1
|
S. V. S, Augustine D, Mushtaq S, Baeshen HA, Ashi H, Hassan RN, Alshahrani M, Patil S. Revitalizing oral cancer research: Crispr-Cas9 technology the promise of genetic editing. Front Oncol 2024; 14:1383062. [PMID: 38915370 PMCID: PMC11194394 DOI: 10.3389/fonc.2024.1383062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 05/08/2024] [Indexed: 06/26/2024] Open
Abstract
This review presents an in-depth analysis of the immense potential of CRISPR-Cas9 technology in revolutionizing oral cancer research. It underscores the inherent limitations of conventional treatments while emphasizing the pressing need for groundbreaking approaches. The unparalleled capability of CRISPR-Cas9 to precisely target and modify specific genes involved in cancer progression heralds a new era in therapeutic intervention. Employing genome-wide CRISPR screens, vulnerabilities in oral cancer cells can be identified, thereby unravelling promising targets for therapeutic interventions. In the realm of oral cancer, the disruptive power of CRISPR-Cas9 manifests through its capacity to perturb genes that are intricately associated with drug resistance, consequently augmenting the efficacy of chemotherapy. To address the challenges that arise, this review diligently examines pertinent issues such as off-target effects, efficient delivery mechanisms, and the ethical considerations surrounding germline editing. Through precise gene editing, facilitated by CRISPR/Cas9, it becomes possible to overcome drug resistance by rectifying mutations, thereby enhancing the efficacy of personalized treatment strategies. This review delves into the prospects of CRISPR-Cas9, illuminating its potential applications in the domains of medicine, agriculture, and biotechnology. It is paramount to emphasize the necessity of ongoing research endeavors and the imperative to develop targeted therapies tailored specifically for oral cancer. By embracing this comprehensive overview, we can pave the way for ground-breaking treatments that instill renewed hope for enhanced outcomes in individuals afflicted by oral cancer.
Collapse
Affiliation(s)
- Sowmya S. V.
- Department of Oral Pathology and Microbiology, Faculty of Dental Sciences, MS Ramaiah University of Applied Sciences, Bengaluru, Karnataka, India
| | - Dominic Augustine
- Department of Oral Pathology and Microbiology, Faculty of Dental Sciences, MS Ramaiah University of Applied Sciences, Bengaluru, Karnataka, India
| | - Shazia Mushtaq
- College of Applied Medical Sciences, Dental Health Department, King Saud University, Riyadh, Saudi Arabia
| | - Hosam Ali Baeshen
- Department of Orthodontics, Faculty of Dentistry, King Abdulziz University, Jeddah, Saudi Arabia
| | - Heba Ashi
- Department of Dental Public Health, Faculty of Dentistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Reem Nabil Hassan
- Biological Sciences Department (Genome), Faculty of Sciences, King Abdul-Aziz University, Jeddah, Saudi Arabia
| | - Mohammed Alshahrani
- Endodontic Department, Faculty of Dentistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Shankargouda Patil
- College of Dental Medicine, Roseman University of Health Sciences, South Jordan, UT, United States
| |
Collapse
|
2
|
Aman Mohammadi M, Maximiano MR, Hosseini SM, Franco OL. CRISPR-Cas engineering in food science and sustainable agriculture: recent advancements and applications. Bioprocess Biosyst Eng 2023; 46:483-497. [PMID: 36707422 DOI: 10.1007/s00449-022-02842-5] [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: 08/20/2022] [Accepted: 12/14/2022] [Indexed: 01/29/2023]
Abstract
The developments in the food supply chain to support the growing population of the world is one of today's most pressing issues, and to achieve this goal improvements should be performed in both crops and microbes. For this purpose, novel approaches such as genome editing (GE) methods have upgraded the biological sciences for genome manipulation and, among such methods, clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) are the main exciting innovations since the Green Revolution. CRISPR/Cas systems can be a potent tool for the food industry, improvement of agricultural crops and even for protecting food-grade bacteria from foreign genetic invasive elements. This review introduces the history and mechanism of the CRISPR-Cas system as a genome editing tool and its applications in the vaccination of starter cultures, production of antimicrobials and bioactive compounds, and genome editing of microorganisms.
Collapse
Affiliation(s)
- Masoud Aman Mohammadi
- Student Research Committee, Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Sciences, Food Science and Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mariana Rocha Maximiano
- S-Inova Biotech, Graduate Program in Biotechnology, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil.,Centro de Análises Proteômicas e Bioquímicas, Graduate Program in Genomic Science and Biotechnology, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Seyede Marzieh Hosseini
- Student Research Committee, Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Sciences, Food Science and Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Octavio Luiz Franco
- S-Inova Biotech, Graduate Program in Biotechnology, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil.,Centro de Análises Proteômicas e Bioquímicas, Graduate Program in Genomic Science and Biotechnology, Universidade Católica de Brasília, Brasília, DF, Brazil
| |
Collapse
|
3
|
Yang Z, Qin F. The battle of crops against drought: Genetic dissection and improvement. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:496-525. [PMID: 36639908 DOI: 10.1111/jipb.13451] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
With ongoing global climate change, water scarcity-induced drought stress remains a major threat to agricultural productivity. Plants undergo a series of physiological and morphological changes to cope with drought stress, including stomatal closure to reduce transpiration and changes in root architecture to optimize water uptake. Combined phenotypic and multi-omics studies have recently identified a number of drought-related genetic resources in different crop species. The functional dissection of these genes using molecular techniques has enriched our understanding of drought responses in crops and has provided genetic targets for enhancing resistance to drought. Here, we review recent advances in the cloning and functional analysis of drought resistance genes and the development of technologies to mitigate the threat of drought to crop production.
Collapse
Affiliation(s)
- Zhirui Yang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Feng Qin
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
4
|
Roy R, Marakkar S, Vayalil MP, Shahanaz A, Anil AP, Kunnathpeedikayil S, Rawal I, Shetty K, Shameer Z, Sathees S, Prasannakumar AP, Mathew OK, Subramanian L, Shameer K, Yadav KK. Drug-food Interactions in the Era of Molecular Big Data, Machine Intelligence, and Personalized Health. RECENT ADVANCES IN FOOD, NUTRITION & AGRICULTURE 2022; 13:27-50. [PMID: 36173075 DOI: 10.2174/2212798412666220620104809] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/04/2022] [Accepted: 03/30/2022] [Indexed: 12/29/2022]
Abstract
The drug-food interaction brings forth changes in the clinical effects of drugs. While favourable interactions bring positive clinical outcomes, unfavourable interactions may lead to toxicity. This article reviews the impact of food intake on drug-food interactions, the clinical effects of drugs, and the effect of drug-food in correlation with diet and precision medicine. Emerging areas in drug-food interactions are the food-genome interface (nutrigenomics) and nutrigenetics. Understanding the molecular basis of food ingredients, including genomic sequencing and pharmacological implications of food molecules, helps to reduce the impact of drug-food interactions. Various strategies are being leveraged to alleviate drug-food interactions; measures including patient engagement, digital health, approaches involving machine intelligence, and big data are a few of them. Furthermore, delineating the molecular communications across dietmicrobiome- drug-food-drug interactions in a pharmacomicrobiome framework may also play a vital role in personalized nutrition. Determining nutrient-gene interactions aids in making nutrition deeply personalized and helps mitigate unwanted drug-food interactions, chronic diseases, and adverse events from their onset. Translational bioinformatics approaches could play an essential role in the next generation of drug-food interaction research. In this landscape review, we discuss important tools, databases, and approaches along with key challenges and opportunities in drug-food interaction and its immediate impact on precision medicine.
Collapse
Affiliation(s)
- Romy Roy
- Molecular Robotics, Cochin, Kerala, India
| | | | | | - Alisha Shahanaz
- Molecular Robotics, Cochin, Kerala, India.,Sanaria Inc, Rockville, MD, USA
| | - Athira Panicker Anil
- Molecular Robotics, Cochin, Kerala, India.,Mar Athanasious College for Advanced Studies, Tiruvalla, India
| | - Shameer Kunnathpeedikayil
- Molecular Robotics, Cochin, Kerala, India.,Thiruvalla, Kerala; People Care Health LLP Thrissur, Kerala, India
| | | | | | | | - Saraswathi Sathees
- Molecular Robotics, Cochin, Kerala, India.,University of Washington Seattle, Washington WA, USA
| | | | | | - Lakshminarayanan Subramanian
- Department of Computer Science, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
| | - Khader Shameer
- Northwell Health, New York, NY, USA and Faculty of Medicine, Imperial College London, London, UK
| | - Kamlesh K Yadav
- School of Engineering Medicine, Center for Genomic and Precision Medicine, Texas A&M University, Houston, TX 77030, USA.,Department of Translational Medical Sciences, Center for Genomic and Precision Medicine, Texas A&M University, Houston, TX 77030, USA
| |
Collapse
|
5
|
Kumar P, Rani A, Singh S, Kumar A. Recent advances on
DNA
and omics‐based technology in Food testing and authentication: A review. J Food Saf 2022. [DOI: 10.1111/jfs.12986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Pramod Kumar
- National Institute of Cancer Prevention and Research Indian Council for Medical Research (ICMR‐NICPR) Noida India
| | - Alka Rani
- National Institute of Cancer Prevention and Research Indian Council for Medical Research (ICMR‐NICPR) Noida India
| | - Shalini Singh
- National Institute of Cancer Prevention and Research Indian Council for Medical Research (ICMR‐NICPR) Noida India
| | - Anuj Kumar
- National Institute of Cancer Prevention and Research Indian Council for Medical Research (ICMR‐NICPR) Noida India
| |
Collapse
|
6
|
Bhattacharjee R, Nandi A, Mitra P, Saha K, Patel P, Jha E, Panda PK, Singh SK, Dutt A, Mishra YK, Verma SK, Suar M. Theragnostic application of nanoparticle and CRISPR against food-borne multi-drug resistant pathogens. Mater Today Bio 2022; 15:100291. [PMID: 35711292 PMCID: PMC9194658 DOI: 10.1016/j.mtbio.2022.100291] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 12/25/2022] Open
Abstract
Foodborne infection is one of the leading sources of infections spreading across the world. Foodborne pathogens are recognized as multidrug-resistant (MDR) pathogens posing a significant problem in the food industry and healthy consumers resulting in enhanced economic burden, and nosocomial infections. The continued search for enhanced microbial detection tools has piqued the interest of the CRISPR-Cas system and Nanoparticles. CRISPR-Cas system is present in the bacterial genome of some prokaryotes and is repurposed as a theragnostic tool against MDR pathogens. Nanoparticles and composites have also emerged as an efficient tool in theragnostic applications against MDR pathogens. The diagnostic limitations of the CRISPR-Cas system are believed to be overcome by a synergistic combination of the nanoparticles system and CRISPR-Cas using nanoparticles as vehicles. In this review, we have discussed the diagnostic application of CRISPR-Cas technologies along with their potential usage in applications like phage resistance, phage vaccination, strain typing, genome editing, and antimicrobial. we have also elucidated the antimicrobial and detection role of nanoparticles against foodborne MDR pathogens. Moreover, the novel combinatorial approach of CRISPR-Cas and nanoparticles for their synergistic effects in pathogen clearance and drug delivery vehicles has also been discussed. Bacterial CRISPR Cas system are repurposed as a thergodiganostic tool against MDR pathogen. Combinatorial approach of CRISPR-Cas and Nanoparticle is used as delivery vehicle and clearing pathogens. CRISPR-Cas and Nanoparticles is a tool for the food safety profiling of MDR food-borne pathogen.
Collapse
Affiliation(s)
- Rahul Bhattacharjee
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
| | - Aditya Nandi
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
| | - Priya Mitra
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
| | - Koustav Saha
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
| | - Paritosh Patel
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
| | - Ealisha Jha
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
| | - Pritam Kumar Panda
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20, Uppsala, Sweden
- Corresponding author.
| | - Sushil Kumar Singh
- DBT- NECAB, Department of Agricultural Biotechnology, Assam Agriculture University, Jorhat, 785013, Assam, India
| | - Ateet Dutt
- Instituto de Investigaciones en Materiales, UNAM, CDMX, Mexico
| | - Yogendra Kumar Mishra
- Mads Clausen Institute, NanoSYD, University of Southern Denmark, Alsion 2, DK-6400, Sønderborg, Denmark
- Corresponding author.
| | - Suresh K. Verma
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20, Uppsala, Sweden
- Corresponding author. KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India.
| | - Mrutyunjay Suar
- KIIT School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU), Bhubaneswar, Odisha, India
- Corresponding author.
| |
Collapse
|
7
|
De B, Goswami TK. Feeding the Future—Challenges and Limitations. Food Chem 2021. [DOI: 10.1002/9781119792130.ch9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
8
|
Asin-Garcia E, Martin-Pascual M, Garcia-Morales L, van Kranenburg R, Martins dos Santos VAP. ReScribe: An Unrestrained Tool Combining Multiplex Recombineering and Minimal-PAM ScCas9 for Genome Recoding Pseudomonas putida. ACS Synth Biol 2021; 10:2672-2688. [PMID: 34547891 PMCID: PMC8524654 DOI: 10.1021/acssynbio.1c00297] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Indexed: 12/11/2022]
Abstract
Genome recoding enables incorporating new functions into the DNA of microorganisms. By reassigning codons to noncanonical amino acids, the generation of new-to-nature proteins offers countless opportunities for bioproduction and biocontainment in industrial chassis. A key bottleneck in genome recoding efforts, however, is the low efficiency of recombineering, which hinders large-scale applications at acceptable speed and cost. To relieve this bottleneck, we developed ReScribe, a highly optimized recombineering tool enhanced by CRISPR-Cas9-mediated counterselection built upon the minimal PAM 5'-NNG-3' of the Streptococcus canis Cas9 (ScCas9). As a proof of concept, we used ReScribe to generate a minimally recoded strain of the industrial chassis Pseudomonas putida by replacing TAG stop codons (functioning as PAMs) of essential metabolic genes with the synonymous TAA. We showed that ReScribe enables nearly 100% engineering efficiency of multiple loci in P. putida, opening promising avenues for genome editing and applications thereof in this bacterium and beyond.
Collapse
Affiliation(s)
- Enrique Asin-Garcia
- Laboratory
of Systems and Synthetic Biology, Wageningen
University & Research, Wageningen 6708 WE, The Netherlands
| | - Maria Martin-Pascual
- Laboratory
of Systems and Synthetic Biology, Wageningen
University & Research, Wageningen 6708 WE, The Netherlands
| | - Luis Garcia-Morales
- Laboratory
of Systems and Synthetic Biology, Wageningen
University & Research, Wageningen 6708 WE, The Netherlands
| | - Richard van Kranenburg
- Corbion, Gorinchem 4206 AC, The Netherlands
- Laboratory
of Microbiology, Wageningen University &
Research, Wageningen 6708 WE, The Netherlands
| | - Vitor A. P. Martins dos Santos
- Laboratory
of Systems and Synthetic Biology, Wageningen
University & Research, Wageningen 6708 WE, The Netherlands
- LifeGlimmer
GmbH, Berlin 12163, Germany
- Bioprocess
Engineering Group, Wageningen University
& Research, Wageningen 6700 AA, The Netherlands
| |
Collapse
|
9
|
Pavlova YS, Paez-Espino D, Morozov AY, Belalov IS. Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling. PLoS Comput Biol 2021; 17:e1008841. [PMID: 33770071 PMCID: PMC8026048 DOI: 10.1371/journal.pcbi.1008841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 04/07/2021] [Accepted: 03/01/2021] [Indexed: 12/28/2022] Open
Abstract
Understanding CRISPR-Cas systems-the adaptive defence mechanism that about half of bacterial species and most of archaea use to neutralise viral attacks-is important for explaining the biodiversity observed in the microbial world as well as for editing animal and plant genomes effectively. The CRISPR-Cas system learns from previous viral infections and integrates small pieces from phage genomes called spacers into the microbial genome. The resulting library of spacers collected in CRISPR arrays is then compared with the DNA of potential invaders. One of the most intriguing and least well understood questions about CRISPR-Cas systems is the distribution of spacers across the microbial population. Here, using empirical data, we show that the global distribution of spacer numbers in CRISPR arrays across multiple biomes worldwide typically exhibits scale-invariant power law behaviour, and the standard deviation is greater than the sample mean. We develop a mathematical model of spacer loss and acquisition dynamics which fits observed data from almost four thousand metagenomes well. In analogy to the classical 'rich-get-richer' mechanism of power law emergence, the rate of spacer acquisition is proportional to the CRISPR array size, which allows a small proportion of CRISPRs within the population to possess a significant number of spacers. Our study provides an alternative explanation for the rarity of all-resistant super microbes in nature and why proliferation of phages can be highly successful despite the effectiveness of CRISPR-Cas systems.
Collapse
Affiliation(s)
- Yekaterina S. Pavlova
- Mathematics Department, Palomar College, San Marcos, California, United States of America
| | - David Paez-Espino
- Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America
- Mammoth BioSciences, South San Francisco, California, United States of America
| | - Andrew Yu. Morozov
- School of Mathematics and Actuarial Science, University of Leicester, Leicester, United Kingdom
- Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Ilya S. Belalov
- Laboratory of Microbial Viruses, Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, Moscow, Russia
| |
Collapse
|
10
|
Cañez C, Selle K, Goh YJ, Barrangou R. Outcomes and characterization of chromosomal self-targeting by native CRISPR-Cas systems in Streptococcus thermophilus. FEMS Microbiol Lett 2020; 366:5488433. [PMID: 31077282 DOI: 10.1093/femsle/fnz105] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/09/2019] [Indexed: 12/21/2022] Open
Abstract
CRISPR-Cas systems provide adaptive immunity against phages in prokaryotes via DNA-encoded, RNA-mediated, nuclease-dependent targeting and cleavage. Due to inefficient and relatively limited DNA repair pathways in bacteria, CRISPR-Cas systems can be repurposed for lethal DNA targeting that selects for sequence variants. In this study, the relative killing efficiencies of endogenous Type I and Type II CRISPR-Cas systems in the model organism Streptococcus thermophilus DGCC7710 were assessed. Additionally, the genetic and phenotypic outcomes of chromosomal targeting by plasmid-programmed Type I-E or Type II-A systems were analyzed. Efficient killing was observed using both systems, in a dose-dependent manner when delivering 0.4-400 ng of plasmid DNA. Targeted PCR screening and genome sequencing were used to determine the genetic basis enabling survival, showing that evasion of Type I-E self-targeting was primarily the result of low-frequency defective plasmids that excised the targeting spacer. The most notable genotype recovered from Type II-A targeting of genomic locus, lacZ, was a 34 kb-deletion derived from homologous recombination (HR) between identical conserved sequences in two separate galE coding regions, resulting in 2% loss of the genome. Collectively, these results suggest that HR contributes to the plasticity and remodeling of bacterial genomes, leading to evasion of genome targeting by CRISPR-Cas systems.
Collapse
Affiliation(s)
- Cassandra Cañez
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA.,Functional Genomics Graduate Program, North Carolina State University, Raleigh, NC 27695, USA
| | - Kurt Selle
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA.,Functional Genomics Graduate Program, North Carolina State University, Raleigh, NC 27695, USA
| | - Yong Jun Goh
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA.,Functional Genomics Graduate Program, North Carolina State University, Raleigh, NC 27695, USA
| |
Collapse
|
11
|
Abstract
The food industry faces a 2050 deadline for the advancement and expansion of the food supply chain to support the world's growing population. Improvements are needed across crops, livestock, and microbes to achieve this goal. Since 2005, researchers have been attempting to make the necessary strides to reach this milestone, but attempts have fallen short. With the introduction of clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins, the food production field is now able to achieve some of its most exciting advancements since the Green Revolution. This review introduces the concept of applying CRISPR-Cas technology as a genome-editing tool for use in the food supply chain, focusing on its implementation to date in crop, livestock, and microbe production, advancement of products to market, and regulatory and societal hurdles that need to be overcome.
Collapse
Affiliation(s)
- Katelyn Brandt
- Genomic Sciences, Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27695, USA; .,Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Rodolphe Barrangou
- Genomic Sciences, Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27695, USA; .,Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| |
Collapse
|
12
|
Westra ER, van Houte S, Gandon S, Whitaker R. The ecology and evolution of microbial CRISPR-Cas adaptive immune systems. Philos Trans R Soc Lond B Biol Sci 2020; 374:20190101. [PMID: 30905294 DOI: 10.1098/rstb.2019.0101] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Edze R Westra
- 1 ESI and CEC, Biosciences, University of Exeter , Cornwall Campus, Penryn TR10 9EZ , UK
| | - Stineke van Houte
- 1 ESI and CEC, Biosciences, University of Exeter , Cornwall Campus, Penryn TR10 9EZ , UK
| | - Sylvain Gandon
- 2 CEFE UMR 5175, CNRS Université de Montpellier Université Paul-Valéry Montpellier EPHE , 34293 Montpellier Cedex 5 , France
| | - Rachel Whitaker
- 3 Department of Microbiology, University of Illinois , Urbana-Champaign, 601 S. Goodwin Avenue, Urbana, IL 61801 , USA
| |
Collapse
|
13
|
Rogalski E, Vogel RF, Ehrmann MA. Monitoring of Lactobacillus sanfranciscensis strains during wheat and rye sourdough fermentations by CRISPR locus length polymorphism PCR. Int J Food Microbiol 2019; 316:108475. [PMID: 31874326 DOI: 10.1016/j.ijfoodmicro.2019.108475] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 11/05/2019] [Accepted: 12/07/2019] [Indexed: 12/26/2022]
Abstract
Lactobacillus (L.) sanfranciscensis is a competitive key species in sourdough fermentations. However, the principles involved in establishing the commonly observed phenomenon of strain dominance are unresolved. This has been studied little because the methods for fast and reliable differentiation of strains and their monitoring during fermentation are tedious and cannot be done with large numbers of isolates. In this contribution, we present a strain-specific, PCR-based typing method that uses length heterogeneities of the clustered regularly interspaced short palindromic repeats (CRISPR) loci as they occur in the genomes of different strains. In silico analysis of 21 genomes revealed 14 different CRISPR genotypes. We then designed a primer set to simultaneously detect different strains in a multiplex PCR assay designated CRISPR locus length polymorphism PCR (CLLP-PCR). The usefulness of this method was evaluated in lab-scale sourdough fermentations conducted with rye and wheat flours. First, the flour was mixed with water to a dough yield of 200. Then each dough was inoculated with four different L. sanfranciscensis strains (TMW 1.1150, TMW 1.392, TMW 1.2142, and TMW 1.2138) at levels of 109 cfu/g each. Sourdoughs were propagated at 28 °C for 5 days by back slopping 5% to the flour mass every 24 h. Samples were collected each day; DNA was isolated, and the presence of strains was detected qualitatively in the sourdoughs with PCR. L. sanfranciscensis TMW 1.392 became dominant as early as 2 days into the fermentation and remained the only detectable strain for the rest of the sampling period. CLLP-PCR proved to be useful in investigating the assertiveness of different strains of L. sanfranciscensis in sourdoughs. Therefore, CLLP-PCR may be used as a tool to investigate assertiveness of microorganisms in food fermentations at the strain level.
Collapse
Affiliation(s)
- Esther Rogalski
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany
| | - Rudi F Vogel
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany
| | - Matthias A Ehrmann
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany.
| |
Collapse
|
14
|
Bakhtin P, Khabirova E, Kuzminov I, Thurner T. The future of food production – a text-mining approach. TECHNOLOGY ANALYSIS & STRATEGIC MANAGEMENT 2019. [DOI: 10.1080/09537325.2019.1674802] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Pavel Bakhtin
- Institute of Statistical Studies and Economics of Knowledge, National Research University Higher School of Economics, Moscow, Russian Federation
| | - Elena Khabirova
- Institute of Statistical Studies and Economics of Knowledge, National Research University Higher School of Economics, Moscow, Russian Federation
| | - Ilya Kuzminov
- Institute of Statistical Studies and Economics of Knowledge, National Research University Higher School of Economics, Moscow, Russian Federation
| | - Thomas Thurner
- Institute of Statistical Studies and Economics of Knowledge, National Research University Higher School of Economics, Moscow, Russian Federation
| |
Collapse
|
15
|
Shiferaw Terefe N, Augustin MA. Fermentation for tailoring the technological and health related functionality of food products. Crit Rev Food Sci Nutr 2019; 60:2887-2913. [PMID: 31583891 DOI: 10.1080/10408398.2019.1666250] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fermented foods are experiencing a resurgence due to the consumers' growing interest in foods that are natural and health promoting. Microbial fermentation is a biotechnological process which transforms food raw materials into palatable, nutritious and healthy food products. Fermentation imparts unique aroma, flavor and texture to food, improves digestibility, degrades anti-nutritional factors, toxins and allergens, converts phytochemicals such as polyphenols into more bioactive and bioavailable forms, and enriches the nutritional quality of food. Fermentation also modifies the physical functional properties of food materials, rendering them differentiated ingredients for use in formulated foods. The science of fermentation and the technological and health functionality of fermented foods is reviewed considering the growing interest worldwide in fermented foods and beverages and the huge potential of the technology for reducing food loss and improving nutritional food security.
Collapse
|
16
|
Stephanie MC, Santiago JV. Genetically Engineered Probiotics and Therapies Applications. BIONATURA 2019. [DOI: 10.21931/rb/cs/2019.02.01.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The idea of using probiotics for health benefits in the human body is still biased since there is skepticism and since it is quite a new field of research. However, recent experiments are trying to debate that given the naturality of their consumption and the successful results from in vitro tests in combination with other therapies. Food scientists are eager to take advantage of the known beneficial properties of probiotics by using engineering technologies in order to enhance them. Using CRISPR systems present in lactobacilli aids in strain identification, while offering information on phylogeny and ecological interactions. Also, the use of genetic engineering tools could also allow the use of plasmid vaccines to prevent antibiotic resistance and the development of synthetic probiotics as microbial treatments.
Collapse
Affiliation(s)
| | - Jijón V. Santiago
- School of Biological Sciences and Engineering, YachayTech, Urcuquí. Ecuador
| |
Collapse
|
17
|
Zhai J, Wang Q, Gao Y, Zhang R, Li S, Wei B, You Y, Sun X, Lu C. The mechanisms of Ag85A DNA vaccine activates RNA sensors through new signal transduction. Int Immunopharmacol 2018; 59:1-11. [PMID: 29604449 DOI: 10.1016/j.intimp.2017.11.041] [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: 09/01/2017] [Revised: 11/26/2017] [Accepted: 11/28/2017] [Indexed: 10/17/2022]
Abstract
Low immunogenicity is one of the major problems limiting the clinical use for DNA vaccines, which makes it impossible to obtain a strong protective immune response after vaccination. In order to explore whether Ag85A DNA vaccine could mount more efficiently protective immune response through new RNA sensor and its signal transduction pathway of antigen presentation we designed and synthesized Ag85A gene fragment containing multiple points mutations and transfected the gene fragment into the dendritic cell line (DC2.4) by CRISPR/Cas9. Subsequently, we focused on the changes of RNA sensors RIG-I, Mda-5, and the downstream adaptors MAVS, IRF3, IRF7 and IFN-β. The results indicated the significant increases in the mRNA and protein expression of RNA sensors RIG-I, Mda-5 and related adaptors MAVS, IRF3, IRF7, and IFN-β in the mutant DC 2.4 cells. The flow cytometry results demonstrated that the expression of MHC II on the surface of DC 2.4 significantly increased when compared with that in control. Therefore, it is suggested that Ag85A mutant DNA could release immunogenic message through RNA sensors and related adaptors via non protein pathway. There is at least one RNA signal transduction pathway of Ag85A DNA in DC2.4 cell. The work provides a new mode of action for nucleic acid vaccine to improve immunogenicity and meaningful data for the better understanding of the mechanisms of DNA vaccine.
Collapse
Affiliation(s)
- Jingbo Zhai
- Department of Immunology, China Medical University, Shenyang 110122, China; Brucellosis Institute of Inner Mongolia University for the Nationalities, Tongliao 028000, China
| | - Qiubo Wang
- Department of Immunology, China Medical University, Shenyang 110122, China
| | - Yunfeng Gao
- Department of Immunology, China Medical University, Shenyang 110122, China
| | - Ran Zhang
- Department of Immunology, China Medical University, Shenyang 110122, China
| | - Shengjun Li
- Department of Immunology, China Medical University, Shenyang 110122, China
| | - Bing Wei
- Department of Immunology, China Medical University, Shenyang 110122, China
| | - Yong You
- Department of Immunology, China Medical University, Shenyang 110122, China
| | - Xun Sun
- Department of Immunology, China Medical University, Shenyang 110122, China
| | - Changlong Lu
- Department of Immunology, China Medical University, Shenyang 110122, China; Brucellosis Institute of Inner Mongolia University for the Nationalities, Tongliao 028000, China.
| |
Collapse
|
18
|
Schmid M, Muri J, Melidis D, Varadarajan AR, Somerville V, Wicki A, Moser A, Bourqui M, Wenzel C, Eugster-Meier E, Frey JE, Irmler S, Ahrens CH. Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level. Front Microbiol 2018; 9:63. [PMID: 29441050 PMCID: PMC5797582 DOI: 10.3389/fmicb.2018.00063] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/10/2018] [Indexed: 11/20/2022] Open
Abstract
Although complete genome sequences hold particular value for an accurate description of core genomes, the identification of strain-specific genes, and as the optimal basis for functional genomics studies, they are still largely underrepresented in public repositories. Based on an assessment of the genome assembly complexity for all lactobacilli, we used Pacific Biosciences' long read technology to sequence and de novo assemble the genomes of three Lactobacillus helveticus starter strains, raising the number of completely sequenced strains to 12. The first comparative genomics study for L. helveticus—to our knowledge—identified a core genome of 988 genes and sets of unique, strain-specific genes ranging from about 30 to more than 200 genes. Importantly, the comparison of MiSeq- and PacBio-based assemblies uncovered that not only accessory but also core genes can be missed in incomplete genome assemblies based on short reads. Analysis of the three genomes revealed that a large number of pseudogenes were enriched for functional Gene Ontology categories such as amino acid transmembrane transport and carbohydrate metabolism, which is in line with a reductive genome evolution in the rich natural habitat of L. helveticus. Notably, the functional Clusters of Orthologous Groups of proteins categories “cell wall/membrane biogenesis” and “defense mechanisms” were found to be enriched among the strain-specific genes. A genome mining effort uncovered examples where an experimentally observed phenotype could be linked to the underlying genotype, such as for cell envelope proteinase PrtH3 of strain FAM8627. Another possible link identified for peptidoglycan hydrolases will require further experiments. Of note, strain FAM22155 did not harbor a CRISPR/Cas system; its loss was also observed in other L. helveticus strains and lactobacillus species, thus questioning the value of the CRISPR/Cas system for diagnostic purposes. Importantly, the complete genome sequences proved to be very useful for the analysis of natural whey starter cultures with metagenomics, as a larger percentage of the sequenced reads of these complex mixtures could be unambiguously assigned down to the strain level.
Collapse
Affiliation(s)
- Michael Schmid
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland.,Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Jonathan Muri
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland
| | - Damianos Melidis
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland
| | - Adithi R Varadarajan
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland.,Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Vincent Somerville
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland.,Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Adrian Wicki
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland
| | - Aline Moser
- Agroscope, Research Group Biochemistry of Milk and Microorganisms, Bern, Switzerland
| | - Marc Bourqui
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland.,Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Claudia Wenzel
- Agroscope, Research Group Biochemistry of Milk and Microorganisms, Bern, Switzerland
| | - Elisabeth Eugster-Meier
- School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Zollikofen, Switzerland
| | - Juerg E Frey
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland
| | - Stefan Irmler
- Agroscope, Research Group Biochemistry of Milk and Microorganisms, Bern, Switzerland
| | - Christian H Ahrens
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland.,Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| |
Collapse
|
19
|
Emerging crossover technologies: How to organize a biotechnology that becomes mainstream? ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s10669-017-9666-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
20
|
King T, Cole M, Farber JM, Eisenbrand G, Zabaras D, Fox EM, Hill JP. Food safety for food security: Relationship between global megatrends and developments in food safety. Trends Food Sci Technol 2017. [DOI: 10.1016/j.tifs.2017.08.014] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
|
21
|
Abstract
The complex carbohydrates of terrestrial and marine biomass represent a rich nutrient source for free-living and mutualistic microbes alike. The enzymatic saccharification of these diverse substrates is of critical importance for fueling a variety of complex microbial communities, including marine, soil, ruminant, and monogastric microbiota. Consequently, highly specific carbohydrate-active enzymes, recognition proteins, and transporters are enriched in the genomes of certain species and are of critical importance in competitive environments. In Bacteroidetes bacteria, these systems are organized as polysaccharide utilization loci (PULs), which are strictly regulated, colocalized gene clusters that encode enzyme and protein ensembles required for the saccharification of complex carbohydrates. This review provides historical perspectives and summarizes key findings in the study of these systems, highlighting a critical shift from sequence-based PUL discovery to systems-based analyses combining reverse genetics, biochemistry, enzymology, and structural biology to precisely illuminate the molecular mechanisms underpinning PUL function. The ecological implications of dynamic PUL deployment by key species in the human gastrointestinal tract are explored, as well as the wider distribution of these systems in other gut, terrestrial, and marine environments.
Collapse
|
22
|
A decade of discovery: CRISPR functions and applications. Nat Microbiol 2017; 2:17092. [PMID: 28581505 DOI: 10.1038/nmicrobiol.2017.92] [Citation(s) in RCA: 180] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 05/05/2017] [Indexed: 12/26/2022]
Abstract
This year marks the tenth anniversary of the identification of the biological function of CRISPR-Cas as adaptive immune systems in bacteria. In just a decade, the characterization of CRISPR-Cas systems has established a novel means of adaptive immunity in bacteria and archaea and deepened our understanding of the interplay between prokaryotes and their environment, and CRISPR-based molecular machines have been repurposed to enable a genome editing revolution. Here, we look back on the historical milestones that have paved the way for the discovery of CRISPR and its function, and discuss the related technological applications that have emerged, with a focus on microbiology. Lastly, we provide a perspective on the impacts the field has had on science and beyond.
Collapse
|
23
|
Liu X, Xie C, Si H, Yang J. CRISPR/Cas9-mediated genome editing in plants. Methods 2017; 121-122:94-102. [PMID: 28315486 DOI: 10.1016/j.ymeth.2017.03.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 02/09/2017] [Accepted: 03/03/2017] [Indexed: 01/09/2023] Open
Abstract
The increasing burden of the world's population on agriculture necessitates the development of more robust crops. As the amount of information from sequenced crop genomes increases, technology can be used to investigate the function of genes in detail and to design improved crops at the molecular level. Recently, an RNA-programmed genome-editing system composed of a clustered regularly interspaced short palindromic repeats (CRISPR)-encoded guide RNA and the nuclease Cas9 has provided a powerful platform to achieve these goals. By combining versatile tools to study and modify plants at different molecular levels, the CRISPR/Cas9 system is paving the way towards a new horizon for basic research and crop development. In this review, the accomplishments, problems and improvements of this technology in plants, including target sequence cleavage, knock-in/gene replacement, transcriptional regulation, epigenetic modification, off-target effects, delivery system and potential applications, will be highlighted.
Collapse
Affiliation(s)
- Xuejun Liu
- TianJin Crops Research Institute, China.
| | - Chuanxiao Xie
- Institute of Crop Science of Chinese Academy of Agricultural Sciences, China.
| | - Huaijun Si
- College of Life Science and Technology, GanSu Agricultural University, China.
| | | |
Collapse
|
24
|
Carroll M, Zhou X. Panacea in progress: CRISPR and the future of its biological research introduction. Microbiol Res 2017; 201:63-74. [PMID: 28602403 DOI: 10.1016/j.micres.2017.04.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 04/27/2017] [Indexed: 01/21/2023]
Abstract
The elucidation of the CRISPR (clustered, regularly interspaced, short palindromic repeats) adaptive immune system endogenous to most microbial life has culminated in progress in a diversity of scientific disciplines. The concurrently promising and eccentric nature of its theoretically plausible applications has wrought enthusiasm in the research community globally, potentiating advancements in human and animal health, ecological stability, and economic wellbeing, that would hitherto be considered the unattainable fancies of a futurist. It may be supposed that the tomes of science fiction are the true books of prophecy. Here, we narrate the scientific dialogue regarding CRISPR/Cas biotechnologies, from the happenstantial initial observation of the locus to the litany of intriguing contemporary endeavors. We discuss the mechanistic underpinnings in detail, and the corpulent body of literature on CRISPR-based biotech is digested into a germane and informative review. CRISPR applications such as microbiome engineering in order to enhance the human immune system beyond the fortitude of the wild type, bacterial genome editing in industrial and medical aspects, conquering antibiotic resistance, the development of novel antimicrobial techniques, the harvesting of solventogenic microbes, the development of antifungal therapies, and investigation of the genetic properties of fungi, are here represented, and the authors posit unconventional, and at times gainfully tangential, thoughts and concepts in order to encourage a reflective disposition towards this sophisticated device of nature: a panacea in progress, such that the most impassive and technical writing still carries the ring of poetry.
Collapse
Affiliation(s)
- Michael Carroll
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
| | - Xiaohui Zhou
- Department of Pathobiology and Veterinary Science, the University of Connecticut, 61 N. Eagleville Rd, Storrs, CT, 06269-3089, United States; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.
| |
Collapse
|
25
|
Survey on the phage resistance mechanisms displayed by a dairy Lactobacillus helveticus strain. Food Microbiol 2017; 66:110-116. [PMID: 28576359 DOI: 10.1016/j.fm.2017.04.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/20/2017] [Accepted: 04/23/2017] [Indexed: 11/20/2022]
Abstract
In this study the presence and functionality of phage defence mechanisms in Lactobacillus helveticus ATCC 10386, a strain of dairy origin which is sensitive to ΦLh56, were investigated. After exposure of ATCC 10386 to ΦLh56, the whole-genome sequences of ATCC 10386 and of a phage-resistant derivative (LhM3) were compared. LhM3 showed deletions in the S-layer protein and a higher expression of the genes involved in the restriction/modification (R/M) system. Genetic data were substantiated by measurements of bacteriophage adsorption rates, efficiency of plaquing, cell wall protein size and by gene expression analysis. In LhM3 two phage resistance mechanisms, the inhibition of phage adsorption and the upregulation of Type I R/M genes, take place and explain its resistance to ΦLh56. Although present in both ATCC 10386 and LhM3 genomes, the CRISPR machinery did not seem to play a role in the phage resistance of LhM3. Overall, the natural selection of phage resistant strains resulted successful in detecting variants carrying multiple phage defence mechanisms in L. helveticus. The concurrent presence of multiple phage-resistance systems should provide starter strains with increased fitness and robustness in dairy ecosystems.
Collapse
|
26
|
Stout E, Klaenhammer T, Barrangou R. CRISPR-Cas Technologies and Applications in Food Bacteria. Annu Rev Food Sci Technol 2017; 8:413-437. [DOI: 10.1146/annurev-food-072816-024723] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins form adaptive immune systems that occur in many bacteria and most archaea. In addition to protecting bacteria from phages and other invasive mobile genetic elements, CRISPR-Cas molecular machines can be repurposed as tool kits for applications relevant to the food industry. A primary concern of the food industry has long been the proper management of food-related bacteria, with a focus on both enhancing the outcomes of beneficial microorganisms such as starter cultures and probiotics and limiting the presence of detrimental organisms such as pathogens and spoilage microorganisms. This review introduces CRISPR-Cas as a novel set of technologies to manage food bacteria and offers insights into CRISPR-Cas biology. It primarily focuses on the applications of CRISPR-Cas systems and tools in starter cultures and probiotics, encompassing strain-typing, phage resistance, plasmid vaccination, genome editing, and antimicrobial activity.
Collapse
Affiliation(s)
- Emily Stout
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695
| | - Todd Klaenhammer
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695
| |
Collapse
|
27
|
Hough SH, Ajetunmobi A. The Future of CRISPR Applications in the Lab, the Clinic and Society. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1016:157-178. [PMID: 29130159 DOI: 10.1007/978-3-319-63904-8_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats) has emerged as one of the premiere biological tools of the century. Even more so than older genome editing techniques such as TALENs and ZFNs, CRISPR provides speed and ease-of-use heretofore unheard of in agriculture, the environment and human health. The ability to map the function of virtually every component of the genome in a scalable, multiplexed manner is unprecedented. Once those regions have been explored, CRISPR also presents an opportunity to take advantage of endogenous cellular repair pathways to change and precisely edit the genome [1-3]. In the case of human health, CRISPR operates as both a tool of discovery and a solution to fundamental problems behind disease and undesirable mutations.
Collapse
Affiliation(s)
- Soren H Hough
- Department of Microbiology, University of Massachusetts Amherst, 418 Morrill Science Center IVN, 649 North Pleasant Street, Amherst, MA, 01003, USA.
| | - Ayokunmi Ajetunmobi
- Department of Clinical Medicine, St. James' Hospital, Dublin, Ireland, James's Street, Dublin 8, Dublin, Leinster, D08 NHY1, Ireland
| |
Collapse
|
28
|
Barrangou R, Doudna JA. Applications of CRISPR technologies in research and beyond. Nat Biotechnol 2016; 34:933-941. [DOI: 10.1038/nbt.3659] [Citation(s) in RCA: 577] [Impact Index Per Article: 72.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 07/31/2016] [Indexed: 02/06/2023]
|
29
|
Hooton SPT, Brathwaite KJ, Connerton IF. The Bacteriophage Carrier State of Campylobacter jejuni Features Changes in Host Non-coding RNAs and the Acquisition of New Host-derived CRISPR Spacer Sequences. Front Microbiol 2016; 7:355. [PMID: 27047470 PMCID: PMC4804229 DOI: 10.3389/fmicb.2016.00355] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 03/07/2016] [Indexed: 12/21/2022] Open
Abstract
Incorporation of self-derived CRISPR DNA protospacers in Campylobacter jejuni PT14 occurs in the presence of bacteriophages encoding a CRISPR-like Cas4 protein. This phenomenon was evident in carrier state infections where both bacteriophages and host are maintained for seemingly indefinite periods as stable populations following serial passage. Carrier state cultures of C. jejuni PT14 have greater aerotolerance in nutrient limited conditions, and may have arisen as an evolutionary response to selective pressures imposed during periods in the extra-intestinal environment. A consequence of this is that bacteriophage and host remain associated and able to survive transition periods where the chances of replicative success are greatly diminished. The majority of the bacteriophage population do not commit to lytic infection, and conversely the bacterial population tolerates low-level bacteriophage replication. We recently examined the effects of Campylobacter bacteriophage/C. jejuni PT14 CRISPR spacer acquisition using deep sequencing strategies of DNA and RNA-Seq to analyze carrier state cultures. This approach identified de novo spacer acquisition in C. jejuni PT14 associated with Class III Campylobacter phages CP8/CP30A but spacer acquisition was oriented toward the capture of host DNA. In the absence of bacteriophage predation the CRISPR spacers in uninfected C. jejuni PT14 cultures remain unchanged. A distinct preference was observed for incorporation of self-derived protospacers into the third spacer position of the C. jejuni PT14 CRISPR array, with the first and second spacers remaining fixed. RNA-Seq also revealed the variation in the synthesis of non-coding RNAs with the potential to bind bacteriophage genes and/or transcript sequences.
Collapse
Affiliation(s)
- Steven P T Hooton
- Division of Food Sciences, School of Biosciences, University of Nottingham Loughborough, UK
| | - Kelly J Brathwaite
- Division of Food Sciences, School of Biosciences, University of Nottingham Loughborough, UK
| | - Ian F Connerton
- Division of Food Sciences, School of Biosciences, University of Nottingham Loughborough, UK
| |
Collapse
|