The CRISPR-Cas system in Enterobacteriaceae

Medina-Aparicio, Liliana; Dávila-Ramos, Sonia; Rebollar-Flores, Javier E; Calva, Edmundo; Hernández-Lucas, Ismael

doi:10.1093/femspd/fty002

Cited by 48 publications

(54 citation statements)

References 153 publications

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“…The results showed that all CRISPR candidates belong to the host species, and they were excluded as possible foreign genetic elements, e.g., from bacteriophages or plasmids. As described by Medina-Aparicio et al 40 , more than 98 (43%) out of 228 complete Enterobacteriaceae genomes analysed lacked CRISPR/Cas systems, including 11 genomes out of all 12 tested from the genus Enterobacter. The results of these analyses and of our research indicate that the distribution of the CRISPR/Cas system in the Enterobacteriaceae family is not regular and rarely found in the genus Enterobacter.…”

Section: Bacteriocin Biosynthesismentioning

confidence: 75%

“…Genetic defence mechanism. The use of clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated proteins (Cas) is one of many bacterial immunological strategies for phage attack or invasion by foreign DNA 40 . This defence mechanism plays a special role, particularly in protecting bacteria against bacteriophage invasion, which is possible during the industrial-scale production of metabolites 31 .…”

Section: Bacteriocin Biosynthesismentioning

confidence: 99%

See 1 more Smart Citation

Genome analysis of a wild rumen bacterium Enterobacter aerogenes LU2 - a novel bio-based succinic acid producer

Szczerba

Komoń-Janczara

Krawczyk

et al. 2020

Sci Rep

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Enterobacter aerogenes LU2 was isolated from cow rumen and recognized as a potential succinic acid producer in our previous study. Here, we present the first complete genome sequence of this new, wild strain and report its basic genetic features from a biotechnological perspective. The MinION singlemolecule nanopore sequencer supported by the Illumina MiSeq platform yielded a circular 5,062,651 bp chromosome with a GC content of 55% that lacked plasmids. A total of 4,986 genes, including 4,741 protein-coding genes, 22 rRNA-, 86 tRNA-, and 10 ncRNA-encoding genes and 127 pseudogenes, were predicted. The genome features of the studied strain and other Enterobacteriaceae strains were compared. Functional studies on the genome content, metabolic pathways, growth, and carbon transport and utilization were performed. The genomic analysis indicates that succinic acid can be produced by the LU2 strain through the reductive branch of the tricarboxylic acid cycle (TCA) and the glyoxylate pathway. Antibiotic resistance genes were determined, and the potential for bacteriocin production was verified. Furthermore, one intact prophage region of length ~31,9 kb, 47 genomic islands (GIs) and many insertion sequences (ISs) as well as tandem repeats (TRs) were identified. No clustered regularly interspaced short palindromic repeats (CRISPRs) were found. Finally, comparative genome analysis with well-known succinic acid producers was conducted. The genome sequence illustrates that the LU2 strain has several desirable traits, which confirm its potential to be a highly efficient platform for the production of bulk chemicals. Enterobacter aerogenes LU2 is a gram-negative, wild bacterium that was isolated from cow rumen as a part of environmental screening for succinic acid-producing bacteria identification. Succinic acid (SA) plays an important role as a metabolic intermediate in the rumen by increasing propionate production, a crucial energy source for the ruminant 1,2. Anaerobic conditions and the presence of carbon dioxide, methane and trace amounts of hydrogen create an excellent environment for the biosynthesis of succinate by some bacteria existing in the rumen 3. In reports of the U.S. Department of Energy (DOE) from 2004 and 2010, SA was recognized as one of the top 10 most promising C4-building chemical platforms for the production of high-value commodity and specialty chemicals with great industrial potential 2,4. Succinate is widely applied as an additive in food, pharmaceuticals, detergents, solvents, and surfactants as well as in biodegradable polymer production 5,6. Until recently, industrial production of succinate was based on chemical synthesis. However, petroleum-based production of SA from n-butane through maleic anhydrate requires the use of high pressure, high temperature and costly catalysts 7. Therefore, because of the current global trend regarding sustainable development, including the support of green technologies, rational waste biomass management and pollution-reducing standards, the bio-based production of...

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Section: Bacteriocin Biosynthesismentioning

confidence: 75%

Section: Bacteriocin Biosynthesismentioning

confidence: 99%

Genome analysis of a wild rumen bacterium Enterobacter aerogenes LU2 - a novel bio-based succinic acid producer

Szczerba

Komoń-Janczara

Krawczyk

et al. 2020

Sci Rep

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“…Equivalent arrays show a considerable intraspecific polymorphism in terms of spacer number and sequence. Fundamental knowledge about the CRISPR-Cas mechanism has been generated from the analysis of these two systems in E. coli 10 11 12 13 and related Enterobacteriaceae 14 .…”

Section: Introductionmentioning

confidence: 99%

The CRISPR conundrum: evolve and maybe die, or survive and risk stagnation

Garcı́a-Martı́nez¹,

Maldonado²,

Guzmán³

et al. 2018

Microb Cell

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CRISPR-Cas represents a prokaryotic defense mechanism against invading genetic elements. Although there is a diversity of CRISPR-Cas systems, they all share similar, essential traits. In general, a CRISPR-Cas system consists of one or more groups of DNA repeats named CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), regularly separated by unique sequences referred to as spacers, and a set of functionally associated cas (CRISPR associated) genes typically located next to one of the repeat arrays. The origin of spacers is in many cases unknown but, when ascertained, they usually match foreign genetic molecules. The proteins encoded by some of the cas genes are in charge of the incorporation of new spacers upon entry of a genetic element. Other Cas proteins participate in generating CRISPR-spacer RNAs and perform the task of destroying nucleic acid molecules carrying sequences similar to the spacer. In this way, CRISPR-Cas provides protection against genetic intruders that could substantially affect the cell viability, thus acting as an adaptive immune system. However, this defensive action also hampers the acquisition of potentially beneficial, horizontally transferred genes, undermining evolution. Here we cover how the model bacterium Escherichia coli deals with CRISPR-Cas to tackle this major dilemma, evolution versus survival.

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“…Since there are other effective methods for genome editing in microorganisms such as HR; few studies have been reported on the development of CRISPR-Cas genome editing in various bacteria (i.e., E. coli, Cyanobacteria, Streptomyces, Riemerella anatipestifer, Clostridium, Corynebacterium, Bacillus, Salmonella, Pseudomonas putida, Lactobacillus casei) (63)(64)(65)(66)(67)(68)(69)(70)(71)(72). Identification of strains (73), detection of natural or engineered immunity against mobile genetic elements (74,75), manipulation of microbial consortium (76), and programmable transcriptional regulation (77) are some issues that have been tried to be solved using CRISPR.…”

Section: Bacterial Genome Editing With Crisprmentioning

confidence: 99%

Untitled

2019

Eur J Biol

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The CRISPR-Cas 9 system, which is known as a natural way of bacteria to defend against phage infection and plasmid transfer, has been re-purposed as a RNA-guided DNA targeting strategy for genome editing. Together with the advances gained in DNA sequencing technology, this platform opened a new era in molecular biology since its recognition was specified by 20-nt single-guide RNA which made technique easier, efficient and simple for application in any organism. Thus, many studies have discussed and performed the applications of CRISPR-Cas systems on different organisms for genome editing. Moreover, targeted gene regulations, epigenetic modulation, chromatin imaging and manipulation could also be applied with this system. Besides all its potential promising aspects, this tool might have some side effects like off-target mutations. In addition, unexpected results have also been reported after some gene editing applications. Thus, this review provides a brief history of gene editing tools together with the overview of the latest applications, regulations and ethical/structural aspects of the CRISPR Cas system.

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The CRISPR-Cas system in Enterobacteriaceae

Cited by 48 publications

References 153 publications

Genome analysis of a wild rumen bacterium Enterobacter aerogenes LU2 - a novel bio-based succinic acid producer

Genome analysis of a wild rumen bacterium Enterobacter aerogenes LU2 - a novel bio-based succinic acid producer

The CRISPR conundrum: evolve and maybe die, or survive and risk stagnation

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