1
|
Díaz-Rullo J, González-Pastor JE. tRNA queuosine modification is involved in biofilm formation and virulence in bacteria. Nucleic Acids Res 2023; 51:9821-9837. [PMID: 37638766 PMCID: PMC10570037 DOI: 10.1093/nar/gkad667] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/27/2023] [Accepted: 08/11/2023] [Indexed: 08/29/2023] Open
Abstract
tRNA modifications are crucial for fine-tuning of protein translation. Queuosine (Q) modification of tRNAs is thought to modulate the translation rate of NAU codons, but its physiological role remains elusive. Therefore, we hypothesize that Q-tRNAs control those physiological processes involving NAU codon-enriched genes (Q-genes). Here, we report a novel bioinformatic strategy to predict Q-genes, revealing a widespread enrichment in functions, especially those related to biofilm formation and virulence in bacteria, and particularly in human pathogens. Indeed, we experimentally verified that these processes were significantly affected by altering the degree of tRNA Q-modification in different model bacteria, representing the first report of a general mechanism controlling biofilm formation and virulence in Gram-positive and Gram-negative bacteria possibly through the coordination of the expression of functionally related genes. Furthermore, we propose that changes in Q availability in a microbiome would affect its functionality. Our findings open the door to the control of bacterial infections and biofilm formation by inhibition of tRNA Q-modification.
Collapse
Affiliation(s)
- Jorge Díaz-Rullo
- Department of Molecular Evolution, Centro de Astrobiología (CAB), CSIC-INTA, Carretera de Ajalvir km 4, Torrejón de Ardoz 28850, Madrid, Spain
| | - José Eduardo González-Pastor
- Department of Molecular Evolution, Centro de Astrobiología (CAB), CSIC-INTA, Carretera de Ajalvir km 4, Torrejón de Ardoz 28850, Madrid, Spain
| |
Collapse
|
2
|
Liang Z, Carothers K, Holmes A, Donahue D, Lee SW, Castellino FJ, Ploplis VA. Stable genetic integration of a red fluorescent protein in a virulent Group A Streptococcus strain. Access Microbiol 2020; 1:e000062. [PMID: 32974562 PMCID: PMC7472541 DOI: 10.1099/acmi.0.000062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/27/2019] [Indexed: 11/29/2022] Open
Abstract
There are several advantages, both in vitro and in vivo, in utilizing bacteria that express a fluorescent protein. Such a protein can be transiently incorporated into the bacteria or integrated within the bacterial genome. The most widely utilized fluorescent protein is green fluorescent protein (GFP), but limitations exist on its use. Additional fluorescent proteins have been designed that have many advantages over GFP and technologies for their incorporation into bacteria have been optimized. In the current study, we report the successful integration and expression of a stable fluorescent reporter, mCherry (red fluorescent protein, RFP), into the genome of a human pathogen, Group A Streptococcus pyogenes (GAS) isolate AP53(S-). RFP was targeted at the atg codon of the fcR pseudogene that is present in the mga regulon of AP53(S-). Transcription of critical bacterial genes was not functionally altered by the genomic integration of mCherry. Host virulence both in vitro (keratinocyte infection and cytotoxicity) and in vivo (skin infection) was maintained in AP53(S-)-RFP. Additionally, survival of mice infected with either AP53(S-) or AP53(S-)-RFP was similar, demonstrating that overall pathogenicity of the AP53(S-) strain was not altered by the expression of mCherry. These studies demonstrate the feasibility of integrating a fluorescent reporter into the bacterial genome of a naturally virulent isolate of Group A S. pyogenes for comparative experimental studies.
Collapse
Affiliation(s)
- Zhong Liang
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Katelyn Carothers
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Adam Holmes
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Deborah Donahue
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Shaun W Lee
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Francis J Castellino
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, USA.,Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Victoria A Ploplis
- W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, USA.,Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| |
Collapse
|
3
|
Sharma M, Tyagi JL, Poluri KM. Quantifying bacterial cell lysis using GFP based fluorimetric assay. Int J Biol Macromol 2019; 138:881-889. [PMID: 31356938 DOI: 10.1016/j.ijbiomac.2019.07.172] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 11/24/2022]
Abstract
Quantitative measurement of cell lysis against a given microbial strain is essential to calculate the antimicrobial potency of protein/peptide/nanomaterial based formulations. Fluorescence spectroscopy based measurements offer precise quantification of a process via selected flurophore emission profile. In this context, we elucidate a reliable and robust green fluorescent protein (GFP) based fluorescence spectroscopy protocol to evaluate the antimicrobial activity of proteins. The technique is based on the fact that the intensity of the GFP emission released from cells correlates with cell lysis and henceforth the antimicrobial potential of the chosen agent. The technique was demonstrated with two different families of bacteriophage endolysins (T7 and T4 endolysins) using GFP expressing E. coli cells. The GFP based method allowed the absolute quantification of T4 and T7 endolysins cell lysis characteristics at different pH, salt concentrations, and metal ions. The results obtained from GFP based fluorimetric assay were substantiated with turbidimetric assay and fluorescence microscopy. This fluorimetric method in conjugation with different GFP expressing microbial strains and antimicrobial agents can be efficiently applied as a quantification technique to precisely measure cell lysis.
Collapse
Affiliation(s)
- Meenakshi Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Jaya Lakshmi Tyagi
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Krishna Mohan Poluri
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India; Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India.
| |
Collapse
|
4
|
Kellermann SJ, Rentmeister A. A FACS-based screening strategy to assess sequence-specific RNA-binding of Pumilio protein variants in E. coli. Biol Chem 2017; 398:69-75. [DOI: 10.1515/hsz-2016-0214] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 09/15/2016] [Indexed: 12/22/2022]
Abstract
Abstract
Sequence-specific and programmable binding of proteins to RNA bears the potential to detect and manipulate target RNAs. Applications include analysis of subcellular RNA localization or post-transcriptional regulation but require sequence-specificity to be readily adjustable to any target RNA. The Pumilio homology domain binds an eight nucleotide target sequence in a predictable manner allowing for rational design of variants with new specificities. We describe a high-throughput system for screening Pumilio variants based on fluorescence-activated cell sorting of E. coli. Our approach should help optimizing variants obtained from rational design regarding folding and stability or identifying new variants with alternative binding modes.
Collapse
|
5
|
Trachtmann N, Alvarez Fong KF, Guitart Font E, Sprenger GA. Construction of chromosomally encoded lacZ
and gfp
reporter strains of Escherichia coli
for the study of global regulation of metabolism. Eng Life Sci 2016. [DOI: 10.1002/elsc.201600056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
| | | | - Emma Guitart Font
- Institut für Mikrobiologie; Universität Stuttgart; Stuttgart Germany
| | - Georg A. Sprenger
- Institut für Mikrobiologie; Universität Stuttgart; Stuttgart Germany
| |
Collapse
|
6
|
Oosterik LH, Tuntufye HN, Tsonos J, Luyten T, Noppen S, Liekens S, Lavigne R, Butaye P, Goddeeris BM. Bioluminescent avian pathogenic Escherichia coli for monitoring colibacillosis in experimentally infected chickens. Vet J 2016; 216:87-92. [PMID: 27687932 DOI: 10.1016/j.tvjl.2016.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 07/17/2016] [Accepted: 07/18/2016] [Indexed: 11/30/2022]
Abstract
Avian pathogenic Escherichia coli (APEC) are responsible for significant economic losses in the poultry industry. In this study, a model for investigating the pathogenesis of APEC infections was established. APEC strain CH2 (O78) was marked with the luciferase operon (luxCDABE) using a Tn7 transposon and tissues of experimentally infected chickens were analysed for a correlation between the bioluminescent signal and the number of bacteria. Transposition of the lux operon into the chromosome of the APEC isolate did not affect sensitivity to lytic bacteriophages and there was no effect on virulence in an intratracheal infection model in 1-day-old chicks, although results with a subcutaneous infection model were inconclusive. A correlation between the number of bacteria and the luminescent signal was found in liquid medium, as well as in homogenised heart, liver, spleen and lung of 4-week-old experimentally infected chickens. This study showed that lux could be used for identification of the infecting strain after experimental infection with APEC in poultry.
Collapse
Affiliation(s)
- Leon H Oosterik
- Department of Biosystems, Division of Gene Technology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 30, Leuven 3000, Belgium; Department of General Bacteriology, Centrum voor Onderzoek in Diergeneeskunde en Agrochemie-Centre d'Etude et de Recherches Vétérinaires et Agrochimiques (CODA-CERVA), Groeselenberg 99, Brussels 1180, Belgium.
| | - Huruma N Tuntufye
- Department of Biosystems, Division of Gene Technology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 30, Leuven 3000, Belgium
| | - Jessica Tsonos
- Department of Biosystems, Division of Gene Technology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 30, Leuven 3000, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, Vlaams Instituut voor Biotechnologie (VIB), Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium
| | - Tom Luyten
- Department of Biosystems, Division of Gene Technology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 30, Leuven 3000, Belgium
| | - Sam Noppen
- Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, Leuven 3000, Belgium
| | - Sandra Liekens
- Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, Leuven 3000, Belgium
| | - Rob Lavigne
- Department of Biosystems, Division of Gene Technology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 30, Leuven 3000, Belgium
| | - Patrick Butaye
- Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, Merelbeke 9820, Belgium
| | - Bruno M Goddeeris
- Department of Biosystems, Division of Gene Technology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 30, Leuven 3000, Belgium
| |
Collapse
|
7
|
Bacteria Removal from Stormwater Runoff Using Tree Filters: A Comparison of a Conventional and an Innovative System. WATER 2016. [DOI: 10.3390/w8030076] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
8
|
Krishnamurthy M, Hennelly SP, Dale T, Starkenburg SR, Martí-Arbona R, Fox DT, Twary SN, Sanbonmatsu KY, Unkefer CJ. Tunable Riboregulator Switches for Post-transcriptional Control of Gene Expression. ACS Synth Biol 2015; 4:1326-34. [PMID: 26165796 DOI: 10.1021/acssynbio.5b00041] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Until recently, engineering strategies for altering gene expression have focused on transcription control using strong inducible promoters or one of several methods to knock down wasteful genes. Recently, synthetic riboregulators have been developed for translational regulation of gene expression. Here, we report a new modular synthetic riboregulator class that has the potential to finely tune protein expression and independently control the concentration of each enzyme in an engineered metabolic pathway. This development is important because the most straightforward approach to altering the flux through a particular metabolic step is to increase or decrease the concentration of the enzyme. Our design includes a cis-repressor at the 5' end of the mRNA that forms a stem-loop helix, occluding the ribosomal binding sequence and blocking translation. A trans-expressed activating-RNA frees the ribosomal-binding sequence, which turns on translation. The overall architecture of the riboregulators is designed using Watson-Crick base-pairing stability. We describe here a cis-repressor that can completely shut off translation of antibiotic-resistance reporters and a trans-activator that restores translation. We have established that it is possible to use these riboregulators to achieve translational control of gene expression over a wide dynamic range. We have also found that a targeting sequence can be modified to develop riboregulators that can, in principle, independently regulate translation of many genes. In a selection experiment, we demonstrated that by subtly altering the sequence of the trans-activator it is possible to alter the ratio of the repressed and activated states and to achieve intermediate translational control.
Collapse
Affiliation(s)
- Malathy Krishnamurthy
- Bioenergy and Biome Sciences, Bioscience
Division, ‡Theoretical Biology and Biophysics,
Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Scott P. Hennelly
- Bioenergy and Biome Sciences, Bioscience
Division, ‡Theoretical Biology and Biophysics,
Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Taraka Dale
- Bioenergy and Biome Sciences, Bioscience
Division, ‡Theoretical Biology and Biophysics,
Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Shawn R. Starkenburg
- Bioenergy and Biome Sciences, Bioscience
Division, ‡Theoretical Biology and Biophysics,
Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Ricardo Martí-Arbona
- Bioenergy and Biome Sciences, Bioscience
Division, ‡Theoretical Biology and Biophysics,
Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - David T. Fox
- Bioenergy and Biome Sciences, Bioscience
Division, ‡Theoretical Biology and Biophysics,
Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Scott N. Twary
- Bioenergy and Biome Sciences, Bioscience
Division, ‡Theoretical Biology and Biophysics,
Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Karissa Y. Sanbonmatsu
- Bioenergy and Biome Sciences, Bioscience
Division, ‡Theoretical Biology and Biophysics,
Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Clifford J. Unkefer
- Bioenergy and Biome Sciences, Bioscience
Division, ‡Theoretical Biology and Biophysics,
Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| |
Collapse
|
9
|
van Zyl WF, Deane SM, Dicks LMT. Reporter systems for in vivo tracking of lactic acid bacteria in animal model studies. Gut Microbes 2015; 6:291-9. [PMID: 26516656 PMCID: PMC4826117 DOI: 10.1080/19490976.2015.1086058] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Bioluminescence (BLI) and fluorescence imaging (FI) allow for non-invasive detection of viable microorganisms from within living tissue and are thus ideally suited for in vivo probiotic studies. Highly sensitive optical imaging techniques detect signals from the excitation of fluorescent proteins, or luciferase-catalyzed oxidation reactions. The excellent relation between microbial numbers and photon emission allow for quantification of tagged bacteria in vivo with extreme accuracy. More information is gained over a shorter period compared to traditional pre-clinical animal studies. The review summarizes the latest advances in in vivo bioluminescence and fluorescence imaging and points out the advantages and limitations of different techniques. The practical application of BLI and FI in the tracking of lactic acid bacteria in animal models is addressed.
Collapse
Affiliation(s)
- Winschau F van Zyl
- Department of Microbiology; Stellenbosch University; Matieland, Stellenbosch, South Africa
| | - Shelly M Deane
- Department of Microbiology; Stellenbosch University; Matieland, Stellenbosch, South Africa
| | - Leon M T Dicks
- Department of Microbiology; Stellenbosch University; Matieland, Stellenbosch, South Africa,Correspondence to: Leon M T Dicks;
| |
Collapse
|
10
|
van Zyl WF, Deane SM, Dicks LMT. Use of the mCherry Fluorescent Protein To Study Intestinal Colonization by Enterococcus mundtii ST4SA and Lactobacillus plantarum 423 in Mice. Appl Environ Microbiol 2015; 81:5993-6002. [PMID: 26116681 PMCID: PMC4551250 DOI: 10.1128/aem.01247-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 05/22/2015] [Indexed: 12/19/2022] Open
Abstract
Lactic acid bacteria (LAB) are natural inhabitants of the gastrointestinal tract (GIT) of humans and animals, and some LAB species receive considerable attention due to their health benefits. Although many papers have been published on probiotic LAB, only a few reports have been published on the migration and colonization of the cells in the GIT. This is due mostly to the lack of efficient reporter systems. In this study, we report on the application of the fluorescent mCherry protein in the in vivo tagging of the probiotic strains Enterococcus mundtii ST4SA and Lactobacillus plantarum 423. The mCherry gene, encoding a red fluorescent protein (RFP), was integrated into a nonfunctional region on the genome of L. plantarum 423 by homologous recombination. In the case of E. mundtii ST4SA, the mCherry gene was cloned into the pGKV223D LAB/Escherichia coli expression vector. Expression of the mCherry gene did not alter the growth rate of the two strains and had no effect on bacteriocin production. Both strains colonized the cecum and colon of mice.
Collapse
Affiliation(s)
- Winschau F van Zyl
- Department of Microbiology, University of Stellenbosch, Stellenbosch, South Africa
| | - Shelly M Deane
- Department of Microbiology, University of Stellenbosch, Stellenbosch, South Africa
| | - Leon M T Dicks
- Department of Microbiology, University of Stellenbosch, Stellenbosch, South Africa
| |
Collapse
|
11
|
Bridier A, Hammes F, Canette A, Bouchez T, Briandet R. Fluorescence-based tools for single-cell approaches in food microbiology. Int J Food Microbiol 2015; 213:2-16. [PMID: 26163933 DOI: 10.1016/j.ijfoodmicro.2015.07.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 06/26/2015] [Accepted: 07/03/2015] [Indexed: 12/31/2022]
Abstract
The better understanding of the functioning of microbial communities is a challenging and crucial issue in the field of food microbiology, as it constitutes a prerequisite to the optimization of positive and technological microbial population functioning, as well as for the better control of pathogen contamination of food. Heterogeneity appears now as an intrinsic and multi-origin feature of microbial populations and is a major determinant of their beneficial or detrimental functional properties. The understanding of the molecular and cellular mechanisms behind the behavior of bacteria in microbial communities requires therefore observations at the single-cell level in order to overcome "averaging" effects inherent to traditional global approaches. Recent advances in the development of fluorescence-based approaches dedicated to single-cell analysis provide the opportunity to study microbial communities with an unprecedented level of resolution and to obtain detailed insights on the cell structure, metabolism activity, multicellular behavior and bacterial interactions in complex communities. These methods are now increasingly applied in the field of food microbiology in different areas ranging from research laboratories to industry. In this perspective, we reviewed the main fluorescence-based tools used for single-cell approaches and their concrete applications with specific focus on food microbiology.
Collapse
Affiliation(s)
| | - F Hammes
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - A Canette
- INRA, UMR1319 Micalis, Jouy-en-Josas, France; AgroParisTech, UMR Micalis, Jouy-en-Josas, France
| | | | - R Briandet
- INRA, UMR1319 Micalis, Jouy-en-Josas, France; AgroParisTech, UMR Micalis, Jouy-en-Josas, France.
| |
Collapse
|
12
|
Transport of Pathogen Surrogates in Soil Treatment Units: Numerical Modeling. WATER 2014. [DOI: 10.3390/w6040818] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
13
|
Bergholz TM, Moreno Switt AI, Wiedmann M. Omics approaches in food safety: fulfilling the promise? Trends Microbiol 2014; 22:275-81. [PMID: 24572764 DOI: 10.1016/j.tim.2014.01.006] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 01/13/2014] [Accepted: 01/22/2014] [Indexed: 12/30/2022]
Abstract
Genomics, transcriptomics, and proteomics are rapidly transforming our approaches to the detection, prevention, and treatment of foodborne pathogens. Microbial genome sequencing in particular has evolved from a research tool into an approach that can be used to characterize foodborne pathogen isolates as part of routine surveillance systems. Genome sequencing efforts will not only improve outbreak detection and source tracking, but will also create large amounts of foodborne pathogen genome sequence data, which will be available for data-mining efforts that could facilitate better source attribution and provide new insights into foodborne pathogen biology and transmission. Although practical uses and application of metagenomics, transcriptomics, and proteomics data and associated tools are less prominent, these tools are also starting to yield practical food safety solutions.
Collapse
Affiliation(s)
- Teresa M Bergholz
- Department of Veterinary and Microbiological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | | | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, New York, USA.
| |
Collapse
|
14
|
Zhao X, Dong T. Multifunctional sample preparation kit and on-chip quantitative nucleic acid sequence-based amplification tests for microbial detection. Anal Chem 2012; 84:8541-8. [PMID: 22985130 DOI: 10.1021/ac3020609] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This study reports a quantitative nucleic acid sequence-based amplification (Q-NASBA) microfluidic platform composed of a membrane-based sampling module, a sample preparation cassette, and a 24-channel Q-NASBA chip for environmental investigations on aquatic microorganisms. This low-cost and highly efficient sampling module, having seamless connection with the subsequent steps of sample preparation and quantitative detection, is designed for the collection of microbial communities from aquatic environments. Eight kinds of commercial membrane filters are relevantly analyzed using Saccharomyces cerevisiae, Escherichia coli, and Staphylococcus aureus as model microorganisms. After the microorganisms are concentrated on the membrane filters, the retentate can be easily conserved in a transport medium (TM) buffer and sent to a remote laboratory. A Q-NASBA-oriented sample preparation cassette is originally designed to extract DNA/RNA molecules directly from the captured cells on the membranes. Sequentially, the extract is analyzed within Q-NASBA chips that are compatible with common microplate readers in laboratories. Particularly, a novel analytical algorithmic method is developed for simple but robust on-chip Q-NASBA assays. The reported multifunctional microfluidic system could detect a few microorganisms quantitatively and simultaneously. Further research should be conducted to simplify and standardize ecological investigations on aquatic environments.
Collapse
Affiliation(s)
- Xinyan Zhao
- (IMST) Department of Micro and Nano Systems Technology, Faculty of Engineering and Marine Sciences, (HiVE) Vestfold University College, Norway
| | | |
Collapse
|
15
|
Fluorescent proteins in microbial biotechnology—new proteins and new applications. Biotechnol Lett 2011; 34:175-86. [DOI: 10.1007/s10529-011-0767-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 09/29/2011] [Indexed: 10/17/2022]
|
16
|
Selective advantage of resistant strains at trace levels of antibiotics: a simple and ultrasensitive color test for detection of antibiotics and genotoxic agents. Antimicrob Agents Chemother 2011; 55:1204-10. [PMID: 21199928 DOI: 10.1128/aac.01182-10] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many studies have examined the evolution of bacterial mutants that are resistant to specific antibiotics, and many of these focus on concentrations at and above the MIC. Here we ask for the minimum concentration at which existing resistant mutants can outgrow sensitive wild-type strains in competition experiments at antibiotic levels significantly below the MIC, and we define a minimum selective concentration (MSC) in Escherichia coli for two antibiotics, which is near 1/5 of the MIC for ciprofloxacin and 1/20 of the MIC for tetracycline. Because of the prevalence of resistant mutants already in the human microbiome, allowable levels of antibiotics to which we are exposed should be below the MSC. Since this concentration often corresponds to low or trace levels of antibiotics, it is helpful to have simple tests to detect such trace levels. We describe a simple ultrasensitive test for detecting the presence of antibiotics and genotoxic agents. The test is based on the use of chromogenic proteins as color markers and the use of single and multiple mutants of Escherichia coli that have greatly increased sensitivity to either a wide range of antibiotics or specific antibiotics, antibiotic families, and genotoxic agents. This test can detect ciprofloxacin at 1/75 of the MIC.
Collapse
|
17
|
Wei XX, Shi ZY, Li ZJ, Cai L, Wu Q, Chen GQ. A mini-Mu transposon-based method for multiple DNA fragment integration into bacterial genomes. Appl Microbiol Biotechnol 2010; 87:1533-41. [DOI: 10.1007/s00253-010-2674-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Revised: 05/10/2010] [Accepted: 05/10/2010] [Indexed: 10/19/2022]
|
18
|
Gregory JA, Becker EC, Jung J, Tuwatananurak I, Pogliano K. Transposon assisted gene insertion technology (TAGIT): a tool for generating fluorescent fusion proteins. PLoS One 2010; 5:e8731. [PMID: 20090956 PMCID: PMC2806921 DOI: 10.1371/journal.pone.0008731] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Accepted: 12/08/2009] [Indexed: 11/30/2022] Open
Abstract
We constructed a transposon (transposon assisted gene insertion technology, or TAGIT) that allows the random insertion of gfp (or other genes) into chromosomal loci without disrupting operon structure or regulation. TAGIT is a modified Tn5 transposon that uses Kan(R) to select for insertions on the chromosome or plasmid, beta-galactosidase to identify in-frame gene fusions, and Cre recombinase to excise the kan and lacZ genes in vivo. The resulting gfp insertions maintain target gene reading frame (to the 5' and 3' of gfp) and are integrated at the native chromosomal locus, thereby maintaining native expression signals. Libraries can be screened to identify GFP insertions that maintain target protein function at native expression levels, allowing more trustworthy localization studies. We here use TAGIT to generate a library of GFP insertions in the Escherichia coli lactose repressor (LacI). We identified fully functional GFP insertions and partially functional insertions that bind DNA but fail to repress the lacZ operon. Several of these latter GFP insertions localize to lacO arrays integrated in the E. coli chromosome without producing the elongated cells frequently observed when functional LacI-GFP fusions are used in chromosome tagging experiments. TAGIT thereby faciliates the isolation of fully functional insertions of fluorescent proteins into target proteins expressed from the native chromosomal locus as well as potentially useful partially functional proteins.
Collapse
Affiliation(s)
- James A. Gregory
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Eric C. Becker
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - James Jung
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Ida Tuwatananurak
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Kit Pogliano
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| |
Collapse
|