/embj.2021108542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 11/22/2022] Open
Abstract
Bacterial small RNAs (sRNAs) are well known to modulate gene expression by base pairing with trans‐encoded transcripts and are typically non‐coding. However, several sRNAs have been reported to also contain an open reading frame and thus are considered dual‐function RNAs. In this study, we discovered a dual‐function RNA from Vibrio cholerae, called VcdRP, harboring a 29 amino acid small protein (VcdP), as well as a base‐pairing sequence. Using a forward genetic screen, we identified VcdRP as a repressor of cholera toxin production and link this phenotype to the inhibition of carbon transport by the base‐pairing segment of the regulator. By contrast, we demonstrate that the VcdP small protein acts downstream of carbon transport by binding to citrate synthase (GltA), the first enzyme of the citric acid cycle. Interaction of VcdP with GltA results in increased enzyme activity and together VcdR and VcdP reroute carbon metabolism. We further show that transcription of vcdRP is repressed by CRP allowing us to provide a model in which VcdRP employs two different molecular mechanisms to synchronize central metabolism in V. cholerae.
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Affiliation(s)
- Kavyaa Venkat
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Mona Hoyos
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - James Rj Haycocks
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Liam Cassidy
- Systematic Proteome Research & Bioanalytics, University of Kiel, Kiel, Germany
| | | | | | | | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, University of Kiel, Kiel, Germany
| | - David C Grainger
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Kai Papenfort
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany.,Microverse Cluster, Friedrich Schiller University Jena, Jena, Germany
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207
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Zeng H, Rohani R, Huang WE, Yang A. Understanding and mathematical modelling of cellular resource allocation in microorganisms: a comparative synthesis. BMC Bioinformatics 2021; 22:467. [PMID: 34583645 PMCID: PMC8479906 DOI: 10.1186/s12859-021-04382-3] [Citation(s) in RCA: 2] [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: 03/02/2021] [Accepted: 09/20/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The rising consensus that the cell can dynamically allocate its resources provides an interesting angle for discovering the governing principles of cell growth and metabolism. Extensive efforts have been made in the past decade to elucidate the relationship between resource allocation and phenotypic patterns of microorganisms. Despite these exciting developments, there is still a lack of explicit comparison between potentially competing propositions and a lack of synthesis of inter-related proposals and findings. RESULTS In this work, we have reviewed resource allocation-derived principles, hypotheses and mathematical models to recapitulate important achievements in this area. In particular, the emergence of resource allocation phenomena is deciphered by the putative tug of war between the cellular objectives, demands and the supply capability. Competing hypotheses for explaining the most-studied phenomenon arising from resource allocation, i.e. the overflow metabolism, have been re-examined towards uncovering the potential physiological root cause. The possible link between proteome fractions and the partition of the ribosomal machinery has been analysed through mathematical derivations. Finally, open questions are highlighted and an outlook on the practical applications is provided. It is the authors' intention that this review contributes to a clearer understanding of the role of resource allocation in resolving bacterial growth strategies, one of the central questions in microbiology. CONCLUSIONS We have shown the importance of resource allocation in understanding various aspects of cellular systems. Several important questions such as the physiological root cause of overflow metabolism and the correct interpretation of 'protein costs' are shown to remain open. As the understanding of the mechanisms and utility of resource application in cellular systems further develops, we anticipate that mathematical modelling tools incorporating resource allocation will facilitate the circuit-host design in synthetic biology.
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Affiliation(s)
- Hong Zeng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, 100048, China
| | - Reza Rohani
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Aidong Yang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK.
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208
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Kurgan G, Onyeabor M, Holland SC, Taylor E, Schneider A, Kurgan L, Billings T, Wang X. Directed evolution of Zymomonas mobilis sugar facilitator Glf to overcome glucose inhibition. J Ind Microbiol Biotechnol 2021; 49:6371102. [PMID: 34529081 PMCID: PMC9118996 DOI: 10.1093/jimb/kuab066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/04/2021] [Indexed: 12/01/2022]
Abstract
Cellular import of D-xylose, the second most abundant sugar in typical lignocellulosic biomass, has been evidenced to be an energy-depriving process in bacterial biocatalysts. The sugar facilitator of Zymomonas mobilis, Glf, is capable of importing xylose at high rates without extra energy input, but is inhibited by D-glucose (the primary biomass sugar), potentially limiting the utility of this transporter for fermentation of sugar mixtures derived from lignocellulose. In this work we developed an Escherichia coli platform strain deficient in glucose and xylose transport to facilitate directed evolution of Glf to overcome glucose inhibition. Using this platform, we isolated nine Glf variants created by both random and site-saturation mutagenesis with increased xylose utilization rates ranging from 4.8-fold to 13-fold relative to wild-type Glf when fermenting 100 g l–1 glucose–xylose mixtures. Diverse point mutations such as A165M and L445I were discovered leading to released glucose inhibition. Most of these mutations likely alter sugar coordinating pocket for the 6-hydroxymethyl group of D-glucose. These discovered glucose-resistant Glf variants can be potentially used as energy-conservative alternatives to the native sugar transport systems of bacterial biocatalysts for fermentation of lignocellulose-derived sugars.
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Affiliation(s)
- Gavin Kurgan
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Moses Onyeabor
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Steven C Holland
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Eric Taylor
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Aidan Schneider
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Logan Kurgan
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Tommy Billings
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Xuan Wang
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
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209
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Mucolytic bacteria: prevalence in various pathological diseases. World J Microbiol Biotechnol 2021; 37:176. [PMID: 34519941 DOI: 10.1007/s11274-021-03145-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/07/2021] [Indexed: 02/07/2023]
Abstract
All mucins are highly glycosylated and a key constituent of the mucus layer that is vigilant against pathogens in many organ systems of animals and humans. The viscous layer is organized in bilayers, i.e., an outer layer that is loosely arranged, variable in thickness, home to the commensal microbiota that grows in the complex environment, and an innermost layer that is stratified, non-aspirated, firmly adherent to the epithelial cells and devoid of any microorganisms. The O-glycosylation moiety represents the site of adhesion for pathogens and due to the increase of motility, mucolytic activity, and upregulation of virulence factors, some microorganisms can circumvent the component of the mucus layer and cause disruption in organ homeostasis. A dysbiotic microbiome, defective mucus barrier, and altered immune response often result in various diseases. In this review, paramount emphasis is given to the role played by the bacterial species directly or indirectly involved in mucin degradation, alteration in mucus secretion or its composition or mucin gene expression, which instigates many diseases in the digestive, respiratory, and other organ systems. A systematic view can help better understand the etiology of some complex disorders such as cystic fibrosis, ulcerative colitis and expand our knowledge about mucin degraders to develop new therapeutic approaches to correct ill effects caused by these mucin-dwelling pathogens.
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210
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El-Ghonemy DH. Antioxidant and antimicrobial activities of exopolysaccharides produced by a novel Aspergillus sp. DHE6 under optimized submerged fermentation conditions. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102150] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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211
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Rong G, Zhang Y, Chen Y, Chen J, Jiang N, Merchuk JC. The prodigiosin change on the surface of Serratia marcescens detected by flow cytometry. Cytometry A 2021; 101:254-263. [PMID: 34448526 DOI: 10.1002/cyto.a.24497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 07/25/2021] [Accepted: 08/06/2021] [Indexed: 11/11/2022]
Abstract
The potential of flow cytometry for the study of changes in prodigiosin on the cell surface of Serratia marcescens is of academic and practical interest. This is because S. marcescens can produce prodigiosin, a secondary metabolite, with potential use as a cancer-cell inhibitor. In this study, three groups of bacterial cultures with different carbon sources were compared, and the effect of the addition of cAMP to the sucrose-based culture was studied. Both cellular morphology and DNA content were detected by flow cytometry, rendering a broad description of the bacterial behavior. It is the first use of flow cytometry to investigate the dynamics of prodigiosin on the surface of S. marcescens during growth in different media. The fluorescence intensity is related to the DNA content, the forward-scattered light is related to cell volume, and the side-scattered light is related to the surface morphology, especially the surface prodigiosin. These may contribute to the potential development of a bacterial metabolic monitoring strategy using both DNA content analysis and bacterial morphology based on flow cytometry technique.
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Affiliation(s)
- Guangjian Rong
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China.,Key Laboratory for Green Chemical Process of Ministry of Education, Wuhan Institute of Technology, LiuFang Campus, Wuhan, China.,Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, Wuhan Institute of Technology, LiuFang Campus, Wuhan, China
| | - Youhong Zhang
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China.,Key Laboratory for Green Chemical Process of Ministry of Education, Wuhan Institute of Technology, LiuFang Campus, Wuhan, China.,Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, Wuhan Institute of Technology, LiuFang Campus, Wuhan, China.,School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, China
| | - Yan Chen
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Jie Chen
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Nan Jiang
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Jose C Merchuk
- Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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212
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Allmann S, Wargnies M, Plazolles N, Cahoreau E, Biran M, Morand P, Pineda E, Kulyk H, Asencio C, Villafraz O, Rivière L, Tetaud E, Rotureau B, Mourier A, Portais JC, Bringaud F. Glycerol suppresses glucose consumption in trypanosomes through metabolic contest. PLoS Biol 2021; 19:e3001359. [PMID: 34388147 PMCID: PMC8386887 DOI: 10.1371/journal.pbio.3001359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/25/2021] [Accepted: 07/09/2021] [Indexed: 11/18/2022] Open
Abstract
Microorganisms must make the right choice for nutrient consumption to adapt to their changing environment. As a consequence, bacteria and yeasts have developed regulatory mechanisms involving nutrient sensing and signaling, known as "catabolite repression," allowing redirection of cell metabolism to maximize the consumption of an energy-efficient carbon source. Here, we report a new mechanism named "metabolic contest" for regulating the use of carbon sources without nutrient sensing and signaling. Trypanosoma brucei is a unicellular eukaryote transmitted by tsetse flies and causing human African trypanosomiasis, or sleeping sickness. We showed that, in contrast to most microorganisms, the insect stages of this parasite developed a preference for glycerol over glucose, with glucose consumption beginning after the depletion of glycerol present in the medium. This "metabolic contest" depends on the combination of 3 conditions: (i) the sequestration of both metabolic pathways in the same subcellular compartment, here in the peroxisomal-related organelles named glycosomes; (ii) the competition for the same substrate, here ATP, with the first enzymatic step of the glycerol and glucose metabolic pathways both being ATP-dependent (glycerol kinase and hexokinase, respectively); and (iii) an unbalanced activity between the competing enzymes, here the glycerol kinase activity being approximately 80-fold higher than the hexokinase activity. As predicted by our model, an approximately 50-fold down-regulation of the GK expression abolished the preference for glycerol over glucose, with glucose and glycerol being metabolized concomitantly. In theory, a metabolic contest could be found in any organism provided that the 3 conditions listed above are met.
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Affiliation(s)
- Stefan Allmann
- Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux University, CNRS, Bordeaux, France
- Centre de Résonance Magnétique des Systèmes Biologiques, UMR 5536, Bordeaux University, CNRS, Bordeaux, France
| | - Marion Wargnies
- Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux University, CNRS, Bordeaux, France
- Centre de Résonance Magnétique des Systèmes Biologiques, UMR 5536, Bordeaux University, CNRS, Bordeaux, France
| | - Nicolas Plazolles
- Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux University, CNRS, Bordeaux, France
| | - Edern Cahoreau
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- MetaToul–MetaboHUB, Toulouse, France
| | - Marc Biran
- Centre de Résonance Magnétique des Systèmes Biologiques, UMR 5536, Bordeaux University, CNRS, Bordeaux, France
| | - Pauline Morand
- Centre de Résonance Magnétique des Systèmes Biologiques, UMR 5536, Bordeaux University, CNRS, Bordeaux, France
| | - Erika Pineda
- Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux University, CNRS, Bordeaux, France
| | - Hanna Kulyk
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- MetaToul–MetaboHUB, Toulouse, France
| | - Corinne Asencio
- Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux University, CNRS, Bordeaux, France
| | - Oriana Villafraz
- Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux University, CNRS, Bordeaux, France
| | - Loïc Rivière
- Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux University, CNRS, Bordeaux, France
| | - Emmanuel Tetaud
- Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux University, CNRS, Bordeaux, France
| | - Brice Rotureau
- Trypanosome Transmission Group, Trypanosome Cell Biology Unit, Department of Parasites and Insect Vectors, INSERM U1201, Institut Pasteur, Paris, France
| | - Arnaud Mourier
- Institute of Biochemistry and Genetics of the Cell (IBGC), CNRS, Bordeaux University, Bordeaux, France
| | - Jean-Charles Portais
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- MetaToul–MetaboHUB, Toulouse, France
- STROMALab, Université de Toulouse, INSERM U1031, EFS, INP-ENVT, UPS, Toulouse, France
| | - Frédéric Bringaud
- Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux University, CNRS, Bordeaux, France
- Centre de Résonance Magnétique des Systèmes Biologiques, UMR 5536, Bordeaux University, CNRS, Bordeaux, France
- * E-mail:
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Regulation of β-amylase synthesis: a brief overview. Mol Biol Rep 2021; 48:6503-6511. [PMID: 34379288 DOI: 10.1007/s11033-021-06613-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 07/29/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND The major activity of β-amylase (BMY) is the production of maltose by the hydrolytic degradation of starch. BMY is found to be produced by some plants and few microorganisms only. The industrial importance of the enzyme warrants its application in a larger scale with the help of genetic engineering, for which the regulatory mechanism is to be clearly understood. RESULTS AND CONCLUSION In plants, the activities of BMY are regulated by various environmental stimuli including stress of drought, cold and heat. In vascular plant, Arabidopsis sp. the enzyme is coded by nine BAM genes, whereas in most bacteria, BMY enzymes are coded by the spoII gene family. The activities of these genes are in turn controlled by various compounds. Production and inhibition of the microbial BMY is regulated by the activation and inactivation of various BAM genes. Various types of transcriptional regulators associated with the plant- BMYs regulate the production of BMY enzyme. The enhancement in the expression of such genes reflects evolutionary significance. Bacterial genes, on the other hand, as exemplified by Bacillus sp and Clostridium sp, clearly depict the importance of a single regulatory gene, the absence or mutation of which totally abolishes the BMY activity.
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214
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Tsujikawa Y, Ishikawa S, Sakane I, Yoshida KI, Osawa R. Identification of genes encoding a novel ABC transporter in Lactobacillus delbrueckii for inulin polymers uptake. Sci Rep 2021; 11:16007. [PMID: 34362962 PMCID: PMC8346543 DOI: 10.1038/s41598-021-95356-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023] Open
Abstract
Lactobacillus delbrueckii JCM 1002T grows on highly polymerized inulin-type fructans as its sole carbon source. When it was grown on inulin, a > 10 kb long gene cluster inuABCDEF (Ldb1381-1386) encoding a plausible ABC transporter was suggested to be induced, since a transcriptome analysis revealed that the fourth gene inuD (Ldb1384) was up-regulated most prominently. Although Bacillus subtilis 168 is originally unable to utilize inulin, it became to grow on inulin upon heterologous expression of inuABCDEF. When freshly cultured cells of the recombinant B. subtilis were then densely suspended in buffer containing inulin polymers and incubated, inulin gradually disappeared from the buffer and accumulated in the cells without being degraded, whereas levan-type fructans did not disappear. The results imply that inuABCDEF might encode a novel ABC transporter in L. delbrueckii to "monopolize" inulin polymers selectively, thereby, providing a possible advantage in competition with other concomitant inulin-utilizing bacteria.
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Affiliation(s)
- Yuji Tsujikawa
- Central Research Institute, ITO EN, Ltd., 21 Mekami, Makinohara, Shizuoka 421-0516 Japan ,grid.31432.370000 0001 1092 3077Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501 Japan
| | - Shu Ishikawa
- grid.31432.370000 0001 1092 3077Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501 Japan
| | - Iwao Sakane
- Central Research Institute, ITO EN, Ltd., 21 Mekami, Makinohara, Shizuoka 421-0516 Japan
| | - Ken-ichi Yoshida
- grid.31432.370000 0001 1092 3077Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501 Japan
| | - Ro Osawa
- grid.31432.370000 0001 1092 3077Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501 Japan
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215
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Li D, Li G, Zhang D. Field-scale studies on the change of soil microbial community structure and functions after stabilization at a chromium-contaminated site. JOURNAL OF HAZARDOUS MATERIALS 2021; 415:125727. [PMID: 34088197 DOI: 10.1016/j.jhazmat.2021.125727] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/14/2021] [Accepted: 03/19/2021] [Indexed: 05/20/2023]
Abstract
Various remediation strategies have been developed to eliminate soil chromium (Cr) contamination which challenges the ecosystem and human health, and chemical stabilization is the most popular one. Limited work focuses on the change of soil microbial community and functions after chemical stabilization. The present study examined the diversity and structure of bacterial, fungal and archaeal communities in 20 soils from a Cr-contaminated site in China after chemical stabilization and ageing. Cr contamination significantly reduced microbial diversity and shaped microbial community structure. After chemical stabilization, bacterial and fungal communities had higher richness and evenness, whereas archaea behaved oppositely. Microbial community structure after stabilization were more similar to uncontaminated soils. Among all environmental variables, pH and Al explained 25.2% and 9.4% of the total variance of bacterial diversity, whereas the major variable affecting fungal community was pH (29.3%). Cr, organic matters, extractable-Al and moisture explained 25.8%, 22.4%, 9.9% and 9.9% of the total variance in archaeal community, respectively. This work for the first time unraveled the change of the whole soil microbial community structures and functions at Cr-contaminated sites after chemical stabilization on field scale and proved chemical stabilization as an effective approach to detoxicate Cr(VI) and recover microbial communities in soils.
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Affiliation(s)
- Danni Li
- School of Environment, Tsinghua University, Beijing 100084, China; National Engineering Laboratory for Site Remediation Technologies, Beijing 100015, China
| | - Guanghe Li
- School of Environment, Tsinghua University, Beijing 100084, China; National Engineering Laboratory for Site Remediation Technologies, Beijing 100015, China
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing 100084, China; National Engineering Laboratory for Site Remediation Technologies, Beijing 100015, China.
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216
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Phale PS, Mohapatra B, Malhotra H, Shah BA. Eco-physiological portrait of a novel Pseudomonas sp. CSV86: an ideal host/candidate for metabolic engineering and bioremediation. Environ Microbiol 2021; 24:2797-2816. [PMID: 34347343 DOI: 10.1111/1462-2920.15694] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 11/30/2022]
Abstract
Pseudomonas sp. CSV86, an Indian soil isolate, degrades wide range of aromatic compounds like naphthalene, benzoate and phenylpropanoids, amongst others. Isolate displays the unique and novel property of preferential utilization of aromatics over glucose and co-metabolizes them with organic acids. Interestingly, as compared to other Pseudomonads, strain CSV86 harbours only high-affinity glucokinase pathway (and absence of low-affinity oxidative route) for glucose metabolism. Such lack of gluconate loop might be responsible for the novel phenotype of preferential utilization of aromatics. The genome analysis and comparative functional mining indicated a large genome (6.79 Mb) with significant enrichment of regulators, transporters as well as presence of various secondary metabolite production clusters, suggesting its eco-physiological and metabolic versatility. Strain harbours various integrative conjugative elements (ICEs) and genomic islands, probably acquired through horizontal gene transfer events, leading to genome mosaicity and plasticity. Naphthalene degradation genes are arranged as regulonic clusters and found to be part of ICECSV86nah . Various eco-physiological properties and absence of major pathogenicity and virulence factors (risk group-1) in CSV86 suggest it to be an ideal candidate for bioremediation. Further, strain can serve as an ideal chassis for metabolic engineering to degrade various xenobiotics preferentially over simple carbon sources for efficient remediation.
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Affiliation(s)
- Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, Maharashtra, 400076, India
| | - Balaram Mohapatra
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, Maharashtra, 400076, India
| | - Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, Maharashtra, 400076, India
| | - Bhavik A Shah
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Mumbai, Maharashtra, 400076, India
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217
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Wang Z, Huang X, Jan M, Kong D, Pan J, Zhang X. The global regulator Hfq exhibits far more extensive and intensive regulation than Crc in Pseudomonas protegens H78. MOLECULAR PLANT PATHOLOGY 2021; 22:921-938. [PMID: 33963656 PMCID: PMC8295515 DOI: 10.1111/mpp.13070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 01/22/2021] [Accepted: 03/24/2021] [Indexed: 05/10/2023]
Abstract
The biocontrol rhizobacterium Pseudomonas protegens H78 can produce a large array of antimicrobial secondary metabolites, including pyoluteorin (Plt), 2,4-diacetylphloroglucinol (DAPG), and pyrrolnitrin (Prn). Our preliminary study showed that the biosynthesis of antibiotics including Plt is activated by the RNA chaperone Hfq in P. protegens H78. This prompted us to explore the global regulatory mechanism of Hfq, as well as the catabolite repression control (Crc) protein in H78. The antimicrobial capacity of H78 was positively controlled by Hfq while slightly down-regulated by knockout of crc. Similarly, cell growth of H78 was significantly impaired by deletion of hfq and slightly inhibited by knockout of crc. Transcriptomic profiling revealed that hfq mutation resulted in significant down-regulation of 688 genes and up-regulation of 683 genes. However, only 113 genes were significantly down-regulated and 105 genes up-regulated by the crc mutation in H78. Hfq positively regulated the expression of gene clusters involved in secondary metabolism (plt, prn, phl, hcn, and pvd), the type VI secretion system, and aromatic compound degradation. However, Crc only positively regulated the biosynthesis of Plt but not other antibiotics. Hfq also regulated expression of genes involved in oxidative phosphorylation and flagellar biogenesis. In addition, Hfq and Crc activated transcription of crcY/Z sRNAs by feedback. In summary, Hfq processes far more extensive and intensive regulatory capacity than Crc and shows small cross-regulation with Crc in H78. This study lays the foundation for clarifying the Hfq and/or Crc-dependent global regulatory network and improving antibiotic production by genetic engineering in P. protegens.
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Affiliation(s)
- Zheng Wang
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic and Developmental SciencesSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Xianqing Huang
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic and Developmental SciencesSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Malik Jan
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic and Developmental SciencesSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Deyu Kong
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic and Developmental SciencesSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Jingwen Pan
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic and Developmental SciencesSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Xuehong Zhang
- State Key Laboratory of Microbial MetabolismJoint International Research Laboratory of Metabolic and Developmental SciencesSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
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218
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Tan Z, Chen J, Liu Y, Chen L, Xu Y, Zou Y, Li Y, Gong B. The survival and removal mechanism of Sphingobacterium changzhouense TC931 under tetracycline stress and its' ecological safety after application. BIORESOURCE TECHNOLOGY 2021; 333:125067. [PMID: 33878498 DOI: 10.1016/j.biortech.2021.125067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/21/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Sphingobacterium changzhouense TC931 was isolated as a novel TC (tetracycline) removal bacterium through adsorption on extracellular polymerase substances (EPS) and cellular surface and biodegradation. TC biodegradation efficiency by strain TC931 was affected by solution initial pH and carbon source. Polysaccharides and hydrocarbons in EPS and cellular surface were responsible for TC biosorption. Eight possible biodegradation products were identified and the biodegradation pathway was proposed. Strain TC931 was rich in antibiotic resistance genes, and tetX-TC931 and antibiotics resistance genome island (GI) may be acquired via horizontal gene transfer in early evolutionary history. The GI was incomplete and may stable in strain TC931, but it could develop into an intact and transferability GI with help of other mobile genetic elements. This work offers a theoretical basis for understanding the survival and biodegradation mechanisms of S. changzhouense TC931 under TC stress, and offers an ecological safety assessment for its application in environmental bioremediation.
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Affiliation(s)
- Zewen Tan
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Jiacheng Chen
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Yiling Liu
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Lian Chen
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Yuqing Xu
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Yixuan Zou
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Yongtao Li
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Beini Gong
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China.
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219
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Pseudomonas aeruginosa Consumption of Airway Metabolites Promotes Lung Infection. Pathogens 2021; 10:pathogens10080957. [PMID: 34451421 PMCID: PMC8401524 DOI: 10.3390/pathogens10080957] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 12/03/2022] Open
Abstract
Prevailing dogma indicates that the lung of cystic fibrosis (CF) individuals is infected by multiple pathogens due to the abundant accumulation of mucus, which traps most of inhaled organisms. However, this hypothesis does not explain how specific opportunists, like Pseudomonas aeruginosa, are selected in the CF lung to cause chronic disease. This strongly suggests that other factors than mucus are accrued in the human airway and might predispose to bacterial disease, especially by P. aeruginosa. In this review we discuss the role of macrophage metabolites, like succinate and itaconate, in P. aeruginosa pneumonia. We analyze how dysfunction of the CF transmembrane conductance regulator (CFTR) favors release of these metabolites into the infected airway, and how P. aeruginosa exploits these elements to induce transcriptomic and metabolic changes that increase its capacity to cause intractable disease. We describe the host and pathogen pathways associated with succinate and itaconate catabolism, mechanisms of bacterial adaptation to these determinants, and suggest how both experimental settings and future therapies should consider macrophage metabolites abundance to better study P. aeruginosa pathogenesis.
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220
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Malecka EM, Bassani F, Dendooven T, Sonnleitner E, Rozner M, Albanese TG, Resch A, Luisi B, Woodson S, Bläsi U. Stabilization of Hfq-mediated translational repression by the co-repressor Crc in Pseudomonas aeruginosa. Nucleic Acids Res 2021; 49:7075-7087. [PMID: 34139006 PMCID: PMC8266614 DOI: 10.1093/nar/gkab510] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/26/2021] [Accepted: 06/15/2021] [Indexed: 01/02/2023] Open
Abstract
In Pseudomonas aeruginosa the RNA chaperone Hfq and the catabolite repression control protein (Crc) govern translation of numerous transcripts during carbon catabolite repression. Here, Crc was shown to enhance Hfq-mediated translational repression of several mRNAs. We have developed a single-molecule fluorescence assay to quantitatively assess the cooperation of Hfq and Crc to form a repressive complex on a RNA, encompassing the translation initiation region and the proximal coding sequence of the P. aeruginosa amiE gene. The presence of Crc did not change the amiE RNA-Hfq interaction lifetimes, whereas it changed the equilibrium towards more stable repressive complexes. This observation is in accord with Cryo-EM analyses, which showed an increased compactness of the repressive Hfq/Crc/RNA assemblies. These biophysical studies revealed how Crc protein kinetically stabilizes Hfq/RNA complexes, and how the two proteins together fold a large segment of the mRNA into a more compact translationally repressive structure. In fact, the presence of Crc resulted in stronger translational repression in vitro and in a significantly reduced half-life of the target amiE mRNA in vivo. Although Hfq is well-known to act with small regulatory RNAs, this study shows how Hfq can collaborate with another protein to down-regulate translation of mRNAs that become targets for the degradative machinery.
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Affiliation(s)
- Ewelina M Malecka
- Department of Biophysics, 3400 N. Charles Street, Johns Hopkins University, Baltimore, MD-21218, USA
| | - Flavia Bassani
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Tom Dendooven
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Elisabeth Sonnleitner
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Marlena Rozner
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Tanino G Albanese
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Armin Resch
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Ben Luisi
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Sarah Woodson
- Department of Biophysics, 3400 N. Charles Street, Johns Hopkins University, Baltimore, MD-21218, USA
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Dr. Bohrgasse 9/4, 1030 Vienna, Austria
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221
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An aptly industrialized bioprocess for lactic acid production from corn stover using thermotolerant microbial consortia. Bioprocess Biosyst Eng 2021; 44:2445-2454. [PMID: 34304345 DOI: 10.1007/s00449-021-02616-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 07/16/2021] [Indexed: 10/20/2022]
Abstract
Chemical pretreatment of lignocellulosic biomass is a critical step in the conversion of lignocellulose to biofuels and biochemical. The main drawback of this pretreatment process is the formation of inhibitors which exhibit combined toxicity to microorganisms and result to low product concentrations and yields. In this study, the selection of microbial consortia by enrichment on hydrolysate of H2SO4-pretreated corn stover (pre-CS) without detoxification has been investigated as an efficient way to develop new strategies for lignocellulose utilization. The analysis of cattle stomach-dervied microbial consortia domesticated to degrade hydrolysate of pre-CS to produce lactic acid (LA) at different temperatures was investigated. Bacterial 16S rRNA gene amplicon sequencing analyses indicated that the three microbial consortia were taxonomically distinct and Enterococcus became dominant at high temperature. The highest glucose consumption rate was observed at 45 °C, while the three microbial consortia showed similar consumption rates of xylose and arabinose. The selected microbial consortia DUT37, DUT45 and DUT47 showed preferable resistances to inhibitors in hydrolysate of pre-CS and abilities of xylose utilization. A batch simultaneous saccharification and fermentation (SSF) process was developed by microbial consortium DUT47 at 47 °C to produce LA from pre-CS under non-detoxified and non-sterile conditions. The LA concentration and yield were 43.73 g/L and 0.50 g/g-corn stover (CS), respectively. Microbial consortium DUT47 has been shown to be suitable for LA production from H2SO4-pretreated corn stover without detoxification due to its thermophilic growth characteristics, robust tolerance of inhibitors, and the simultaneous utilization of glucose and xylose.
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222
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Nair A, Sarma SJ. The impact of carbon and nitrogen catabolite repression in microorganisms. Microbiol Res 2021; 251:126831. [PMID: 34325194 DOI: 10.1016/j.micres.2021.126831] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 07/15/2021] [Accepted: 07/21/2021] [Indexed: 02/06/2023]
Abstract
Organisms have cellular machinery that is focused on optimum utilization of resources to maximize growth and survival depending on various environmental and developmental factors. Catabolite repression is a strategy utilized by various species of bacteria and fungi to accommodate changes in the environment such as the depletion of resources, or an abundance of less-favored nutrient sources. Catabolite repression allows for the rapid use of certain substrates like glucose over other carbon sources. Effective handling of carbon and nitrogen catabolite repression in microorganisms is crucial to outcompete others in nutrient limiting conditions. Investigations into genes and proteins linked to preferential uptake of different nutrients under various environmental conditions can aid in identifying regulatory mechanisms that are crucial for optimum growth and survival of microorganisms. The exact time and way bacteria and fungi switch their utilization of certain nutrients is of great interest for scientific, industrial, and clinical reasons. Catabolite repression is of great significance for industrial applications that rely on microorganisms for the generation of valuable bio-products. The impact catabolite repression has on virulence of pathogenic bacteria and fungi and disease progression in hosts makes it important area of interest in medical research for the prevention of diseases and developing new treatment strategies. Regulatory networks under catabolite repression exemplify the flexibility and the tremendous diversity that is found in microorganisms and provides an impetus for newer insights into these networks.
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Affiliation(s)
- Abhinav Nair
- Department of Biotechnology, School of Engineering and Applied Sciences, Bennett University, Greater Noida, Uttar Pradesh, India
| | - Saurabh Jyoti Sarma
- Department of Biotechnology, School of Engineering and Applied Sciences, Bennett University, Greater Noida, Uttar Pradesh, India.
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223
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Kim J, Silva-Rocha R, de Lorenzo V. Picking the right metaphors for addressing microbial systems: economic theory helps understanding biological complexity. Int Microbiol 2021; 24:507-519. [PMID: 34269947 DOI: 10.1007/s10123-021-00194-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 11/28/2022]
Abstract
Any descriptive language is necessarily metaphoric and interpretative. Two somewhat overlapping-but not identical-languages have been thoroughly employed in the last decade to address the issue of regulatory complexity in biological systems: the terminology of network theory and the jargon of electric circuitry. These approaches have found many formal equivalences between the layout of extant genetic circuits and the architecture of man-made counterparts. However, these languages still fail to describe accurately key features of biological objects, in particular the diversity of signal-transfer molecules and the diffusion that is inherent to any biochemical system. Furthermore, current formalisms associated with networks and circuits can hardly face the problem of multi-scale regulatory complexity-from single molecules to entire ecosystems. We argue that the language of economic theory might be instrumental not only to portray accurately many features of regulatory networks, but also to unveil aspects of the biological complexity problem that remain opaque to other types of analyses. The main perspective opened by the economic metaphor when applied to control of microbiological activities is a focus on metabolism, not gene selfishness, as the necessary background to make sense of regulatory phenomena. As an example, we analyse and reinterpret the widespread phenomenon of catabolite repression with the formal frame of the consumer's choice theory.
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Affiliation(s)
- Juhyun Kim
- Department of Chemical Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Rafael Silva-Rocha
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, 14049-900, Brazil
| | - Víctor de Lorenzo
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, 28049, Madrid, Spain.
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Bharwad K, Ghoghari N, Rajkumar S. Crc Regulates Succinate-Mediated Repression of Mineral Phosphate Solubilization in Acinetobacter sp. SK2 by Modulating Membrane Glucose Dehydrogenase. Front Microbiol 2021; 12:641119. [PMID: 34322095 PMCID: PMC8312277 DOI: 10.3389/fmicb.2021.641119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 04/30/2021] [Indexed: 11/13/2022] Open
Abstract
The plant growth-promoting Acinetobacter sp. SK2 isolated from Vigna radiata rhizosphere was characterized for mineral phosphate solubilization (MPS). To understand the contribution of the membrane glucose dehydrogenase (mGDH) and soluble glucose dehydrogenase (sGDH) in glucose oxidation and MPS, insertional inactivation of the corresponding genes was carried out. The disruption of mGDH encoding gene gdhA resulted in complete loss of mGDH activity, which confirmed its role in periplasmic glucose oxidation and gluconate-mediated MPS phenotype. The inactivation of sGDH encoding gene gdhB resulted in loss of sGDH activity, which did not alter the MPS or mGDH activity. Thus, it was also concluded that the sGDH was dispensable in gluconate-mediated MPS. Supplementation of succinate in glucose-containing medium suppressed the activity of mGDH (and sGDH) and therefore repressed the MPS phenotype. The catabolite repression control protein (Crc) of Pseudomonas was implicated in Acinetobacter sp. for a similar function in the presence of preferred and non-preferred carbon sources. To understand the regulatory linkage between Crc and genes for glucose oxidation, crc mutants were generated. The inactivation of crc resulted in increased activity of the mGDH in glucose + succinate-grown cells, indicating derepression. An increase in phosphate solubilization up to 44% in glucose + succinate-grown crc - compared with glucose-grown cells was recorded, which was significantly repressed in the wild-type strain under similar conditions. It is therefore proposed that in Acinetobacter sp. SK2, Crc is involved in the succinate-provoked repression of the MPS phenotype. The gene expression data indicated that Hfq may also have a regulating role in preferential utilization of carbon source by perhaps modulating Crc-Hfq functionality. V. radiata plants inoculated with the wild type improved both root and shoot length by 1.3 to 1.4-fold. However, crc - increased the root and shoot length by 1.6-fold, compared with the uninoculated controls. In mimicking the soil condition (in the presence of multiple carbon sources, e.g., succinate along with glucose), the crc - strain of Acinetobacter sp. SK2 performed better in supporting the growth of V. radiata in pot experiments.
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225
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Challenges and opportunities in biological funneling of heterogeneous and toxic substrates beyond lignin. Curr Opin Biotechnol 2021; 73:1-13. [PMID: 34242853 DOI: 10.1016/j.copbio.2021.06.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/02/2021] [Accepted: 06/07/2021] [Indexed: 12/12/2022]
Abstract
Significant developments in the understanding and manipulation of microbial metabolism have enabled the use of engineered biological systems toward a more sustainable energy and materials economy. While developments in metabolic engineering have primarily focused on the conversion of carbohydrates, substantial opportunities exist for using these same principles to extract value from more heterogeneous and toxic waste streams, such as those derived from lignin, biomass pyrolysis, or industrial waste. Funneling heterogeneous substrates from these streams toward valuable products, termed biological funneling, presents new challenges in balancing multiple catabolic pathways competing for shared cellular resources and engineering against perturbation from toxic substrates. Solutions to many of these challenges have been explored within the field of lignin valorization. This perspective aims to extend beyond lignin to highlight the challenges and discuss opportunities for use of biological systems to upgrade previously inaccessible waste streams.
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226
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Yu AO, Goldman EA, Brooks JT, Golomb BL, Yim IS, Gotcheva V, Angelov A, Kim EB, Marco ML. Strain diversity of plant-associated Lactiplantibacillus plantarum. Microb Biotechnol 2021; 14:1990-2008. [PMID: 34171185 PMCID: PMC8449665 DOI: 10.1111/1751-7915.13871] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 06/04/2021] [Accepted: 06/06/2021] [Indexed: 01/05/2023] Open
Abstract
Lactiplantibacillus plantarum (formerly Lactobacillus plantarum) is a lactic acid bacteria species found on plants that is essential for many plant food fermentations. In this study, we investigated the intraspecific phenotypic and genetic diversity of 13 L. plantarum strains isolated from different plant foods, including fermented olives and tomatoes, cactus fruit, teff injera, wheat boza and wheat sourdough starter. We found that strains from the same or similar plant food types frequently exhibited similar carbohydrate metabolism and stress tolerance responses. The isolates from acidic, brine‐containing ferments (olives and tomatoes) were more resistant to MRS adjusted to pH 3.5 or containing 4% w/v NaCl, than those recovered from grain fermentations. Strains from fermented olives grew robustly on raffinose as the sole carbon source and were better able to grow in the presence of ethanol (8% v/v or sequential exposure of 8% (v/v) and then 12% (v/v) ethanol) than most isolates from other plant types and the reference strain NCIMB8826R. Cell free culture supernatants from the olive‐associated strains were also more effective at inhibiting growth of an olive spoilage strain of Saccharomyces cerevisiae. Multi‐locus sequence typing and comparative genomics indicated that isolates from the same source tended to be genetically related. However, despite these similarities, other traits were highly variable between strains from the same plant source, including the capacity for biofilm formation and survival at pH 2 or 50°C. Genomic comparisons were unable to resolve strain differences, with the exception of the most phenotypically impaired and robust isolates, highlighting the importance of utilizing phenotypic studies to investigate differences between strains of L. plantarum. The findings show that L. plantarum is adapted for growth on specific plants or plant food types, but that intraspecific variation may be important for ecological fitness and strain coexistence within individual habitats.
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Affiliation(s)
- Annabelle O Yu
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
| | - Elissa A Goldman
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
| | - Jason T Brooks
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
| | - Benjamin L Golomb
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
| | - Irene S Yim
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
| | - Velitchka Gotcheva
- Department of Biotechnology, University of Food Technologies, Plovdiv, Bulgaria
| | - Angel Angelov
- Department of Biotechnology, University of Food Technologies, Plovdiv, Bulgaria
| | - Eun Bae Kim
- Department of Applied Animal Science, Kangwon National University, Chuncheon, Gangwon-Do, South Korea
| | - Maria L Marco
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
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227
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Covington BC, Xu F, Seyedsayamdost MR. A Natural Product Chemist's Guide to Unlocking Silent Biosynthetic Gene Clusters. Annu Rev Biochem 2021; 90:763-788. [PMID: 33848426 PMCID: PMC9148385 DOI: 10.1146/annurev-biochem-081420-102432] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microbial natural products have provided an important source of therapeutic leads and motivated research and innovation in diverse scientific disciplines. In recent years, it has become evident that bacteria harbor a large, hidden reservoir of potential natural products in the form of silent or cryptic biosynthetic gene clusters (BGCs). These can be readily identified in microbial genome sequences but do not give rise to detectable levels of a natural product. Herein, we provide a useful organizational framework for the various methods that have been implemented for interrogating silent BGCs. We divide all available approaches into four categories. The first three are endogenous strategies that utilize the native host in conjunction with classical genetics, chemical genetics, or different culture modalities. The last category comprises expression of the entire BGC in a heterologous host. For each category, we describe the rationale, recent applications, and associated advantages and limitations.
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Affiliation(s)
- Brett C Covington
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA; ,
| | - Fei Xu
- Institute of Pharmaceutical Biotechnology and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China;
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA; ,
- Department of Molecular Biology, Princeton University, New Jersey 08544, USA
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228
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Bailey SF, Alonso Morales LA, Kassen R. Effects of synonymous mutations beyond codon bias: The evidence for adaptive synonymous substitutions from microbial evolution experiments. Genome Biol Evol 2021; 13:6300525. [PMID: 34132772 PMCID: PMC8410137 DOI: 10.1093/gbe/evab141] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2021] [Indexed: 12/22/2022] Open
Abstract
Synonymous mutations are often assumed to be neutral with respect to fitness because they do not alter the encoded amino acid and so cannot be 'seen' by natural selection. Yet a growing body of evidence suggests that synonymous mutations can have fitness effects that drive adaptive evolution through their impacts on gene expression and protein folding. Here, we review what microbial experiments have taught us about the contribution of synonymous mutations to adaptation. A survey of site-directed mutagenesis experiments reveals the distributions of fitness effects for nonsynonymous and synonymous mutations are more similar, especially for beneficial mutations, than expected if all synonymous mutations were neutral, suggesting they should drive adaptive evolution more often than is typically observed. A review of experimental evolution studies where synonymous mutations have contributed to adaptation shows they can impact fitness through a range of mechanisms including the creation of illicit RNA polymerase binding sites impacting transcription and changes to mRNA folding stability that modulate translation. We suggest that clonal interference in evolving microbial populations may be the reason synonymous mutations play a smaller role in adaptive evolution than expected based on their observed fitness effects. We finish by discussing the impacts of falsely assuming synonymous mutations are neutral and discuss directions for future work exploring the role of synonymous mutations in adaptive evolution.
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Affiliation(s)
- Susan F Bailey
- Department of Biology, Clarkson University, Potsdam, NY 13699, USA
| | | | - Rees Kassen
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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229
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Ji G, Xu L, Lyu Q, Liu Y, Gong X, Li X, Yan Z. Poly-γ-glutamic acid production by simultaneous saccharification and fermentation using corn straw and its fertilizer synergistic effect evaluation. Bioprocess Biosyst Eng 2021; 44:2181-2191. [PMID: 34086133 DOI: 10.1007/s00449-021-02593-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/25/2021] [Indexed: 10/21/2022]
Abstract
Agricultural wastes rich in lignocellulosic biomass have been used in the production of poly-γ-glutamic acid (γ-PGA) through separate hydrolysis and fermentation (SHF), but this process is complicated and generates a lot of wastes. In order to find a simpler and greener way to produce γ-PGA using agricultural wastes, this study attempted to establish simultaneous saccharification and fermentation (SSF) with citric acid-pretreated corn straw. The possibility of Bacillus amyloliquefaciens JX-6 using corn straw as substrate to synthesize γ-PGA was validated, and the results showed that increasing the proportion of glucose in the substrate could improve the γ-PGA yield. Based on these preliminary results, the corn straw was pretreated using citric acid. Then, the liquid fraction (xylan-rich) was used for cultivation of seed culture, and the solid fraction (glucan-rich) was used as the substrate for SSF. In a 10-L fermenter, the maximum cumulative γ-PGA concentration in batch and fed-batch SSF were 5.08 ± 0.78 g/L and 10.78 ± 0.32 g/L, respectively. Moreover, the product from SSF without γ-PGA extraction was used as a fertilizer synergist, increasing the yield of pepper by 13.46% (P < 0.05). Our study greatly simplified the production steps of γ-PGA, and each step achieved zero emission as far as possible. The SSF process for γ-PGA production provided a simple and green way for lignocellulose biorefinery and sustainable cultivation in agriculture.
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Affiliation(s)
- Gaosheng Ji
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lishan Xu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, People's Republic of China
| | - Qingyang Lyu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, People's Republic of China
| | - Yang Liu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, People's Republic of China
| | - Xuefeng Gong
- Institute of Horticulture, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Xudong Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, People's Republic of China
| | - Zhiying Yan
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, People's Republic of China.
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230
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Matuszewska M, Maciąg T, Rajewska M, Wierzbicka A, Jafra S. The carbon source-dependent pattern of antimicrobial activity and gene expression in Pseudomonas donghuensis P482. Sci Rep 2021; 11:10994. [PMID: 34040089 PMCID: PMC8154892 DOI: 10.1038/s41598-021-90488-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/12/2021] [Indexed: 02/04/2023] Open
Abstract
Pseudomonas donghuensis P482 is a tomato rhizosphere isolate with the ability to inhibit growth of bacterial and fungal plant pathogens. Herein, we analysed the impact of the carbon source on the antibacterial activity of P482 and expression of the selected genes of three genomic regions in the P482 genome. These regions are involved in the synthesis of pyoverdine, 7-hydroxytropolone (7-HT) and an unknown compound ("cluster 17") and are responsible for the antimicrobial activity of P482. We showed that the P482 mutants, defective in these regions, show variations and contrasting patterns of growth inhibition of the target pathogen under given nutritional conditions (with glucose or glycerol as a carbon source). We also selected and validated the reference genes for gene expression studies in P. donghuensis P482. Amongst ten candidate genes, we found gyrB, rpoD and mrdA the most stably expressed. Using selected reference genes in RT-qPCR, we assessed the expression of the genes of interest under minimal medium conditions with glucose or glycerol as carbon sources. Glycerol was shown to negatively affect the expression of genes necessary for 7-HT synthesis. The significance of this finding in the light of the role of nutrient (carbon) availability in biological plant protection is discussed.
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Affiliation(s)
- Marta Matuszewska
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Tomasz Maciąg
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Magdalena Rajewska
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Aldona Wierzbicka
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Sylwia Jafra
- Laboratory of Plant Microbiology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland.
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231
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Bazurto JV, Nayak DD, Ticak T, Davlieva M, Lee JA, Hellenbrand CN, Lambert LB, Benski OJ, Quates CJ, Johnson JL, Patel JS, Ytreberg FM, Shamoo Y, Marx CJ. EfgA is a conserved formaldehyde sensor that leads to bacterial growth arrest in response to elevated formaldehyde. PLoS Biol 2021; 19:e3001208. [PMID: 34038406 PMCID: PMC8153426 DOI: 10.1371/journal.pbio.3001208] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/25/2021] [Indexed: 01/07/2023] Open
Abstract
Normal cellular processes give rise to toxic metabolites that cells must mitigate. Formaldehyde is a universal stressor and potent metabolic toxin that is generated in organisms from bacteria to humans. Methylotrophic bacteria such as Methylorubrum extorquens face an acute challenge due to their production of formaldehyde as an obligate central intermediate of single-carbon metabolism. Mechanisms to sense and respond to formaldehyde were speculated to exist in methylotrophs for decades but had never been discovered. Here, we identify a member of the DUF336 domain family, named efgA for enhanced formaldehyde growth, that plays an important role in endogenous formaldehyde stress response in M. extorquens PA1 and is found almost exclusively in methylotrophic taxa. Our experimental analyses reveal that EfgA is a formaldehyde sensor that rapidly arrests growth in response to elevated levels of formaldehyde. Heterologous expression of EfgA in Escherichia coli increases formaldehyde resistance, indicating that its interaction partners are widespread and conserved. EfgA represents the first example of a formaldehyde stress response system that does not involve enzymatic detoxification. Thus, EfgA comprises a unique stress response mechanism in bacteria, whereby a single protein directly senses elevated levels of a toxic intracellular metabolite and safeguards cells from potential damage.
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Affiliation(s)
- Jannell V. Bazurto
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, Minnesota, United States of America
- Microbial and Plant Genomics Institute, University of Minnesota, Twin Cities, Minnesota, United States of America
- Biotechnology Institute, University of Minnesota, Twin Cities, Minnesota, United States of America
- * E-mail: (JVB); (CJM)
| | - Dipti D. Nayak
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
| | - Tomislav Ticak
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
| | - Milya Davlieva
- Department of Biosciences, Rice University, Houston, Texas, United States of America
| | - Jessica A. Lee
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- Space Biosciences Research Branch, NASA Ames Research Center, Moffett Field, California, United States of America
| | - Chandler N. Hellenbrand
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, Minnesota, United States of America
| | - Leah B. Lambert
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Olivia J. Benski
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Caleb J. Quates
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, United States of America
| | - Jill L. Johnson
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
| | - Jagdish Suresh Patel
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, United States of America
| | - F. Marty Ytreberg
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- Department of Physics, University of Idaho, Moscow, Idaho, United States of America
| | - Yousif Shamoo
- Department of Biosciences, Rice University, Houston, Texas, United States of America
| | - Christopher J. Marx
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail: (JVB); (CJM)
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232
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Influence of the Alternative Sigma Factor RpoN on Global Gene Expression and Carbon Catabolism in Enterococcus faecalis V583. mBio 2021; 12:mBio.00380-21. [PMID: 34006651 PMCID: PMC8262876 DOI: 10.1128/mbio.00380-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The alternative sigma factor σ54 has been shown to regulate the expression of a wide array of virulence-associated genes, as well as central metabolism, in bacterial pathogens. In Gram-positive organisms, the σ54 is commonly associated with carbon metabolism. In this study, we show that the Enterococcus faecalis alternative sigma factor σ54 (RpoN) and its cognate enhancer binding protein MptR are essential for mannose utilization and are primary contributors to glucose uptake through the Mpt phosphotransferase system. To gain further insight into how RpoN contributes to global transcriptional changes, we performed microarray transcriptional analysis of strain V583 and an isogenic rpoN mutant grown in a chemically defined medium with glucose as the sole carbon source. Transcripts of 340 genes were differentially affected in the rpoN mutant; the predicted functions of these genes mainly related to nutrient acquisition. These differentially expressed genes included those with predicted catabolite-responsive element (cre) sites, consistent with loss of repression by the major carbon catabolite repressor CcpA. To determine if the inability to efficiently metabolize glucose/mannose affected infection outcome, we utilized two distinct infection models. We found that the rpoN mutant is significantly attenuated in both rabbit endocarditis and murine catheter-associated urinary tract infection (CAUTI). Here, we examined a ccpA mutant in the CAUTI model and showed that the absence of carbon catabolite control also significantly attenuates bacterial tissue burden in this model. Our data highlight the contribution of central carbon metabolism to growth of E. faecalis at various sites of infection.
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233
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Lee Y, Sathesh-Prabu C, Kwak GH, Bang I, Jung HW, Kim D, Lee SK. Enhanced production of nonanedioic acid from nonanoic acid by engineered Escherichia coli. Biotechnol J 2021; 17:e2000416. [PMID: 33964181 DOI: 10.1002/biot.202000416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 05/06/2021] [Accepted: 05/06/2021] [Indexed: 11/06/2022]
Abstract
In this study, whole-cell biotransformation was conducted to produce nonanedioic acid from nonanoic acid by expressing the alkane hydroxylating system (AlkBGT) from Pseudomonas putida GPo1 in Escherichia coli. Following adaptive laboratory evolution, an efficient E. coli mutant strain, designated as MRE, was successfully obtained, demonstrating the fastest growth (27-fold higher) on nonanoic acid as the sole carbon source compared to the wild-type strain. Additionally, the MRE strain was engineered to block nonanoic acid degradation by deleting fadE. The resulting strain exhibited a 12.8-fold increase in nonanedioic acid production compared to the wild-type strain. Six mutations in acrR, Pcrp , dppA, PfadD , e14, and yeaR were identified in the mutant MRE strain, which was characterized using genomic modifications and RNA-sequencing. The acquired mutations were found to be beneficial for rapid growth and nonanedioic acid production.
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Affiliation(s)
- Yongjoo Lee
- School of Energy & Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Chandran Sathesh-Prabu
- School of Energy & Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Geun Hwa Kwak
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Ina Bang
- School of Energy & Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Hyun Wook Jung
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Donghyuk Kim
- School of Energy & Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.,Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Sung Kuk Lee
- School of Energy & Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.,Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
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234
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Pacciani-Mori L, Suweis S, Maritan A, Giometto A. Constrained proteome allocation affects coexistence in models of competitive microbial communities. THE ISME JOURNAL 2021; 15:1458-1477. [PMID: 33432139 PMCID: PMC8115080 DOI: 10.1038/s41396-020-00863-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 11/19/2020] [Accepted: 11/30/2020] [Indexed: 02/08/2023]
Abstract
Microbial communities are ubiquitous and play crucial roles in many natural processes. Despite their importance for the environment, industry and human health, there are still many aspects of microbial community dynamics that we do not understand quantitatively. Recent experiments have shown that the structure and composition of microbial communities are intertwined with the metabolism of the species that inhabit them, suggesting that properties at the intracellular level such as the allocation of cellular proteomic resources must be taken into account when describing microbial communities with a population dynamics approach. In this work, we reconsider one of the theoretical frameworks most commonly used to model population dynamics in competitive ecosystems, MacArthur's consumer-resource model, in light of experimental evidence showing how proteome allocation affects microbial growth. This new framework allows us to describe community dynamics at an intermediate level of complexity between classical consumer-resource models and biochemical models of microbial metabolism, accounting for temporally-varying proteome allocation subject to constraints on growth and protein synthesis in the presence of multiple resources, while preserving analytical insight into the dynamics of the system. We first show with a simple experiment that proteome allocation needs to be accounted for to properly understand the dynamics of even the simplest microbial community, i.e. two bacterial strains competing for one common resource. Then, we study our consumer-proteome-resource model analytically and numerically to determine the conditions that allow multiple species to coexist in systems with arbitrary numbers of species and resources.
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Affiliation(s)
- Leonardo Pacciani-Mori
- grid.5608.b0000 0004 1757 3470Dipartimento di Fisica e Astronomia “Galileo Galilei”, Università degli Studi di Padova, Via Francesco Marzolo 8, 35131 Padova, Italy ,grid.38142.3c000000041936754XDepartment of Physics, Harvard University, 17 Oxford St, Cambridge, MA 02138 USA
| | - Samir Suweis
- grid.5608.b0000 0004 1757 3470Dipartimento di Fisica e Astronomia “Galileo Galilei”, Università degli Studi di Padova, Via Francesco Marzolo 8, 35131 Padova, Italy
| | - Amos Maritan
- grid.5608.b0000 0004 1757 3470Dipartimento di Fisica e Astronomia “Galileo Galilei”, Università degli Studi di Padova, Via Francesco Marzolo 8, 35131 Padova, Italy
| | - Andrea Giometto
- grid.5386.8000000041936877XSchool of Civil and Environmental Engineering, Cornell University, 220 Hollister Dr, Ithaca, NY 14853 USA
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235
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Gabriel A, Costa S, Henriques I, Lopes I. Effects of Long-Term Exposure to Increased Salinity on the Amphibian Skin Bacterium Erwinia toletana. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2021; 80:779-788. [PMID: 33877369 DOI: 10.1007/s00244-021-00845-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
Amphibian's skin bacterial community may help them to cope with several types of environmental perturbations, including osmotic stress caused by increased salinity. This work assessed whether an amphibian skin bacterium could increase its tolerance to NaCl after a long-term exposure to this salt. A strain of Erwinia toletana, isolated from the skin of Pelophylax perezi, was exposed to two salinity scenarios (with 18 g/L of NaCl): (1) long-term exposure (for 46 days; Et-NaCl), and (2) long-term exposure followed by a recovery period (exposure for 30 days to NaCl and then to LB medium for 16 days; Et-R). After exposure, the sensitivity of E. toletana clonal populations to NaCl was assessed by exposing them to 6 NaCl concentrations (LB medium spiked with NaCl) plus a control (LB medium). Genotypic alterations were assessed by PCR-based molecular typing method (BOX-PCR). The results showed that tolerance of E. toletana to NaCl slightly increased after the long-term exposure, EC50 for growth were: 22.5 g/L (8.64-36.4) for Et-LB; 30.3 g/L (23.2-37.4) for Et-NaCl; and 26.1 g/L (19.332.9) for Et-R. Differences in metabolic activity were observed between Et-LB and Et-R and between Et-NaCl and Et-R, suggesting the use of different substrates by this bacterium when exposed to salinized environments. NaCl-induced genotypic alterations were not detected. This work suggests that E. toletana exposed to low levels of salinity, activate different metabolic pathways to cope with osmotic stress. These findings may be further explored to be used in bioaugmentation procedures through the supplementation with this bacterium of the skin microbiome of natural populations of amphibians exposed to salinization.
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Affiliation(s)
- Antonieta Gabriel
- Department of Biology, CESAM, University of Aveiro, Campus Universitario de Santiago, Aveiro, Portugal.
| | - Sara Costa
- Department of Biology, CESAM, University of Aveiro, Campus Universitario de Santiago, Aveiro, Portugal
| | - Isabel Henriques
- Department of Life Sciences, CESAM, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - Isabel Lopes
- Department of Biology, CESAM, University of Aveiro, Campus Universitario de Santiago, Aveiro, Portugal
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236
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Tsevelkhoroloo M, Shim SH, Lee CR, Hong SK, Hong YS. LacI-Family Transcriptional Regulator DagR Acts as a Repressor of the Agarolytic Pathway Genes in Streptomyces coelicolor A3(2). Front Microbiol 2021; 12:658657. [PMID: 33889146 PMCID: PMC8055832 DOI: 10.3389/fmicb.2021.658657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/08/2021] [Indexed: 11/15/2022] Open
Abstract
Actinobacteria utilize various polysaccharides in the soil as carbon source by degrading them via extracellular hydrolytic enzymes. Agarose, a marine algal polysaccharide composed of D-galactose and 3,6-anhydro-L-galactose (AHG), is one of the carbon sources used by S. coelicolor A3(2). However, little is known about agar hydrolysis in S. coelicolor A3(2), except that the regulation of agar hydrolysis metabolism is strongly inhibited by glucose as in the catabolic pathways of other polysaccharides. In this study, we elucidated the role of DagR in regulating the expression of three agarase genes (dagA, dagB, and dagC) in S. coelicolor A3(2) by developing a dagR-deletion mutant (Δsco3485). We observed that the Δsco3485 mutant had increased mRNA level of the agarolytic pathway genes and 1.3-folds higher agarase production than the wild type strain, indicating that the dagR gene encodes a cluster-suited repressor. Electrophoretic mobility shift assay revealed that DagR bound to the upstream regions of the three agarase genes. DNase 1 footprinting analysis demonstrated that a palindromic sequence present in the upstream region of the three agarase genes was essential for DagR-binding. Uniquely, the DNA-binding activity of DagR was inhibited by AHG, one of the final degradation products of agarose. AHG-induced agarase production was not observed in the Δsco3485 mutant, as opposed to that in the wild type strain. Therefore, DagR acts as a repressor that binds to the promoter region of the agarase genes, inhibits gene expression at the transcriptional level, and is derepressed by AHG. This is the first report on the regulation of gene expression regarding agar metabolism in S. coelicolor A3(2).
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Affiliation(s)
- Maral Tsevelkhoroloo
- Department of Bioscience and Bioinformatics, Myong-Ji University, Yongin-si, South Korea
| | - So Heon Shim
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju-si, South Korea
| | - Chang-Ro Lee
- Department of Bioscience and Bioinformatics, Myong-Ji University, Yongin-si, South Korea
| | - Soon-Kwang Hong
- Department of Bioscience and Bioinformatics, Myong-Ji University, Yongin-si, South Korea
| | - Young-Soo Hong
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju-si, South Korea
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237
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Estrela S, Sanchez-Gorostiaga A, Vila JCC, Sanchez A. Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments. eLife 2021; 10:e65948. [PMID: 33877964 PMCID: PMC8057819 DOI: 10.7554/elife.65948] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 04/02/2021] [Indexed: 12/12/2022] Open
Abstract
A major open question in microbial community ecology is whether we can predict how the components of a diet collectively determine the taxonomic composition of microbial communities. Motivated by this challenge, we investigate whether communities assembled in pairs of nutrients can be predicted from those assembled in every single nutrient alone. We find that although the null, naturally additive model generally predicts well the family-level community composition, there exist systematic deviations from the additive predictions that reflect generic patterns of nutrient dominance at the family level. Pairs of more-similar nutrients (e.g. two sugars) are on average more additive than pairs of more dissimilar nutrients (one sugar-one organic acid). Furthermore, sugar-acid communities are generally more similar to the sugar than the acid community, which may be explained by family-level asymmetries in nutrient benefits. Overall, our results suggest that regularities in how nutrients interact may help predict community responses to dietary changes.
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Affiliation(s)
- Sylvie Estrela
- Department of Ecology & Evolutionary Biology and Microbial Sciences Institute, Yale UniversityNew HavenUnited States
| | - Alicia Sanchez-Gorostiaga
- Department of Ecology & Evolutionary Biology and Microbial Sciences Institute, Yale UniversityNew HavenUnited States
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, CantoblancoMadridSpain
| | - Jean CC Vila
- Department of Ecology & Evolutionary Biology and Microbial Sciences Institute, Yale UniversityNew HavenUnited States
| | - Alvaro Sanchez
- Department of Ecology & Evolutionary Biology and Microbial Sciences Institute, Yale UniversityNew HavenUnited States
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238
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Wilhelm C, Surendar J, Karagiannis F. Enemy or ally? Fasting as an essential regulator of immune responses. Trends Immunol 2021; 42:389-400. [PMID: 33865714 DOI: 10.1016/j.it.2021.03.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 12/11/2022]
Abstract
Nutrition is essential for supplying an organism with sufficient energy to maintain its bodily functions. Apart from serving as an energy supply, the immunomodulatory effects of diet are emerging as a central aspect of human health. The latest evidence suggests that dietary restriction may play an important regulatory role by influencing the activation and effector functions of immune cells. However, depending on the context, nutrient restriction may have both pathogenic and beneficial effects. Here, we discuss the diverse roles of fasting programs, including ketogenesis in infection and chronic inflammation, aiming to clarify their detrimental and/or beneficial effects. Understanding these differences may help identify conditions under which dietary interventions might serve as putative effective approaches to treat various diseases.
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Affiliation(s)
- Christoph Wilhelm
- Immunopathology Unit, Institute of Clinical Chemistry and Clinical Pharmacology, Medical Faculty, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany.
| | - Jayagopi Surendar
- Immunopathology Unit, Institute of Clinical Chemistry and Clinical Pharmacology, Medical Faculty, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany
| | - Fotios Karagiannis
- Immunopathology Unit, Institute of Clinical Chemistry and Clinical Pharmacology, Medical Faculty, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany
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239
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Inactivation of the Pta-AckA pathway impairs fitness of Bacillus anthracis during overflow metabolism. J Bacteriol 2021; 203:JB.00660-20. [PMID: 33593944 PMCID: PMC8092162 DOI: 10.1128/jb.00660-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Under conditions of glucose excess, aerobically growing bacteria predominantly direct carbon flux towards acetate fermentation, a phenomenon known as overflow metabolism or the bacterial 'Crabtree effect'. Numerous studies of the major acetate-generating pathway, the Pta-AckA, revealed its important role in bacterial fitness through the control of central metabolism to sustain balanced growth and cellular homeostasis. In this work, we highlight the contribution of the Pta-AckA pathway to fitness of the spore-forming bacterium, Bacillus anthracis We demonstrate that disruption of the Pta-AckA pathway causes a drastic growth reduction in the mutants and alters the metabolic and energy status of the cells. Our results revealed that inactivation of the Pta-AckA pathway increases the glucose consumption rate, affects intracellular ATP, NAD+ and NADH levels and leads to a metabolic block at the pyruvate and acetyl-CoA nodes. Consequently, accumulation of intracellular acetyl-CoA and pyruvate forces bacteria to direct carbon into the TCA and/or glyoxylate cycles as well as fatty acid and poly(3-hydroxybutyrate) (PHB) biosynthesis pathways. Notably, the presence of phosphate butyryltransferase in B. anthracis partially compensates for the loss of phosphotransacetylase activity. Furthermore, overexpression of the ptb gene not only eliminates the negative impact of the pta mutation on B. anthracis fitness, but also restores normal growth in the pta mutant of the non-butyrate-producing bacterium, Staphylococcus aureus Taken together, the results of this study demonstrate the importance of the Pta-AckA pathway for B. anthracis fitness by revealing its critical contribution to the maintenance of metabolic homeostasis during aerobic growth under conditions of carbon overflow.IMPORTANCE B. anthracis, the etiologic agent of anthrax, is a highly pathogenic, spore-forming bacterium that causes acute, life-threatening disease in both humans and livestock. A greater understanding of the metabolic determinants governing fitness of B. anthracis is essential for the development of successful therapeutic and vaccination strategies aimed at lessening the potential impact of this important biodefense pathogen. This study is the first to demonstrate the vital role of the Pta-AckA pathway in preserving energy and metabolic homeostasis in B. anthracis under conditions of carbon overflow, therefore, highlighting this pathway as a potential therapeutic target for drug discovery. Overall, the results of this study provide important insight into understanding the metabolic processes and requirements driving rapid B. anthracis proliferation during vegetative growth.
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240
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Gevorgyan H, Khalatyan S, Vassilian A, Trchounian K. The role of Escherichia coli FhlA transcriptional activator in generation of proton motive force and F O F 1 -ATPase activity at pH 7.5. IUBMB Life 2021; 73:883-892. [PMID: 33773019 DOI: 10.1002/iub.2470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/08/2021] [Accepted: 03/19/2021] [Indexed: 12/29/2022]
Abstract
Escherichia coli is able to utilize the mixture of carbon sources and produce molecular hydrogen (H2 ) via formate hydrogen lyase (FHL) complexes. In current work role of transcriptional activator of formate regulon FhlA in generation of fermentation end products and proton motive force, N'N'-dicyclohexylcarbodiimide (DCCD)-sensitive ATPase activity at 20 and 72 hr growth during utilization of mixture of glucose, glycerol, and formate were investigated. It was shown that in fhlA mutant specific growth rate was ~1.5 fold lower compared to wt, while addition of DCCD abolished the growth in fhlA but not in wt. Formate was not utilized in fhlA mutant but wt cells simultaneously utilized formate with glucose. Glycerol utilization started earlier (from 2 hr) in fhlA than in wt. The DCCD-sensitive ATPase activity in wt cells membrane vesicles increased ~2 fold at 72 hr and was decreased 70% in fhlA. Addition of formate in the assays increased proton ATPase activity in wt and mutant strain. FhlA absence mainly affected the ΔpH but not ΔΨ component of Δp in the cells grown at 72 hr but not in 24 hr. The Δp in wt cells decreased from 24 to 72 hr of growth ~40 mV while in fhlA mutant it was stable. Taken together, it is suggested that FhlA regulates the concentration of fermentation end products and via influencing FO F1 -ATPase activity contributes to the proton motive force generation.
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Affiliation(s)
- Heghine Gevorgyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, Yerevan, Armenia.,Faculty of Biology, Scientific-Research Institute of Biology, Yerevan State University, Yerevan, Armenia.,Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, Yerevan, Armenia
| | - Satenik Khalatyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, Yerevan, Armenia.,Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, Yerevan, Armenia.,Laboratory of Neuroscience, Yerevan State Medical University, Yerevan, Armenia
| | - Anait Vassilian
- Department of Ecology and Nature Protection, Faculty of Biology, Yerevan State University, Yerevan, Armenia
| | - Karen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, Yerevan, Armenia.,Faculty of Biology, Scientific-Research Institute of Biology, Yerevan State University, Yerevan, Armenia.,Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, Yerevan, Armenia
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241
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Xiao F, Li Y, Zhang Y, Wang H, Zhang L, Ding Z, Gu Z, Xu S, Shi G. A new CcpA binding site plays a bidirectional role in carbon catabolism in Bacillus licheniformis. iScience 2021; 24:102400. [PMID: 33997685 PMCID: PMC8091064 DOI: 10.1016/j.isci.2021.102400] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/06/2021] [Accepted: 04/05/2021] [Indexed: 11/17/2022] Open
Abstract
Bacillus licheniformis is widely used to produce various valuable products, such as food enzymes, industrial chemicals, and biocides. The carbon catabolite regulation process in the utilization of raw materials is crucial to maximizing the efficiency of this microbial cell factory. The current understanding of the molecular mechanism of this regulation is based on limited motif patterns in protein-DNA recognition, where the typical catabolite-responsive element (CRE) motif is "TGWNANCGNTNWCA". Here, CRETre is identified and characterized as a new CRE. It consists of two palindrome arms of 6 nucleotides (AGCTTT/AAAGCT) and an intermediate spacer. CRETre is involved in bidirectional regulation in a glucose stress environment. When AGCTTT appears in the 5' end, the regulatory element exhibits a carbon catabolite activation effect, while AAAGCT in the 5' end corresponds to carbon catabolite repression. Further investigation indicated a wide occurrence of CRETre in the genome of B. licheniformis.
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Affiliation(s)
- Fengxu Xiao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Youran Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Yupeng Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Hanrong Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Liang Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Zhongyang Ding
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Zhenghua Gu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Sha Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Guiyang Shi
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, People's Republic of China.,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
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242
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Bacterial-induced pH shifts link individual cell physiology to macroscale collective behavior. Proc Natl Acad Sci U S A 2021; 118:2014346118. [PMID: 33795512 DOI: 10.1073/pnas.2014346118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteria have evolved a diverse array of signaling pathways that enable them to quickly respond to environmental changes. Understanding how these pathways reflect environmental conditions and produce an orchestrated response is an ongoing challenge. Herein, we present a role for collective modifications of environmental pH carried out by microbial colonies living on a surface. We show that by collectively adjusting the local pH value, Paenibacillus spp., specifically, regulate their swarming motility. Moreover, we show that such pH-dependent regulation can converge with the carbon repression pathway to down-regulate flagellin expression and inhibit swarming in the presence of glucose. Interestingly, our results demonstrate that the observed glucose-dependent swarming repression is not mediated by the glucose molecule per se, as commonly thought to occur in carbon repression pathways, but rather is governed by a decrease in pH due to glucose metabolism. In fact, modification of the environmental pH by neighboring bacterial species could override this glucose-dependent repression and induce swarming of Paenibacillus spp. away from a glucose-rich area. Our results suggest that bacteria can use local pH modulations to reflect nutrient availability and link individual bacterial physiology to macroscale collective behavior.
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243
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Zhang A, Sun L, Bai Y, Yu H, McArthur JB, Chen X, Atsumi S. Microbial production of human milk oligosaccharide lactodifucotetraose. Metab Eng 2021; 66:12-20. [PMID: 33812022 DOI: 10.1016/j.ymben.2021.03.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/04/2021] [Accepted: 03/25/2021] [Indexed: 12/17/2022]
Abstract
Human milk oligosaccharides (HMOs) are potent bioactive compounds that modulate neonatal health and are of interest for development as potential drug treatments for adult diseases. The potential of these molecules, their limited access from natural sources, and difficulty in large-scale isolation of individual HMOs for studies and applications have motivated the development of chemical syntheses and in vitro enzymatic catalysis strategies. Whole cell biocatalysts are emerging as alternative self-regulating production platforms that have the potential to reduce the cost for enzymatic synthesis of HMOs. Whole cell biocatalysts for the production of short-chained, linear and small monofucosylated HMOs have been reported but those for fucosylated structures with higher complexity have not been explored. In this study, we established a strategy for producing a difucosylated HMO, lactodifucotetraose (LDFT), from lactose and L-fucose in Escherichia coli. We used two bacterial fucosyltransferases with narrow acceptor selectivity to drive the sequential fucosylation of lactose and intermediate 2'-fucosyllactose (2'-FL) to produce LDFT. Deletion of substrate degradation pathways that decoupled cellular growth from LDFT production, enhanced expression of native substrate transporters and modular induction of the genes in the LDFT biosynthetic pathway allowed complete conversion of lactose into LDFT and minor quantities of the side product 3-fucosyllactose (3-FL). Overall, 5.1 g/L of LDFT was produced from 3 g/L lactose and 3 g/L L-fucose in 24 h. Our results demonstrate promising applications of engineered microbial biosystems for the production of multi-fucosylated HMOs for biochemical studies.
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Affiliation(s)
- Angela Zhang
- Department of Chemistry, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Lei Sun
- Department of Chemistry, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA; School of Biotechnology, Jiangnan University, Wuxi, 214122, PR China
| | - Yuanyuan Bai
- Department of Chemistry, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Hai Yu
- Department of Chemistry, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA
| | - John B McArthur
- Department of Chemistry, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Xi Chen
- Department of Chemistry, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Shota Atsumi
- Department of Chemistry, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA.
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244
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Horne CR, Venugopal H, Panjikar S, Wood DM, Henrickson A, Brookes E, North RA, Murphy JM, Friemann R, Griffin MDW, Ramm G, Demeler B, Dobson RCJ. Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism. Nat Commun 2021; 12:1988. [PMID: 33790291 PMCID: PMC8012715 DOI: 10.1038/s41467-021-22253-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 03/03/2021] [Indexed: 12/20/2022] Open
Abstract
Bacteria respond to environmental changes by inducing transcription of some genes and repressing others. Sialic acids, which coat human cell surfaces, are a nutrient source for pathogenic and commensal bacteria. The Escherichia coli GntR-type transcriptional repressor, NanR, regulates sialic acid metabolism, but the mechanism is unclear. Here, we demonstrate that three NanR dimers bind a (GGTATA)3-repeat operator cooperatively and with high affinity. Single-particle cryo-electron microscopy structures reveal the DNA-binding domain is reorganized to engage DNA, while three dimers assemble in close proximity across the (GGTATA)3-repeat operator. Such an interaction allows cooperative protein-protein interactions between NanR dimers via their N-terminal extensions. The effector, N-acetylneuraminate, binds NanR and attenuates the NanR-DNA interaction. The crystal structure of NanR in complex with N-acetylneuraminate reveals a domain rearrangement upon N-acetylneuraminate binding to lock NanR in a conformation that weakens DNA binding. Our data provide a molecular basis for the regulation of bacterial sialic acid metabolism. The GntR superfamily is one of the largest families of transcription factors in prokaryotes. Here the authors combine biophysical analysis and structural biology to dissect the mechanism by which NanR — a GntR-family regulator — binds to its promoter to repress the transcription of genes necessary for sialic acid metabolism.
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Affiliation(s)
- Christopher R Horne
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Hariprasad Venugopal
- Clive and Vera Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, VIC, Australia
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, Clayton, VIC, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - David M Wood
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Amy Henrickson
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada
| | - Emre Brookes
- Department of Chemistry, University of Montana, Missoula, MT, USA
| | - Rachel A North
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Rosmarie Friemann
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Michael D W Griffin
- Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia
| | - Georg Ramm
- Clive and Vera Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, VIC, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada.,Department of Chemistry, University of Montana, Missoula, MT, USA
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand. .,Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia.
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245
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Matilla MA, Ortega Á, Krell T. The role of solute binding proteins in signal transduction. Comput Struct Biotechnol J 2021; 19:1786-1805. [PMID: 33897981 PMCID: PMC8050422 DOI: 10.1016/j.csbj.2021.03.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
The solute binding proteins (SBPs) of prokaryotes are present in the extracytosolic space. Although their primary function is providing substrates to transporters, SBPs also stimulate different signaling proteins, including chemoreceptors, sensor kinases, diguanylate cyclases/phosphodiesterases and Ser/Thr kinases, thereby causing a wide range of responses. While relatively few such systems have been identified, several pieces of evidence suggest that SBP-mediated receptor activation is a widespread mechanism. (1) These systems have been identified in Gram-positive and Gram-negative bacteria and archaea. (2) There is a structural diversity in the receptor domains that bind SBPs. (3) SBPs belonging to thirteen different families interact with receptor ligand binding domains (LBDs). (4) For the two most abundant receptor LBD families, dCache and four-helix-bundle, there are different modes of interaction with SBPs. (5) SBP-stimulated receptors carry out many different functions. The advantage of SBP-mediated receptor stimulation is attributed to a strict control of SBP levels, which allows a precise adjustment of the systeḿs sensitivity. We have compiled information on the effect of ligands on the transcript/protein levels of their cognate SBPs. In 87 % of the cases analysed, ligands altered SBP expression levels. The nature of the regulatory effect depended on the ligand family. Whereas inorganic ligands typically downregulate SBP expression, an upregulation was observed in response to most sugars and organic acids. A major unknown is the role that SBPs play in signaling and in receptor stimulation. This review attempts to summarize what is known and to present new information to narrow this gap in knowledge.
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Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, Granada 18008, Spain
| | - Álvaro Ortega
- Department of Biochemistry and Molecular Biology 'B' and Immunology, Faculty of Chemistry, University of Murcia, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, Granada 18008, Spain
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246
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Sivaloganathan DM, Brynildsen MP. Pseudomonas aeruginosa prioritizes detoxification of hydrogen peroxide over nitric oxide. BMC Res Notes 2021; 14:120. [PMID: 33771209 PMCID: PMC7995768 DOI: 10.1186/s13104-021-05534-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 03/16/2021] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Bacteria are exposed to multiple concurrent antimicrobial stressors within phagosomes. Among the antimicrobials produced, hydrogen peroxide and nitric oxide are two of the most deleterious products. In a previous study, we discovered that when faced with both stressors simultaneously, Escherichia coli prioritized detoxification of hydrogen peroxide over nitric oxide. In this study, we investigated whether such a process was conserved in another bacterium, Pseudomonas aeruginosa. RESULTS P. aeruginosa prioritized hydrogen peroxide detoxification in a dose-dependent manner. Specifically, hydrogen peroxide detoxification was unperturbed by the presence of nitric oxide, whereas larger doses of hydrogen peroxide produced longer delays in nitric oxide detoxification. Computational modelling revealed that the rate of nitric oxide consumption in co-treated cultures was biphasic, with cells entering the second phase of detoxification only after hydrogen peroxide was eliminated from the culture.
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Affiliation(s)
| | - Mark P. Brynildsen
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ USA
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Neira JL, Cámara-Artigas A, Hernández-Cifre JG, Ortore MG. The Histidine Phosphocarrier Kinase/Phosphorylase from Bacillus Subtilis Is an Oligomer in Solution with a High Thermal Stability. Int J Mol Sci 2021; 22:3231. [PMID: 33810099 PMCID: PMC8004850 DOI: 10.3390/ijms22063231] [Citation(s) in RCA: 2] [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: 01/31/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 01/25/2023] Open
Abstract
The histidine phosphocarrier protein (HPr) kinase/phosphorylase (HPrK/P) modulates the phosphorylation state of the HPr protein, and it is involved in the use of carbon sources by Gram-positive bacteria. Its X-ray structure, as concluded from crystals of proteins from several species, is a hexamer; however, there are no studies about its conformational stability, and how its structure is modified by the pH. We have embarked on the conformational characterization of HPrK/P of Bacillus subtilis (bsHPrK/P) in solution by using several spectroscopic (namely, fluorescence and circular dichroism (CD)) and biophysical techniques (namely, small-angle X-ray-scattering (SAXS) and dynamic light-scattering (DLS)). bsHPrK/P was mainly a hexamer in solution at pH 7.0, in the presence of phosphate. The protein had a high conformational stability, with an apparent thermal denaturation midpoint of ~70 °C, at pH 7.0, as monitored by fluorescence and CD. The protein was very pH-sensitive, precipitated between pH 3.5 and 6.5; below pH 3.5, it had a molten-globule-like conformation; and it acquired a native-like structure in a narrow pH range (between pH 7.0 and 8.0). Guanidinium hydrochloride (GdmCl) denaturation occurred through an oligomeric intermediate. On the other hand, urea denaturation occurred as a single transition, in the range of concentrations between 1.8 and 18 µM, as detected by far-UV CD and fluorescence.
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Affiliation(s)
- José L. Neira
- IDIBE, Universidad Miguel Hernández, 03202 Alicante, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Ana Cámara-Artigas
- Departamento de Química y Física, Research Center CIAIMBITAL, Universidad de Almería- ceiA3, 04120 Almería, Spain;
| | - José Ginés Hernández-Cifre
- Departamento de Química Física, Facultad de Química, Campus de Espinardo, Universidad de Murcia, 30100 Murcia, Spain;
| | - María Grazia Ortore
- Dipartimento DiSVA, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy;
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Recent Development of Rapid Antimicrobial Susceptibility Testing Methods through Metabolic Profiling of Bacteria. Antibiotics (Basel) 2021; 10:antibiotics10030311. [PMID: 33803002 PMCID: PMC8002737 DOI: 10.3390/antibiotics10030311] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 11/17/2022] Open
Abstract
Due to the inappropriate use and overuse of antibiotics, the emergence and spread of antibiotic-resistant bacteria are increasing and have become a major threat to human health. A key factor in the treatment of bacterial infections and slowing down the emergence of antibiotic resistance is to perform antimicrobial susceptibility testing (AST) of infecting bacteria rapidly to prescribe appropriate drugs and reduce the use of broad-spectrum antibiotics. Current phenotypic AST methods based on the detection of bacterial growth are generally reliable but are too slow. There is an urgent need for new methods that can perform AST rapidly. Bacterial metabolism is a fast process, as bacterial cells double about every 20 to 30 min for fast-growing species. Moreover, bacterial metabolism has shown to be related to drug resistance, so a comparison of differences in microbial metabolic processes in the presence or absence of antimicrobials provides an alternative approach to traditional culture for faster AST. In this review, we summarize recent developments in rapid AST methods through metabolic profiling of bacteria under antibiotic treatment.
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249
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Lac Operon Boolean Models: Dynamical Robustness and Alternative Improvements. MATHEMATICS 2021. [DOI: 10.3390/math9060600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In Veliz-Cuba and Stigler 2011, Boolean models were proposed for the lac operon in Escherichia coli capable of reproducing the operon being OFF, ON and bistable for three (low, medium and high) and two (low and high) parameters, representing the concentration ranges of lactose and glucose, respectively. Of these 6 possible combinations of parameters, 5 produce results that match with the biological experiments of Ozbudak et al., 2004. In the remaining one, the models predict the operon being OFF while biological experiments show a bistable behavior. In this paper, we first explore the robustness of two such models in the sense of how much its attractors change against any deterministic update schedule. We prove mathematically that, in cases where there is no bistability, all the dynamics in both models lack limit cycles while, when bistability appears, one model presents 30% of its dynamics with limit cycles while the other only 23%. Secondly, we propose two alternative improvements consisting of biologically supported modifications; one in which both models match with Ozbudak et al., 2004 in all 6 combinations of parameters and, the other one, where we increase the number of parameters to 9, matching in all these cases with the biological experiments of Ozbudak et al., 2004.
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250
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Guo J, Hu X, Gao Z, Li G, Fu F, Shang X, Liang Z, Shan Y. Global transcriptomic response of Listeria monocytogenes exposed to Fingered Citron (Citrus medica L. var. sarcodactylis Swingle) essential oil. Food Res Int 2021; 143:110274. [PMID: 33992374 DOI: 10.1016/j.foodres.2021.110274] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/15/2020] [Accepted: 02/23/2021] [Indexed: 11/26/2022]
Abstract
Listeria monocytogenes, which could cause severe disease of listeriosis, is one of the most concerned foodborne pathogens worldwide. Citrus medica L. var. sarcodactylis Swingle (Fingered Citron) is one of the citrus species cultivated in south China. Here, we investigated the efficacy of Fingered Citron essential oil (FCEO) against L. monocytogenes and explored the response of L. monocytogenes in the presence of FCEO using genome-wide transcriptome analysis. FCEO exhibited strong anti-listeria activity and obvious alterations of cell morphology were observed by scanning electron microscopy and transmission electron microscopy. Moreover, GO analysis demonstrated many potential cell responses, including metabolic process, cellular process, single-organism process, cell part, membrane, catalytic activity, binding, and transporter activity. KEGG analysis suggests that L. monocytogenes respond and adapt by (1) increasing motility through the enhancement of flagella rotation; (2) promoting cell tumbles and re-orientating to escape from FCEO; (3) enhancing the uptake of carbohydrates from environment to gain more energy; (4) changing the uptake of several metallic cations, including iron, zinc, cobalt, and nickel. Our research contributes to the understanding of the adaptive responses of L. monocytogenes exposed to FCEO and provides novel insights for finding new targets of anti-listeria therapy.
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Affiliation(s)
- Jiajing Guo
- Hunan Agriculture Product Processing Institute, International Joint Lab on Fruits & Vegetables Processing, Quality and Safety, Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha 410125, Hunan Province, China; Longping Branch, Graduate School of Hunan University, Changsha 410125, Hunan Province, China
| | - Xiao Hu
- Hunan Agriculture Product Processing Institute, International Joint Lab on Fruits & Vegetables Processing, Quality and Safety, Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha 410125, Hunan Province, China; Longping Branch, Graduate School of Hunan University, Changsha 410125, Hunan Province, China
| | - Zhipeng Gao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, Hunan Province, China.
| | - Gaoyang Li
- Hunan Agriculture Product Processing Institute, International Joint Lab on Fruits & Vegetables Processing, Quality and Safety, Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha 410125, Hunan Province, China; Longping Branch, Graduate School of Hunan University, Changsha 410125, Hunan Province, China
| | - Fuhua Fu
- Hunan Agriculture Product Processing Institute, International Joint Lab on Fruits & Vegetables Processing, Quality and Safety, Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha 410125, Hunan Province, China; Longping Branch, Graduate School of Hunan University, Changsha 410125, Hunan Province, China
| | - Xuebo Shang
- Hunan Agriculture Product Processing Institute, International Joint Lab on Fruits & Vegetables Processing, Quality and Safety, Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha 410125, Hunan Province, China
| | - Zengenni Liang
- Hunan Agriculture Product Processing Institute, International Joint Lab on Fruits & Vegetables Processing, Quality and Safety, Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha 410125, Hunan Province, China
| | - Yang Shan
- Hunan Agriculture Product Processing Institute, International Joint Lab on Fruits & Vegetables Processing, Quality and Safety, Hunan Key Lab of Fruits & Vegetables Storage, Processing, Quality and Safety, Hunan Academy of Agricultural Sciences, Changsha 410125, Hunan Province, China; Longping Branch, Graduate School of Hunan University, Changsha 410125, Hunan Province, China.
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