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Zhen J, Wang ZB, Ni BJ, Ismail S, El-Baz A, Cui Z, Ni SQ. Synergistic Integration of Anammox and Endogenous Denitrification Processes for the Simultaneous Carbon, Nitrogen, and Phosphorus Removal. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:10632-10643. [PMID: 38817146 DOI: 10.1021/acs.est.4c00558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
The feasibility of a synergistic endogenous partial denitrification-phosphorus removal coupled anammox (SEPD-PR/A) system was investigated in a modified anaerobic baffled reactor (mABR) for synchronous carbon, nitrogen, and phosphorus removal. The mABR comprising four identical compartments (i.e., C1-C4) was inoculated with precultured denitrifying glycogen-accumulating organisms (DGAOs), denitrifying polyphosphate-accumulating organisms, and anammox bacteria. After 136 days of operation, the chemical oxygen demand (COD), total nitrogen, and phosphorus removal efficiencies reached 88.6 ± 1.0, 97.2 ± 1.5, and 89.1 ± 4.2%, respectively. Network-based analysis revealed that the biofilmed community demonstrated stable nutrient removal performance under oligotrophic conditions in C4. The metagenome-assembled genomes (MAGs) such as MAG106, MAG127, MAG52, and MAG37 annotated as denitrifying phosphorus-accumulating organisms (DPAOs) and MAG146 as a DGAO were dominated in C1 and C2 and contributed to 89.2% of COD consumption. MAG54 and MAG16 annotated as Candidatus_Brocadia (total relative abundance of 16.5% in C3 and 4.3% in C4) were responsible for 74.4% of the total nitrogen removal through the anammox-mediated pathway. Functional gene analysis based on metagenomic sequencing confirmed that different compartments of the mABR were capable of performing distinct functions with specific advantageous microbial groups, facilitating targeted nutrient removal. Additionally, under oligotrophic conditions, the activity of the anammox bacteria-related genes of hzs was higher compared to that of hdh. Thus, an innovative method for the treatment of low-strength municipal and nitrate-containing wastewaters without aeration was presented, mediated by an anammox process with less land area and excellent quality effluent.
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Affiliation(s)
- Jianyuan Zhen
- School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, China
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Zhi-Bin Wang
- School of Life Sciences, Shandong University, Jinan 250100, China
| | - Bing-Jie Ni
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
- School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Sherif Ismail
- School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, China
- Environmental Engineering Department, Faculty of Engineering, Zagazig University, Zagazig 44519, Egypt
| | - Amro El-Baz
- Environmental Engineering Department, Faculty of Engineering, Zagazig University, Zagazig 44519, Egypt
| | - Zhaojie Cui
- School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, China
| | - Shou-Qing Ni
- School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, China
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Han D, Ma S, He C, Yang Y, Li P, Lu L. Unveiling the genetic architecture and transmission dynamics of a novel multidrug-resistant plasmid harboring bla NDM-5 in E. Coli ST167: implications for antibiotic resistance management. BMC Microbiol 2024; 24:178. [PMID: 38783210 PMCID: PMC11112900 DOI: 10.1186/s12866-024-03333-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND The emergence of multidrug-resistant (MDR) Escherichia coli strains poses significant challenges in clinical settings, particularly when these strains harbor New Delhi metallo-ß-lactamase (NDM) gene, which confer resistance to carbapenems, a critical class of last-resort antibiotics. This study investigates the genetic characteristics and implications of a novel blaNDM-5-carrying plasmid pNDM-5-0083 isolated from an E. coli strain GZ04-0083 from clinical specimen in Zhongshan, China. RESULTS Phenotypic and genotypic evaluations confirmed that the E. coli ST167 strain GZ04-0083 is a multidrug-resistant organism, showing resistance to diverse classes of antibiotics including ß-lactams, carbapenems, fluoroquinolones, aminoglycosides, and sulfonamides, while maintaining susceptibility to monobactams. Investigations involving S1 pulsed-field gel electrophoresis, Southern blot analysis, and conjugation experiments, alongside genomic sequencing, confirmed the presence of the blaNDM-5 gene within a 146-kb IncFIB plasmid pNDM-5-0083. This evidence underscores a significant risk for the horizontal transfer of resistance genes among bacterial populations. Detailed annotations of genetic elements-such as resistance genes, transposons, and insertion sequences-and comparative BLAST analyses with other blaNDM-5-carrying plasmids, revealed a unique architectural configuration in the pNDM-5-0083. The MDR region of this plasmid shares a conserved gene arrangement (repA-IS15DIV-blaNDM-5-bleMBL-IS91-suI2-aadA2-dfrA12) with three previously reported plasmids, indicating a potential for dynamic genetic recombination and evolution within the MDR region. Additionally, the integration of virulence factors, including the iro and sit gene clusters and enolase, into its genetic architecture poses further therapeutic challenges by enhancing the strain's pathogenicity through improved host tissue colonization, immune evasion, and increased infection severity. CONCLUSIONS The detailed identification and characterization of pNDM-5-0083 enhance our understanding of the mechanisms facilitating the spread of carbapenem resistance. This study illuminates the intricate interplay among various genetic elements within the novel blaNDM-5-carrying plasmid, which are crucial for the stability and mobility of resistance genes across bacterial populations. These insights highlight the urgent need for ongoing surveillance and the development of effective strategies to curb the proliferation of antibiotic resistance.
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Affiliation(s)
- Dengke Han
- Department of Laboratory Medicine, Zhongshan City People's Hospital, Zhongshan, 528403, Guangdong, China
| | - Suzhen Ma
- Department of Laboratory Medicine, Zhongshan City People's Hospital, Zhongshan, 528403, Guangdong, China
| | - Chenhong He
- Department of Emergency, Zhongshan City People's Hospital, Zhongshan, 528403, Guangdong, China
| | - Yuxing Yang
- Department of Laboratory Medicine, Zhongshan City People's Hospital, Zhongshan, 528403, Guangdong, China
| | - Peng Li
- Chinese PLA Center for Disease Control and Prevention, 20 DongDa Street, Fengtai District, Beijing, 100071, China
| | - Lanfen Lu
- Department of Laboratory Medicine, Zhongshan City People's Hospital, Zhongshan, 528403, Guangdong, China.
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Borghi F, Saiardi A. Evolutionary perspective on mammalian inorganic polyphosphate (polyP) biology. Biochem Soc Trans 2023; 51:1947-1956. [PMID: 37844192 PMCID: PMC10657179 DOI: 10.1042/bst20230483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 10/18/2023]
Abstract
Inorganic polyphosphate (polyP), the polymeric form of phosphate, is attracting ever-growing attention due to the many functions it appears to perform within mammalian cells. This essay does not aim to systematically review the copious mammalian polyP literature. Instead, we examined polyP synthesis and functions in various microorganisms and used an evolutionary perspective to theorise key issues of this field and propose solutions. By highlighting the presence of VTC4 in distinct species of very divergent eucaryote clades (Opisthokonta, Viridiplantae, Discoba, and the SAR), we propose that whilst polyP synthesising machinery was present in the ancestral eukaryote, most lineages subsequently lost it during evolution. The analysis of the bacteria-acquired amoeba PPK1 and its unique polyP physiology suggests that eukaryote cells must have developed mechanisms to limit cytosolic polyP accumulation. We reviewed the literature on polyP in the mitochondria from the perspective of its endosymbiotic origin from bacteria, highlighting how mitochondria could possess a polyP physiology reminiscent of their 'bacterial' beginning that is not yet investigated. Finally, we emphasised the similarities that the anionic polyP shares with the better-understood negatively charged polymers DNA and RNA, postulating that the nucleus offers an ideal environment where polyP physiology might thrive.
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Affiliation(s)
- Filipy Borghi
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, U.K
| | - Adolfo Saiardi
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, U.K
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4
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Nicholls JWF, Chin JP, Williams TA, Lenton TM, O’Flaherty V, McGrath JW. On the potential roles of phosphorus in the early evolution of energy metabolism. Front Microbiol 2023; 14:1239189. [PMID: 37601379 PMCID: PMC10433651 DOI: 10.3389/fmicb.2023.1239189] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/20/2023] [Indexed: 08/22/2023] Open
Abstract
Energy metabolism in extant life is centered around phosphate and the energy-dense phosphoanhydride bonds of adenosine triphosphate (ATP), a deeply conserved and ancient bioenergetic system. Yet, ATP synthesis relies on numerous complex enzymes and has an autocatalytic requirement for ATP itself. This implies the existence of evolutionarily simpler bioenergetic pathways and potentially primordial alternatives to ATP. The centrality of phosphate in modern bioenergetics, coupled with the energetic properties of phosphorylated compounds, may suggest that primordial precursors to ATP also utilized phosphate in compounds such as pyrophosphate, acetyl phosphate and polyphosphate. However, bioavailable phosphate may have been notably scarce on the early Earth, raising doubts about the roles that phosphorylated molecules might have played in the early evolution of life. A largely overlooked phosphorus redox cycle on the ancient Earth might have provided phosphorus and energy, with reduced phosphorus compounds potentially playing a key role in the early evolution of energy metabolism. Here, we speculate on the biological phosphorus compounds that may have acted as primordial energy currencies, sources of environmental energy, or sources of phosphorus for the synthesis of phosphorylated energy currencies. This review encompasses discussions on the evolutionary history of modern bioenergetics, and specifically those pathways with primordial relevance, and the geochemistry of bioavailable phosphorus on the ancient Earth. We highlight the importance of phosphorus, not only in the form of phosphate, to early biology and suggest future directions of study that may improve our understanding of the early evolution of bioenergetics.
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Affiliation(s)
- Jack W. F. Nicholls
- School of Biological Sciences, Queen’s University of Belfast, Belfast, United Kingdom
| | - Jason P. Chin
- School of Biological Sciences, Queen’s University of Belfast, Belfast, United Kingdom
| | - Tom A. Williams
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Timothy M. Lenton
- Global Systems Institute, University of Exeter, Exeter, United Kingdom
| | | | - John W. McGrath
- School of Biological Sciences, Queen’s University of Belfast, Belfast, United Kingdom
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5
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Villard D, Nesbø Goa IA, Leena Angell I, Eikaas S, Saltnes T, Johansen W, Rudi K. Spatiotemporal succession of phosphorous accumulating biofilms during the first year of establishment. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2023; 88:381-391. [PMID: 37522440 PMCID: wst_2023_214 DOI: 10.2166/wst.2023.214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
Many wastewater treatment plants are dependent on the utilization of microorganisms in biofilms. Our knowledge about the establishment of these biofilms is limited, particular with respect to biofilms involved in enhanced biological phosphorus removal (EBPR). These biofilms rely on polyphosphate-accumulating organisms (PAOs), requiring alternating oxic and anaerobic conditions for phosphorous uptake. This challenge has been solved using the Hias process, which combines moving-bed biofilm-reactor (MBBR) technology with physical transfer of biofilm-carriers from oxic to anaerobic zones. We combined biofilm fractionation with temporal analyses to unveil the establishment in the Hias process. A stable phosphorous removal efficiency of >95% was reached within 16 weeks of operation. Phosphorus removal, however, was not correlated with the establishment of known PAOs. The biofilms seemed associated with an outer microbiota layer with rapid turnover and an inner layer with a slow expansion. The inner layer showed an overrepresentation of known PAOs. In conclusion, our spatiotemporal analyses of phosphorous accumulating biofilm establishment lead to a new model for biofilm growth, while the mechanisms for phosphorous removal remain largely unresolved.
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Affiliation(s)
- Didrik Villard
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway E-mail:
| | - Inger Andrea Nesbø Goa
- Faculty of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway
| | - Inga Leena Angell
- Faculty of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway
| | | | - Torgeir Saltnes
- Hias, Ottestad, Hamar, Norway; Hias How2O, Ottestad, Hamar, Norway
| | - Wenche Johansen
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Knut Rudi
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway; Faculty of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway
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Palmer M, Covington JK, Zhou EM, Thomas SC, Habib N, Seymour CO, Lai D, Johnston J, Hashimi A, Jiao JY, Muok AR, Liu L, Xian WD, Zhi XY, Li MM, Silva LP, Bowen BP, Louie K, Briegel A, Pett-Ridge J, Weber PK, Tocheva EI, Woyke T, Northen TR, Mayali X, Li WJ, Hedlund BP. Thermophilic Dehalococcoidia with unusual traits shed light on an unexpected past. THE ISME JOURNAL 2023:10.1038/s41396-023-01405-0. [PMID: 37041326 DOI: 10.1038/s41396-023-01405-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/13/2023]
Abstract
Although the phylum Chloroflexota is ubiquitous, its biology and evolution are poorly understood due to limited cultivability. Here, we isolated two motile, thermophilic bacteria from hot spring sediments belonging to the genus Tepidiforma and class Dehalococcoidia within the phylum Chloroflexota. A combination of cryo-electron tomography, exometabolomics, and cultivation experiments using stable isotopes of carbon revealed three unusual traits: flagellar motility, a peptidoglycan-containing cell envelope, and heterotrophic activity on aromatics and plant-associated compounds. Outside of this genus, flagellar motility has not been observed in Chloroflexota, and peptidoglycan-containing cell envelopes have not been described in Dehalococcoidia. Although these traits are unusual among cultivated Chloroflexota and Dehalococcoidia, ancestral character state reconstructions showed flagellar motility and peptidoglycan-containing cell envelopes were ancestral within the Dehalococcoidia, and subsequently lost prior to a major adaptive radiation of Dehalococcoidia into marine environments. However, despite the predominantly vertical evolutionary histories of flagellar motility and peptidoglycan biosynthesis, the evolution of enzymes for degradation of aromatics and plant-associated compounds was predominantly horizontal and complex. Together, the presence of these unusual traits in Dehalococcoidia and their evolutionary histories raise new questions about the timing and selective forces driving their successful niche expansion into global oceans.
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Affiliation(s)
- Marike Palmer
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
| | - Jonathan K Covington
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - En-Min Zhou
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 650091, Kunming, People's Republic of China
| | - Scott C Thomas
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Neeli Habib
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 650091, Kunming, People's Republic of China
- Department of Microbiology, Shaheed Benazir Bhutto Women University, Peshawar, Khyber Pakhtunkhwa (KPK), Pakistan
| | - Cale O Seymour
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Dengxun Lai
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Juliet Johnston
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Ameena Hashimi
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Alise R Muok
- Institute of Biology, Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Xiao-Yang Zhi
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 650091, Kunming, People's Republic of China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Leslie P Silva
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Benjamin P Bowen
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Katherine Louie
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ariane Briegel
- Institute of Biology, Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life and Environmental Sciences, University of California Merced, Merced, CA, 95343, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Elitza I Tocheva
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Tanja Woyke
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Life and Environmental Sciences, University of California Merced, Merced, CA, 95343, USA
| | - Trent R Northen
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
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Computational Insight into Intraspecies Distinctions in Pseudoalteromonas distincta: Carotenoid-like Synthesis Traits and Genomic Heterogeneity. Int J Mol Sci 2023; 24:ijms24044158. [PMID: 36835570 PMCID: PMC9966250 DOI: 10.3390/ijms24044158] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/10/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Advances in the computational annotation of genomes and the predictive potential of current metabolic models, based on more than thousands of experimental phenotypes, allow them to be applied to identify the diversity of metabolic pathways at the level of ecophysiology differentiation within taxa and to predict phenotypes, secondary metabolites, host-associated interactions, survivability, and biochemical productivity under proposed environmental conditions. The significantly distinctive phenotypes of members of the marine bacterial species Pseudoalteromonas distincta and an inability to use common molecular markers make their identification within the genus Pseudoalteromonas and prediction of their biotechnology potential impossible without genome-scale analysis and metabolic reconstruction. A new strain, KMM 6257, of a carotenoid-like phenotype, isolated from a deep-habituating starfish, emended the description of P. distincta, particularly in the temperature growth range from 4 to 37 °C. The taxonomic status of all available closely related species was elucidated by phylogenomics. P. distincta possesses putative methylerythritol phosphate pathway II and 4,4'-diapolycopenedioate biosynthesis, related to C30 carotenoids, and their functional analogues, aryl polyene biosynthetic gene clusters (BGC). However, the yellow-orange pigmentation phenotypes in some strains coincide with the presence of a hybrid BGC encoding for aryl polyene esterified with resorcinol. The alginate degradation and glycosylated immunosuppressant production, similar to brasilicardin, streptorubin, and nucleocidines, are the common predicted features. Starch, agar, carrageenan, xylose, lignin-derived compound degradation, polysaccharide, folate, and cobalamin biosynthesis are all strain-specific.
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Wang L, Zhan LJ, Wise MJ. Editorial: What does not kill you makes you stronger: Interactions between environmental stresses and microbial virulence. Front Microbiol 2023; 13:1127058. [PMID: 36699596 PMCID: PMC9869246 DOI: 10.3389/fmicb.2022.1127058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 01/12/2023] Open
Affiliation(s)
- Liang Wang
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China,Centre for Precision Health, School of Medical and Health Sciences, Edith Cowan University, Perth, WA, Australia,Liang Wang ✉
| | - Ling-Jun Zhan
- Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, Beijing, China,Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences, Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Michael J. Wise
- Department of Computer Science and Software Engineering, The University of Western Australia, Perth, WA, Australia,The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Perth, WA, Australia,*Correspondence: Michael J. Wise ✉
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9
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Gautam LK, Sharma P, Capalash N. Structural insight into substrate binding of Acinetobacter baumannii polyphosphate-AMP phosphotransferase (PPK2), a novel drug target. Biochem Biophys Res Commun 2022; 626:107-113. [PMID: 35987095 DOI: 10.1016/j.bbrc.2022.07.090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 07/23/2022] [Indexed: 11/02/2022]
Abstract
Acinetobacter baumannii is an opportunistic pathogen known for high morbidity and mortality. It causes life-threatening infections, such as ventilator-associated pneumonia (VAP), bacteremia, meningitis, wound and urinary tract infections (UTI). Increase in carbapenem resistance exhibited by A. baumannii has accentuated the need for novel targets for effective treatment. Despite the pronounced relevance of PPK2 as a pathogenicity determinant in several pathogens, it has not been explored as a drug target in A. baumannii. The present study was piloted to investigate the substrate binding by A. baumannii PPK2 (AbPPK2), a two-domain Class II polyphosphate kinase 2. A homology model of AbPPK2 was developed and validated for molecular docking of ATP and ADP in the predicted binding pocket. Further analysis of AbPPK2 revealed a set of common residues in the catalytic cleft interacting with ATP and ADP which would be useful for the screening of inhibitors against A. baumannii.
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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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10
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Geerlings NMJ, Kienhuis MVM, Hidalgo-Martinez S, Hageman R, Vasquez-Cardenas D, Middelburg JJ, Meysman FJR, Polerecky L. Polyphosphate Dynamics in Cable Bacteria. Front Microbiol 2022; 13:883807. [PMID: 35663875 PMCID: PMC9159916 DOI: 10.3389/fmicb.2022.883807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/18/2022] [Indexed: 11/14/2022] Open
Abstract
Cable bacteria are multicellular sulfide oxidizing bacteria that display a unique metabolism based on long-distance electron transport. Cells in deeper sediment layers perform the sulfide oxidizing half-reaction whereas cells in the surface layers of the sediment perform the oxygen-reducing half-reaction. These half-reactions are coupled via electron transport through a conductive fiber network that runs along the shared cell envelope. Remarkably, only the sulfide oxidizing half-reaction is coupled to biosynthesis and growth whereas the oxygen reducing half-reaction serves to rapidly remove electrons from the conductive fiber network and is not coupled to energy generation and growth. Cells residing in the oxic zone are believed to (temporarily) rely on storage compounds of which polyphosphate (poly-P) is prominently present in cable bacteria. Here we investigate the role of poly-P in the metabolism of cable bacteria within the different redox environments. To this end, we combined nanoscale secondary ion mass spectrometry with dual-stable isotope probing (13C-DIC and 18O-H2O) to visualize the relationship between growth in the cytoplasm (13C-enrichment) and poly-P activity (18O-enrichment). We found that poly-P was synthesized in almost all cells, as indicated by 18O enrichment of poly-P granules. Hence, poly-P must have an important function in the metabolism of cable bacteria. Within the oxic zone of the sediment, where little growth is observed, 18O enrichment in poly-P granules was significantly lower than in the suboxic zone. Thus, both growth and poly-P metabolism appear to be correlated to the redox environment. However, the poly-P metabolism is not coupled to growth in cable bacteria, as many filaments from the suboxic zone showed poly-P activity but did not grow. We hypothesize that within the oxic zone, poly-P is used to protect the cells against oxidative stress and/or as a resource to support motility, while within the suboxic zone, poly-P is involved in the metabolic regulation before cells enter a non-growing stage.
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Affiliation(s)
- Nicole M. J. Geerlings
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
- *Correspondence: Nicole M. J. Geerlings,
| | | | - Silvia Hidalgo-Martinez
- Excellence centre for Microbial Systems Technology, University of Antwerp, Wilrijk, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Renee Hageman
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
| | - Diana Vasquez-Cardenas
- Excellence centre for Microbial Systems Technology, University of Antwerp, Wilrijk, Belgium
| | | | - Filip J. R. Meysman
- Excellence centre for Microbial Systems Technology, University of Antwerp, Wilrijk, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Lubos Polerecky
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
- Lubos Polerecky,
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11
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Bowlin MQ, Long AR, Huffines JT, Gray MJ. The role of nitrogen-responsive regulators in controlling inorganic polyphosphate synthesis in Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2022; 168:001185. [PMID: 35482529 PMCID: PMC10233264 DOI: 10.1099/mic.0.001185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/10/2022] [Indexed: 12/22/2022]
Abstract
Inorganic polyphosphate (polyP) is synthesized by bacteria under stressful environmental conditions and acts by a variety of mechanisms to promote cell survival. While the kinase that synthesizes polyP (PPK, encoded by the ppk gene) is well known, ppk transcription is not activated by environmental stress and little is understood about how environmental stress signals lead to polyP accumulation. Previous work has shown that the transcriptional regulators DksA, RpoN (σ54) and RpoE (σ24) positively regulate polyP production, but not ppk transcription, in Escherichia coli. In this work, we examine the role of the alternative sigma factor RpoN and nitrogen starvation stress response pathways in controlling polyP synthesis. We show that the RpoN enhancer binding proteins GlnG and GlrR impact polyP production, and uncover a new role for the nitrogen phosphotransferase regulator PtsN (EIIANtr) as a positive regulator of polyP production, acting upstream of DksA, downstream of RpoN and apparently independently of RpoE. However, neither these regulatory proteins nor common nitrogen metabolites appear to act directly on PPK, and the precise mechanism(s) by which polyP production is modulated after stress remain(s) unclear. Unexpectedly, we also found that the genes that impact polyP production vary depending on the composition of the rich media in which the cells were grown before exposure to polyP-inducing stress. These results constitute progress towards deciphering the regulatory networks driving polyP production under stress, and highlight the remarkable complexity of this regulation and its connections to a broad range of stress-sensing pathways.
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Affiliation(s)
- Marvin Q. Bowlin
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Abagail Renee Long
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Joshua T. Huffines
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Michael Jeffrey Gray
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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12
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Bidaud CC, Monteil CL, Menguy N, Busigny V, Jézéquel D, Viollier É, Travert C, Skouri-Panet F, Benzerara K, Lefevre CT, Duprat É. Biogeochemical Niche of Magnetotactic Cocci Capable of Sequestering Large Polyphosphate Inclusions in the Anoxic Layer of the Lake Pavin Water Column. Front Microbiol 2022; 12:789134. [PMID: 35082768 PMCID: PMC8786505 DOI: 10.3389/fmicb.2021.789134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/19/2021] [Indexed: 11/13/2022] Open
Abstract
Magnetotactic bacteria (MTB) are microorganisms thriving mostly at oxic–anoxic boundaries of aquatic habitats. MTB are efficient in biomineralising or sequestering diverse elements intracellularly, which makes them potentially important actors in biogeochemical cycles. Lake Pavin is a unique aqueous system populated by a wide diversity of MTB with two communities harbouring the capability to sequester not only iron under the form of magnetosomes but also phosphorus and magnesium under the form of polyphosphates, or calcium carbonates, respectively. MTB thrive in the water column of Lake Pavin over a few metres along strong redox and chemical gradients representing a series of different microenvironments. In this study, we investigate the relative abundance and the vertical stratification of the diverse populations of MTB in relation to environmental parameters, by using a new method coupling a precise sampling for geochemical analyses, MTB morphotype description, and in situ measurement of the physicochemical parameters. We assess the ultrastructure of MTB as a function of depth using light and electron microscopy. We evidence the biogeochemical niche of magnetotactic cocci, capable of sequestering large PolyP inclusions below the oxic–anoxic transition zone. Our results suggest a tight link between the S and P metabolisms of these bacteria and pave the way to better understand the implication of MTB for the P cycle in stratified environmental conditions.
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Affiliation(s)
- Cécile C Bidaud
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590 - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France.,Aix-Marseille University, CNRS, CEA, UMR 7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, France.,Université de Paris, Centre de Recherches Interdisciplinaires (CRI), Paris, France
| | - Caroline L Monteil
- Aix-Marseille University, CNRS, CEA, UMR 7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, France
| | - Nicolas Menguy
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590 - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Vincent Busigny
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, France
| | - Didier Jézéquel
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris, France.,INRAE & Université Savoie Mont Blanc, UMR CARRTEL, Thonon-les-Bains, France
| | - Éric Viollier
- LSCE, CEA/CNRS/UVSQ/IPSL, Université Paris Saclay & Université de Paris France, Gif-sur-Yvette Cedex, France
| | - Cynthia Travert
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590 - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Fériel Skouri-Panet
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590 - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Karim Benzerara
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590 - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Christopher T Lefevre
- Aix-Marseille University, CNRS, CEA, UMR 7265 Institute of Biosciences and Biotechnologies of Aix-Marseille, CEA Cadarache, Saint-Paul-lez-Durance, France
| | - Élodie Duprat
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590 - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
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13
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Bhalla K, Qu X, Kretschmer M, Kronstad JW. The phosphate language of fungi. Trends Microbiol 2021; 30:338-349. [PMID: 34479774 DOI: 10.1016/j.tim.2021.08.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 11/20/2022]
Abstract
Phosphate is an essential macronutrient for fungal proliferation as well as a key mediator of antagonistic, beneficial, and pathogenic interactions between fungi and other organisms. In this review, we summarize recent insights into the integration of phosphate metabolism with mechanisms of fungal adaptation that support growth and survival. In particular, we highlight aspects of phosphate sensing important for responses to stress and regulation of cell-surface changes with an impact on fungal pathogenesis, host immune responses, and disease outcomes. Additionally, new studies provide insights into the influence of phosphate availability on cooperative or antagonistic interactions between fungi and other microbes, the associations of mycorrhizal and endophytic fungi with plants, and connections with plant immunity. Overall, phosphate homeostasis is emerging as an integral part of fungal metabolism and communication to support diverse lifestyles.
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Affiliation(s)
- Kabir Bhalla
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Xianya Qu
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Matthias Kretschmer
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - James W Kronstad
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.
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14
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Bacterial Biopolymer: Its Role in Pathogenesis to Effective Biomaterials. Polymers (Basel) 2021; 13:polym13081242. [PMID: 33921239 PMCID: PMC8069653 DOI: 10.3390/polym13081242] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 12/17/2022] Open
Abstract
Bacteria are considered as the major cell factories, which can effectively convert nitrogen and carbon sources to a wide variety of extracellular and intracellular biopolymers like polyamides, polysaccharides, polyphosphates, polyesters, proteinaceous compounds, and extracellular DNA. Bacterial biopolymers find applications in pathogenicity, and their diverse materialistic and chemical properties make them suitable to be used in medicinal industries. When these biopolymer compounds are obtained from pathogenic bacteria, they serve as important virulence factors, but when they are produced by non-pathogenic bacteria, they act as food components or biomaterials. There have been interdisciplinary studies going on to focus on the molecular mechanism of synthesis of bacterial biopolymers and identification of new targets for antimicrobial drugs, utilizing synthetic biology for designing and production of innovative biomaterials. This review sheds light on the mechanism of synthesis of bacterial biopolymers and its necessary modifications to be used as cell based micro-factories for the production of tailor-made biomaterials for high-end applications and their role in pathogenesis.
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15
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Roy S, Guanglei Q, Zuniga-Montanez R, Williams RB, Wuertz S. Recent advances in understanding the ecophysiology of enhanced biological phosphorus removal. Curr Opin Biotechnol 2021; 67:166-174. [PMID: 33582603 DOI: 10.1016/j.copbio.2021.01.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 01/02/2023]
Abstract
Enhanced biological phosphorus removal (EBPR) is an efficient, cost-effective, and sustainable method for removing excess phosphorus from wastewater. Polyphosphate accumulating organisms (PAOs) exhibit a unique physiology alternating between anaerobic conditions for uptake of carbon substrates and aerobic or anoxic conditions for phosphorus uptake. The implementation of high-throughput sequencing technologies and advanced molecular tools along with biochemical characterization has provided many new perspectives on the EBPR process. These approaches have helped identify a wide range of carbon substrates and electron acceptors utilized by PAOs that in turn influence interactions with microbial community members and determine overall phosphorus removal efficiency. In this review, we systematically discuss the microbial diversity and metabolic response to a range of environmental conditions and process control strategies in EBPR.
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Affiliation(s)
- Samarpita Roy
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore 119077, Singapore
| | - Qiu Guanglei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Rogelio Zuniga-Montanez
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; Department of Civil and Environmental Engineering, University of California, One Shields Avenue, Davis, CA 95616, United States
| | - Rohan Bh Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore 119077, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; Department of Civil and Environmental Engineering, University of California, One Shields Avenue, Davis, CA 95616, United States; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798, Singapore.
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16
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Requirement of the exopolyphosphatase gene for cellular acclimation to phosphorus starvation in a cyanobacterium, Synechocystis sp. PCC 6803. Biochem Biophys Res Commun 2021; 540:16-21. [PMID: 33429195 DOI: 10.1016/j.bbrc.2020.12.095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 12/28/2020] [Indexed: 11/22/2022]
Abstract
Polyphosphate, which is ubiquitous in cells in nature, is involved in a myriad of cellular functions, and has been recently focused on its metabolism related with microbial acclimation to phosphorus-source fluctuation. In view of the ecological importance of cyanobacteria as the primary producers, this study investigated the responsibility of polyphosphate metabolism for cellular acclimation to phosphorus starvation in a cyanobacterium, Synechocystis sp. PCC 6803, with the use of a disruptant (Δppx) as to the gene of exopolyphosphatase that is responsible for polyphosphate degradation. Δppx was similar to the wild type in the cellular content of polyphosphate to show no defect in cell growth under phosphorus-replete conditions. However, under phosphorus-starved conditions, Δppx cells were defective in a phosphorus-starvation dependent decrease of polyphosphate to show deleterious phenotypes as to their survival and the stabilization of the photosystem complexes. These results demonstrated some crucial role of exopolyphosphatase to degrade polyP in the acclimation of cyanobacterial cells to phosphorus-starved conditions. Besides, it was found that ppx expression is induced in Synechocystis cells in response to phosphorus starvation through the action of the two-component system, SphS and SphR, in the phosphate regulon. The information will be a foundation for a fuller understanding of the process of cyanobacterial acclimation to phosphorus fluctuation.
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17
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Chen H, Zhang YHPJ. Enzymatic regeneration and conservation of ATP: challenges and opportunities. Crit Rev Biotechnol 2020; 41:16-33. [PMID: 33012193 DOI: 10.1080/07388551.2020.1826403] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Adenosine triphosphate (ATP), the universal energy currency of life, has a central role in numerous biochemical reactions with potential for the synthesis of numerous high-value products. ATP can be regenerated by three types of mechanisms: substrate level phosphorylation, oxidative phosphorylation, and photophosphorylation. Current ATP regeneration methods are mainly based on substrate level phosphorylation catalyzed by one enzyme, several cascade enzymes, or in vitro synthetic enzymatic pathways. Among them, polyphosphate kinases and acetate kinase, along with their respective phosphate donors, are the most popular approaches for in vitro ATP regeneration. For in vitro artificial pathways, either ATP-free or ATP-balancing strategies can be implemented via smart pathway design by choosing ATP-independent enzymes. Also, we discuss some remaining challenges and suggest perspectives, especially for industrial biomanufacturing. Development of ATP regeneration systems featuring low cost, high volumetric productivity, long lifetime, flexible compatibility, and great robustness could be one of the bottom-up strategies for cascade biocatalysis and in vitro synthetic biology.
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Affiliation(s)
- Hongge Chen
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yi-Heng P Job Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin Airport Economic Area, Tianjin, China
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18
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Abstract
Bacteria are prime cell factories that can efficiently convert carbon and nitrogen sources into a large diversity of intracellular and extracellular biopolymers, such as polysaccharides, polyamides, polyesters, polyphosphates, extracellular DNA and proteinaceous components. Bacterial polymers have important roles in pathogenicity, and their varied chemical and material properties make them suitable for medical and industrial applications. The same biopolymers when produced by pathogenic bacteria function as major virulence factors, whereas when they are produced by non-pathogenic bacteria, they become food ingredients or biomaterials. Interdisciplinary research has shed light on the molecular mechanisms of bacterial polymer synthesis, identified new targets for antibacterial drugs and informed synthetic biology approaches to design and manufacture innovative materials. This Review summarizes the role of bacterial polymers in pathogenesis, their synthesis and their material properties as well as approaches to design cell factories for production of tailor-made bio-based materials suitable for high-value applications.
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Affiliation(s)
- M Fata Moradali
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Bernd H A Rehm
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD, Australia.
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19
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Wang L, Wang M, Wise MJ, Liu Q, Yang T, Zhu Z, Li C, Tan X, Tang D, Wang W. Recent progress in the structure of glycogen serving as a durable energy reserve in bacteria. World J Microbiol Biotechnol 2020; 36:14. [PMID: 31897771 DOI: 10.1007/s11274-019-2795-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 12/23/2019] [Indexed: 12/18/2022]
Abstract
Glycogen is conventionally considered as a transient energy reserve that can be rapidly synthesized for glucose accumulation and mobilized for ATP production. However, this conception is not completely applicable to prokaryotes due to glycogen structural heterogeneity. A number of studies noticed that glycogen with small average chain length gc in bacteria has the potential to degrade slowly, which might prolong bacterial environment survival. This phenomenon was previously examined and later formulated as the durable energy storage mechanism hypothesis. Although recent research has been warming to the hypothesis, experimental validation is still missing at current stage. In this review, we summarized recent progress of the hypothesis, provided a supporting mathematical model, and explored the technical pitfalls that shall be avoided in glycogen study.
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Affiliation(s)
- Liang Wang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China.
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China.
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
| | - Mengmeng Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
- Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
| | - Michael J Wise
- The Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Perth, WA, 6009, Australia
- Computer Science and Software Engineering, Faculty of Engineering and Mathematical Sciences, University of Western Australia, Perth, WA, 6009, Australia
| | - Qinghua Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
- Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
| | - Ting Yang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
| | - Zuobin Zhu
- Department of Genetics, School of Life Science, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
| | - Chengcheng Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Xinle Tan
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Daoquan Tang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
- Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
| | - Wei Wang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, 221000, Jiangsu, China
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, 6027, Australia
- The First Affiliated Hospital, Medical College of Shantou University, Shantou, 515041, Guangdong, China
- School of Public Health, Taishan Medical University, Tai'an, 271000, Shandong, China
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20
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Complex Responses to Hydrogen Peroxide and Hypochlorous Acid by the Probiotic Bacterium Lactobacillus reuteri. mSystems 2019; 4:4/5/e00453-19. [PMID: 31481604 PMCID: PMC6722424 DOI: 10.1128/msystems.00453-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Inflammatory diseases of the gut are associated with increased intestinal oxygen concentrations and high levels of inflammatory oxidants, including hydrogen peroxide (H2O2) and hypochlorous acid (HOCl), which are antimicrobial compounds produced by the innate immune system. This contributes to dysbiotic changes in the gut microbiome, including increased populations of proinflammatory enterobacteria (Escherichia coli and related species) and decreased levels of health-associated anaerobic Firmicutes and Bacteroidetes The pathways for H2O2 and HOCl resistance in E. coli have been well studied, but little is known about how commensal and probiotic bacteria respond to inflammatory oxidants. In this work, we have characterized the transcriptomic response of the anti-inflammatory, gut-colonizing Gram-positive probiotic Lactobacillus reuteri to both H2O2 and HOCl. L. reuteri mounts distinct but overlapping responses to each of these stressors, and both gene expression and survival were strongly affected by the presence or absence of oxygen. Oxidative stress response in L. reuteri required several factors not found in enterobacteria, including the small heat shock protein Lo18, polyphosphate kinase 2, and RsiR, an L. reuteri-specific regulator of anti-inflammatory mechanisms.IMPORTANCE Reactive oxidants, including hydrogen peroxide and hypochlorous acid, are antimicrobial compounds produced by the immune system during inflammation. Little is known, however, about how many important types of bacteria present in the human microbiome respond to these oxidants, especially commensal and other health-associated species. We have now mapped the stress response to both H2O2 and HOCl in the intestinal lactic acid bacterium Lactobacillus reuteri.
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Abstract
Cable bacteria of the family Desulfobulbaceae form centimeter-long filaments comprising thousands of cells. They occur worldwide in the surface of aquatic sediments, where they connect sulfide oxidation with oxygen or nitrate reduction via long-distance electron transport. In the absence of pure cultures, we used single-filament genomics and metagenomics to retrieve draft genomes of 3 marine Candidatus Electrothrix and 1 freshwater Ca. Electronema species. These genomes contain >50% unknown genes but still share their core genomic makeup with sulfate-reducing and sulfur-disproportionating Desulfobulbaceae, with few core genes lost and 212 unique genes (from 197 gene families) conserved among cable bacteria. Last common ancestor analysis indicates gene divergence and lateral gene transfer as equally important origins of these unique genes. With support from metaproteomics of a Ca. Electronema enrichment, the genomes suggest that cable bacteria oxidize sulfide by reversing the canonical sulfate reduction pathway and fix CO2 using the Wood-Ljungdahl pathway. Cable bacteria show limited organotrophic potential, may assimilate smaller organic acids and alcohols, fix N2, and synthesize polyphosphates and polyglucose as storage compounds; several of these traits were confirmed by cell-level experimental analyses. We propose a model for electron flow from sulfide to oxygen that involves periplasmic cytochromes, yet-unidentified conductive periplasmic fibers, and periplasmic oxygen reduction. This model proposes that an active cable bacterium gains energy in the anodic, sulfide-oxidizing cells, whereas cells in the oxic zone flare off electrons through intense cathodic oxygen respiration without energy conservation; this peculiar form of multicellularity seems unparalleled in the microbial world.
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Wang L, Yang J, Huang Y, Liu Q, Xu Y, Piao X, Wise MJ. Systematic Analysis of Metabolic Pathway Distributions of Bacterial Energy Reserves. G3 (BETHESDA, MD.) 2019; 9:2489-2496. [PMID: 31151997 PMCID: PMC6686919 DOI: 10.1534/g3.119.400123] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/28/2019] [Indexed: 01/08/2023]
Abstract
Previous bioinformatics studies have linked gain or loss of energy reserves with host-pathogen interactions and bacterial virulence based on a comparatively small number of bacterial genomes or proteomes. Thus, understanding the theoretical distribution patterns of energy reserves across bacterial species could provide a shortcut route to look into bacterial lifestyle and physiology. So far, five major energy reserves have been identified in bacteria due to their capacity to support bacterial persistence under nutrient deprivation conditions. These include polyphosphate (polyP), glycogen, wax ester (WE), triacylglycerol (TAG), and polyhydroxyalkanoates (PHAs). Although the enzymes related with metabolism of energy reserves are well understood, there is a lack of systematic investigations into the distribution of bacterial energy reserves from an evolutionary point of view. In this study, we sourced 8282 manually reviewed bacterial reference proteomes and combined a set of hidden Markov sequence models (HMMs) to search homologs of key enzymes related with the metabolism of energy reserves. Our results revealed that specific pathways like trehalose-related glycogen metabolism and enzymes such as wax ester synthase/acyl-CoA:diacylglycerol acyltransferase (WS/DGAT) are mainly restricted within specific types of bacterial groups, which provides evolutionary insights into the understanding of their origins and functions. In addition, the study also confirms that loss of energy reserves like polyP metabolism absence in Mollicutes is correlated with bacterial genome reduction. Through this analysis, a clearer picture about the metabolism of energy reserves in bacteria is presented, which could serve as a guide for further theoretical and experimental analyses of bacterial energy metabolism.
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Affiliation(s)
- Liang Wang
- Department of Bioinformatics, School of Medical Informatics,
- Jiangsu Key Lab of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu Province, 221000, China
| | - Jianye Yang
- Department of Bioinformatics, School of Medical Informatics
| | - Yue Huang
- Department of Bioinformatics, School of Medical Informatics
| | - Qinghua Liu
- Jiangsu Key Lab of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu Province, 221000, China
| | - Yaping Xu
- Department of Bioinformatics, School of Medical Informatics
| | - Xue Piao
- Department of Bioinformatics, School of Medical Informatics
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, Jiangsu, 221116, China
| | - Michael J Wise
- Department of Computer Science and Software Engineering, and
- The Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Perth 6009, WA, Australia
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23
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Wang L, Yang J, Xu Y, Piao X, Lv J. Domain-based Comparative Analysis of Bacterial Proteomes: Uniqueness, Interactions, and the Dark Matter. Curr Genomics 2019; 20:115-123. [PMID: 31555062 PMCID: PMC6728903 DOI: 10.2174/1389202920666190320134438] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 11/15/2018] [Accepted: 01/10/2019] [Indexed: 01/05/2023] Open
Abstract
Background Proteins may have none, single, double, or multiple domains, while a single domain may appear in multiple proteins. Their distribution patterns may have impacts on bacterial physi-ology and lifestyle.Objective: This study aims to understand how domains are distributed and duplicated in bacterial prote-omes, in order to better understand bacterial physiology and lifestyles. Methods In this study, we used 16712 Hidden Markov Models to screen 944 bacterial reference prote-omes versus a threshold E-value<0.001. The number of non-redundant domains and duplication rates of redundant domains for each species were calculated. The unique domains, if any, were also identified for each species. In addition, the properties of no-domain proteins were investigated in terms of physico-chemical properties. Results The increasing number of non-redundant domains for a bacterial proteome follows the trend of an asymptotic function. The domain duplication rate is positively correlated with proteome size and in-creases more rapidly. The high percentage of single-domain proteins is more associated with small pro-teome size. For each proteome, unique domains were also obtained. Moreover, no-domain proteins show differences with the other three groups for several physicochemical properties analysed in this study. Conclusion The study confirmed that a low domain duplication rate and a high percentage of single-domain proteins are more likely to be associated with bacterial host-dependent or restricted niche-adapted lifestyle. In addition, the unique lifestyle and physiology were revealed based on the analysis of species-specific domains and core domain interactions or co-occurrences.
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Affiliation(s)
- Liang Wang
- 1Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, P.R. China; 2Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, P.R. China; 3School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, Jiangsu, 221116, P.R. China
| | - Jianye Yang
- 1Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, P.R. China; 2Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, P.R. China; 3School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, Jiangsu, 221116, P.R. China
| | - Yaping Xu
- 1Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, P.R. China; 2Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, P.R. China; 3School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, Jiangsu, 221116, P.R. China
| | - Xue Piao
- 1Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, P.R. China; 2Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, P.R. China; 3School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, Jiangsu, 221116, P.R. China
| | - Jichang Lv
- 1Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, P.R. China; 2Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, Xuzhou Medical University, Xuzhou, Jiangsu, 221000, P.R. China; 3School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, Jiangsu, 221116, P.R. China
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Mailer RKW, Hänel L, Allende M, Renné T. Polyphosphate as a Target for Interference With Inflammation and Thrombosis. Front Med (Lausanne) 2019; 6:76. [PMID: 31106204 PMCID: PMC6499166 DOI: 10.3389/fmed.2019.00076] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/28/2019] [Indexed: 12/19/2022] Open
Abstract
Activated platelets and mast cells expose the inorganic polymer, polyphosphate (polyP) on their surfaces. PolyP initiates procoagulant and proinflammatory reactions and the polymer has been recognized as a therapeutic target for interference with blood coagulation and vascular hyperpermeability. PolyP content and chain length depend on the specific cell type and energy status, which may affect cellular functions. PolyP metabolism has mainly been studied in bacteria and yeast, but its roles in eukaryotic cells and mammalian systems have remained enigmatic. In this review, we will present an overview of polyP functions, focusing on intra- and extracellular roles of the polymer and discuss open questions that emerge from the current knowledge on polyP regulation.
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Affiliation(s)
- Reiner K W Mailer
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lorena Hänel
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mikel Allende
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Renné
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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25
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Inorganic Polyphosphate Accumulation in Escherichia coli Is Regulated by DksA but Not by (p)ppGpp. J Bacteriol 2019; 201:JB.00664-18. [PMID: 30745375 DOI: 10.1128/jb.00664-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/07/2019] [Indexed: 12/25/2022] Open
Abstract
Production of inorganic polyphosphate (polyP) by bacteria is triggered by a variety of different stress conditions. polyP is required for stress survival and virulence in diverse pathogenic microbes. Previous studies have hypothesized a model for regulation of polyP synthesis in which production of the stringent-response second messenger (p)ppGpp directly stimulates polyP accumulation. In this work, I have now shown that this model is incorrect, and (p)ppGpp is not required for polyP synthesis in Escherichia coli However, stringent mutations of RNA polymerase that frequently arise spontaneously in strains defective in (p)ppGpp synthesis and null mutations of the stringent-response-associated transcription factor DksA both strongly inhibit polyP accumulation. The loss of polyP synthesis in a mutant lacking DksA was reversed by deletion of the transcription elongation factor GreA, suggesting that competition between these proteins for binding to the secondary channel of RNA polymerase plays an important role in controlling polyP activation. These results provide new insights into the poorly understood regulation of polyP synthesis in bacteria and indicate that the relationship between polyP and the stringent response is more complex than previously suspected.IMPORTANCE Production of polyP in bacteria is required for virulence and stress response, but little is known about how bacteria regulate polyP levels in response to changes in their environments. Understanding this regulation is important for understanding how pathogenic microbes resist killing by disinfectants, antibiotics, and the immune system. In this work, I have clarified the connections between polyP regulation and the stringent response to starvation stress in Escherichia coli and demonstrated an important and previously unknown role for the transcription factor DksA in controlling polyP levels.
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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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27
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Wang L, Liu Q, Wu X, Huang Y, Wise MJ, Liu Z, Wang W, Hu J, Wang C. Bioinformatics Analysis of Metabolism Pathways of Archaeal Energy Reserves. Sci Rep 2019; 9:1034. [PMID: 30705313 PMCID: PMC6355812 DOI: 10.1038/s41598-018-37768-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 12/13/2018] [Indexed: 11/08/2022] Open
Abstract
Energy storage compounds play crucial roles in prokaryotic physiology. Five chemical compounds have been identified in prokaryotes as energy reserves: polyphosphate (polyP), polyhydroxyalkanoates (PHAs), glycogen, wax ester (WE) and triacylglycerol (TAG). Currently, no systematic study of archaeal energy storage metabolism exists. In this study, we collected 427 archaeal reference sequences from UniProt database. A thorough pathway screening of energy reserves led to an overview of distribution patterns of energy metabolism in archaea. We also explored how energy metabolism might have impact on archaeal extremophilic phenotypes. Based on the systematic analyses of archaeal proteomes, we confirmed that metabolism pathways of polyP, PHAs and glycogen are present in archaea, but TAG and WE are completely absent. It was also confirmed that PHAs are tightly related to halophilic archaea with larger proteome size and higher GC contents, while polyP is mainly present in methanogens. In sum, this study systematically investigates energy storage metabolism in archaea and provides a clear correlation between energy metabolism and the ability to survive in extreme environments. With more genomic editing tools developed for archaea and molecular mechanisms unravelled for energy storage metabolisms (ESMs), there will be a better understanding of the unique lifestyle of archaea in extreme environments.
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Affiliation(s)
- Liang Wang
- Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, Jiangsu, China.
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China.
| | - Qinghua Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xiang Wu
- Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yue Huang
- Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Michael J Wise
- The Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Perth, Western Australia, Australia
- Department of Computer Science and Software Engineering, School of Physics, Mathematics and Computing, University of Western Australia, Perth, Western Australia, Australia
| | - Zhanzhong Liu
- Xuzhou Infectious Diseases Hospital, Xuzhou, Jiangsu, China
| | - Wei Wang
- Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, Jiangsu, China
- School of Public Health, Capital Medical University, Beijing, China
- School of Medical Sciences, Edith Cowan University, Perth, WA, Australia
| | - Junfeng Hu
- Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Department of Computer Science, School of Medical Informatics, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Chunying Wang
- Xuzhou Infectious Diseases Hospital, Xuzhou, Jiangsu, China
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