scholarly journals Genetic Manipulation of a Lipolytic Yeast Candida aaseri SH14 Using CRISPR-Cas9 System

2020 ◽  
Vol 8 (4) ◽  
pp. 526 ◽  
Author(s):  
Zool Hilmi Ibrahim ◽  
Jung-Hoon Bae ◽  
Sun-Hee Lee ◽  
Bong Hyun Sung ◽  
Ahmad Hazri Ab Rashid ◽  
...  
Keyword(s):  
Genome Engineering ◽  
Genetic Manipulation ◽  
Plant Oils ◽  
Long Chain Fatty Acids ◽  
Temporal Expression ◽  
Autonomously Replicating Sequence ◽  
Manipulation System ◽  
Episomal Vectors ◽  
Dodecanedioic Acid ◽  
Diploid Cells

A lipolytic yeast Candida aaseri SH14 that can utilise long-chain fatty acids as the sole carbon source was isolated from oil palm compost. To develop this strain as a platform yeast for the production of bio-based chemicals from renewable plant oils, a genetic manipulation system using CRISPR-Cas9 was developed. Episomal vectors for expression of Cas9 and sgRNA were constructed using an autonomously replicating sequence isolated from C. aaseri SH14. This system guaranteed temporal expression of Cas9 for genetic manipulation and rapid curing of the vector from transformed strains. A β-oxidation mutant was directly constructed by simultaneous disruption of six copies of acyl-CoA oxidases genes (AOX2, AOX4 and AOX5) in diploid cells using a single sgRNA with 70% efficiency and the Cas9 vector was efficiently removed. Blocking of β-oxidation in the triple AOX mutant was confirmed by the accumulation of dodecanedioic acid from dodecane. Targeted integration of the expression cassette for C. aaseri lipase2 was demonstrated with 60% efficiency using this CRISPR-Cas9 system. This genome engineering tool could accelerate industrial application of C. aaseri SH14 for production of bio-based chemicals from renewable oils.

scholarly journals Blocking drug efflux mechanisms facilitate genome engineering process in hypercellulolytic fungus, Penicillium funiculosum NCIM1228

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Anmoldeep Randhawa ◽  
Nandita Pasari ◽  
Tulika Sinha ◽  
Mayank Gupta ◽  
Anju M. Nair ◽  
...  
Keyword(s):  
Homologous Recombination ◽  
Genome Engineering ◽  
Efflux Pump ◽  
Genetic Manipulation ◽  
Function Analysis ◽  
Drug Tolerance ◽  
Growth Media ◽  
Penicillium Funiculosum ◽  
Cellobiohydrolase I ◽  
Drug Tolerability

Abstract Background Penicillium funiculosum NCIM1228 is a non-model filamentous fungus that produces high-quality secretome for lignocellulosic biomass saccharification. Despite having desirable traits to be an industrial workhorse, P. funiculosum has been underestimated due to a lack of reliable genetic engineering tools. Tolerance towards common fungal antibiotics had been one of the major hindrances towards development of reliable transformation tools against the non-model fungi. In this study, we sought to understand the mechanism of drug tolerance of P. funiculosum and the provision to counter it. We then attempted to identify a robust method of transformation for genome engineering of this fungus. Results Penicillium funiculosum showed a high degree of drug tolerance towards hygromycin, zeocin and nourseothricin, thereby hindering their use as selectable markers to obtain recombinant transformants. Transcriptome analysis suggested a high level expression of efflux pumps belonging to ABC and MFS family, especially when complex carbon was used in growth media. Antibiotic selection medium was optimized using a combination of efflux pump inhibitors and suitable carbon source to prevent drug tolerability. Protoplast-mediated and Agrobacterium-mediated transformation were attempted for identifying efficiencies of linear and circular DNA in performing genetic manipulation. After finding Ti-plasmid-based Agrobacterium-mediated transformation more suitable for P. funiculosum, we improvised the system to achieve random and homologous recombination-based gene integration and deletion, respectively. We found single-copy random integration of the T-DNA cassette and could achieve 60% efficiency in homologous recombination-based gene deletions. A faster, plasmid-free, and protoplast-based CRISPR/Cas9 gene-editing system was also developed for P. funiculosum. To show its utility in P. funiculosum, we deleted the gene coding for the most abundant cellulase Cellobiohydrolase I (CBH1) using a pair of sgRNA directed towards both ends of cbh1 open reading frame. Functional analysis of ∆cbh1 strain revealed its essentiality for the cellulolytic trait of P. funiculosum secretome. Conclusions In this study, we addressed drug tolerability of P. funiculosum and developed an optimized toolkit for its genome modification. Hence, we set the foundation for gene function analysis and further genetic improvements of P. funiculosum using both traditional and advanced methods.

scholarly journals Development of an efficient conjugation-based genetic manipulation system for Pseudoalteromonas

2015 ◽  
Vol 14 (1) ◽  
pp. 11 ◽  
Author(s):  
Pengxia Wang ◽  
Zichao Yu ◽  
Baiyuan Li ◽  
Xingsheng Cai ◽  
Zhenshun Zeng ◽  
...  
Keyword(s):  
Genetic Manipulation ◽  
Manipulation System

Genetic manipulation system in propionibacteria

2002 ◽  
Vol 93 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Pornpimon Kiatpapan ◽  
Yoshikatsu Murooka
Keyword(s):  
Genetic Manipulation ◽  
Manipulation System

Genetic Manipulation System in Propionibacteria.

2002 ◽  
Vol 93 (1) ◽  
pp. 1-8 ◽  
Author(s):  
PORNPIMON KIATPAPAN ◽  
YOSHIKATSU MUROOKA
Keyword(s):  
Genetic Manipulation ◽  
Manipulation System

scholarly journals CRISPR-nRAGE, a Cas9 nickase-reverse transcriptase assisted versatile genetic engineering toolkit for E. coli

2020 ◽  
Author(s):  
Yaojun Tong ◽  
Tue S. Jørgensen ◽  
Christopher M. Whitford ◽  
Tilmann Weber ◽  
Sang Yup Lee
Keyword(s):  
Reverse Transcriptase ◽  
Genome Engineering ◽  
Genetic Manipulation ◽  
Fragment Size ◽  
Leukemia Virus ◽  
Strand Break ◽  
Engineering System ◽  
E Coli ◽  
Dna Engineering ◽  
Nucleotide Resolution

AbstractIn most prokaryotes, missing and poorly active non-homologous end joining (NHEJ) DNA repair pathways heavily restrict the direct application of CRISPR-Cas for DNA double-strand break (DSB)-based genome engineering without providing editing templates. CRISPR base editors, on the other hand, can be directly used for genome engineering in a number of bacteria, including E. coli, showing advantages over CRISPR-Cas9, since they do not require DSBs. However, as the current CRISPR base editors can only engineer DNA by A to G or C to T/G/A substitutions, they are incapable of mediating deletions, insertions, and combinations of deletions, insertions and substitutions. To address these challenges, we developed a Cas9 nickase (Cas9n)-reverse transcriptase (Moloney Murine Leukemia Virus, M-MLV) mediated, DSB-free, versatile, and single-nucleotide resolution genetic manipulation toolkit for prokaryotes, termed CRISPR-nRAGE (CRISPR-Cas9n Reverse transcriptase Assisted Genome Engineering) system. CRISPR-nRAGE can be used to introduce substitutions, deletions, insertions, and the combination thereof, both in plasmids and the chromosome of E. coli. Notably, small sized-deletion shows better editing efficiency compared to other kinds of DNA engineering. CRISPR-nRAGE has been used to delete and insert DNA fragments up to 97 bp and 33 bp, respectively. Efficiencies, however, drop sharply with the increase of the fragment size. It is not only a useful addition to the genome engineering arsenal for E. coli, but also may be the basis for the development of similar toolkits for other organisms.

scholarly journals An Efficient Genetic Manipulation Protocol for Dark Septate Endophyte Falciphora Oryzae

2021 ◽  
Author(s):  
Zhen-Zhu Su ◽  
Meng-Di Dai ◽  
Jia-Nan Zhu ◽  
Yu-Lan Zeng ◽  
Xuan-Jun Lu ◽  
...  
Keyword(s):  
Endophytic Fungus ◽  
Plant Biomass ◽  
Genetic Manipulation ◽  
Blast Resistance ◽  
Enzyme Digestion ◽  
Dark Septate Endophyte ◽  
Rice Blast Resistance ◽  
Rice Roots ◽  
Manipulation System ◽  
Protoplast Preparation

Abstract Falciphora oryzae is a dark septate endophyte (DSE) isolated from wild rice roots (Oryza sativa L.). It was classified as a non-clavicitaceous endophyte. The fungus colonizes rice roots, showing a significant increase in agronomic parameters with plant biomass, rice blast resistance, yield, and quality. The construction of the genetic manipulation system is critical to study the relationship between F. oryzae and O. sativa. In the present study, the protoplast preparation and transformation system of F. oryzae was investigated. The key parameters affecting the efficiency of protoplast production, such as osmotic pressure stabilizer, enzyme digestion conditions, and fungal age, were studied. The results showed that F. oryzae strain obtained higher protoplast yield and effective transformation when treated with enzyme digestion solution containing 0.9mol L-1 KCl solution and 10 mg mL−1 glucanase at 30℃ with shaking 80 rpm for 2-3 h. When the protoplasts were plated on a regenerations-agar (RgA) medium containing 1M sucrose, the re-growth rate of protoplasts was the highest. We successfully acquired GFP-expressing transformants by transforming the pKD6-GFP vector into protoplasts. Further, the GFP expression in fungal hyphae possessed good stability and intensity during symbiosis in rice roots.The genetic manipulation system of endophytic fungus facilitates the further exploration the interaction between the endophytic fungus and their hosts.

scholarly journals Establishment and application of a CRISPR–Cas12a assisted genome-editing system in Zymomonas mobilis

2019 ◽  
Vol 18 (1) ◽  
Author(s):  
Wei Shen ◽  
Jun Zhang ◽  
Binan Geng ◽  
Mengyue Qiu ◽  
Mimi Hu ◽  
...  
Keyword(s):  
Genome Editing ◽  
Dna Cleavage ◽  
Zymomonas Mobilis ◽  
Genome Engineering ◽  
Gene Deletion ◽  
Genetic Manipulation ◽  
Strain Improvement ◽  
Genomic Research ◽  
Francisella Novicida ◽  
A Genome

Abstract Background Efficient and convenient genome-editing toolkits can expedite genomic research and strain improvement for desirable phenotypes. Zymomonas mobilis is a highly efficient ethanol-producing bacterium with a small genome size and desirable industrial characteristics, which makes it a promising chassis for biorefinery and synthetic biology studies. While classical techniques for genetic manipulation are available for Z. mobilis, efficient genetic engineering toolkits enabling rapidly systematic and high-throughput genome editing in Z. mobilis are still lacking. Results Using Cas12a (Cpf1) from Francisella novicida, a recombinant strain with inducible cas12a expression for genome editing was constructed in Z. mobilis ZM4, which can be used to mediate RNA-guided DNA cleavage at targeted genomic loci. gRNAs were then designed targeting the replicons of native plasmids of ZM4 with about 100% curing efficiency for three native plasmids. In addition, CRISPR–Cas12a recombineering was used to promote gene deletion and insertion in one step efficiently and precisely with efficiency up to 90%. Combined with single-stranded DNA (ssDNA), CRISPR–Cas12a system was also applied to introduce minor nucleotide modification precisely into the genome with high fidelity. Furthermore, the CRISPR–Cas12a system was employed to introduce a heterologous lactate dehydrogenase into Z. mobilis with a recombinant lactate-producing strain constructed. Conclusions This study applied CRISPR–Cas12a in Z. mobilis and established a genome editing tool for efficient and convenient genome engineering in Z. mobilis including plasmid curing, gene deletion and insertion, as well as nucleotide substitution, which can also be employed for metabolic engineering to help divert the carbon flux from ethanol production to other products such as lactate demonstrated in this work. The CRISPR–Cas12a system established in this study thus provides a versatile and powerful genome-editing tool in Z. mobilis for functional genomic research, strain improvement, as well as synthetic microbial chassis development for economic biochemical production.

scholarly journals A versatile genetic engineering toolkit for E. coli based on CRISPR-prime editing

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yaojun Tong ◽  
Tue S. Jørgensen ◽  
Christopher M. Whitford ◽  
Tilmann Weber ◽  
Sang Yup Lee
Keyword(s):  
Genome Engineering ◽  
Genetic Manipulation ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Base Editing ◽  
Guide Rna ◽  
E Coli ◽  
Potential Basis ◽  
Low Efficiency ◽  
Nucleotide Resolution

AbstractCRISPR base editing is a powerful method to engineer bacterial genomes. However, it restricts editing to single-nucleotide substitutions. Here, to address this challenge, we adapt a CRISPR-Prime Editing-based, DSB-free, versatile, and single-nucleotide resolution genetic manipulation toolkit for prokaryotes. It can introduce substitutions, deletions, insertions, and the combination thereof, both in plasmids and the chromosome of E. coli with high fidelity. Notably, under optimal conditions, the efficiency of 1-bp deletions reach up to 40%. Moreover, deletions of up to 97 bp and insertions up to 33 bp were successful with the toolkit in E. coli, however, efficiencies dropped sharply with increased fragment sizes. With a second guide RNA, our toolkit can achieve multiplexed editing albeit with low efficiency. Here we report not only a useful addition to the genome engineering arsenal for E. coli, but also a potential basis for the development of similar toolkits for other bacteria.

Development of a genetic manipulation system for Haemophilus parasuis

2005 ◽  
Vol 105 (3-4) ◽  
pp. 223-228 ◽  
Author(s):  
Anna Bigas ◽  
M. Elena Garrido ◽  
Ana M. Pérez de Rozas ◽  
Ignacio Badiola ◽  
Jordi Barbé ◽  
...  
Keyword(s):  
Genetic Manipulation ◽  
Haemophilus Parasuis ◽  
Manipulation System

Using 16S rDNA as Target Site for Homologous Recombination to Improve the Alkaline Protease Production of Bacillus alcalophilus

2014 ◽  
Vol 886 ◽  
pp. 349-354
Author(s):  
Qing Shan Mo ◽  
Yao Tian ◽  
Hui Tu Zhang ◽  
Ling Jun Bu ◽  
Fu Ping Lu
Keyword(s):  
16S Rdna ◽  
Alkaline Protease ◽  
Genetic Manipulation ◽  
Protease Production ◽  
Protease Gene ◽  
Wild Type ◽  
Recombinant Strains ◽  
Manipulation System ◽  
Rdna Sites ◽  
Alkaline Protease Gene

Bacillus alcalophilusisolated was used for the production of alkaline protease. The enzyme encoded by alkaline protease gene (apr4) gene. To further improve the production of the strain for industrial requirement, a genetic manipulation system forBacillus alcalophiluswas developed. Additional copies of theapr4 gene were transferred into the strainBacillus alcalophilusand integrated into the 16S rDNA sites, yielding a series of recombinant strains. One of these recombinant strains, designated K23, exhibited superior properties for production of alkaline protease. the protease activity of K23 achieved by (6.19 ± 0.34) × 104U/ml, which is approximately 111.3% higher than that of the wild-type ones for 50-h fermentation. In addition, the new strain was genetically stable for more than 100 generations. These superior characteristics make it to be more suitable than the wild-type strain for alkaline protease production.

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