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Zhu YX, Zhang X, Yang WC, Li JF. Enhancement of Biomass Conservation and Bioethanol Production of Sweet Sorghum Silage by Constructing Synergistic Microbial Consortia. Microbiol Spectr 2023; 11:e0365922. [PMID: 36645314 PMCID: PMC9927380 DOI: 10.1128/spectrum.03659-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/20/2022] [Indexed: 01/17/2023] Open
Abstract
The efficient storage of materials before bioethanol production could be key to improving pretreatment protocol and facilitating biodegradation, in turn improving the cost-effectiveness of biomass utilization. Biological inoculants were investigated for their effects on ensiling performance, biodegradability of silage materials, and final bioethanol yield from sweet sorghum. Two cellulolytic microbial consortia (CF and PY) were used to inoculate silages of sweet sorghum, with and without combined lactic acid bacteria (Xa), for up to 60 days of ensiling. We found that the consortia notably decreased pH and ammonia nitrogen content while increasing lactic acid/acetic acid ratios. The microbes also functioned in synergy with Xa, significantly reducing lignocellulose content and improving biomass preservation. First-order exponential decay models captured the kinetics of nonstructural carbohydrates and suggested high water-soluble carbohydrate (grams per kilogram dry matter [DM]) preservation potential in PY-Xa (33.48), followed by CF-Xa (30.51). Combined addition efficiently improved enzymatic hydrolysis and enhanced bioethanol yield, and sweet sorghum treated with PY-Xa had the highest ethanol yield (28.42 g L-1). Thus, combined bioaugmentation of synergistic microbes provides an effective method of improving biomass preservation and bioethanol production from sweet sorghum silages. IMPORTANCE Ensiling is an effective storage approach to ensure stable year-round supply for downstream biofuel production; it offers combined facilities of storage and pretreatment. There are challenges in ensiling sweet sorghum due to its coarse structure and high fiber content. This study provides a meaningful evaluation of the effects of adding microbial consortia, with and without lactic acid bacteria, on changes in key properties of sweet sorghum. This study highlighted the bioaugmented ensiling using cellulolytic synergistic microbes to outline a cost-effective strategy to store and pretreat sweet sorghum for bioethanol production.
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Affiliation(s)
- Yu-Xi Zhu
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Xu Zhang
- College of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Nanjing, China
| | - Wen-Chao Yang
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Jun-Feng Li
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, China
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2
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Broten CJ, Wydallis JB, Reilly TH, Bisha B. Development and Evaluation of a Paper-Based Microfluidic Device for Detection of Listeria monocytogenes on Food Contact and Non-Food Contact Surfaces. Foods 2022; 11:foods11070947. [PMID: 35407034 PMCID: PMC8997480 DOI: 10.3390/foods11070947] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/14/2022] [Accepted: 03/21/2022] [Indexed: 01/27/2023] Open
Abstract
Listeria monocytogenes is the third most deadly foodborne pathogen in the United States. The bacterium is found in soil and water, contaminating raw food products and the processing environment, where it can persist for an extended period. Currently, testing of food contact and non-food contact surfaces is performed using an array of sampling devices and endpoint technologies, offering various levels of sensitivity, cost, user skill, and time to detection. Paper-based microfluidic devices (µPADs) are a rapid detection platform amenable to low-cost, user-friendly, and portable diagnostics. In this study, we developed and evaluated a µPAD platform specific for the colorimetric detection of the Listeria genus following recovery from food contact and non-food contact surfaces. For detection, four colorimetric substrates specific for the detection of β-glucosidase, two broths selective for the detection of Listeria spp., and a nonselective broth were evaluated to facilitate detection of Listeria spp. The limit of detection and time to detection were determined by using pure bacterial cultures. After 8 h enrichment, L. monocytogenes (102 Colony Forming Units (CFU)/coupon) was detected on every surface. After 18 h enrichment, L. monocytogenes (102 CFU/coupon) was detected on all surfaces with all swabbing devices. This study demonstrated the ability of the µPAD-based method to detect potentially stressed cells at low levels of environmental contamination.
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Affiliation(s)
- Codi Jo Broten
- Department of Animal Science, University of Wyoming, Laramie, WY 82071, USA;
| | - John B. Wydallis
- Access Sensor Technologies, Fort Collins, CO 80524, USA; (J.B.W.); (T.H.R.III)
| | - Thomas H. Reilly
- Access Sensor Technologies, Fort Collins, CO 80524, USA; (J.B.W.); (T.H.R.III)
| | - Bledar Bisha
- Department of Animal Science, University of Wyoming, Laramie, WY 82071, USA;
- Correspondence:
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3
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Shivaperumal N, Knight DR, Imwattana K, Androga GO, Chang BJ, Riley TV. Esculin hydrolysis negative and TcdA‐only producing strains of
Clostridium (Clostridiodes) difficile
from the environment in Western Australia. J Appl Microbiol 2022; 133:1183-1196. [PMID: 35184359 PMCID: PMC9544920 DOI: 10.1111/jam.15500] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 02/10/2022] [Accepted: 02/15/2022] [Indexed: 12/03/2022]
Abstract
Background and Aims Clostridium (Clostridiodes) difficile clade 3 ribotype (RT) 023 strains that fail to produce black colonies on bioMérieux ChromID agar have been reported, as well as variant strains of C. difficile that produce only toxin A. We have recently isolated strains of C. difficile from the environment in Western Australia (WA) with similar characteristics. The objective of this study was to characterize these strains. It was hypothesized that a putative β‐glucosidase gene was lacking in these strains of C. difficile, including RT 023, leading to white colonies. Methods and Results A total of 17 environmental isolates of C. difficile from garden soil and compost, and gardening shoe soles in Perth, WA, failed to produce black colonies on ChromID agar. MALDI‐TOF MS analysis confirmed these strains as C. difficile. Four strains contained only a tcdA gene (A+B−CDT−) by PCR and were a novel RT (QX 597). All isolates were susceptible to all antimicrobials tested except one with low‐level resistance to clindamycin (MIC = 8 mg/L). The four tcdA‐positive strains were motile. All isolates contained neither bgl locus but only bgl K or a putative β‐glucosidase gene by PCR. Whole‐genome sequencing showed the 17 strains belonged to novel multi‐locus sequence types 632, 848, 849, 850, 851, 852 and 853, part of the evolutionarily divergent clade C‐III. Four isolates carried a full‐length tcdA but not tcdB nor binary toxin genes. Conclusions ChromID C. difficile agar is used for the specific detection of C. difficile in the samples. To date, all strains except RT 023 strains from clinical samples hydrolyse esculin. This is the first report to provide insights into the identification of esculin hydrolysis negative and TcdA‐only producing (A+B−CDT−) strains of C. difficile from environmental samples. Significance and Impact of the Study White colonies of C. difficile from environmental samples could be overlooked when using ChromID C. difficile agar, leading to false‐negative results, however, whether these strains are truly pathogenic remains to be proven.
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Affiliation(s)
| | - Daniel R. Knight
- Biosecurity and One Health Research Centre, Harry Butler Institute Murdoch University Murdoch Western Australia Australia
| | | | - Grace O. Androga
- School of Biomedical Sciences Nedlands Western Australia Australia
- Current address: HIV, Inflammation and Microbiome Group Burnet Institute Melbourne Victoria Australia
| | - Barbara J. Chang
- School of Biomedical Sciences Nedlands Western Australia Australia
| | - Thomas V. Riley
- School of Biomedical Sciences Nedlands Western Australia Australia
- Biosecurity and One Health Research Centre, Harry Butler Institute Murdoch University Murdoch Western Australia Australia
- PathWest Laboratory Medicine, Department of Microbiology, Queen Elizabeth II Medical Centre Nedlands Western Australia Australia
- School of Medical and Health Sciences Edith Cowan University Joondalup Western Australia Australia
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4
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Li J, Wang S, Zhao J, Dong Z, Liu Q, Dong D, Shao T. Two novel screened microbial consortia and their application in combination with Lactobacillus plantarum for improving fermentation quality of high-moisture alfalfa. J Appl Microbiol 2021; 132:2572-2582. [PMID: 34839576 DOI: 10.1111/jam.15388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 11/02/2021] [Accepted: 11/24/2021] [Indexed: 11/29/2022]
Abstract
AIMS To enrich lignocellulolytic microbial consortia and evaluate whether a combination of these consortia and Lactobacillus plantarum can facilitate degradation of structural carbohydrates and improve fermentation quality of high-moisture alfalfa silage. METHODS AND RESULTS Two novel microbial consortia (CL and YL) with high lignocellulolytic potential were enriched, and had higher enzyme activities at slightly acidic conditions (pH 3.5-6.5). Two consortia were inoculated with and without combined L. plantarum (LP) to alfalfa for up to 120 days of ensiling. The two consortia alone or combined with LP significantly (p < 0.05) increased lactic-to-acetic acid ratios and decreased contents of volatile organic acids and NH3 -N as compared to the control. Treatments that combining microbial consortia and LP further resulted in the higher contents of lactic acid (LA), water soluble carbohydrates (WSC) and crude protein, dry matter (DM) recovery, and lower neutral detergent fibre, acid detergent lignin and cellulose contents, with YLP silage showing the lowest pH (4.41) and highest LA content (76.72 g kg-1 DM) and the conversion of WSC into LA (184.03%). CONCLUSIONS The addition of lignocellulolytic microbial consortia (CL or YL) to alfalfa silages as attractive silage inoculants could improve fermentation quality, and that their combination with L. plantarum appeared more effective on the degradation of structural carbohydrates and conversion of soluble carbohydrates into LA. SIGNIFICANCE AND IMPACT OF THE STUDY High-moisture alfalfa is difficult to ensile due to its high buffering capacity and low readily fermentable carbohydrate contents. Microbial consortia (CL and YL) can encode a broad selection of multi-functional CAZymes, and their combination with LP could be promising for the degradation of structural carbohydrates simultaneously with improvement fermentation quality, with high performance in LA production.
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Affiliation(s)
- Junfeng Li
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Siran Wang
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Jie Zhao
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Zhihao Dong
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Qinhua Liu
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Dong Dong
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Tao Shao
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
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5
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A Galactosidase-Activatable Fluorescent Probe for Detection of Bacteria Based on BODIPY. Molecules 2021; 26:molecules26196072. [PMID: 34641615 PMCID: PMC8512000 DOI: 10.3390/molecules26196072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/03/2021] [Accepted: 10/05/2021] [Indexed: 11/16/2022] Open
Abstract
Pathogenic E. coli infection is one of the most widespread foodborne diseases, so the development of sensitive, reliable and easy operating detection tests is a key issue for food safety. Identifying bacteria with a fluorescent medium is more sensitive and faster than using chromogenic media. This study designed and synthesized a β-galactosidase-activatable fluorescent probe BOD-Gal for the sensitive detection of E. coli. It employed a biocompatible and photostable 4,4-difluoro-3a,4a-diaza-s-indancene (BODIPY) as the fluorophore to form a β-O-glycosidic bond with galactose, allowing the BOD-Gal to show significant on-off fluorescent signals for in vitro and in vivo bacterial detection. This work shows the potential for the use of a BODIPY based enzyme substrate for pathogen detection.
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6
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Karnaouri A, Zerva A, Christakopoulos P, Topakas E. Screening of Recombinant Lignocellulolytic Enzymes Through Rapid Plate Assays. Methods Mol Biol 2021; 2178:479-503. [PMID: 33128767 DOI: 10.1007/978-1-0716-0775-6_30] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In the search for novel biomass-degrading enzymes through mining microbial genomes, it is necessary to apply functional tests during high-throughput screenings, which are capable of detecting enzymatic activities directly by way of plate assay. Using the most efficient expression systems of Escherichia coli and Pichia pastoris, the production of a high amount of His-tagged recombinant proteins could be thrived, allowing the one-step isolation by affinity chromatography. Here, we describe simple and efficient assay techniques for the detection of various biomass-degrading enzymatic activities on agar plates, such as cellulolytic, hemicellulolytic, and ligninolytic activities and their isolation using immobilized-metal affinity chromatography.
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Affiliation(s)
- Anthi Karnaouri
- Industrial Biotechnology and Biocatalysis Group, Biotechnology Laboratory, Department of Synthesis and Development of Industrial Processes, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Anastasia Zerva
- Industrial Biotechnology and Biocatalysis Group, Biotechnology Laboratory, Department of Synthesis and Development of Industrial Processes, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Paul Christakopoulos
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
| | - Evangelos Topakas
- Industrial Biotechnology and Biocatalysis Group, Biotechnology Laboratory, Department of Synthesis and Development of Industrial Processes, School of Chemical Engineering, National Technical University of Athens, Athens, Greece.
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden.
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7
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Jeong H, Han N, Hwang DW, Ko HM. B(C 6F 5) 3-Catalyzed Highly Chemoselective Reduction of Isatins: Synthesis of Indolin-3-ones and Indolines. Org Lett 2020; 22:8150-8155. [PMID: 33021380 DOI: 10.1021/acs.orglett.0c03150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A chemo- and site-selective reduction reaction of isatin derivatives using catalyst B(C6F5)3 and hydrosilanes is described. This transformation is operationally simple, proceeds under mild conditions, and is resistant to various functional groups. Thus, this efficient reaction using a combination of B(C6F5)3 and BnMe2SiH or B(C6F5)3 and Et2SiH2 could potentially be utilized to produce various indolin-3-ones and indolines, without the need for multistep procedures and metal catalysis conditions.
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Affiliation(s)
- Hyojin Jeong
- Department of Chemistry, Wonkwang University, 460 Iksandae-ro, Iksan, Jeonbuk 54538, Republic of Korea
| | - Nara Han
- Department of Chemistry, Wonkwang University, 460 Iksandae-ro, Iksan, Jeonbuk 54538, Republic of Korea
| | - Dong Wook Hwang
- Department of Chemistry, Wonkwang University, 460 Iksandae-ro, Iksan, Jeonbuk 54538, Republic of Korea
| | - Haye Min Ko
- Department of Chemistry, Wonkwang University, 460 Iksandae-ro, Iksan, Jeonbuk 54538, Republic of Korea.,Wonkwang Institute of Materials Science and Technology, Wonkwang University, 460 Iksandae-ro, Iksan, Jeonbuk 54538, Republic of Korea
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8
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Pala L, Sirec T, Spitz U. Modified Enzyme Substrates for the Detection of Bacteria: A Review. Molecules 2020; 25:E3690. [PMID: 32823590 PMCID: PMC7465704 DOI: 10.3390/molecules25163690] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/05/2020] [Accepted: 08/11/2020] [Indexed: 12/13/2022] Open
Abstract
The ability to detect, identify and quantify bacteria is crucial in clinical diagnostics, environmental testing, food security settings and in microbiology research. Recently, the threat of multidrug-resistant bacterial pathogens pushed the global scientific community to develop fast, reliable, specific and affordable methods to detect bacterial species. The use of synthetically modified enzyme substrates is a convenient approach to detect bacteria in a specific, economic and rapid manner. The method is based on the use of specific enzyme substrates for a given bacterial marker enzyme, conjugated to a signalogenic moiety. Following enzymatic reaction, the signalophor is released from the synthetic substrate, generating a specific and measurable signal. Several types of signalophors have been described and are defined by the type of signal they generate, such as chromogenic, fluorogenic, luminogenic, electrogenic and redox. Signalophors are further subdivided into groups based on their solubility in water, which is key in defining their application on solid or liquid media for bacterial culturing. This comprehensive review describes synthetic enzyme substrates and their applications for bacterial detection, showing their mechanism of action and their synthetic routes.
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Affiliation(s)
| | | | - Urs Spitz
- Biosynth Carbosynth, Axis House, High Street, Compton, Berkshire RG20 6NL, UK; (L.P.); (T.S.)
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9
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Rong Z, Hu W, Dai N, Qian G. A Hg(OTf)2-Catalyzed Enolate Umpolung Reaction Enables the Synthesis of Coumaran-3-ones and Indolin-3-ones. Org Lett 2020; 22:3286-3290. [DOI: 10.1021/acs.orglett.0c01096] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhouting Rong
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, People’s Republic of China
| | - Weican Hu
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, People’s Republic of China
| | - Ning Dai
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, People’s Republic of China
| | - Guoying Qian
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, People’s Republic of China
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10
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Sanderson H, Ortega-Polo R, McDermott K, Hall G, Zaheer R, Brown RS, Majury A, McAllister TA, Liss SN. Quantification and Multidrug Resistance Profiles of Vancomycin-Resistant Enterococci Isolated from Two Wastewater Treatment Plants in the Same Municipality. Microorganisms 2019; 7:microorganisms7120626. [PMID: 31795349 PMCID: PMC6956375 DOI: 10.3390/microorganisms7120626] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 11/23/2019] [Accepted: 11/25/2019] [Indexed: 11/16/2022] Open
Abstract
Wastewater treatment plants (WWTPs) are points of control for the environmental dissemination of antimicrobial resistant bacteria. Vancomycin-resistant enterococci (VRE) were used as indicators of antimicrobial resistance (AMR) in two WWTPs (biologically aerated filter (BAF) and conventional activated sludge (CAS)) in the same municipality. The removal and abundance of enterococci and VRE as well as the species and antimicrobial resistance profiles of VRE were assessed. Enterococci and VRE from the primary and final effluents were enumerated. Results were assessed from an ecological context. VRE was not selected for by either WWTP but the BAF system outperformed the CAS system for the removal of enterococci/VRE. Enterococcus faecalis (n = 151), E. faecium (n = 94) and E. casseliflavus/E. gallinarum (n = 59) were the dominant VRE species isolated. A decrease in levofloxacin resistance in enterococci was observed in the BAF WWTP. An increase in nitrofurantoin resistant (p < 0.001) and a decrease in quinupristin/dalfopristin (p = 0.003) and streptomycin (p = 0.022) resistant enterococci were observed in the CAS WWTP, corresponding to a shift of VRE from E. faecalis to E. faecium. Wastewater treatment processes can be managed to limit the dissemination of antimicrobial resistance determinants into the surrounding environment.
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Affiliation(s)
- Haley Sanderson
- School of Environmental Studies, Queen’s University, Kingston, ON K7L 3N6, Canada; (H.S.); (G.H.); (R.S.B.); (A.M.)
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Center, Lethbridge, AB T1J 4B1, Canada; (R.O.-P.); (R.Z.)
| | - Rodrigo Ortega-Polo
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Center, Lethbridge, AB T1J 4B1, Canada; (R.O.-P.); (R.Z.)
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 6T5, Canada
| | | | - Geoffrey Hall
- School of Environmental Studies, Queen’s University, Kingston, ON K7L 3N6, Canada; (H.S.); (G.H.); (R.S.B.); (A.M.)
- Department of Civil Engineering, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Rahat Zaheer
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Center, Lethbridge, AB T1J 4B1, Canada; (R.O.-P.); (R.Z.)
| | - R. Stephen Brown
- School of Environmental Studies, Queen’s University, Kingston, ON K7L 3N6, Canada; (H.S.); (G.H.); (R.S.B.); (A.M.)
- Department of Chemistry, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Anna Majury
- School of Environmental Studies, Queen’s University, Kingston, ON K7L 3N6, Canada; (H.S.); (G.H.); (R.S.B.); (A.M.)
- Public Health Ontario, Kingston, ON K7L 3K3, Canada;
| | - Tim A. McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Center, Lethbridge, AB T1J 4B1, Canada; (R.O.-P.); (R.Z.)
- Correspondence: (T.A.M.); (S.N.L.)
| | - Steven N. Liss
- School of Environmental Studies, Queen’s University, Kingston, ON K7L 3N6, Canada; (H.S.); (G.H.); (R.S.B.); (A.M.)
- Department of Biology, Ryerson University, Toronto, ON M5B 2K3, Canada
- Correspondence: (T.A.M.); (S.N.L.)
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11
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A Selective, Dual Emission β-Alanine Aminopeptidase Activated Fluorescent Probe for the Detection of Pseudomonas aeruginosa, Burkholderia cepacia, and Serratia marcescens. Molecules 2019; 24:molecules24193550. [PMID: 31575027 PMCID: PMC6804094 DOI: 10.3390/molecules24193550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/26/2019] [Accepted: 09/26/2019] [Indexed: 11/17/2022] Open
Abstract
Selective detection of β-alanyl aminopeptidase (BAP)-producing Pseudomonas aeruginosa, Serratia marcescens, and Burkholderia cepacia was achieved by employing the blue-to-yellow fluorescent transition of a BAP-specific enzyme substrate, 3-hydroxy-2-(p-dimethylaminophenyl)flavone derivative, incorporating a self-immolative linker to β-alanine. Upon cellular uptake and accumulation of the substrate by viable bacterial colonies, blue fluorescence was generated, while hydrolysis of the N-terminal peptide bond by BAP resulted in the elimination of the self-immolative linker and the restoration of the original fluorescence of the flavone derivative.
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12
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Kim HJ, Kwon C, Lee BS, Noh H. One-step sensing of foodborne pathogenic bacteria using a 3D paper-based device. Analyst 2019; 144:2248-2255. [PMID: 30775740 DOI: 10.1039/c8an02151a] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Managing food contamination from bacteria has been an ongoing issue in the public health and industrial fields. Enzymatic substrates possessing optical properties, e.g. fluorescence or color manifestation, are widely exploited in pathogenic/non-pathogenic bacteria culture methods. Recently, various chromogenic substrates have been utilized in the development of point-of-care diagnostic tools. Herein, four types of chromogenic substrates were exploited to develop paper-based sensors for major foodborne pathogens. We designed a compact sized three-dimensional paper device with a simple user interface. By inserting functional layers in the middle of multilayers, pre-lysis and pH regulation steps were excluded and the analysis time was subsequently reduced, while only one sample droplet was needed for the whole analysis process. After the enzymatic reactions had proceeded, target-specific colors appeared. When it was combined with enrichment, 101 cfu mL-1 of pathogens were successfully detected in 4-8 hours, while those in milk samples were readily sensed in 12 hours. The proposed bacteria sensor exhibited great advantages of low cost, portability and simple operation, while showing a respectable limit-of-detection as low as 101 cfu mL-1 and below. Significantly, we emphasize that it takes fewer steps than existing methods and provides a reduced analysis time owing to the layer functionalization.
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Affiliation(s)
- Hyeok Jung Kim
- Department of Optometry, Seoul National University of Science and Technology (Seoultech), 232 Gongneung-ro, Nowon-gu, Seoul 01811, Korea.
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13
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Lagacé-Wiens PRS, Abbott AA, Karlowsky JA. CHROMagar™ orientation urine culture medium produces matrix-assisted laser desorption ionization-time-of-flight mass spectrometry spectra misidentified as Mycoplasma arginini and Mycoplasma alkalescens. Diagn Microbiol Infect Dis 2019; 94:113-115. [PMID: 30718158 DOI: 10.1016/j.diagmicrobio.2018.12.014] [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: 08/21/2018] [Revised: 11/16/2018] [Accepted: 12/24/2018] [Indexed: 10/27/2022]
Abstract
Matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry is commonly used to identify bacteria and yeasts. Studies indicate that MALDI-TOF is relatively indifferent to the medium used for culture. We report on an investigation into high- and low-confidence MALDI-TOF misidentifications of Mycoplasma arginini and Mycoplasma alkalescens from urine specimens plated to CHROMagar™ Orientation medium that appear to be due to the intrinsic mass spectrum of the medium.
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Affiliation(s)
- Philippe R S Lagacé-Wiens
- Shared Health, Diagnostic Services, Clinical Microbiology, Winnipeg, Manitoba, Canada; Department of Medical Microbiology and Infectious Diseases, College of Medicine, University of Manitoba. Winnipeg, Manitoba, Canada.
| | - Amanda A Abbott
- Shared Health, Diagnostic Services, Clinical Microbiology, Winnipeg, Manitoba, Canada
| | - James A Karlowsky
- Shared Health, Diagnostic Services, Clinical Microbiology, Winnipeg, Manitoba, Canada; Department of Medical Microbiology and Infectious Diseases, College of Medicine, University of Manitoba. Winnipeg, Manitoba, Canada
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Luo C, Li Y, Chen Y, Fu C, Nong X, Yang Y. Degradation of bamboo lignocellulose by bamboo snout beetle Cyrtotrachelus buqueti in vivo and vitro: efficiency and mechanism. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:75. [PMID: 30976325 PMCID: PMC6442404 DOI: 10.1186/s13068-019-1406-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/12/2019] [Indexed: 05/15/2023]
Abstract
BACKGROUND As an important biomass raw material, the lignocellulose in bamboo is of significant value in energy conversion. The conversion of bamboo lignocellulose into fermentable reducing sugar, i.e. the degradation of bamboo lignocellulose, is an important step in lignocellulose conversion. However, little research has focussed on excavating the enzymes and microbes that are related to the degradation of bamboo lignocellulose, which is important for its utilisation. This study used Cyrtotrachelus buqueti (bamboo snout beetle) to evaluate the efficiency of bamboo lignocellulose degradation. RESULTS RNA sequencing was conducted to sequence the transcriptome of the insect before and after feeding on bamboo shoots. The expression levels of genes encoding several carbohydrate-active enzymes, such as endoglucanase (evgtrinloc27093t1 and evgtrinloc16407t0) and laccase (evgtrinloc15173t0 and evgtrinloc11252t0), were found to be upregulated after feeding. Faecal component analysis showed that the degradation efficiencies of cellulose, hemicellulose and lignin were 61.82%, 87.65% and 69.05%, respectively. After 6 days of co-culture with crude enzymes in vitro, the degradation efficiencies of cellulose, hemicellulose and lignin in bamboo shoot particles (BSPs) were 24.98%, 37.52% and 26.67%, respectively. These results indicated that lignocellulosic enzymes and related enzymes within the insect itself co-degraded bamboo lignocellulose. These finding can potentially be used for the pre-treatment and enzymatic hydrolysis of bamboo lignocellulose. CONCLUSION Our results showed that intestinal digestive enzymes from C. buqueti degraded bamboo shoot lignocellulose both in vivo and in vitro. In addition, the expression levels of many carbohydrate-active enzyme (CAZyme) genes were upregulated in the transcriptome, including those for cellulase, xylanase and ligninase genes. Therefore, we proposed a scheme for applying the lignocellulolytic enzymes from C. buqueti to degrade bamboo lignocellulose using genetic, enzymatic and fermentation engineering techniques to overexpress the lignocellulolytic enzymes genes in vitro and obtain large quantities of enzymes that could efficiently degrade bamboo lignocellulose and be used for lignocellulose bioconversion.
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Affiliation(s)
- Chaobing Luo
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Riverside Road, Central District, Leshan, 614000 China
| | - Yuanqiu Li
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Riverside Road, Central District, Leshan, 614000 China
- College of Food and Biological Engineering, Xihua University, Chengdu, 610039 China
| | - Ying Chen
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Riverside Road, Central District, Leshan, 614000 China
- College of Food and Biological Engineering, Xihua University, Chengdu, 610039 China
| | - Chun Fu
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Riverside Road, Central District, Leshan, 614000 China
| | - Xiang Nong
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Riverside Road, Central District, Leshan, 614000 China
| | - Yaojun Yang
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, Leshan Normal University, No. 778, Riverside Road, Central District, Leshan, 614000 China
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15
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Howse GL, Bovill RA, Stephens PJ, Osborn HM. Synthesis and antibacterial profiles of targeted triclosan derivatives. Eur J Med Chem 2019; 162:51-58. [DOI: 10.1016/j.ejmech.2018.10.053] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 10/22/2018] [Indexed: 01/29/2023]
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16
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Luo C, Li Y, Liao H, Yang Y. De novo transcriptome assembly of the bamboo snout beetle Cyrtotrachelus buqueti reveals ability to degrade lignocellulose of bamboo feedstock. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:292. [PMID: 30386429 PMCID: PMC6204003 DOI: 10.1186/s13068-018-1291-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/15/2018] [Indexed: 05/27/2023]
Abstract
BACKGROUND The bamboo weevil Cyrtotrachelus buqueti, which is considered a pest species, damages bamboo shoots via its piercing-sucking mode of feeding. C. buqueti is well known for its ability to transform bamboo shoot biomass into nutrients and energy for growth, development and reproduction with high specificity and efficacy of bioconversion. Woody bamboo is a perennial grass that is a potential feedstock for lignocellulosic biomass because of its high growth rate and lignocellulose content. To verify our hypothesis that C. buqueti efficiently degrades bamboo lignocellulose, we assessed the bamboo lignocellulose-degrading ability of this insect through RNA sequencing for identifying a potential route for utilisation of bamboo biomass. RESULTS Analysis of carbohydrate-active enzyme (CAZyme) family genes in the developmental transcriptome of C. buqueti revealed 1082 unigenes, including 55 glycoside hydrolases (GH) families containing 309 GHs, 51 glycosyltransferases (GT) families containing 329 GTs, 8 carbohydrate esterases (CE) families containing 174 CEs, 6 polysaccharide lyases (PL) families containing 11 PLs, 8 auxiliary activities (AA) families containing 131 enzymes with AAs and 17 carbohydrate-binding modules (CBM) families containing 128 CBMs. We used weighted gene co-expression network analysis to analyse developmental RNA sequencing data, and 19 unique modules were identified in the analysis. Of these modules, the expression of MEyellow module genes was unique and the module included numerous CAZyme family genes. CAZyme genes in this module were divided into two groups depending on whether gene expression was higher in the adult/larval stages or in the egg/pupal stages. Enzyme assays revealed that cellulase activity was highest in the midgut whereas lignin-degrading enzyme activity was highest in the hindgut, consistent with findings from intestinal gene expression studies. We also analysed the expression of CAZyme genes in the transcriptome of C. buqueti from two cities and found that several genes were also assigned to CAZyme families. The insect had genes and enzymes associated with lignocellulose degradation, the expression of which differed with developmental stage and intestinal region. CONCLUSION Cyrtotrachelus buqueti exhibits lignocellulose degradation-related enzymes and genes, most notably CAZyme family genes. CAZyme family genes showed differences in expression at different developmental stages, with adults being more effective at cellulose degradation and larvae at lignin degradation, as well as at different regions of the intestine, with the midgut being more cellulolytic than the hindgut. This degradative system could be utilised for the bioconversion of bamboo lignocellulosic biomass.
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Affiliation(s)
- Chaobing Luo
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, No. 778, Riverside Road, Central District, Leshan, 614000 China
| | - Yuanqiu Li
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, No. 778, Riverside Road, Central District, Leshan, 614000 China
- College of Food and Biological Engineering, Xihua University, Chengdu, China
| | - Hong Liao
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, No. 778, Riverside Road, Central District, Leshan, 614000 China
| | - Yaojun Yang
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, No. 778, Riverside Road, Central District, Leshan, 614000 China
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17
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Burton M, Perry JD, Stanforth SP, Turner HJ. The synthesis of novel chromogenic enzyme substrates for detection of bacterial glycosidases and their applications in diagnostic microbiology. Bioorg Med Chem 2018; 26:4841-4849. [PMID: 30170924 DOI: 10.1016/j.bmc.2018.08.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 08/01/2018] [Accepted: 08/16/2018] [Indexed: 10/28/2022]
Abstract
The preparation and evaluation of chromogenic substrates for detecting bacterial glycosidase enzymes is reported. These substrates are monoglycoside derivatives of the metal chelators catechol, 2,3-dihydroxynaphthalene (DHN) and 6,7-dibromo-2,3-dihydroxynaphthalene (6,7-dibromo-DHN). When hydrolysed by appropriate bacterial enzymes these substrates produced coloured chelates in the presence of ammonium iron(III) citrate, thus enabling bacterial detection. A β-d-riboside of DHN and a β-d-glucuronide derivative of 6,7-dibromo-DHN were particularly effective for the detection of S. aureus and E. coli respectively.
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Affiliation(s)
- Michael Burton
- Glycosynth Ltd, 14 Craven Court, Winwick Quay, Warrington, Cheshire WA2 8QU, UK
| | - John D Perry
- Department of Microbiology, Freeman Hospital, Newcastle upon Tyne NE7 7DN, UK
| | - Stephen P Stanforth
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Hayley J Turner
- Glycosynth Ltd, 14 Craven Court, Winwick Quay, Warrington, Cheshire WA2 8QU, UK.
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18
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Coch C, Stümpel JP, Lilien-Waldau V, Wohlleber D, Kümmerer BM, Bekeredjian-Ding I, Kochs G, Garbi N, Herberhold S, Schuberth-Wagner C, Ludwig J, Barchet W, Schlee M, Hoerauf A, Bootz F, Staeheli P, Hartmann G, Hartmann E. RIG-I Activation Protects and Rescues from Lethal Influenza Virus Infection and Bacterial Superinfection. Mol Ther 2017; 25:2093-2103. [PMID: 28760668 DOI: 10.1016/j.ymthe.2017.07.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 07/02/2017] [Accepted: 07/05/2017] [Indexed: 12/25/2022] Open
Abstract
Influenza A virus infection causes substantial morbidity and mortality in seasonal epidemic outbreaks, and more efficient treatments are urgently needed. Innate immune sensing of viral nucleic acids stimulates antiviral immunity, including cell-autonomous antiviral defense mechanisms that restrict viral replication. RNA oligonucleotide ligands that potently activate the cytoplasmic helicase retinoic-acid-inducible gene I (RIG-I) are promising candidates for the development of new antiviral therapies. Here, we demonstrate in an Mx1-expressing mouse model of influenza A virus infection that a single intravenous injection of low-dose RIG-I ligand 5'-triphosphate RNA (3pRNA) completely protected mice from a lethal challenge with influenza A virus for at least 7 days. Furthermore, systemic administration of 3pRNA rescued mice with pre-established fulminant influenza infection and prevented the fatal effects of a streptococcal superinfection. Type I interferon, but not interferon-λ, was required for the therapeutic effect. Our results suggest that the use of RIG-I activating oligonucleotide ligands has the clinical potential to confine influenza epidemics when a strain-specific vaccine is not yet available and to reduce lethality of influenza in severely infected patients.
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Affiliation(s)
- Christoph Coch
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany.
| | - Jan Phillip Stümpel
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - Vanessa Lilien-Waldau
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - Dirk Wohlleber
- Institute of Molecular Immunology and Experimental Oncology, TU Munich, 81675 Munich, Germany
| | - Beate M Kümmerer
- Institute of Virology, University Hospital Bonn, 53105 Bonn, Germany
| | - Isabelle Bekeredjian-Ding
- Division of Microbiology, Paul-Ehrlich Institute, 63225 Langen, Germany; Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, 53127 Bonn, Germany
| | - Georg Kochs
- Institute of Virology, Medical Center Freiburg, 79104 Freiburg, Germany
| | - Natalio Garbi
- Institute of Experimental Immunology, University Hospital Bonn, 53127 Bonn, Germany
| | - Stephan Herberhold
- Department of Otolaryngology, University Hospital Bonn, 53127 Bonn, Germany
| | - Christine Schuberth-Wagner
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - Janos Ludwig
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - Winfried Barchet
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - Martin Schlee
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - Achim Hoerauf
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, 53127 Bonn, Germany
| | - Friedrich Bootz
- Department of Otolaryngology, University Hospital Bonn, 53127 Bonn, Germany
| | - Peter Staeheli
- Institute of Virology, Medical Center Freiburg, 79104 Freiburg, Germany
| | - Gunther Hartmann
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - Evelyn Hartmann
- Department of Otolaryngology, University Hospital Bonn, 53127 Bonn, Germany
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19
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Cellier M, James AL, Orenga S, Perry JD, Rasul AK, Stanforth SP. Detection of l-alanylaminopeptidase activity in microorganisms using chromogenic self-immolative enzyme substrates. Bioorg Med Chem Lett 2017; 27:2102-2106. [PMID: 28389152 DOI: 10.1016/j.bmcl.2017.03.080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/23/2017] [Accepted: 03/25/2017] [Indexed: 11/19/2022]
Abstract
Three potential chromogenic enzymatic probes, each possessing a self-immolative spacer unit, were synthesised for the purpose of detecting l-alanylaminopeptidase activity in microorganisms. An Alizarin-based probe was the most effective, allowing several species to generate strongly coloured colonies in the presence of metal ions.
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Affiliation(s)
- Marie Cellier
- Research & Development Microbiology, bioMérieux SA, 3 route de Port Michaud, 38 390 La-Balme-les-Grottes, France
| | - Arthur L James
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Sylvain Orenga
- Research & Development Microbiology, bioMérieux SA, 3 route de Port Michaud, 38 390 La-Balme-les-Grottes, France
| | - John D Perry
- Department of Microbiology, Freeman Hospital, Newcastle upon Tyne NE7 7DN, UK
| | - Ari K Rasul
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Stephen P Stanforth
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK.
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20
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Bovill R, Evans PG, Howse GL, Osborn HMI. Synthesis and biological analysis of novel glycoside derivatives of l-AEP, as targeted antibacterial agents. Bioorg Med Chem Lett 2016; 26:3774-9. [PMID: 27268308 DOI: 10.1016/j.bmcl.2016.05.052] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 05/16/2016] [Accepted: 05/18/2016] [Indexed: 11/19/2022]
Abstract
To develop targeted methods for treating bacterial infections, the feasibility of using glycoside derivatives of the antibacterial compound l-R-aminoethylphosphonic acid (l-AEP) has been investigated. These derivatives are hypothesized to be taken up by bacterial cells via carbohydrate uptake mechanisms, and then hydrolyzed in situ by bacterial borne glycosidase enzymes, to selectively afford l-AEP. Therefore the synthesis and analysis of ten glycoside derivatives of l-AEP, for selective targeting of specific bacteria, is reported. The ability of these derivatives to inhibit the growth of a panel of Gram-negative bacteria in two different media is discussed. β-Glycosides (12a) and (12b) that contained l-AEP linked to glucose or galactose via a carbamate linkage inhibited growth of a range of organisms with the best MICs being <0.75mg/ml; for most species the inhibition was closely related to the hydrolysis of the equivalent chromogenic glycosides. This suggests that for (12a) and (12b), release of l-AEP was indeed dependent upon the presence of the respective glycosidase enzyme.
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Affiliation(s)
- Richard Bovill
- Thermofisher Scientific, Wade Road, Basingstoke, Hampshire RG24 8PW, UK
| | - Philip G Evans
- Reading School of Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - Gemma L Howse
- Reading School of Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - Helen M I Osborn
- Reading School of Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, UK
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21
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Ma J, Zhang K, Liao H, Hector SB, Shi X, Li J, Liu B, Xu T, Tong C, Liu X, Zhu Y. Genomic and secretomic insight into lignocellulolytic system of an endophytic bacterium Pantoea ananatis Sd-1. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:25. [PMID: 26839588 PMCID: PMC4736469 DOI: 10.1186/s13068-016-0439-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 01/14/2016] [Indexed: 05/06/2023]
Abstract
BACKGROUND Exploring microorganisms especially bacteria associated with the degradation of lignocellulosic biomass shows great potentials in biofuels production. The rice endophytic bacterium Pantoea ananatis Sd-1 with strong lignocellulose degradation capacity has been reported in our previous study. However, a comprehensive analysis of its corresponding degradative system has not yet been conducted. The aim of this work is to identify and characterize the lignocellulolytic enzymes of the bacterium to understand its mechanism of lignocellulose degradation and facilitate its application in sustainable energy production. RESULTS The genomic analysis revealed that there are 154 genes encoding putative carbohydrate-active enzymes (CAZy) in P. ananatis Sd-1. This number is higher than that of compared cellulolytic and ligninolytic bacteria as well as other eight P. ananatis strains. The CAZy in P. ananatis Sd-1 contains a complete repertoire of enzymes required for cellulose and hemicellulose degradation. In addition, P. ananatis Sd-1 also possesses plenty of genes encoding potential ligninolytic relevant enzymes, such as multicopper oxidase, catalase/hydroperoxidase, glutathione S-transferase, and quinone oxidoreductase. Quantitative real-time PCR analysis of parts of genes encoding lignocellulolytic enzymes revealed that they were significantly up-regulated (at least P < 0.05) in presence of rice straw. Further identification of secretome of P. ananatis Sd-1 by nano liquid chromatography-tandem mass spectrometry confirmed that considerable amounts of proteins involved in lignocellulose degradation were only detected in rice straw cultures. Rice straw saccharification levels by the secretome of P. ananatis Sd-1 reached 129.11 ± 2.7 mg/gds. Correspondingly, the assay of several lignocellulolytic enzymes including endoglucanase, exoglucanase, β-glucosidase, xylanase-like, lignin peroxidase-like, and laccase-like activities showed that these enzymes were more active in rice straw relative to glucose substrates. The high enzymes activities were not attributed to bacterial cell densities but to the difference of secreted protein contents. CONCLUSION Our results indicate that P. ananatis Sd-1 can produce considerable lignocellulolytic enzymes including cellulases, hemicellulases, and ligninolytic relevant enzymes. The high activities of those enzymes could be efficiently induced by lignocellulosic biomass. This identified degradative system is valuable for the lignocellulosic bioenergy industry.
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Affiliation(s)
- Jiangshan Ma
- />Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Keke Zhang
- />Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Hongdong Liao
- />Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Stanton B. Hector
- />Department of Genetics, Institute for Plant Biotechnology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602 South Africa
- />DNA Sequencing Unit, Central Analytical Facility, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602 South Africa
| | - Xiaowei Shi
- />Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Jianglin Li
- />State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Bin Liu
- />Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Ting Xu
- />Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Chunyi Tong
- />Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Xuanming Liu
- />Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
| | - Yonghua Zhu
- />Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, College of Biology, Hunan University, Changsha, 410008 Hunan People’s Republic of China
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22
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Renchinkhand G, Park YW, Song GY, Cho SH, Urgamal M, Bae HC, Choi JW, Nam MS. Identification of β-Glucosidase Activity of E
nterococcus Faecalis
CRNB-A3 in Airag and Its Potential to Convert Ginsenoside Rb1
from Panax Ginseng. J Food Biochem 2015. [DOI: 10.1111/jfbc.12201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gereltuya Renchinkhand
- Department of Animal Bio-system Science; College of Agriculture and Life Sciences; Chungnam National University; Yuseong-gu Daejeon 305-764 Korea
| | - Young W. Park
- Agricultural Research Station; Fort Valley State University; Fort Valley GA
| | - Gyu-Yong Song
- Department of Pharmacology Science; College of Pharmacology; Chungnam National University; Yuseong-gu Daejeon 305-764 Korea
| | - Soo-Hyun Cho
- Department of Pharmacology Science; College of Pharmacology; Chungnam National University; Yuseong-gu Daejeon 305-764 Korea
| | - Magsar Urgamal
- Department of Animal Bio-system Science; College of Agriculture and Life Sciences; Chungnam National University; Yuseong-gu Daejeon 305-764 Korea
| | - Hyoung C. Bae
- Department of Animal Bio-system Science; College of Agriculture and Life Sciences; Chungnam National University; Yuseong-gu Daejeon 305-764 Korea
| | - Jong-Woo Choi
- National Institute of Animal Science; Rural Development Administration; Jeonju Korea
| | - Myoung Soo Nam
- Department of Animal Bio-system Science; College of Agriculture and Life Sciences; Chungnam National University; Yuseong-gu Daejeon 305-764 Korea
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23
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Burke HM, Gunnlaugsson T, Scanlan EM. Recent advances in the development of synthetic chemical probes for glycosidase enzymes. Chem Commun (Camb) 2015; 51:10576-88. [PMID: 26051717 DOI: 10.1039/c5cc02793d] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The emergence of synthetic glycoconjugates as chemical probes for the detection of glycosidase enzymes has resulted in the development of a range of useful chemical tools with applications in glycobiology, biotechnology, medical and industrial research. Critical to the function of these probes is the preparation of substrates containing a glycosidic linkage that when activated by a specific enzyme or group of enzymes, irreversibly releases a reporter molecule that can be detected. Starting from the earliest examples of colourimetric probes, increasingly sensitive and sophisticated substrates have been reported. In this review we present an overview of the recent advances in this field, covering an array of strategies including chromogenic and fluorogenic substrates, lanthanide complexes, gels and nanoparticles. The applications of these substrates for the detection of various glycosidases and the scope and limitations for each approach are discussed.
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Affiliation(s)
- Helen M Burke
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College, Pearse St, Dublin 2, Ireland.
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24
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Orenga S, James AL, Manafi M, Perry JD, Pincus DH. Enzymatic substrates in microbiology. J Microbiol Methods 2009; 79:139-55. [PMID: 19679151 DOI: 10.1016/j.mimet.2009.08.001] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 07/24/2009] [Accepted: 08/03/2009] [Indexed: 11/15/2022]
Abstract
Enzymatic substrates are powerful tools in biochemistry. They are widely used in microbiology to study metabolic pathways, to monitor metabolism and to detect, enumerate and identify microorganisms. Synthetic enzymatic substrates have been customized for various microbial assays, to detect an expanding range of both new enzymatic activities and target microorganisms. Recent developments in synthetic enzymatic substrates with new spectral, chemical and biochemical properties allow improved detection, enumeration and identification of food-borne microorganisms, clinical pathogens and multi-resistant bacteria in various sample types. In the past 20 years, the range of synthetic enzymatic substrates used in microbiology has been markedly extended supporting the development of new multi-test systems (e.g., Microscan, Vitek 2, Phoenix) and chromogenic culture media. The use of such substrates enables an improvement in time to detection and specificity over conventional tests that employ natural substrates. In the era of intense developments in molecular biology, phenotypic tests involving enzymatic substrates remain useful to analyse both simple and complex samples. Such tests are applicable to diagnostic and research laboratories all over the world.
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Affiliation(s)
- Sylvain Orenga
- Research & Development Microbiology, bioMérieux, 3 route de Port Michaud, La Balme-les-Grottes, France.
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25
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Abstract
Since 1990, a wide range of chromogenic culture media has been made commercially available providing useful tools for diagnostic clinical microbiology. By the inclusion of chromogenic enzyme substrates targeting microbial enzymes, such media are able to target pathogens with high specificity. Examples of target pathogens include Staphylococcus aureus, Streptococcus agalactiae, Salmonella spp. and Candida spp. The inclusion of multiple chromogenic substrates into culture media facilitates the differentiation of polymicrobial cultures, thus allowing for the development of improved media for diagnosis of urinary tract infections and media for the enhanced discrimination of yeasts. The purpose of this review is to provide some insight into how such media work and appraise their utility in routine clinical diagnostics, in comparison with conventional media.
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Affiliation(s)
- J D Perry
- Microbiology Department, Freeman Hospital, Newcastle upon Tyne, UK.
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