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Müller WE, Schröder HC, Wang X. Inorganic Polyphosphates As Storage for and Generator of Metabolic Energy in the Extracellular Matrix. Chem Rev 2019; 119:12337-12374. [PMID: 31738523 PMCID: PMC6935868 DOI: 10.1021/acs.chemrev.9b00460] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Indexed: 12/14/2022]
Abstract
Inorganic polyphosphates (polyP) consist of linear chains of orthophosphate residues, linked by high-energy phosphoanhydride bonds. They are evolutionarily old biopolymers that are present from bacteria to man. No other molecule concentrates as much (bio)chemically usable energy as polyP. However, the function and metabolism of this long-neglected polymer are scarcely known, especially in higher eukaryotes. In recent years, interest in polyP experienced a renaissance, beginning with the discovery of polyP as phosphate source in bone mineralization. Later, two discoveries placed polyP into the focus of regenerative medicine applications. First, polyP shows morphogenetic activity, i.e., induces cell differentiation via gene induction, and, second, acts as an energy storage and donor in the extracellular space. Studies on acidocalcisomes and mitochondria provided first insights into the enzymatic basis of eukaryotic polyP formation. In addition, a concerted action of alkaline phosphatase and adenylate kinase proved crucial for ADP/ATP generation from polyP. PolyP added extracellularly to mammalian cells resulted in a 3-fold increase of ATP. The importance and mechanism of this phosphotransfer reaction for energy-consuming processes in the extracellular matrix are discussed. This review aims to give a critical overview about the formation and function of this unique polymer that is capable of storing (bio)chemically useful energy.
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Affiliation(s)
- Werner E.G. Müller
- ERC Advanced Investigator
Grant Research
Group at the Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Duesbergweg 6, D-55128 Mainz, Germany
| | - Heinz C. Schröder
- ERC Advanced Investigator
Grant Research
Group at the Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Duesbergweg 6, D-55128 Mainz, Germany
| | - Xiaohong Wang
- ERC Advanced Investigator
Grant Research
Group at the Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Duesbergweg 6, D-55128 Mainz, Germany
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Azimi L, Lari AR. Colistin-resistant Pseudomonas aeruginosa clinical strains with defective biofilm formation. GMS HYGIENE AND INFECTION CONTROL 2019; 14:Doc12. [PMID: 31728266 PMCID: PMC6838732 DOI: 10.3205/dgkh000328] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aim: Colistin is the only effective antibiotic in some cases of Pseudo monas aeruginosa resistance to all tested antibiotics, even carbapenem. On the other hand, biofilm formation is one of the antibiotic resistance mechanisms in this bacterium. The aim of this study was to examine biofilm formation in colistin-resistant P. aeruginosa for the first time. Method: Two groups of P. aeruginosa were included in this study: 1) colistin-resistant and 2) colistin-susceptible. Biofilm formation was determined in these groups using the micro-tube test well as PCR to detect the genes involved in biofilm formation (ppk and molA). The plasmids for colistin resistance, mcr-1 and mcr-2, were also determined. P. aeruginosa ATCC 27853 was used as a control for all tests. Results: Strong biofilm formation was observed only in colistin-susceptible strains, and ppk and modA were not detected in colistin-resistant strains. The control strain P. aeruginosa ATCC 27853 possesses ppk and modA and is categorized as a strong biofilm formation group. According to the results of this study, colistin resistance is associated with defective biofilm formation, as reported by other studies on Acinetobacter baumannii.
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Affiliation(s)
- Leila Azimi
- Pediatric Infections Research Center, Research Institute of Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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53
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Velmourougane K, Prasanna R, Supriya P, Ramakrishnan B, Thapa S, Saxena AK. Transcriptome profiling provides insights into regulatory factors involved in Trichoderma viride-Azotobacter chroococcum biofilm formation. Microbiol Res 2019; 227:126292. [PMID: 31421719 DOI: 10.1016/j.micres.2019.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/30/2019] [Accepted: 06/15/2019] [Indexed: 12/14/2022]
Abstract
Azotobacter chroococcum (Az) and Trichoderma viride (Tv) represent agriculturally important and beneficial plant growth promoting options which contribute towards nutrient management and biocontrol, respectively. When Az and Tv are co-cultured, they form a biofilm, which has proved promising as an inoculant in several crops; however, the basic aspects related to regulation of biofilm formation were not investigated. Therefore, whole transcriptome sequencing (Illumina NextSeq500) and gene expression analyses were undertaken, related to biofilm formation vis a vis Tv and Az growing individually. Significant changes in the transcriptome profiles of biofilm were recorded and validated through qPCR analyses. In-depth evaluation also identified several genes (phoA, phoB, glgP, alg8, sipW, purB, pssA, fadD) specifically involved in biofilm formation in Az, Tv and Tv-Az. Genes coding for RNA-dependent RNA polymerase, ABC transporters, translation elongation factor EF-1, molecular chaperones and double homeobox 4 were either up-regulated or down-regulated during biofilm formation. To our knowledge, this is the first report on the modulation of gene expression in an agriculturally beneficial association, as a biofilm. Our results provide insights into the regulatory factors involved during biofilm formation, which can help to improve the beneficial effects and develop more effective and promising plant- microbe associations.
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Affiliation(s)
| | - Radha Prasanna
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | - Puram Supriya
- Centre for Agricultural Bioinformatics, ICAR- Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Shobit Thapa
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kusmaur, PO Kaitholi, Mau Nath Bhanjan, Uttar Pradesh 275101, India
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54
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Matange N. Deorphanizing NUDIX hydrolases from Trypanosoma: tantalizing links with metabolic regulation and stress tolerance. Biosci Rep 2019; 39:BSR20191369. [PMID: 31160481 PMCID: PMC6616042 DOI: 10.1042/bsr20191369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/01/2019] [Accepted: 06/03/2019] [Indexed: 12/15/2022] Open
Abstract
An explosion of sequence information in the genomics era has thrown up thousands of protein sequences without functional assignment. Though our ability to predict function based on sequence alone is improving steadily, we still have a long way to go. Proteins with common evolutionary origins carry telling sequence signatures, which ought to reveal their biological roles. These sequence signatures have allowed us to classify proteins into families with similar structures, and possibly, functions. Yet, evolution is a perpetual tinkerer, and hence, sequence signatures alone have proved inadequate in understanding the physiological activities of proteins. One such enigmatic family of enzymes is the NUDIX ( nu cleoside di phosphate linked to a moiety X ) hydrolase family that has over 80000 members from all branches of the tree of life. Though MutT, the founding member of this family, was identified in 1954, we are only now beginning to understand the diversity of substrates and biological roles that these enzymes demonstrate. In a recent article by Cordeiro et al. in Bioscience Reports [Biosci. Rep. (2019)], two members of this protein family from the human pathogen Trypanosoma brucei were deorphanized as being polyphosphate hydrolases. The authors show that of the five NUDIX hydrolases coded by the T. brucei genomes, TbNH2 and TbNH4, show in vitro hydrolytic activity against inorganic polyphosphate. Through classical biochemistry and immunostaining microscopy, differences in their substrate specificities and sub-cellular localization were revealed. These new data provide a compelling direction to the study of Trypanosome stress biology as well as our understanding of the NUDIX enzyme family.
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Affiliation(s)
- Nishad Matange
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, India
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55
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Tiwari P, Gosain TP, Singh M, Sankhe GD, Arora G, Kidwai S, Agarwal S, Chugh S, Saini DK, Singh R. Inorganic polyphosphate accumulation suppresses the dormancy response and virulence in Mycobacterium tuberculosis. J Biol Chem 2019; 294:10819-10832. [PMID: 31113860 DOI: 10.1074/jbc.ra119.008370] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/07/2019] [Indexed: 11/06/2022] Open
Abstract
Stringent response pathways involving inorganic polyphosphate (PolyP) play an essential role in bacterial stress adaptation and virulence. The intracellular levels of PolyP are modulated by the activities of polyphosphate kinase-1 (PPK1), polyphosphate kinase-2 (PPK2), and exopolyphosphatases (PPXs). The genome of Mycobacterium tuberculosis encodes two functional PPXs, and simultaneous deletion of ppx1 and ppx2 results in a defect in biofilm formation. We demonstrate here that these PPXs cumulatively contribute to the ability of M. tuberculosis to survive in nutrient-limiting, low-oxygen growth conditions and also in macrophages. Characterization of single (Δppx2) and double knockout (dkppx) strains of M. tuberculosis indicated that PPX-mediated PolyP degradation is essential for establishing bacterial infection in guinea pigs. RNA-Seq-based transcriptional profiling revealed that relative to the parental strain, the expression levels of DosR regulon-regulated dormancy genes were significantly reduced in the dkppx mutant strain. In concordance, we also provide evidence that PolyP inhibits the autophosphorylation activities associated with DosT and DosS sensor kinases. The results in this study uncover that enzymes involved in PolyP homeostasis play a critical role in M. tuberculosis physiology and virulence and are attractive targets for developing more effective therapeutic interventions.
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Affiliation(s)
- Prabhakar Tiwari
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Haryana 121001, India and
| | - Tannu Priya Gosain
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Haryana 121001, India and
| | - Mamta Singh
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Haryana 121001, India and
| | | | - Garima Arora
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Haryana 121001, India and
| | - Saqib Kidwai
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Haryana 121001, India and
| | - Sakshi Agarwal
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Haryana 121001, India and
| | - Saurabh Chugh
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Haryana 121001, India and
| | - Deepak K Saini
- Centre for BioSystems Science and Engineering and; Department of Molecular Reproduction, Development, and Genetics, Biological Sciences Building, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Ramandeep Singh
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Haryana 121001, India and.
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Abstract
Polyphosphate (polyP), an extremely simple polyanion, has long been known to be involved in a variety of different cellular processes, ranging from stress resistance, biofilm formation, and virulence in bacteria to bone mineralization, blood clotting, and mammalian target of rapamycin (mTOR) signaling in mammalian organisms. Our laboratory recently discovered a completely unexpected role of polyP as a stabilizing scaffold for β-sheet-containing protein-folding intermediates. This realization led us to investigate the effects of polyP on amyloidogenic processes and the novel concept that polyP might play a role in neurodegenerative diseases. In this review, we will summarize recent results that show that polyP is a physiological modifier that accelerates amyloid fiber formation, alters fiber morphology, and protects cells against amyloid toxicity. We will review the current knowledge on the distribution, levels, and roles of polyP in the mammalian brain, and discuss potential mechanisms by which polyP might ameliorate amyloid toxicity.
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57
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A Stringent Analysis of Polyphosphate Dynamics in Escherichia coli. J Bacteriol 2019; 201:JB.00070-19. [PMID: 30782636 DOI: 10.1128/jb.00070-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
During stress, bacterial cells activate a conserved pathway called the stringent response that promotes survival. Polyphosphates are long chains of inorganic phosphates that modulate this response in diverse bacterial species. In this issue, Michael J. Gray provides an important correction to the model of how polyphosphate accumulation is regulated during the stringent response in Escherichia coli (M. J. Gray, J. Bacteriol, 201:e00664-18, 2019, https://doi.org/10.1128/JB.00664-18). With other recent publications, this study provides a revised framework for understanding how bacterial polyphosphate dynamics might be exploited in infection control and industrial applications.
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58
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Srisanga K, Suthapot P, Permsirivisarn P, Govitrapong P, Tungpradabkul S, Wongtrakoongate P. Polyphosphate kinase 1 of Burkholderia pseudomallei controls quorum sensing, RpoS and host cell invasion. J Proteomics 2019; 194:14-24. [DOI: 10.1016/j.jprot.2018.12.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 12/16/2018] [Accepted: 12/25/2018] [Indexed: 12/18/2022]
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59
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Suess PM, Tang Y, Gomer RH. The putative G protein-coupled receptor GrlD mediates extracellular polyphosphate sensing in Dictyostelium discoideum. Mol Biol Cell 2019; 30:1118-1128. [PMID: 30785840 PMCID: PMC6724513 DOI: 10.1091/mbc.e18-10-0686] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Five or more orthophosphates bound together by high-energy phosphoanhydride bonds are highly ubiquitous inorganic molecules called polyphosphate. Polyphosphate acts as a signaling molecule eliciting a number of responses in eukaryotic cells, but the mechanisms mediating these effects are poorly understood. Proliferating Dictyostelium discoideum cells accumulate extracellular polyphosphate. At extracellular concentrations similar to those observed in stationary phase cells, polyphosphate inhibits proteasome activity and proliferation, and induces aggregation. Here we identify GrlD as a putative G protein–coupled receptor that mediates binding of extracellular polyphosphate to the cell surface. Cells lacking GrlD do not respond to polyphosphate-induced proteasome inhibition, aggregation, or proliferation inhibition. Polyphosphate also elicits differential effects on cell-substratum adhesion and cytoskeletal F-actin levels based on nutrient availability, and these effects were also mediated by GrlD. Starving cells also accumulate extracellular polyphosphate. Starved cells treated with exopolyphosphatase failed to aggregate effectively, suggesting that polyphosphate also acts as a signaling molecule during starvation-induced development of Dictyostelium. Together, these results suggest that a eukaryotic cell uses a G protein–coupled receptor to mediate the sensing and response to extracellular polyphosphate.
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Affiliation(s)
- Patrick M Suess
- Department of Biology, Texas A&M University, College Station, TX 77843-3474
| | - Yu Tang
- Department of Biology, Texas A&M University, College Station, TX 77843-3474
| | - Richard H Gomer
- Department of Biology, Texas A&M University, College Station, TX 77843-3474
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60
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Abstract
Polyphosphate (polyP) consists of a linear arrangement of inorganic phosphates and defies its structural simplicity with an astounding number of different activities in the cell. Already well known for its ability to partake in phosphate, calcium, and energy metabolism, polyP recently gained a new functional dimension with the discovery that it serves as a stabilizing scaffold for protein-folding intermediates. In this review, we summarize and discuss the recent studies that have identified polyP not only as a potent protein-like chaperone that protects cells against stress-induced protein aggregation, but also as a robust modifier of amyloidogenic processes that shields neuronal cells from amyloid toxicity. We consider some of the most pressing questions in the field, the obstacles faced, and the potential avenues to take to provide a complete picture about the working mechanism and physiological relevance of this intriguing biopolymer.
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Affiliation(s)
- Lihan Xie
- From the Departments of Molecular, Cellular and Developmental Biology and
| | - Ursula Jakob
- From the Departments of Molecular, Cellular and Developmental Biology and
- Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1085
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61
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Gautam LK, Sharma P, Capalash N. Bacterial Polyphosphate Kinases Revisited: Role in Pathogenesis and Therapeutic Potential. Curr Drug Targets 2019; 20:292-301. [DOI: 10.2174/1389450119666180801120231] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/02/2018] [Accepted: 07/31/2018] [Indexed: 11/22/2022]
Abstract
Bacterial infections have always been an unrestrained challenge to the medical community due to the rise of multi-drug tolerant and resistant strains. Pioneering work on Escherichia coli polyphosphate kinase (PPK) by Arthur Kornberg has generated great interest in this polyphosphate (PolyP) synthesizing enzyme. PPK has wide distribution among pathogens and is involved in promoting pathogenesis, stress management and susceptibility to antibiotics. Further, the absence of a PPK orthologue in humans makes it a potential drug target. This review covers the functional and structural aspects of polyphosphate kinases in bacterial pathogens. A description of molecules being designed against PPKs has been provided, challenges associated with PPK inhibitor design are highlighted and the strategies to enable development of efficient drug against this enzyme have also been discussed.
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Affiliation(s)
- Lalit Kumar Gautam
- Department of Biotechnology, Panjab University, BMS Block-I, Sector- 25, Chandigarh, 160014, India
| | - Prince Sharma
- Department of Microbiology, Panjab University, BMS Block-I, Sector- 25, Chandigarh, 160014, India
| | - Neena Capalash
- Department of Biotechnology, Panjab University, BMS Block-I, Sector- 25, Chandigarh, 160014, India
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62
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Pokhrel A, Lingo JC, Wolschendorf F, Gray MJ. Assaying for Inorganic Polyphosphate in Bacteria. J Vis Exp 2019. [PMID: 30735204 DOI: 10.3791/58818] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Inorganic polyphosphate (polyP) is a biological polymer found in cells from all domains of life, and is required for virulence and stress response in many bacteria. There are a variety of methods for quantifying polyP in biological materials, many of which are either labor-intensive or insensitive, limiting their usefulness. We present here a streamlined method for polyP quantification in bacteria, using a silica membrane column extraction optimized for rapid processing of multiple samples, digestion of polyP with the polyP-specific exopolyphosphatase ScPPX, and detection of the resulting free phosphate with a sensitive ascorbic acid-based colorimetric assay. This procedure is straightforward, inexpensive, and allows reliable polyP quantification in diverse bacterial species. We present representative polyP quantification from the Gram-negative bacterium (Escherichia coli), the Gram-positive lactic acid bacterium (Lactobacillus reuteri), and the mycobacterial species (Mycobacterium smegmatis). We also include a simple protocol for nickel affinity purification of mg quantities of ScPPX, which is not currently commercially available.
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Affiliation(s)
- Arya Pokhrel
- Department of Microbiology, University of Alabama at Birmingham
| | - Jordan C Lingo
- Division of Infectious Diseases, University of Alabama at Birmingham
| | | | - Michael J Gray
- Department of Microbiology, University of Alabama at Birmingham;
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63
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Guo XW, Zhang Y, Li LL, Guan XY, Guo J, Wu DG, Chen YF, Xiao DG. Improved xylose tolerance and 2,3-butanediol production of Klebsiella pneumoniae by directed evolution of rpoD and the mechanisms revealed by transcriptomics. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:307. [PMID: 30455736 PMCID: PMC6225576 DOI: 10.1186/s13068-018-1312-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 11/01/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND The biological production of 2,3-butanediol from xylose-rich raw materials from Klebsiella pneumoniae is a low-cost process. RpoD, an encoding gene of the sigma factor, is the key element in global transcription machinery engineering and has been successfully used to improve the fermentation with Escherichia coli. However, whether it can regulate the tolerance in K. pneumoniae remains unclear. RESULTS In this study, the kpC mutant strain was constructed by altering the expression quantity and genotype of the rpoD gene, and this exhibited high xylose tolerance and 2,3-butanediol production. The xylose tolerance of kpC strain was increased from 75 to 125 g/L, and the yield of 2,3-butanediol increased by 228.5% compared with the parent strain kpG, reaching 38.6 g/L at 62 h. The RNA sequencing results showed an upregulated expression level of 500 genes and downregulated expression level of 174 genes in the kpC mutant strain. The pathway analysis further showed that the differentially expressed genes were mainly related to signal transduction, membrane transport, carbohydrate metabolism, and energy metabolism. The nine most-promising genes were selected based on transcriptome sequencing, and were evaluated for their effects on xylose tolerance. The overexpression of the tktA encoding transketolase, pntA encoding NAD(P) transhydrogenase subunit alpha, and nuoF encoding NADH dehydrogenase subunit F conferred increased xylose consumption and increased 2,3-butanediol production to K. pneumoniae. CONCLUSIONS These results suggest that the xylose tolerance and 2,3-butanediol production of K. pneumoniae can be greatly improved by the directed evolution of rpoD. By applying transcriptomic analysis, the upregulation of tktA, pntA, and nuoF that were coded are essential for the xylose consumption and 2,3-butanediol production. This study will provide reference for further research on improving the fermentation abilities by means of other organisms.
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Affiliation(s)
- Xue-Wu Guo
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin, 300547 China
- Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, Tianjin, 300547 China
| | - Yu Zhang
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin, 300547 China
- Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, Tianjin, 300547 China
| | - Lu-Lu Li
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin, 300547 China
- Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, Tianjin, 300547 China
| | - Xiang-Yu Guan
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin, 300547 China
- Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, Tianjin, 300547 China
| | - Jian Guo
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin, 300547 China
- Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, Tianjin, 300547 China
| | - De-Guang Wu
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin, 300547 China
- Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, Tianjin, 300457 China
| | - Ye-Fu Chen
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin, 300547 China
- Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, Tianjin, 300547 China
| | - Dong-Guang Xiao
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Industrial Microbiology Key Lab, College of Biotechnology of Tianjin University of Science and Technology, Tianjin, 300547 China
- Tianjin Food Safety & Low Carbon Manufacturing Collaborative Innovation Center, Tianjin, 300547 China
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Zhao Y, Guo L, Li J, Fang B, Huang X. Molecular epidemiology, antimicrobial susceptibility, and pulsed-field gel electrophoresis genotyping of Pseudomonas aeruginosa isolates from mink. CANADIAN JOURNAL OF VETERINARY RESEARCH = REVUE CANADIENNE DE RECHERCHE VETERINAIRE 2018; 82:256-263. [PMID: 30363376 PMCID: PMC6168023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/30/2018] [Indexed: 06/08/2023]
Abstract
Pseudomonas aeruginosa is an important animal pathogen and contributes to hemorrhagic pneumonia in mink. Between April 2011 and December 2016, samples of lung, liver, and spleen were collected from mink with this disease on 11 mink farms in 5 Chinese provinces. From these samples, we obtained 98 isolates of P. aeruginosa that belonged to 5 serotypes: G (n = 58), I (n = 15), C (n = 8), M (n = 5), and B (n = 2); 10 isolates were not typeable (10/98). More than 90% of the isolates formed biofilms, and 85% produced slime. All 98 isolates were resistant to 10 antibiotics (oxacillin, ampicillin, penicillin G, amoxicillin, ceftriaxone, cefazolin, cefaclor, tilmicosin, tildipirosin, and sulfonamide). However, almost all were susceptible to gentamicin, polymyxin B, and amikacin. We identified 56 unique genotypes by pulsed-field gel electrophoresis. These findings have revealed genetic diversity and high antimicrobial resistance in P. aeruginosa isolated from mink with hemorrhagic pneumonia and will facilitate the prevention and control of this disease.
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Affiliation(s)
- Yongda Zhao
- College of Veterinary Medicine, National Risk Assessment Laboratory for Antimicrobial Resistance of Microorganisms in Animals, South China Agricultural University, 483 WuShan Road, Tianhe District, Guangzhou 510642, China (Zhao, Li, Fang, Huang); Qingdao Yebio Biological Engineering Company Ltd., Qingdao, China (Guo)
| | - Lili Guo
- College of Veterinary Medicine, National Risk Assessment Laboratory for Antimicrobial Resistance of Microorganisms in Animals, South China Agricultural University, 483 WuShan Road, Tianhe District, Guangzhou 510642, China (Zhao, Li, Fang, Huang); Qingdao Yebio Biological Engineering Company Ltd., Qingdao, China (Guo)
| | - Jie Li
- College of Veterinary Medicine, National Risk Assessment Laboratory for Antimicrobial Resistance of Microorganisms in Animals, South China Agricultural University, 483 WuShan Road, Tianhe District, Guangzhou 510642, China (Zhao, Li, Fang, Huang); Qingdao Yebio Biological Engineering Company Ltd., Qingdao, China (Guo)
| | - Binghu Fang
- College of Veterinary Medicine, National Risk Assessment Laboratory for Antimicrobial Resistance of Microorganisms in Animals, South China Agricultural University, 483 WuShan Road, Tianhe District, Guangzhou 510642, China (Zhao, Li, Fang, Huang); Qingdao Yebio Biological Engineering Company Ltd., Qingdao, China (Guo)
| | - Xianhui Huang
- College of Veterinary Medicine, National Risk Assessment Laboratory for Antimicrobial Resistance of Microorganisms in Animals, South China Agricultural University, 483 WuShan Road, Tianhe District, Guangzhou 510642, China (Zhao, Li, Fang, Huang); Qingdao Yebio Biological Engineering Company Ltd., Qingdao, China (Guo)
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65
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Yoo NG, Dogra S, Meinen BA, Tse E, Haefliger J, Southworth DR, Gray MJ, Dahl JU, Jakob U. Polyphosphate Stabilizes Protein Unfolding Intermediates as Soluble Amyloid-like Oligomers. J Mol Biol 2018; 430:4195-4208. [PMID: 30130556 DOI: 10.1016/j.jmb.2018.08.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/06/2018] [Accepted: 08/14/2018] [Indexed: 02/03/2023]
Abstract
Inorganic polyphosphate (polyP) constitutes one of the most conserved and ubiquitous molecules in biology. Recent work in bacteria demonstrated that polyP increases oxidative stress resistance by preventing stress-induced protein aggregation and promotes biofilm formation by stimulating functional amyloid formation. To gain insights into these two seemingly contradictory functions of polyP, we investigated the effects of polyP on the folding model lactate dehydrogenase. We discovered that the presence of polyP during the thermal unfolding process stabilizes folding intermediates of lactate dehydrogenase as soluble micro-β-aggregates with amyloid-like properties. Size and heterogeneity of the oligomers formed in this process were dependent on the polyP chain length, with longer chains forming smaller, more homogenous complexes. This ability of polyP to stabilize thermally unfolded proteins even upon exposure to extreme temperatures appears to contribute to the observed resistance of uropathogenic Escherichia coli toward severe heat shock treatment. These results suggest that the working mechanism of polyP is the same for both soluble and amyloidogenic proteins, with the ultimate outcome likely being determined by a combination of polyP chain length and the client protein itself. They help to explain how polyP can simultaneously function as general stress-protective chaperone and instigator of amyloidogenic processes in vivo.
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Affiliation(s)
- Nicholas G Yoo
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N University Ave, Ann Arbor, MI 48109, United States; Biological Chemistry Department, University of Michigan, 830 N University Ave, Ann Arbor, MI 48109, United States
| | - Siddhant Dogra
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N University Ave, Ann Arbor, MI 48109, United States; Biological Chemistry Department, University of Michigan, 830 N University Ave, Ann Arbor, MI 48109, United States
| | - Ben A Meinen
- Howard Hughes Medical Institute, University of Michigan, 2256 Biological Sciences Science Building, 1105 North University Ave, Ann Arbor, MI 48109, United States
| | - Eric Tse
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94158, United States
| | - Janine Haefliger
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N University Ave, Ann Arbor, MI 48109, United States; Biological Chemistry Department, University of Michigan, 830 N University Ave, Ann Arbor, MI 48109, United States
| | - Daniel R Southworth
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, CA 94158, United States
| | - Michael J Gray
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N University Ave, Ann Arbor, MI 48109, United States; Biological Chemistry Department, University of Michigan, 830 N University Ave, Ann Arbor, MI 48109, United States
| | - Jan-Ulrik Dahl
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N University Ave, Ann Arbor, MI 48109, United States; Biological Chemistry Department, University of Michigan, 830 N University Ave, Ann Arbor, MI 48109, United States
| | - Ursula Jakob
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N University Ave, Ann Arbor, MI 48109, United States; Biological Chemistry Department, University of Michigan, 830 N University Ave, Ann Arbor, MI 48109, United States.
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66
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Genetic diversity and phenotypic plasticity of AHL-mediated Quorum sensing in environmental strains of Vibrio mediterranei. ISME JOURNAL 2018; 13:159-169. [PMID: 30116040 DOI: 10.1038/s41396-018-0260-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/12/2018] [Accepted: 07/24/2018] [Indexed: 01/28/2023]
Abstract
N-Acyl homoserine lactone (AHL)-mediated Quorum sensing (QS) is one of the most studied social behavior among Proteobacteria. However, despite the current knowledge on QS-associated phenotypes such as bioluminescence, biofilm formation, or pathogenesis, the characterization of environmental factors driving QS in realistic ecological settings remains scarce. We investigated the dynamics of AHL and AHL-producing Vibrio among 840 isolates collected fortnightly from the Salses-Leucate Mediterranean lagoon in spring and summer 2015 and 2016. Vibrio isolates were characterized by gyrB gene sequencing, Enterobacterial repetitive intergenic consensus polymerase chain reaction, and genome sequencing, and AHL production was investigated by a biosensors-based UHPLC-HRMS/MS approach. Our results revealed, for the first time, a succession of V. mediterranei isolates with different AHL production phenotypes over time and this dynamics was observed in a single genotype (average genomic nucleotide identity >99.9). A multivariate DistLM analysis revealed that 83.4% of the temporal variation of V. mediterranei QS phenotypes was explained by environmental variables. Overall, our results suggest that isolates of a single genotype are able to change their QS phenotypes in response to environmental conditions, highlighting the phenotypic plasticity of bacterial communication in the environment.
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67
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Kose SH, Grice K, Orsi WD, Ballal M, Coolen MJL. Metagenomics of pigmented and cholesterol gallstones: the putative role of bacteria. Sci Rep 2018; 8:11218. [PMID: 30046045 PMCID: PMC6060111 DOI: 10.1038/s41598-018-29571-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/13/2018] [Indexed: 01/10/2023] Open
Abstract
There is growing evidence for bacteria playing a role in the pathogenesis and formation of pigmented gallstones from humans. These studies mainly involved cultivation of gallstone-associated bacteria and 16S rRNA profiling, providing an indirect link between processes involved in gallstone formation by the bacteria in-situ. Here, we provide functional metagenomic evidence of a range of genes involved in bile stress response, biofilm formation, and anaerobic energy metabolism by Gram-negative Klebsiella in pigmented gallstones from a 76-year-old male patient. Klebsiella was also present in one cholesterol-type stone in a 30-year-old female patient who had additional cholesterol gallstones characterised by Gram-positive bacteria. Pigmented stones further revealed a predominance of genes involved in carbohydrate metabolism, whilst cholesterol stones indicated a profile dominanted by protein metabolism possibly reflecting known chemical differences between Gram-negative and Gram-positive biofilm matrices. Archaeal genes were not detected. Complementary carbon and hydrogen isotopic analyses of cholesterol within the patients’ stones revealed homogeneity, suggesting a common diet or cholesterol biosynthesis pathway that has little influence on microbial composition. This pilot study provides a framework to study microbial processes that play a potential role in gallstone formation across markedly different types of stones and patient backgrounds.
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Affiliation(s)
- S H Kose
- School of Molecular and Life Sciences, Curtin University, Perth, WA, 6102, Australia. .,WA-Organic and Isotope Geochemistry Centre, School of Earth and Planetary Science, Curtin University, Perth, WA, 6102, Australia.
| | - K Grice
- WA-Organic and Isotope Geochemistry Centre, School of Earth and Planetary Science, Curtin University, Perth, WA, 6102, Australia
| | - W D Orsi
- Department of Earth and Environmental Science, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, 80333, Munich, Germany.,GeoBio Centre LMU, Ludwig-Maximilians-Universität München, 80333, Munich, Germany
| | - M Ballal
- Fiona Stanley Hospital, 11 Robin Warren Dr, Murdoch, 6150, WA, Australia.,St John of God Murdoch Hospital, Barry Marshall Parade, Murdoch, 6150, WA, Australia
| | - M J L Coolen
- WA-Organic and Isotope Geochemistry Centre, School of Earth and Planetary Science, Curtin University, Perth, WA, 6102, Australia
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68
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Kang D, Kirienko NV. Interdependence between iron acquisition and biofilm formation in Pseudomonas aeruginosa. J Microbiol 2018; 56:449-457. [PMID: 29948830 DOI: 10.1007/s12275-018-8114-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 03/22/2018] [Accepted: 03/22/2018] [Indexed: 11/28/2022]
Abstract
Bacterial biofilms remain a persistent threat to human healthcare due to their role in the development of antimicrobial resistance. To combat multi-drug resistant pathogens, it is crucial to enhance our understanding of not only the regulation of biofilm formation, but also its contribution to bacterial virulence. Iron acquisition lies at the crux of these two subjects. In this review, we discuss the role of iron acquisition in biofilm formation and how hosts impede this mechanism to defend against pathogens. We also discuss recent findings that suggest that biofilm formation can also have the reciprocal effect, influencing siderophore production and iron sequestration.
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Affiliation(s)
- Donghoon Kang
- Department of Biosciences, Rice University, Houston, USA
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69
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Bentley-DeSousa A, Downey M. From underlying chemistry to therapeutic potential: open questions in the new field of lysine polyphosphorylation. Curr Genet 2018; 65:57-64. [PMID: 29881919 DOI: 10.1007/s00294-018-0854-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 06/01/2018] [Accepted: 06/04/2018] [Indexed: 12/14/2022]
Abstract
Polyphosphorylation is a newly described non-enzymatic post-translational modification wherein long chains of inorganic phosphates are attached to lysine residues. The first targets of polyphosphorylation identified were S. cerevisiae proteins Nsr1 and Top1. Building on this theme, we recently exploited functional genomics tools in yeast to identify 15 new targets, including a conserved network of nucleolar proteins implicated in ribosome biogenesis. We also described the polyphosphorylation of six human proteins, suggesting that this unique post-translational modification could be conserved throughout eukaryotes. The study of polyphosphorylation seems poised to uncover novel modes of protein regulation in pathways spanning diverse biological processes. In this review, we establish a framework for future work by outlining critical questions related to the biochemistry of polyphosphorylation, its therapeutic potential, and everything in between.
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Affiliation(s)
- Amanda Bentley-DeSousa
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, KIH 8M5, Canada
| | - Michael Downey
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada. .,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, KIH 8M5, Canada.
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70
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Bharudin I, Abu Bakar MF, Hashim NHF, Mat Isa MN, Alias H, Firdaus-Raih M, Md Illias R, Najimudin N, Mahadi NM, Abu Bakar FD, Abdul Murad AM. Unravelling the adaptation strategies employed by Glaciozyma antarctica PI12 on Antarctic sea ice. MARINE ENVIRONMENTAL RESEARCH 2018; 137:169-176. [PMID: 29598997 DOI: 10.1016/j.marenvres.2018.03.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/09/2018] [Accepted: 03/19/2018] [Indexed: 06/08/2023]
Abstract
Glaciozyma antarctica PI12, is a psychrophilic yeast isolated from Antarctic sea. In this work, Expressed Sequence Tags (EST) from cells exposed to three different temperatures; 15 °C, 0 °C and -12 °C were generated to identify genes associated with cold adaptation. A total of 5376 clones from each library were randomly picked and sequenced. Comparative analyses from the resulting ESTs in each condition identified several groups of genes required for cold adaptation. Additionally, 319 unique transcripts that encoded uncharacterised functions were identified in the -12 °C library and are currently unique to G. antarctica. Gene expression analysis using RT-qPCR revealed two of the unknown genes to be up-regulated at -12 °C compared to 0 °C and 15 °C. These findings further contribute to the collective knowledge into G. antarctica cold adaptation and as a resource for understanding the ecological and physiological tolerance of psychrophilic microbes in general.
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Affiliation(s)
- Izwan Bharudin
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia.
| | | | - Noor Haza Fazlin Hashim
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia
| | - Mohd Noor Mat Isa
- Malaysia Genome Institute, Jalan Bangi Lama, 43000, Kajang, Selangor, Malaysia
| | - Halimah Alias
- Malaysia Genome Institute, Jalan Bangi Lama, 43000, Kajang, Selangor, Malaysia
| | - Mohd Firdaus-Raih
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia; Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia
| | - Rosli Md Illias
- Department of Biosciences Engineering, Faculty of Chemical & Natural Resources Engineering, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Nazalan Najimudin
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Nor Muhammad Mahadi
- Malaysia Genome Institute, Jalan Bangi Lama, 43000, Kajang, Selangor, Malaysia
| | - Farah Diba Abu Bakar
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia
| | - Abdul Munir Abdul Murad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia
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71
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Bashatwah RM, Khanfar MA, Bardaweel SK. Discovery of potent polyphosphate kinase 1 (PPK1) inhibitors using structure-based exploration of PPK1Pharmacophoric space coupled with docking analyses. J Mol Recognit 2018; 31:e2726. [DOI: 10.1002/jmr.2726] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 04/03/2018] [Accepted: 04/13/2018] [Indexed: 01/30/2023]
Affiliation(s)
- Rasha M. Bashatwah
- Department of Pharmaceutical Sciences, School of Pharmacy; The University of Jordan; Amman Jordan
| | - Mohammad A. Khanfar
- Heinrich-Heine-Universitaet Duesseldorf; InstitutfuerPharmazeutische and MedizinischeChemie; Duesseldorf Germany
| | - Sanaa K. Bardaweel
- Department of Pharmaceutical Sciences, School of Pharmacy; The University of Jordan; Amman Jordan
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72
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Wang L, Yan J, Wise MJ, Liu Q, Asenso J, Huang Y, Dai S, Liu Z, Du Y, Tang D. Distribution Patterns of Polyphosphate Metabolism Pathway and Its Relationships With Bacterial Durability and Virulence. Front Microbiol 2018; 9:782. [PMID: 29755430 PMCID: PMC5932413 DOI: 10.3389/fmicb.2018.00782] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 04/06/2018] [Indexed: 12/15/2022] Open
Abstract
Inorganic polyphosphate (polyP) is a linear polymer of orthophosphate residues. It is reported to be present in all life forms. Experimental studies showed that polyP plays important roles in bacterial durability and virulence. Here we investigated the relationships of polyP with bacterial durability and virulence theoretically. Bacterial lifestyle, environmental persistence, virulence factors (VFs), and species evolution are all included in the analysis. The presence of seven genes involved in polyP metabolism (ppk1, ppk2, pap, surE, gppA, ppnK, and ppgK) and 2595 core VFs were verified in 944 bacterial reference proteomes for distribution patterns via HMMER. Proteome size and VFs were compared in terms of gain and loss of polyP pathway. Literature mining and phylogenetic analysis were recruited to support the study. Our analyzes revealed that the presence of polyP metabolism is positively correlated with bacterial proteome size and the number of virulence genes. A potential relationship of polyP in bacterial lifestyle and environmental durability is suggested. Evolutionary analysis shows that polyP genes are randomly lost along the phylogenetic tree. In sum, based on our theoretical analysis, we confirmed that bacteria with polyP metabolism are associated with high environmental durability and more VFs.
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Affiliation(s)
- Liang Wang
- Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, China
| | - Jiawei Yan
- Xuzhou Infectious Diseases Hospital, Xuzhou, China
| | - Michael J Wise
- School of Computer Science and Software Engineering, University of Western Australia, Perth, WA, Australia.,The Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Perth, WA, Australia
| | - Qinghua Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - James Asenso
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Yue Huang
- Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, China
| | - Shiyun Dai
- School of Anesthesiology, Xuzhou Medical University, Xuzhou, China
| | | | - Yan Du
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Daoquan Tang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China.,Center for Experimental Animals, Xuzhou Medical University, Xuzhou, China
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73
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Rudat AK, Pokhrel A, Green TJ, Gray MJ. Mutations in Escherichia coli Polyphosphate Kinase That Lead to Dramatically Increased In Vivo Polyphosphate Levels. J Bacteriol 2018; 200:e00697-17. [PMID: 29311274 PMCID: PMC5826030 DOI: 10.1128/jb.00697-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 12/20/2017] [Indexed: 11/20/2022] Open
Abstract
Bacteria synthesize inorganic polyphosphate (polyP) in response to a wide variety of stresses, and production of polyP is essential for stress response and survival in many important pathogens and bacteria used in biotechnological processes. However, surprisingly little is known about the molecular mechanisms that control polyP synthesis. We have therefore developed a novel genetic screen that specifically links growth of Escherichia coli to polyP synthesis, allowing us to isolate mutations leading to enhanced polyP production. Using this system, we have identified mutations in the polyP-synthesizing enzyme polyP kinase (PPK) that lead to dramatic increases in in vivo polyP synthesis but do not substantially affect the rate of polyP synthesis by PPK in vitro These mutations are distant from the PPK active site and found in interfaces between monomers of the PPK tetramer. We have also shown that high levels of polyP lead to intracellular magnesium starvation. Our results provide new insights into the control of bacterial polyP accumulation and suggest a simple, novel strategy for engineering bacteria with increased polyP contents.IMPORTANCE PolyP is an ancient, universally conserved biomolecule and is important for stress response, energy metabolism, and virulence in a remarkably broad range of microorganisms. PolyP accumulation by bacteria is also important in biotechnology applications. For example, it is critical to enhanced biological phosphate removal (EBPR) from wastewater. Understanding how bacteria control polyP synthesis is therefore of broad importance in both the fields of bacterial pathogenesis and biological engineering. Using Escherichia coli as a model organism, we have identified the first known mutations in polyP kinase that lead to increases in cellular polyP content.
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Affiliation(s)
- Amanda K Rudat
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Arya Pokhrel
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Todd J Green
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Michael J Gray
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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74
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A Screen for Candidate Targets of Lysine Polyphosphorylation Uncovers a Conserved Network Implicated in Ribosome Biogenesis. Cell Rep 2018; 22:3427-3439. [DOI: 10.1016/j.celrep.2018.02.104] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 01/12/2018] [Accepted: 02/27/2018] [Indexed: 11/22/2022] Open
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75
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Varas MA, Riquelme-Barrios S, Valenzuela C, Marcoleta AE, Berríos-Pastén C, Santiviago CA, Chávez FP. Inorganic Polyphosphate Is Essential for Salmonella Typhimurium Virulence and Survival in Dictyostelium discoideum. Front Cell Infect Microbiol 2018; 8:8. [PMID: 29441327 PMCID: PMC5797601 DOI: 10.3389/fcimb.2018.00008] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/09/2018] [Indexed: 01/26/2023] Open
Abstract
Inorganic polyphosphate (polyP) deficiency in enteric bacterial pathogens reduces their ability to invade and establish systemic infections in different hosts. For instance, inactivation of the polyP kinase gene (ppk) encoding the enzyme responsible for polyP biosynthesis reduces invasiveness and intracellular survival of Salmonella enterica serovar Typhimurium (S. Typhimurium) in epithelial cells and macrophages in vitro. In addition, the virulence in vivo of a S. Typhimurium Δppk mutant is significantly reduced in a murine infection model. In spite of these observations, the role played by polyP during the Salmonella-host interaction is not well understood. The social amoeba Dictyostelium discoideum has proven to be a useful model for studying relevant aspects of the host-pathogen interaction. In fact, many intracellular pathogens can survive within D. discoideum cells using molecular mechanisms also required to survive within macrophages. Recently, we established that S. Typhimurium is able to survive intracellularly in D. discoideum and identified relevant genes linked to virulence that are crucial for this process. The aim of this study was to determine the effect of a polyP deficiency in S. Typhimurium during its interaction with D. discoideum. To do this, we evaluated the intracellular survival of wild-type and Δppk strains of S. Typhimurium in D. discoideum and the ability of these strains to delay the social development of the amoeba. In contrast to the wild-type strain, the Δppk mutant was unable to survive intracellularly in D. discoideum and enabled the social development of the amoeba. Both phenotypes were complemented using a plasmid carrying a copy of the ppk gene. Next, we simultaneously evaluated the proteomic response of both S. Typhimurium and D. discoideum during host-pathogen interaction via global proteomic profiling. The analysis of our results allowed the identification of novel molecular signatures that give insight into Salmonella-Dictyostelium interaction. Altogether, our results indicate that inorganic polyP is essential for S. Typhimurium virulence and survival in D. discoideum. In addition, we have validated the use of global proteomic analyses to simultaneously evaluate the host-pathogen interaction of S. Typhimurium and D. discoideum. Furthermore, our infection assays using these organisms can be exploited to screen for novel anti-virulence molecules targeting inorganic polyP biosynthesis.
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Affiliation(s)
- Macarena A Varas
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Sebastián Riquelme-Barrios
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Camila Valenzuela
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Andrés E Marcoleta
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Camilo Berríos-Pastén
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Carlos A Santiviago
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Francisco P Chávez
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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76
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Polyphosphate Kinase Antagonizes Virulence Gene Expression in Francisella tularensis. J Bacteriol 2018; 200:JB.00460-17. [PMID: 29158241 DOI: 10.1128/jb.00460-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/02/2017] [Indexed: 12/31/2022] Open
Abstract
The alarmone ppGpp is a critical regulator of virulence gene expression in Francisella tularensis In this intracellular pathogen, ppGpp is thought to work in concert with the putative DNA-binding protein PigR and the SspA protein family members MglA and SspA to control a common set of genes. MglA and SspA form a complex that interacts with RNA polymerase (RNAP), and PigR functions by interacting with the RNAP-associated MglA-SspA complex. Prior work suggested that ppGpp indirectly exerts its regulatory effects in F. tularensis by promoting the accumulation of polyphosphate in the cell, which in turn was required for formation of the MglA-SspA complex. Here we show that in Escherichia coli, neither polyphosphate nor ppGpp is required for formation of the MglA-SspA complex but that ppGpp promotes the interaction between PigR and the MglA-SspA complex. Moreover, we show that polyphosphate kinase, the enzyme responsible for the synthesis of polyphosphate, antagonizes virulence gene expression in F. tularensis, a finding that is inconsistent with the notion that polyphosphate accumulation promotes virulence gene expression in this organism. Our findings identify polyphosphate kinase as a novel negative regulator of virulence gene expression in F. tularensis and support a model in which ppGpp exerts its positive regulatory effects by promoting the interaction between PigR and the MglA-SspA complex.IMPORTANCE In Francisella tularensis, MglA and SspA form a complex that associates with RNA polymerase to positively control the expression of key virulence genes. The MglA-SspA complex works together with the putative DNA-binding protein PigR and the alarmone ppGpp. PigR functions by interacting directly with the MglA-SspA complex, but how ppGpp exerts its effects was unclear. Prior work indicated that ppGpp acts by promoting the accumulation of polyphosphate, which is required for MglA and SspA to interact. Here we show that formation of the MglA-SspA complex does not require polyphosphate. Furthermore, we find that polyphosphate antagonizes the expression of virulence genes in F. tularensis Thus, ppGpp does not promote virulence gene expression in this organism through an effect on polyphosphate.
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77
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Kamatani S, Takegawa K, Kimura Y. Catalytic Activity Profile of Polyphosphate Kinase 1 from Myxococcus xanthus. Curr Microbiol 2017; 75:379-385. [PMID: 29127456 DOI: 10.1007/s00284-017-1391-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 11/06/2017] [Indexed: 10/18/2022]
Abstract
Polyphosphate kinase 1 (Ppk1) catalyzes reverse transfer of the terminal phosphate from ATP to form polyphosphate (polyP) and from polyP to form ATP, and is responsible for the synthesis of most of cellular polyPs. When Ppk1 from Myxococcus xanthus was incubated with 0.2 mM polyP60-70 and 1 mM ATP or ADP, the rate of ATP synthesis was approximately 1.5-fold higher than that of polyP synthesis. If in the same reaction the proportion of ADP in the ATP/ADP mixture exceeded one-third, the equilibrium shifted to ATP synthesis, suggesting that M. xanthus Ppk1 preferentially catalyzed ATP formation. At the same time, GTP and GDP were not recognized as substrates by Ppk1. In the absence of polyP, Ppk1 generated ATP and AMP from ADP, and ADP from ATP and AMP, suggesting that the enzyme catalyzed the transfer of a phosphate group between ADP molecules yielding ATP and AMP, thus exhibiting adenylate kinase activity.
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Affiliation(s)
- Shiori Kamatani
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa, Japan
| | - Kaoru Takegawa
- Department of Bioscience and Biotechnology, Kyushu University, Hakozaki, Higashi-ku, Fukuoka, Japan
| | - Yoshio Kimura
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa, Japan.
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Wang L, Liu Z, Dai S, Yan J, Wise MJ. The Sit-and-Wait Hypothesis in Bacterial Pathogens: A Theoretical Study of Durability and Virulence. Front Microbiol 2017; 8:2167. [PMID: 29209284 PMCID: PMC5701638 DOI: 10.3389/fmicb.2017.02167] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 10/23/2017] [Indexed: 12/20/2022] Open
Abstract
The intriguing sit-and-wait hypothesis predicts that bacterial durability in the external environment is positively correlated with their virulence. Since its first proposal in 1987, the hypothesis has been spurring debates in terms of its validity in the field of bacterial virulence. As a special case of the vector-borne transmission versus virulence tradeoff, where vector is now replaced by environmental longevity, there are only sporadic studies over the last three decades showing that environmental durability is possibly linked with virulence. However, no systematic study of these works is currently available and epidemiological analysis has not been updated for the sit-and-wait hypothesis since the publication of Walther and Ewald's (2004) review. In this article, we put experimental evidence, epidemiological data and theoretical analysis together to support the sit-and-wait hypothesis. According to the epidemiological data in terms of gain and loss of virulence (+/-) and durability (+/-) phenotypes, we classify bacteria into four groups, which are: sit-and-wait pathogens (++), vector-borne pathogens (+-), obligate-intracellular bacteria (--), and free-living bacteria (-+). After that, we dive into the abundant bacterial proteomic data with the assistance of bioinformatics techniques in order to investigate the two factors at molecular level thanks to the fast development of high-throughput sequencing technology. Sequences of durability-related genes sourced from Gene Ontology and UniProt databases and virulence factors collected from Virulence Factor Database are used to search 20 corresponding bacterial proteomes in batch mode for homologous sequences via the HMMER software package. Statistical analysis only identified a modest, and not statistically significant correlation between mortality and survival time for eight non-vector-borne bacteria with sit-and-wait potentials. Meanwhile, through between-group comparisons, bacteria with higher host-mortality are significantly more durable in the external environment. The results of bioinformatics analysis correspond well with epidemiological data, that is, non-vector-borne pathogens with sit-and-wait potentials have higher number of virulence and durability genes compared with other bacterial groups. However, the conclusions are constrained by the relatively small bacterial sample size and non-standardized experimental data.
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Affiliation(s)
- Liang Wang
- School of Medical Informatics, Xuzhou Medical University, Xuzhou, China
| | - Zhanzhong Liu
- Department of Clinical Pharmacology, Xuzhou Infectious Diseases Hospital, Xuzhou, China
| | - Shiyun Dai
- School of Anaesthesia, Xuzhou Medical University, Xuzhou, China
| | - Jiawei Yan
- Clinical Laboratory of Tuberculosis, Xuzhou Infectious Diseases Hospital, Xuzhou, China
| | - Michael J. Wise
- School of Computer Science and Software Engineering, University of Western Australia, Perth, WA, Australia
- The Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Perth, WA, Australia
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79
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Velmourougane K, Prasanna R, Saxena AK. Agriculturally important microbial biofilms: Present status and future prospects. J Basic Microbiol 2017; 57:548-573. [PMID: 28407275 DOI: 10.1002/jobm.201700046] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/17/2017] [Accepted: 03/19/2017] [Indexed: 11/07/2022]
Abstract
Microbial biofilms are a fascinating subject, due to their significant roles in the environment, industry, and health. Advances in biochemical and molecular techniques have helped in enhancing our understanding of biofilm structure and development. In the past, research on biofilms primarily focussed on health and industrial sectors; however, lately, biofilms in agriculture are gaining attention due to their immense potential in crop production, protection, and improvement. Biofilms play an important role in colonization of surfaces - soil, roots, or shoots of plants and enable proliferation in the desired niche, besides enhancing soil fertility. Although reports are available on microbial biofilms in general; scanty information is published on biofilm formation by agriculturally important microorganisms (bacteria, fungi, bacterial-fungal) and their interactions in the ecosystem. Better understanding of agriculturally important bacterial-fungal communities and their interactions can have several implications on climate change, soil quality, plant nutrition, plant protection, bioremediation, etc. Understanding the factors and genes involved in biofilm formation will help to develop more effective strategies for sustainable and environment-friendly agriculture. The present review brings together fundamental aspects of biofilms, in relation to their formation, regulatory mechanisms, genes involved, and their application in different fields, with special emphasis on agriculturally important microbial biofilms.
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Affiliation(s)
| | - Radha Prasanna
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau Nath Bhanjan, Uttar Pradesh, India
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80
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彭 亮, 区 静, 潘 嘉, 邓 聪, 陈 景, 曹 虹. [Expression of Proteus mirabilis polyphosphate kinase and preparation of its polyclonal antibodies]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2017; 37:312-316. [PMID: 28377345 PMCID: PMC6780429 DOI: 10.3969/j.issn.1673-4254.2017.03.06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Indexed: 06/07/2023]
Abstract
OBJECTIVE To express and purify polyphosphate kinase (PPK) from Proteus mirabilis and prepare the polyclonal antibody against PPK. METHODS The antigenicity and hydrophobicity of PPK were analyzed using software. The N-terminal conservative sequence containing 309 amino acids was selected as the target peptide, and its corresponding gene sequence with modification based on prokaryotic cells-preferred codon was synthesized and inserted into plasmid pET28b(+). The constructed recombinant plasmid was transformed into Escherichia coli BL21 (DE3) and induced with IPTG. The expressed fusion protein was purified using Ni-affinity chromatography. The purified protein was injected along with adjuvant in rabbits to prepare the polyclonal antibodies against PPK. RESULTS AND CONCLUSION PPK fusion protein expressed by E. coli was purified successfully using Ni-affinity chromatography. ELISA result demonstrated that the harvested rabbit anti-sera against PPK had a high titer of 1:512 000, and Western blotting showed a good specificity of the antibody, which can be used further study of the role of PPK in the pathogenesis of Proteus mirabilis infection.
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Affiliation(s)
- 亮 彭
- 广州医科大学附属第二医院 检验科,广东 广州 510260Department of Clinical Laboratory, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - 静怡 区
- 广州医科大学附属第二医院 检验科,广东 广州 510260Department of Clinical Laboratory, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - 嘉韵 潘
- 广州医科大学附属第二医院 检验科,广东 广州 510260Department of Clinical Laboratory, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - 聪 邓
- 广州医科大学附属第二医院 检验科,广东 广州 510260Department of Clinical Laboratory, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - 景红 陈
- 广州医科大学附属第二医院 血液科,广东 广州 510260Department of Hematology, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - 虹 曹
- 南方医科大学公共卫生学院//广东省热带病研究重点实验室,微生物学系,广东 广州 510515Department of Microbiology, Guangdong Provincial Key Laboratory of Tropical Disease Research/ School of Public Health, Southern Medical University, Guangzhou 510515, China
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彭 亮, 区 静, 潘 嘉, 邓 聪, 陈 景, 曹 虹. [Expression of Proteus mirabilis polyphosphate kinase and preparation of its polyclonal antibodies]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2017; 37:312-316. [PMID: 28377345 PMCID: PMC6780429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Indexed: 07/30/2024]
Abstract
OBJECTIVE To express and purify polyphosphate kinase (PPK) from Proteus mirabilis and prepare the polyclonal antibody against PPK. METHODS The antigenicity and hydrophobicity of PPK were analyzed using software. The N-terminal conservative sequence containing 309 amino acids was selected as the target peptide, and its corresponding gene sequence with modification based on prokaryotic cells-preferred codon was synthesized and inserted into plasmid pET28b(+). The constructed recombinant plasmid was transformed into Escherichia coli BL21 (DE3) and induced with IPTG. The expressed fusion protein was purified using Ni-affinity chromatography. The purified protein was injected along with adjuvant in rabbits to prepare the polyclonal antibodies against PPK. RESULTS AND CONCLUSION PPK fusion protein expressed by E. coli was purified successfully using Ni-affinity chromatography. ELISA result demonstrated that the harvested rabbit anti-sera against PPK had a high titer of 1:512 000, and Western blotting showed a good specificity of the antibody, which can be used further study of the role of PPK in the pathogenesis of Proteus mirabilis infection.
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Affiliation(s)
- 亮 彭
- 广州医科大学附属第二医院 检验科,广东 广州 510260Department of Clinical Laboratory, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - 静怡 区
- 广州医科大学附属第二医院 检验科,广东 广州 510260Department of Clinical Laboratory, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - 嘉韵 潘
- 广州医科大学附属第二医院 检验科,广东 广州 510260Department of Clinical Laboratory, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - 聪 邓
- 广州医科大学附属第二医院 检验科,广东 广州 510260Department of Clinical Laboratory, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - 景红 陈
- 广州医科大学附属第二医院 血液科,广东 广州 510260Department of Hematology, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - 虹 曹
- 南方医科大学公共卫生学院//广东省热带病研究重点实验室,微生物学系,广东 广州 510515Department of Microbiology, Guangdong Provincial Key Laboratory of Tropical Disease Research/ School of Public Health, Southern Medical University, Guangzhou 510515, China
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Proteins with CHADs (Conserved Histidine α-Helical Domains) Are Attached to Polyphosphate Granules In Vivo and Constitute a Novel Family of Polyphosphate-Associated Proteins (Phosins). Appl Environ Microbiol 2017; 83:AEM.03399-16. [PMID: 28130300 DOI: 10.1128/aem.03399-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 01/17/2017] [Indexed: 01/13/2023] Open
Abstract
On the basis of bioinformatic evidence, we suspected that proteins with a CYTH (CyaB thiamine triphosphatase) domain and/or a CHAD (conserved histidine α-helical domain) motif might represent polyphosphate (polyP) granule-associated proteins. We found no evidence of polyP targeting by proteins with CYTH domains. In contrast, two CHAD motif-containing proteins from Ralstonia eutropha H16 (A0104 and B1017) that were expressed as fusions with enhanced yellow fluorescent protein (eYFP) colocalized with polyP granules. While the expression of B1017 was not detectable, the A0104 protein was specifically identified in an isolated polyP granule fraction by proteome analysis. Moreover, eYFP fusions with the CHAD motif-containing proteins MGMSRV2-1987 from Magnetospirillum gryphiswaldense and PP2307 from Pseudomonas putida also colocalized with polyP granules in a transspecies-specific manner. These data indicated that CHAD-containing proteins are generally attached to polyP granules. Together with the findings from four previously polyP-attached proteins (polyP kinases), the results of this study raised the number of polyP-associated proteins in R. eutropha to six. We suggest designating polyP granule-bound proteins with CHAD motifs as phosins (phosphate), analogous to phasins and oleosins that are specifically bound to the surface of polyhydroxyalkanoate (PHA) granules in PHA-accumulating bacteria and to oil droplets in oil seed plants, respectively.IMPORTANCE The importance of polyphosphate (polyP) for life is evident from the ubiquitous presence of polyP in all species on earth. In unicellular eukaryotic microorganisms, polyP is located in specific membrane-enclosed organelles, called acidocalcisomes. However, in most prokaryotes, polyP is present as insoluble granules that have been designated previously as volutin granules. Almost nothing is known regarding the macromolecular composition of polyP granules. Particularly, the absence or presence of cellular compounds on the surface of polyP granules has not yet been investigated. In this study, we identified a novel class of proteins that are attached to the surface of polyP granules in three model species of Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria These proteins are characterized by the presence of a CHAD (conserved histidine α-helical domain) motif that functions as a polyP granule-targeting signal. We suggest designating CHAD motif-containing proteins as phosins [analogous to phasins for poly(3-hydroxybutyrate)-associated proteins and to oleosins for oil droplet-associated proteins in oil seed plants]. The expression of phosins in different species confirmed their polyP-targeting function in a transspecies-specific manner. We postulate that polyP granules in prokaryotic species generally have a complex surface structure that consists of one to several polyP kinases and phosin proteins. We suggest differentiating polyP granules from acidocalcisomes by designating them as polyphosphatosomes.
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83
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Ashrafi M, Baguneid M, Alonso-Rasgado T, Rautemaa-Richardson R, Bayat A. Cutaneous wound biofilm and the potential for electrical stimulation in management of the microbiome. Future Microbiol 2017; 12:337-357. [DOI: 10.2217/fmb-2016-0204] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Infection contributes significantly to delayed cutaneous wound healing, which impacts patient care. External application of electrical stimulation (ES) has beneficial effects on wound repair and regeneration. The majority of studies to date have explored ES in relation to planktonic microorganisms, yet evidence indicates that bacteria in chronic wounds reside as antibiotic-resistant polymicrobial biofilms, which contribute to impairing wound healing. Culture-independent sequencing techniques have revolutionized our understanding of the skin microbiome and allowed a more accurate determination of microbial taxa and their relative abundance in wounds allowing a greater understanding of the host–microbial interface. Future studies combining the fields of ES, biofilm and microbiome research are necessary to fully elucidate the use of ES in the management of wound infection.
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Affiliation(s)
- Mohammed Ashrafi
- Plastic & Reconstructive Surgery Research, Centre for Dermatological Research, University of Manchester, Manchester, UK
- University Hospital of South Manchester NHS Foundation Trust, Wythenshawe Hospital, Manchester, UK
- Bioengineering Group, School of Materials, University of Manchester, Manchester, UK
| | - Mohamed Baguneid
- University Hospital of South Manchester NHS Foundation Trust, Wythenshawe Hospital, Manchester, UK
| | | | - Riina Rautemaa-Richardson
- University Hospital of South Manchester NHS Foundation Trust, Wythenshawe Hospital, Manchester, UK
- Manchester Academic Health Science Centre, Institute of Inflammation & Repair, University of Manchester, Manchester, UK
| | - Ardeshir Bayat
- Plastic & Reconstructive Surgery Research, Centre for Dermatological Research, University of Manchester, Manchester, UK
- University Hospital of South Manchester NHS Foundation Trust, Wythenshawe Hospital, Manchester, UK
- Bioengineering Group, School of Materials, University of Manchester, Manchester, UK
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84
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Tarayre C, Charlier R, Delepierre A, Brognaux A, Bauwens J, Francis F, Dermience M, Lognay G, Taminiau B, Daube G, Compère P, Meers E, Michels E, Delvigne F. Looking for phosphate-accumulating bacteria in activated sludge processes: a multidisciplinary approach. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:8017-8032. [PMID: 28132192 DOI: 10.1007/s11356-017-8490-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/19/2017] [Indexed: 06/06/2023]
Abstract
Over the past decades, an increasing need in renewable resources has progressively appeared. This trend concerns not only fossil fuels but also mineral resources. Wastewater and sewage sludge contain significant concentrations in phosphate and can be considered as a fertilizer source of the utmost importance. In wastewater treatment plants, the biological uptake of phosphate is performed by a specific microbiota: the phosphate-accumulating organisms. These microorganisms are recovered in sewage sludge. Here, we aimed to investigate the occurrence of phosphate accumulators in four wastewater treatment plants. A 16S metagenetic analysis identified the main bacterial phyla extracted from the aerobic treatment: α-Proteobacteria, β-Proteobacteria, and Sphingobacteria. An enrichment stage was performed to stimulate the specific growth of phosphate-accumulating bacteria in an acetate medium. An analysis of metabolic activities of sulfur and phosphorus highlighted strong modifications related to phosphorus and much less distinguishable effects with sulfur. A solid acetate medium containing 5-Br-4-Cl-3-indolyl phosphate was used to select potential phosphate-accumulating bacteria from the enriched consortia. The positive strains have been found to belong in the genera Acinetobacter, Corynebacterium, and Pseudomonas. Finally, electron microscopy was applied to the strains and allowed to confirm the presence of polyphosphate granules. Some of these bacteria contained granules the size of which exceeded 100 nm.
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Affiliation(s)
- Cédric Tarayre
- Microbial Processes and Interactions, TERRA Research Centre, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, B-5030, Gembloux, Belgium.
| | - Raphaëlle Charlier
- Microbial Processes and Interactions, TERRA Research Centre, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, B-5030, Gembloux, Belgium
| | - Anissa Delepierre
- Microbial Processes and Interactions, TERRA Research Centre, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, B-5030, Gembloux, Belgium
| | - Alison Brognaux
- Microbial Processes and Interactions, TERRA Research Centre, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, B-5030, Gembloux, Belgium
| | - Julien Bauwens
- Entomologie Fonctionnelle et Évolutive, AgroBioChem, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, B-5030, Gembloux, Belgium
| | - Frédéric Francis
- Entomologie Fonctionnelle et Évolutive, AgroBioChem, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, B-5030, Gembloux, Belgium
| | - Michaël Dermience
- Chimie Analytique, AgroBioChem, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, B-5030, Gembloux, Belgium
| | - Georges Lognay
- Chimie Analytique, AgroBioChem, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, B-5030, Gembloux, Belgium
| | - Bernard Taminiau
- Microbiologie des Denrées alimentaires, Fundamental and Applied Research for Animals and Health, University of Liege, Quartier Vallée 2, Avenue de Cureghem 10, B-4000, Liege, Belgium
| | - Georges Daube
- Microbiologie des Denrées alimentaires, Fundamental and Applied Research for Animals and Health, University of Liege, Quartier Vallée 2, Avenue de Cureghem 10, B-4000, Liege, Belgium
| | - Philippe Compère
- Département de Biologie, Ecologie et Evolution, Université de Liège, Allée du Six Août 15, B-4000, Liège, Belgium
| | - Erik Meers
- Department of Applied Analytical and Physical Chemistry, Laboratory of Analytical Chemistry and Applied Ecochemistry, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Evi Michels
- Department of Applied Analytical and Physical Chemistry, Laboratory of Analytical Chemistry and Applied Ecochemistry, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Frank Delvigne
- Microbial Processes and Interactions, TERRA Research Centre, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, B-5030, Gembloux, Belgium
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85
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Ramos CL, Gomes FM, Girard-Dias W, Almeida FP, Albuquerque PC, Kretschmer M, Kronstad JW, Frases S, de Souza W, Rodrigues ML, Miranda K. Phosphorus-rich structures and capsular architecture in Cryptococcus neoformans. Future Microbiol 2017; 12:227-238. [PMID: 28262043 DOI: 10.2217/fmb-2017-0060] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM In this study, we aimed to analyze the relationship of phosphorus-rich structures with surface architecture in Cryptococcus neoformans. METHODS Phosphorus-rich structures in C. neoformans were analyzed by combining fluorescence microscopy, biochemical extraction, scanning electron microscopy, electron probe x-ray microanalysis and 3D reconstruction of high pressure frozen and freeze substituted cells by focused ion beam-scanning electron microscopy (FIB-SEM). RESULTS & CONCLUSION Intracellular and surface phosphorus-enriched structures were identified. These molecules were required for capsule assembly, as demonstrated in experiments using polysaccharide incorporation by capsule-deficient cells and mutants with defects in polyphosphate synthesis. The demonstration of intracellular and cell wall-associated polyphosphates in C. neoformans may lead to future studies involving their participation in both physiologic and pathogenic events.
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Affiliation(s)
- Caroline L Ramos
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabio M Gomes
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Wendell Girard-Dias
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Instituto Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Fernando P Almeida
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Instituto Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Priscila C Albuquerque
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Matthias Kretschmer
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - James W Kronstad
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.,Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Susana Frases
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Instituto Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Wanderley de Souza
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Instituto Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcio L Rodrigues
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Kildare Miranda
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Instituto Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Agulló L, Romero-Silva MJ, Domenech M, Seeger M. p-Cymene Promotes Its Catabolism through the p-Cymene and the p-Cumate Pathways, Activates a Stress Response and Reduces the Biofilm Formation in Burkholderia xenovorans LB400. PLoS One 2017; 12:e0169544. [PMID: 28072820 PMCID: PMC5224996 DOI: 10.1371/journal.pone.0169544] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 12/18/2016] [Indexed: 11/19/2022] Open
Abstract
p-Cymene is an aromatic terpene that is present in diverse plant species. The aims of this study were to study the p-cymene metabolism in the model aromatic-degrading bacterium Burkholderia xenovorans LB400, and its response to p-cymene. The catabolic p-cymene (cym) and p-cumate (cmt) genes are clustered on the LB400 major chromosome. B. xenovorans LB400 was able to grow on p-cymene as well as on p-cumate as a sole carbon and energy sources. LB400 growth attained higher cell concentration at stationary phase on p-cumate than on p-cymene. The transcription of the key cymAb and cmtAb genes, and p-cumate dioxygenase activity were observed in LB400 cells grown on p-cymene and on p-cumate, but not in glucose-grown cells. Diverse changes on LB400 proteome were observed in p-cymene-grown cells compared to glucose-grown cells. An increase of the molecular chaperones DnaK, GroEL and ClpB, the organic hydroperoxide resistance protein Ohr, the alkyl hydroperoxide reductase AhpC and the copper oxidase CopA during growth on p-cymene strongly suggests that the exposure to p-cymene constitutes a stress condition for strain LB400. Diverse proteins of the energy metabolism such as enolase, pyruvate kinase, aconitase AcnA, succinyl-CoA synthetase beta subunit and ATP synthase beta subunit were induced by p-cymene. Electron microscopy showed that p-cymene-grown cells exhibited fuzzy outer and inner membranes and an increased periplasm. p-Cymene induced diverse membrane and transport proteins including the p-cymene transporter CymD. Biofilm formation was reduced during growth in p-cymene in strain LB400 compared to glucose-grown cells that may be associated with a decrease of diguanylate cyclase protein levels. Overall, these results indicate active p-cymene and p-cumate catabolic pathways in B. xenovorans LB400. In addition, this study showed that p-cymene activated a stress response in strain LB400 and reduced its biofilm formation.
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Affiliation(s)
- Loreine Agulló
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry & Center for Nanotechnology and Systems Biology, Centro de Biotecnología, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - María José Romero-Silva
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry & Center for Nanotechnology and Systems Biology, Centro de Biotecnología, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Mirian Domenech
- Departamento de Microbiología Molecular y Biología de las Infecciones, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
| | - Michael Seeger
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry & Center for Nanotechnology and Systems Biology, Centro de Biotecnología, Universidad Técnica Federico Santa María, Valparaíso, Chile
- * E-mail:
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Varas M, Valdivieso C, Mauriaca C, Ortíz-Severín J, Paradela A, Poblete-Castro I, Cabrera R, Chávez FP. Multi-level evaluation of Escherichia coli polyphosphate related mutants using global transcriptomic, proteomic and phenomic analyses. Biochim Biophys Acta Gen Subj 2017; 1861:871-883. [PMID: 28069396 DOI: 10.1016/j.bbagen.2017.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 12/26/2016] [Accepted: 01/05/2017] [Indexed: 12/20/2022]
Abstract
BACKGROUND Polyphosphate (polyP) is a linear biopolymer found in all living cells. In bacteria, mutants lacking polyphosphate kinase 1 (PPK1), the enzyme responsible for synthesis of most polyP, have many structural and functional defects. However, little is known about the causes of these pleiotropic alterations. The link between ppk1 deletion and those numerous phenotypes observed can be the result of complex molecular interactions that can be elucidated via a systems biology approach. METHODS By integrating different omics levels (transcriptome, proteome and phenome), we described the functioning of various metabolic pathways among Escherichia coli polyphosphate mutant strains (Δppk1, Δppx, and ΔpolyP). Bioinformatic analyses reveal the complex metabolic and regulatory bases of the phenotypes unique to polyP mutants. RESULTS Our results suggest that during polyP deficiency (Δppk1 mutant), metabolic pathways needed for energy supply are up-regulated, including fermentation, aerobic and anaerobic respiration. Transcriptomic and q-proteomic contrasting changes between Δppk1 and Δppx mutant strains were observed in those central metabolic pathways and confirmed by using Phenotypic microarrays. In addition, our results suggest a regulatory connection between polyP, second messenger metabolism, alternative Sigma/Anti-Sigma factors and type-II toxin-antitoxin (TA) systems. CONCLUSIONS We suggest a broader role for polyP via regulation of ATP-dependent proteolysis of type II toxin-antitoxin system and alternative Sigma/Anti-Sigma factors, that could explain the multiple structural and functional deficiencies described due to alteration of polyP metabolism. GENERAL SIGNIFICANCE Understanding the interplay of polyP in bacterial metabolism using a systems biology approach can help to improve design of novel antimicrobials toward pathogens.
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Affiliation(s)
- Macarena Varas
- Systems Microbiology Laboratory, Department of Biology, Faculty of Science, University of Chile, Chile.
| | - Camilo Valdivieso
- Systems Microbiology Laboratory, Department of Biology, Faculty of Science, University of Chile, Chile; Department of Ecology, Faculty of Science, University of Chile, Chile.
| | - Cecilia Mauriaca
- Systems Microbiology Laboratory, Department of Biology, Faculty of Science, University of Chile, Chile.
| | - Javiera Ortíz-Severín
- Systems Microbiology Laboratory, Department of Biology, Faculty of Science, University of Chile, Chile.
| | | | - Ignacio Poblete-Castro
- Facultad de Ciencias Biológicas, Center for Bioinformatics and Integrative Biology, Biosystems Engineering Laboratory, Universidad Andrés Bello, Chile.
| | - Ricardo Cabrera
- Department of Biology, Faculty of Sciences, University of Chile, Chile.
| | - Francisco P Chávez
- Systems Microbiology Laboratory, Department of Biology, Faculty of Science, University of Chile, Chile.
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88
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Abstract
Post-translational modifications (PTMs) add regulatory features to proteins that help establish the complex functional networks that make up higher organisms. Advances in analytical detection methods have led to the identification of more than 200 types of PTMs. However, some modifications are unstable under the present detection methods, anticipating the existence of further modifications and a much more complex map of PTMs. An example is the recently discovered protein modification polyphosphorylation. Polyphosphorylation is mediated by inorganic polyphosphate (polyP) and represents the covalent attachment of this linear polymer of orthophosphate to lysine residues in target proteins. This modification has eluded MS analysis as both polyP itself and the phosphoramidate bonds created upon its reaction with lysine residues are highly unstable in acidic conditions. Polyphosphorylation detection was only possible through extensive biochemical characterization. Two targets have been identified: nuclear signal recognition 1 (Nsr1) and its interacting partner, topoisomerase 1 (Top1). Polyphosphorylation occurs within a conserved N-terminal polyacidic serine (S) and lysine (K) rich (PASK) cluster. It negatively regulates Nsr1-Top1 interaction and impairs Top1 enzymatic activity, namely relaxing supercoiled DNA. Modulation of cellular levels of polyP regulates Top1 activity by modifying its polyphosphorylation status. Here we discuss the significance of the recently identified new role of inorganic polyP.
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89
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Araujo ACV, Morillo V, Cypriano J, Teixeira LCRS, Leão P, Lyra S, Almeida LGD, Bazylinski DA, Ribeiro de Vasconcelos AT, Abreu F, Lins U. Combined genomic and structural analyses of a cultured magnetotactic bacterium reveals its niche adaptation to a dynamic environment. BMC Genomics 2016; 17:726. [PMID: 27801294 PMCID: PMC5088516 DOI: 10.1186/s12864-016-3064-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Magnetotactic bacteria (MTB) are a unique group of prokaryotes that have a potentially high impact on global geochemical cycling of significant primary elements because of their metabolic plasticity and the ability to biomineralize iron-rich magnetic particles called magnetosomes. Understanding the genetic composition of the few cultivated MTB along with the unique morphological features of this group of bacteria may provide an important framework for discerning their potential biogeochemical roles in natural environments. RESULTS Genomic and ultrastructural analyses were combined to characterize the cultivated magnetotactic coccus Magnetofaba australis strain IT-1. Cells of this species synthesize a single chain of elongated, cuboctahedral magnetite (Fe3O4) magnetosomes that cause them to align along magnetic field lines while they swim being propelled by two bundles of flagella at velocities up to 300 μm s-1. High-speed microscopy imaging showed the cells move in a straight line rather than in the helical trajectory described for other magnetotactic cocci. Specific genes within the genome of Mf. australis strain IT-1 suggest the strain is capable of nitrogen fixation, sulfur reduction and oxidation, synthesis of intracellular polyphosphate granules and transporting iron with low and high affinity. Mf. australis strain IT-1 and Magnetococcus marinus strain MC-1 are closely related phylogenetically although similarity values between their homologous proteins are not very high. CONCLUSION Mf. australis strain IT-1 inhabits a constantly changing environment and its complete genome sequence reveals a great metabolic plasticity to deal with these changes. Aside from its chemoautotrophic and chemoheterotrophic metabolism, genomic data indicate the cells are capable of nitrogen fixation, possess high and low affinity iron transporters, and might be capable of reducing and oxidizing a number of sulfur compounds. The relatively large number of genes encoding transporters as well as chemotaxis receptors in the genome of Mf. australis strain IT-1 combined with its rapid swimming velocities, indicate that cells respond rapidly to environmental changes.
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Affiliation(s)
- Ana Carolina Vieira Araujo
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil.,Current institution: Departamento de Biologia, Universidade Federal de São Carlos, 18052-780, Sorocaba, SP, Brazil
| | - Viviana Morillo
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil.,School of Life Sciences, University of Nevada at Las Vegas, Las Vegas, NV, 89154-4004, USA
| | - Jefferson Cypriano
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | | | - Pedro Leão
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Sidcley Lyra
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Luiz Gonzaga de Almeida
- Departamento de Matemática Aplicada e Computacional, Laboratório Nacional de Computação Científica, 25651-070, Petrópolis, RJ, Brazil
| | - Dennis A Bazylinski
- School of Life Sciences, University of Nevada at Las Vegas, Las Vegas, NV, 89154-4004, USA
| | - Ana Tereza Ribeiro de Vasconcelos
- Departamento de Matemática Aplicada e Computacional, Laboratório Nacional de Computação Científica, 25651-070, Petrópolis, RJ, Brazil
| | - Fernanda Abreu
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil
| | - Ulysses Lins
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, RJ, Brazil.
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90
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Yoshida N, Yano T, Kedo K, Fujiyoshi T, Nagai R, Iwano M, Taguchi E, Nishida T, Takagi H. A unique intracellular compartment formed during the oligotrophic growth of Rhodococcus erythropolis N9T-4. Appl Microbiol Biotechnol 2016; 101:331-340. [PMID: 27717963 DOI: 10.1007/s00253-016-7883-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/17/2016] [Accepted: 09/20/2016] [Indexed: 11/29/2022]
Abstract
Rhodococcus erythropolis N9T-4, isolated from stored crude oil, shows extremely oligotrophic features and can grow on a basal medium without any additional carbon, nitrogen, sulfur, and energy sources, but requires CO2 for its oligotrophic growth. Transmission electron microscopic observation showed that a relatively large and spherical compartment was observed in a N9T-4 cell grown under oligotrophic conditions. In most cases, only one compartment was observed per cell, but in some cases, it was localized at each pole of the cell, suggesting that it divides at cell division. We termed this unique bacterial compartment an oligobody. The oligobody was not observed or very rarely observed in small sizes under nutrient rich conditions, whereas additional carbon sources did not affect oligobody formation. Energy dispersive X-ray spectroscopy analysis revealed remarkable peaks corresponding to phosphorus and potassium in the oligobody. The oligobodies in N9T-4 cells could be stained by Toluidine blue, suggesting that the oligobody is composed of inorganic polyphosphate and is a type of acidocalcisome. Two genes-encoding polyphosphate kinases, ppk1 and ppk2, were found in the N9T-4 genome: ppk1 disruption caused a negative effect on the formation of the oligobody. Although it was suggested that the oligobody plays an important role for the oligotrophic growth, both ppk-deleted mutants showed the same level of oligotrophic growth as the wild-type strain.
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Affiliation(s)
- Nobuyuki Yoshida
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, 432-8561, Japan. .,Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, 432-8561, Japan.
| | - Takanori Yano
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, 432-8561, Japan.,The Institute of Enology and Viticulture, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 1-13-1 Kitashin, Kofu, Yamanashi, 400-0005, Japan
| | - Kaori Kedo
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Takuya Fujiyoshi
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Rina Nagai
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
| | - Megumi Iwano
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan.,Department of Biotechnology, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Eiji Taguchi
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, 7-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Tomoki Nishida
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, 7-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Hiroshi Takagi
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
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91
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Cremers CM, Knoefler D, Gates S, Martin N, Dahl JU, Lempart J, Xie L, Chapman MR, Galvan V, Southworth DR, Jakob U. Polyphosphate: A Conserved Modifier of Amyloidogenic Processes. Mol Cell 2016; 63:768-80. [PMID: 27570072 DOI: 10.1016/j.molcel.2016.07.016] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 04/20/2016] [Accepted: 07/19/2016] [Indexed: 01/07/2023]
Abstract
Polyphosphate (polyP), a several billion-year-old biopolymer, is produced in every cell, tissue, and organism studied. Structurally extremely simple, polyP consists of long chains of covalently linked inorganic phosphate groups. We report here the surprising discovery that polyP shows a remarkable efficacy in accelerating amyloid fibril formation. We found that polyP serves as an effective nucleation source for various different amyloid proteins, ranging from bacterial CsgA to human α-synuclein, Aβ1-40/42, and Tau. polyP-associated α-synuclein fibrils show distinct differences in seeding behavior, morphology, and fibril stability compared with fibrils formed in the absence of polyP. In vivo, the amyloid-stimulating and fibril-stabilizing effects of polyP have wide-reaching consequences, increasing the rate of biofilm formation in pathogenic bacteria and mitigating amyloid toxicity in differentiated neuroblastoma cells and C. elegans strains that serve as models for human folding diseases. These results suggest that we have discovered a conserved cytoprotective modifier of amyloidogenic processes.
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Affiliation(s)
- Claudia M Cremers
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniela Knoefler
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Stephanie Gates
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nicholas Martin
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jan-Ulrik Dahl
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Justine Lempart
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lihan Xie
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew R Chapman
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Veronica Galvan
- Department of Physiology and The Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Daniel R Southworth
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ursula Jakob
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
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92
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Suess PM, Gomer RH. Extracellular Polyphosphate Inhibits Proliferation in an Autocrine Negative Feedback Loop in Dictyostelium discoideum. J Biol Chem 2016; 291:20260-9. [PMID: 27519410 DOI: 10.1074/jbc.m116.737825] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Indexed: 11/06/2022] Open
Abstract
Polyphosphate is a polymer of phosphate residues linked by high energy phosphoanhydride bonds. Despite being highly conserved throughout nature, its function is poorly understood. Here we show that Dictyostelium cells accumulate extracellular polyphosphate, and this acts to inhibit proliferation at high cell densities. In shaking culture, extracellular polyphosphate concentrations increase as cell density increases, and if the concentration of polyphosphate observed at the stationary phase is added to cells at mid-log, proliferation is halted. Adding an exopolyphosphatase to cell cultures or stationary phase conditioned medium decreases polyphosphate levels and abrogates the anti-proliferative effect. The cells show saturable binding of polyphosphate, suggesting the presence of a cell surface polyphosphate receptor. Extracellular polyphosphate accumulation is potentiated by decreased nutrient levels, potentially as a means to anticipate starvation. Loss of the Dictyostelium polyphosphate kinase DdPpk1 causes intracellular polyphosphate levels to become undetectable and negatively affects fitness, cytokinesis, and germination. However, cells lacking DdPpk1 accumulate ∼50% normal levels of extracellular polyphosphate, suggesting an additional means of synthesis. We found that cells lacking inositol hexakisphosphate kinase, which is responsible for the synthesis of the inositol pyrophosphates IP7 and IP8, reach abnormally high cell densities and show decreased extracellular polyphosphate levels. Two different enzymes thus appear to mediate the synthesis of Dictyostelium extracellular polyphosphate, which is used as a signal in an autocrine negative feedback loop to regulate cell proliferation.
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Affiliation(s)
- Patrick M Suess
- From the Department of Biology, Texas A&M University, College Station, Texas 77843-3474
| | - Richard H Gomer
- From the Department of Biology, Texas A&M University, College Station, Texas 77843-3474
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93
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A survey of biofilms on wastewater aeration diffusers suggests bacterial community composition and function vary by substrate type and time. Appl Microbiol Biotechnol 2016; 100:6361-6373. [DOI: 10.1007/s00253-016-7604-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 04/27/2016] [Accepted: 05/02/2016] [Indexed: 01/06/2023]
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94
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Establishing Virulence Associated Polyphosphate Kinase 2 as a drug target for Mycobacterium tuberculosis. Sci Rep 2016; 6:26900. [PMID: 27279366 PMCID: PMC4899718 DOI: 10.1038/srep26900] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 05/10/2016] [Indexed: 02/03/2023] Open
Abstract
Inorganic polyphosphate (PolyP) plays an essential role in microbial stress adaptation, virulence and drug tolerance. The genome of Mycobacterium tuberculosis encodes for two polyphosphate kinases (PPK-1, Rv2984 and PPK-2, Rv3232c) and polyphosphatases (ppx-1, Rv0496 and ppx-2, Rv1026) for maintenance of intracellular PolyP levels. Microbial polyphosphate kinases constitute a molecular mechanism, whereby microorganisms utilize PolyP as phosphate donor for synthesis of ATP. In the present study we have constructed ppk-2 mutant strain of M. tuberculosis and demonstrate that PPK-2 enzyme contributes to its ability to cause disease in guinea pigs. We observed that ppk-2 mutant strain infected guinea pigs had significantly reduced bacterial loads and tissue pathology in comparison to wild type infected guinea pigs at later stages of infection. We also report that in comparison to the wild type strain, ppk-2 mutant strain was more tolerant to isoniazid and impaired for survival in THP-1 macrophages. In the present study we have standardized a luciferase based assay system to identify chemical scaffolds that are non-cytotoxic and inhibit M. tuberculosis PPK-2 enzyme. To the best of our knowledge this is the first study demonstrating feasibility of high throughput screening to obtain small molecule PPK-2 inhibitors.
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95
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Chen J, Su L, Wang X, Zhang T, Liu F, Chen H, Tan C. Polyphosphate Kinase Mediates Antibiotic Tolerance in Extraintestinal Pathogenic Escherichia coli PCN033. Front Microbiol 2016; 7:724. [PMID: 27242742 PMCID: PMC4871857 DOI: 10.3389/fmicb.2016.00724] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 05/02/2016] [Indexed: 02/04/2023] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) causes a variety of acute infections in its hosts, and multidrug-resistant strains present significant challenges to public health and animal husbandry. Therefore, it is necessary to explore new drug targets to control E. coli epidemics. Previous studies have reported that ppk mutants of Burkholderia pseudomallei and Mycobacterium tuberculosis are more susceptible than the wild types (WTs) to stress. Therefore, we investigated the stress response to antibiotics mediated by polyphosphate kinase (PPK) in ExPEC strain PCN033. We observed that planktonic cells of a ppk knockout strain (Δppk) were more susceptible to antibiotics than was WT. However, biofilm-grown Δppk cells showed similar susceptibility to that of the WT and were more tolerant than the planktonic cells. During the planktonic lifestyle, the expression of genes involved in antibiotic tolerance (including resistance-conferring genes, and antibiotic influx, and efflux genes) did not change in the Δppk mutant without antibiotic treatment. However, the resistance-conferring gene bla and efflux genes were upregulated more in the WT than in the Δppk mutant by treatment with tazobactam. After treatment with gentamycin, the efflux genes and influx genes were upregulated and downregulated, respectively, more in the WT than in the Δppk mutant. The expression of genes involved in biofilm regulation also changed after treatment with tazobactam or gentamycin, and which is consistent with the results of the biofilm formation. Together, these observations indicate that PPK is important for the antibiotic stress response during the planktonic growth of ExPEC and might be a potential drug target in bacteria.
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Affiliation(s)
- Jing Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University Wuhan, China
| | - Lijie Su
- School of Public Health, Guangzhou Medical University Guangzhou, China
| | - Xiangru Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University Wuhan, China
| | - Tao Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University Wuhan, China
| | - Feng Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University Wuhan, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Key Laboratory for the Development of Veterinary Diagnostic Products, The Cooperative Innovation Center for Sustainable Pig Production, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
| | - Chen Tan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural UniversityWuhan, China; Key Laboratory for the Development of Veterinary Diagnostic Products, The Cooperative Innovation Center for Sustainable Pig Production, Ministry of Agriculture, Huazhong Agricultural UniversityWuhan, China
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96
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Bravo-Toncio C, Álvarez JA, Campos F, Ortíz-Severín J, Varas M, Cabrera R, Lagos CF, Chávez FP. Dictyostelium discoideum as a surrogate host–microbe model for antivirulence screening in Pseudomonas aeruginosa PAO1. Int J Antimicrob Agents 2016; 47:403-9. [DOI: 10.1016/j.ijantimicag.2016.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 02/14/2016] [Accepted: 02/20/2016] [Indexed: 11/25/2022]
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97
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Grillo-Puertas M, Rintoul MR, Rapisarda VA. PhoB activation in non-limiting phosphate condition by the maintenance of high polyphosphate levels in the stationary phase inhibits biofilm formation in Escherichia coli. MICROBIOLOGY-SGM 2016; 162:1000-1008. [PMID: 27023099 DOI: 10.1099/mic.0.000281] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Polyphosphate (polyP) degradation in Escherichia coli stationary phase triggers biofilm formation via the LuxS quorum sensing system. In media containing excess of phosphate (Pi), high polyP levels are maintained in the stationary phase with the consequent inhibition of biofilm formation. The transcriptional-response regulator PhoB, which is activated under Pi limitation, is involved in the inhibition of biofilm formation in several bacterial species. In the current study, we report, for the first time, we believe that E. coli PhoB can be activated in non-limiting Pi conditions, leading to inhibition of biofilm formation. In fact, PhoB was activated when high polyP levels were maintained in the stationary phase, whereas it remained inactive when the polymer was degraded or absent. PhoB activation was mediated by acetyl phosphate with the consequent repression of biofilm formation owing to the downregulation of c-di-GMP synthesis and the inhibition of autoinducer-2 production. These results allowed us to propose a model showing that PhoB is a component in the signal cascade regulating biofilm formation triggered by fluctuations of polyP levels in E. coli cells during stationary phase.
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Affiliation(s)
- M Grillo-Puertas
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, Chacabuco 461, T4000ILI - San Miguel de Tucumán, Tucumán, Argentina.,Instituto de Química Biológica, 'Dr Bernabe Bloj', Facultad de Bioquímica, Química y Farmacia, UNT, Chacabuco 461, T4000ILI - San Miguel de Tucumán, Tucumán, Argentina
| | - M R Rintoul
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, Chacabuco 461, T4000ILI - San Miguel de Tucumán, Tucumán, Argentina.,Instituto de Química Biológica, 'Dr Bernabe Bloj', Facultad de Bioquímica, Química y Farmacia, UNT, Chacabuco 461, T4000ILI - San Miguel de Tucumán, Tucumán, Argentina
| | - V A Rapisarda
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, Chacabuco 461, T4000ILI - San Miguel de Tucumán, Tucumán, Argentina.,Instituto de Química Biológica, 'Dr Bernabe Bloj', Facultad de Bioquímica, Química y Farmacia, UNT, Chacabuco 461, T4000ILI - San Miguel de Tucumán, Tucumán, Argentina
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98
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Major Transcriptome Changes Accompany the Growth of Pseudomonas aeruginosa in Blood from Patients with Severe Thermal Injuries. PLoS One 2016; 11:e0149229. [PMID: 26933952 PMCID: PMC4774932 DOI: 10.1371/journal.pone.0149229] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 01/04/2016] [Indexed: 11/19/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that causes serious infections in immunocompromised hosts including severely burned patients. After multiplying within the burn wound, P. aeruginosa translocate into the bloodstream causing bacterial sepsis frequently leading to organ dysfunction and septic shock. Although the pathogenesis of P. aeruginosa infection of thermally-injured wounds has been extensively analyzed, little is known regarding the ability of P. aeruginosa to adapt and survive within the blood of severely burned patients during systemic infection. To identify such adaptations, transcriptome analyses (RNA-seq) were conducted on P. aeruginosa strain PA14 that was grown in whole blood from a healthy volunteer or three severely burned patients. Compared with growth in blood from healthy volunteers, growth of PA14 in the blood from severely burned patients significantly altered the expression of 2596 genes, with expression of 1060 genes enhanced, while that of 1536 genes was reduced. Genes whose expression was significantly reduced included genes related to quorum sensing, quorum sensing-controlled virulence factors and transport of heme, phosphate, and phosphonate. Genes whose expression was significantly enhanced were related to the type III secretion system, the pyochelin iron-acquisition system, flagellum synthesis, and pyocyanin production. We confirmed changes in expression of many of these genes using qRT-PCR. Although severe burns altered the levels of different blood components in each patient, the growth of PA14 in their blood produced similar changes in the expression of each gene. These results suggest that, in response to changes in the blood of severely burned patients and as part of its survival strategy, P. aeruginosa enhances the expression of certain virulence genes and reduces the expression of others.
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99
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Inorganic polyphosphate in the microbial world. Emerging roles for a multifaceted biopolymer. World J Microbiol Biotechnol 2016; 32:27. [DOI: 10.1007/s11274-015-1983-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/05/2015] [Indexed: 10/22/2022]
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100
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Szymusiak M, Donovan AJ, Smith SA, Ransom R, Shen H, Kalkowski J, Morrissey JH, Liu Y. Colloidal Confinement of Polyphosphate on Gold Nanoparticles Robustly Activates the Contact Pathway of Blood Coagulation. Bioconjug Chem 2015; 27:102-9. [DOI: 10.1021/acs.bioconjchem.5b00524] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Stephanie A. Smith
- Department
of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | | | | | | | - James H. Morrissey
- Department
of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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