Abstract：
:Genome editing is essential for probing genotype-phenotype relationships and for enhancing chemical production and phenotypic robustness in industrial bacteria. Currently, the most popular tools for genome editing couple recombineering with DNA cleavage by the CRISPR nuclease Cas9 from Streptococcus pyogenes. Although successful in some model strains, CRISPR-based genome editing has been slow to extend to the multitude of industrially relevant bacteria. In this review, we analyze existing barriers to implementing CRISPR-based editing across diverse bacterial species. We first compare the efficacy of current CRISPR-based editing strategies. Next, we discuss alternatives when the S. pyogenes Cas9 does not yield colonies. Finally, we describe different ways bacteria can evade editing and how elucidating these failure modes can improve CRISPR-based genome editing across strains. Together, this review highlights existing obstacles to CRISPR-based editing in bacteria and offers guidelines to help achieve and enhance editing in a wider range of bacterial species, including non-model strains.
journal_name
J Ind Microbiol Biotechnoljournal_title
Journal of industrial microbiology & biotechnologyauthors
Vento JM,Crook N,Beisel CLdoi
10.1007/s10295-019-02195-1subject
Has Abstractpub_date
2019-10-01 00:00:00pages
1327-1341issue
9-10eissn
1367-5435issn
1476-5535pii
10.1007/s10295-019-02195-1journal_volume
46pub_type
杂志文章,评审abstract：:A metabolic network consisting of 48 reactions was established to describe intracellular processes during growth and poly-3-hydroxybutyrate (PHB) production for Cupriavidus necator DSM 545. Glycerol acted as the sole carbon source during exponential, steady-state cultivation conditions. Elementary flux modes were obta...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章
doi：10.1007/s10295-014-1439-y
更新日期：2014-06-01 00:00:00
abstract：:Burkholderia cepacia complex (BCC) presence has been the cause of recalls of both sterile and non-sterile pharmaceutical products since these opportunistic pathogens have been implicated to cause infections to susceptible individuals. BCC are ubiquitous in nature, but in pharmaceutical settings the most common source ...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章
doi：10.1007/s10295-014-1442-3
更新日期：2014-07-01 00:00:00
abstract：:This paper summarizes research results and their industrial applications obtained by continuous culture in the former Czechoslovakia. Past achievements as well as recent trends and developments worldwide are presented. The term "Prague School of continuous culture" is put forward and its international activity is outl...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 历史文章,杂志文章
doi：10.1007/s10295-010-0881-8
更新日期：2010-12-01 00:00:00
abstract：:Selection of the ideal microbe is crucial for whole-cell biotransformations, especially if the target reaction intensively interacts with host cell functions. Asymmetric styrene epoxidation is an example of a reaction which is strongly dependent on the host cell owing to its requirement for efficient cofactor regenera...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章
doi：10.1007/s10295-012-1126-9
更新日期：2012-08-01 00:00:00
abstract：:Bioremediation of aromatic hydrocarbons in groundwater and sediments is often limited by dissolved oxygen. Many aromatic hydrocarbons degrade very slowly or not at all under anaerobic conditions. Nitrate is a good alternative electron acceptor to oxygen, and denitrifying bacteria are commonly found in the subsurface a...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章,评审
doi：10.1038/sj.jim.2900288
更新日期：1997-02-01 00:00:00
abstract：:In the online published article, row value "pIB139-metK1-metK2" in table 1 has been processed incorrectly. The correct table is given below. ...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章,已发布勘误
doi：10.1007/s10295-018-2036-2
更新日期：2018-06-01 00:00:00
abstract：:The longer start-up period of the Anammox process is due to the very low cellular yield and growth rates of Anammox bacteria. Nitrite inhibition is considered to be the key factor in the instability of the Anammox process during the operation. However, little attention was paid to the inhibitory effect of pH and free ...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章
doi：10.1007/s10295-009-0593-0
更新日期：2009-08-01 00:00:00
abstract：:The acidification behavior of Lactobacillus bulgaricus and Streptococcus thermophilus for yoghurt production was investigated along temperature profiles within the optimal window of 38-44 degrees C. For the optimal acidification temperature profile search, an optimization engine module built on a modular artificial ne...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章
doi：10.1007/s10295-007-0220-x
更新日期：2007-07-01 00:00:00
abstract：:Bacteriocins produced by lactic acid bacteria are gaining increased importance due to their activity against undesirable microorganisms in foods. In this study, a concentrated acid extract of a culture of Lactobacillus sakei subsp. sakei 2a, a bacteriocinogenic strain isolated from a Brazilian pork product, was purifi...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章
doi：10.1007/s10295-009-0684-y
更新日期：2010-04-01 00:00:00
abstract：:Isoprenoids are a large class of natural products with myriad applications as bioactive and commercial compounds. Their diverse structures are derived from the biosynthetic assembly and tailoring of their scaffolds, ultimately constructed from two C5 hemiterpene building blocks. The modular logic of these platforms ca...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章,评审
doi：10.1007/s10295-020-02306-3
更新日期：2020-10-01 00:00:00
abstract：:The non-conventional yeast Kluyveromyces marxianus is an emerging industrial producer for many biotechnological processes. Here, we show the application of a biomass-linked stoichiometric model of central metabolism that is experimentally validated, and mass and charge balanced for assessing the carbon conversion effi...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章
doi：10.1007/s10295-017-1946-8
更新日期：2017-08-01 00:00:00
abstract：:In this study, the M13 primer was used to distinguish Geotrichum candidum from the anamorphic and teleomorphic forms of other arthrospore-forming species (discriminatory power = 0.99). For intraspecific characterization, the GATA4 primer showed the highest level of discrimination for G. candidum among the 20 microsate...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章
doi：10.1007/s10295-006-0130-3
更新日期：2006-12-01 00:00:00
abstract：:Keratinases are proteolytic enzymes capable of degrading insoluble keratins. The importance of these enzymes is being increasingly recognized in fields as diverse as animal feed production, textile processing, detergent formulation, leather manufacture, and medicine. To enhance the thermostability of Bacillus lichenif...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章
doi：10.1007/s10295-013-1268-4
更新日期：2013-07-01 00:00:00
abstract：:Production of recombinant protein bio-insecticides on a commercial scale can only be cost effective if host strains with very high expression levels are available. A recombinant fusion protein containing an arthropod toxin, ω-hexatoxin-Hv1a, (from funnel web spider Hadronyche versuta) linked to snowdrop lectin (Galant...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章
doi：10.1007/s10295-014-1466-8
更新日期：2014-08-01 00:00:00
abstract：:The survival of a Sphingomonas species that was introduced into pentachlorophenol (PCP)-contaminated soil was monitored with two complementary methods, a respiration-based assay and a most probable number (MPN) technique. Sphingomonas chlorophenolicastrain RA2 is a PCP-mineralizing bacterium that was introduced into s...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章
doi：10.1038/sj.jim.2900718
更新日期：1999-10-01 00:00:00
abstract：:The Red recombinase system, the most convenient genetic tool applied in Escherichia coli and other bacteria, was introduced for gene replacement in Klebsiella pneumoniae. The novel K. pneumoniae gene replacement system comprised the Red and FLP recombinases expression vector pDK6-red and pDK6-flp, and linear DNA fragm...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章
doi：10.1007/s10295-012-1117-x
更新日期：2012-08-01 00:00:00
abstract：:Gordonia alkanivorans S7 is an efficient degrader of fuel oil hydrocarbons that can simultaneously utilize oxygen and nitrate as electron acceptors. The respiratory nitrate reductase (Nar) from this organism has been isolated using ion exchange chromatography and gel filtration, and then preliminarily characterized. P...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章
doi：10.1007/s10295-010-0717-6
更新日期：2010-06-01 00:00:00
abstract：:Amyris is a fermentation product company that leverages synthetic biology and has been bringing novel fermentation products to the market since 2009. Driven by breakthroughs in genome editing, strain construction and testing, analytics, automation, data science, and process development, Amyris has commercialized nine ...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章
doi：10.1007/s10295-020-02314-3
更新日期：2020-11-01 00:00:00
abstract：:Abundant larval transcript (ALT), a novel filarial protein, has been shown to have great potential as a vaccine in the prevention of human lymphatic filariasis. In this study, we report a method for the production of recombinant ALT-2 protein, expressed in the cytoplasm of bacterium Escherichia coli in soluble form an...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章
doi：10.1007/s10295-010-0753-2
更新日期：2010-10-01 00:00:00
abstract：:Toxic heavy metals and metalloids, such as cadmium, lead, mercury, arsenic, and selenium, are constantly released into the environment. There is an urgent need to develop low-cost, effective, and sustainable methods for their removal or detoxification. Plant-based approaches, such as phytoremediation, are relatively i...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章,评审
doi：10.1007/s10295-005-0227-0
更新日期：2005-12-01 00:00:00
abstract：:Experiments based on a 2(3) central composite full factorial design were carried out in 200-ml stainless-steel containers to study the pretreatment, with dilute sulfuric acid, of a sugarcane bagasse sample obtained from a local sugar-alcohol mill. The independent variables selected for study were temperature, varied f...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章
doi：10.1007/s10295-010-0931-2
更新日期：2011-09-01 00:00:00
abstract：:The phytase of the yeast Pichia anomala (PPHY) is a suitable biocatalyst as a food and feed additive because of its adequate thermostability, acid stability, protease insensitivity and broad substrate spectrum. The cell-bound nature and low phytase titres are the main bottlenecks for its utility in food and feed indus...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章
doi：10.1007/s10295-015-1670-1
更新日期：2015-10-01 00:00:00
abstract：:Natural product discovery in the microbial world has historically been biased toward aerobes. Recent in silico analysis demonstrates that genomes of anaerobes encode unexpected biosynthetic potential for natural products, however, chemical data on natural products from the anaerobic world are extremely limited. Here, ...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章,评审
doi：10.1007/s10295-018-2086-5
更新日期：2019-03-01 00:00:00
abstract：:A novel chromatic visible screening method using bromothymol blue (BTB) as a color indicator and cetylpyridinium chloride (CPC) as a mediator was constructed to obtain the high titer surfactin-producing strains. The reliability and quantification accuracy of color shift were also confirmed. Regular chromatic responses...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章
doi：10.1007/s10295-015-1635-4
更新日期：2015-08-01 00:00:00
abstract：:Deficiency in petroleum resources and increasing environmental concerns have pushed a bio-based economy to be built, employing a highly reproducible, metal contaminant free, sustainable and green biomanufacturing method. Here, a chiral drug intermediate L-pipecolic acid has been synthesized from biomass-derived lysine...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章
doi：10.1007/s10295-018-2044-2
更新日期：2018-06-01 00:00:00
abstract：:A superoxide dismutase (SOD) gene was cloned from the thermophilic bacterium Rhodothermus sp. XMH10 for the first time and highly expressed in Escherichia coli. The Rhodothermus sp. XMH10 SOD (RhSOD) gene encodes 209 amino acids with a putative molecular weight of 23.6 kDa and a pI value of 5.53. The recombinant RhSOD...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章
doi：10.1007/s10295-007-0274-9
更新日期：2008-02-01 00:00:00
abstract：:Streptomyces transglutaminase (TGase) has been widely used in food, pharmaceutical and textile industries. Streptomyces TGase is naturally synthesized as zymogen (pro-TGase), which is then processed to produce active enzyme by removing its N-terminal pro-peptide. Although the pro-peptide is essential for TGase folding...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章
doi：10.1007/s10295-012-1221-y
更新日期：2013-04-01 00:00:00
abstract：:A formate dehydrogenase gene (fdh) originated from Candida boidinii was co-expressed in E. coli BL21 (DE3) with the cyclohexanone monooxygenase gene (chmo) cloned from Acinetobacter calcoaceticus NCIMB 9871. The co-expression system was then used as a whole-cell biocatalyst to synthesize chiral phenyl methyl sulfoxide...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章
doi：10.1007/s10295-013-1288-0
更新日期：2013-08-01 00:00:00
abstract：:Microbial diversity is fundamental to maintenance and conservation of global genetic resources. As extreme environments are explored, the richness of microbial diversity is increasingly evident. Measures must be taken to estimate, record, and conserve microbial diversity, not only to sustain human health but also to e...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章,评审
doi：10.1038/sj.jim.2900390
更新日期：1997-05-01 00:00:00
abstract：:Providencia rettgeri strain YL was found to be efficient in heterotrophic nitrogen removal under aerobic conditions. Maximum removal of NH(4) (+)-N occurred under the conditions of pH 7 and supplemented with glucose as the carbon source. Inorganic ions such as Mg(2+), Mn(2+), and Zn(2+) largely influenced the growth a...
journal_title：Journal of industrial microbiology & biotechnology
pub_type： 杂志文章
doi：10.1007/s10295-010-0708-7
更新日期：2010-06-01 00:00:00
