Engineering a xylose fermenting yeast for lignocellulosic ethanol production.

Lignocellulosic ethanol is produced by yeast fermentation of lignocellulosic hydrolysates generated by chemical pretreatment and enzymatic hydrolysis of plant cell walls. The conversion of xylose into ethanol in hydrolysates containing microbial inhibitors is a major bottleneck in biofuel production. We identified sodium salts as the primary yeast inhibitors, and evolved a Saccharomyces cerevisiae strain overexpressing xylose catabolism genes in xylose or glucose-mixed medium containing sodium salts.

Fine-tuning Bacterial Cyclic di-AMP Production for Durable Antitumor Effects Through the Activation of the STING Pathway.

The stimulator of interferon genes (STING) protein is an important and promising innate immune target for tumor therapy. However, the instability of the agonists of STING and their tendency to cause systemic immune activation is a hurdle. The STING activator, cyclic di-adenosine monophosphate (CDA), produced by the modified Nissle 1917, shows high antitumor activity and effectively reduces the systemic effects of the "off-target" caused by the activation of the STING pathway.

Expression of phenylalanine ammonia lyase as an intracellularly free and extracellularly cell surface-immobilized enzyme on a gut microbe as a live biotherapeutic for phenylketonuria.

Phenylketonuria (PKU), a disease resulting in the disability to degrade phenylalanine (Phe) is an inborn error with a 1 in 10,000 morbidity rate on average around the world which leads to neurotoxicity. As an potential alternative to a protein-restricted diet, oral intake of engineered probiotics degrading Phe inside the body is a promising treatment, currently at clinical stage II (Isabella, et al., 2018).

Genome Editing of Corynebacterium glutamicum Using CRISPR-Cpf1 System.

Corynebacterium glutamicum, as an important microbial chassis, has great potential in industrial application. However, complicated genetic modification is severely slowed by lack of efficient genome editing tools. The Streptococcus pyogenes (Sp) CRISPR-Cas9 system has been verified as a very powerful tool for mediating genome alteration in many microorganisms but cannot work well in C.

Reducing glucoamylase usage for commercial-scale ethanol production from starch using glucoamylase expressing Saccharomyces cerevisiae.

The development of yeast that converts raw corn or cassava starch to ethanol without adding the exogenous α-amylase and/or glucoamylase would reduce the overall ethanol production cost. In this study, two copies of codon-optimized Saccharomycopsis fibuligera glucoamylase genes were integrated into the genome of the industrial Saccharomyces cerevisiae strain CCTCC M94055, and the resulting strain CIBTS1522 showed comparable basic growth characters with the parental strain. We systemically evaluated the fermentation performance of the CIBTS1522 strain using the raw corn or cassava starch at small and commercial-scale, and observed that a reduction of at least 40% of the dose of glucoamylase was possible when using the CIBTS1522 yeast under real ethanol production condition.

Development of a RecE/T-Assisted CRISPR-Cas9 Toolbox for Lactobacillus.

Lactobacilli are members of a large family involved in industrial food fermentation, therapeutics, and health promotion. However, the development of genetic manipulation tools for this genus lags behind its relative industrial and medical significance. The development of clustered regularly interspaced short palindromic repeat (CRISPR)-based genome engineering for Lactobacillus is now underway.

Unraveling the genetic basis of fast l-arabinose consumption on top of recombinant xylose-fermenting Saccharomyces cerevisiae.

One major challenge in the bioconversion of lignocelluloses into ethanol is to develop Saccharomyces cerevisiae strains that can utilize all available sugars in biomass hydrolysates, especially the d-xylose and l-arabinose that cannot be fermented by the S. cerevisiae strain naturally. Here, we integrated an l-arabinose utilization cassette (AUC) into the genome of an efficient d-xylose fermenting industrial diploid S.

Genome editing and transcriptional repression in Pseudomonas putida KT2440 via the type II CRISPR system.

Background: The soil bacterium Pseudomonas putida KT2440 is a "generally recognized as safe"-certified strain with robust property and versatile metabolism. Thus, it is an ideal candidate for synthetic biology, biodegradation, and other biotechnology applications. The known genome editing approaches of Pseudomonas are suboptimal; thus, it is necessary to develop a high efficiency genome editing tool.

CRISPR/Cas9-based efficient genome editing in Staphylococcus aureus.

Staphylococcus aureus is an important pathogenic bacterium prevalent in nosocomial infections and associated with high morbidity and mortality rates, which arise from the significant pathogenicity and multi-drug resistance. However, the typical genetic manipulation tools used to explore the relevant molecular mechanisms of S. aureus have multiple limitations: leaving a scar in the genome, comparatively low gene-editing efficiency, and prolonged experimental period.

CRISPR-Cas9 Nickase-Assisted Genome Editing in Lactobacillus casei.

has drawn increasing attention as a health-promoting probiotic, while effective genetic manipulation tools are often not available, e.g., the single-gene knockout in still depends on the classic homologous recombination-dependent double-crossover strategy, which is quite labor-intensive and time-consuming.

CRISPR-Cpf1 assisted genome editing of Corynebacterium glutamicum.

Corynebacterium glutamicum is an important industrial metabolite producer that is difficult to genetically engineer. Although the Streptococcus pyogenes (Sp) CRISPR-Cas9 system has been adapted for genome editing of multiple bacteria, it cannot be introduced into C. glutamicum.

Iterative integration of multiple-copy pathway genes in Yarrowia lipolytica for heterologous β-carotene production.

β-Carotene is a terpenoid molecule with high hydrophobicity that is often used as an additive in foods and feed. Previous work has demonstrated the heterologous biosynthesis of β-carotene from an intrinsic high flux of acetyl-CoA in 12 steps through 11 genes in Yarrowia lipolytica. Here, an efficient biosynthetic pathway capable of producing 100-fold more β-carotene than the baseline construct was generated using strong promoters and multiple gene copies for each of the 12 steps.

Production of β-carotene by expressing a heterologous multifunctional carotene synthase in Yarrowia lipolytica.

Objectives: To obtain functional expression of a heterologous multifunctional carotene synthase containing phytoene synthase, phytoene dehydrogenase, and lycopene β-cyclase activities encoded by carS from Schizochytrium sp. in order to allow Yarrowia lipolytica to produce β-carotene.

Results: To increase the integration efficiency of a 3.

Enhanced solvent production by metabolic engineering of a twin-clostridial consortium.

The efficient fermentative production of solvents (acetone, n-butanol, and ethanol) from a lignocellulosic feedstock using a single process microorganism has yet to be demonstrated. Herein, we developed a consolidated bioprocessing (CBP) based on a twin-clostridial consortium composed of Clostridium cellulovorans and Clostridium beijerinckii capable of producing cellulosic butanol from alkali-extracted, deshelled corn cobs (AECC). To accomplish this a genetic system was developed for C.

Tailor-made biocatalysts enzymes for the fine chemical industry in China.

The Center of Industrial Biotechnology (CIBT) was established in Huzhou for fine chemicals in 2006 and CIBT Shanghai was founded for bulk chemicals in 2008. CIBT is a non-profit organization under auspices of the Shanghai Institutes for Biological Sciences, Shanghai Branch of the Chinese Academy of Sciences (CAS) and Huzhou Municipal Government. CIBT is affiliated with the CAS, which enables it to take advantage of the rich R&D resources and support from CAS; yet CIBT operates as an independent legal entity.

Enzymatic Production of Glutathione by Bifunctional γ-Glutamylcysteine Synthetase/Glutathione Synthetase Coupled with In Vitro Acetate Kinase-Based ATP Generation.

Glutathione (γ-glutamyl-L-cysteinylglycine, GSH) is a pharmaceutical compound often used in food additives and the cosmetics industry. GSH can be produced biologically from L-glutamic acid, L-cysteine, and glycine through an enzymatic process traditionally involving two sequential adenosine triphosphate (ATP)-dependent reactions catalyzed by γ-glutamylcysteine synthetase (γ-GCS or GSHI, EC 6.3.

Multiplex gene editing of the Yarrowia lipolytica genome using the CRISPR-Cas9 system.

Yarrowia lipolytica is categorized as a generally recognized as safe (GRAS) organism and is a heavily documented, unconventional yeast that has been widely incorporated into multiple industrial fields to produce valuable biochemicals. This study describes the construction of a CRISPR-Cas9 system for genome editing in Y. lipolytica using a single plasmid (pCAS1yl or pCAS2yl) to transport Cas9 and relevant guide RNA expression cassettes, with or without donor DNA, to target genes.

CRISPR-based genome editing and expression control systems in Clostridium acetobutylicum and Clostridium beijerinckii.

Solventogenic clostridia are important industrial microorganisms that produce various chemicals and fuels. Effective genetic tools would facilitate physiological studies aimed both at improving our understanding of metabolism and optimizing solvent productivity through metabolic engineering. Here we have developed an all-in-one, CRISPR-based genome editing plasmid, pNICKclos, that can be used to achieve successive rounds of gene editing in Clostridium acetobutylicum ATCC 824 and Clostridium beijerinckii NCIMB 8052 with efficiencies varying from 6.

Synergy between methylerythritol phosphate pathway and mevalonate pathway for isoprene production in Escherichia coli.

Isoprene, a key building block of synthetic rubber, is currently produced entirely from petrochemical sources. In this work, we engineered both the methylerythritol phosphate (MEP) pathway and the mevalonate (MVA) pathway for isoprene production in E. coli.

Complete genome sequence of Clostridium carboxidivorans P7(T), a syngas-fermenting bacterium capable of producing long-chain alcohols.

Clostridium carboxidivorans P7(T) is an anaerobe that can ferment syngas (mainly CO or CO2 and H2) to produce acids (acetic and butyric acid), ethanol and long-chain alcohols (butanol and hexanol). Here, the first complete genome sequence for C. carboxidivorans P7(T) is presented.

Multiple-site genetic modifications in Escherichia coli using lambda-Red recombination and I-SceI cleavage.

Objectives: Genetic modifications to bacterial chromosomes are important for research; recently we reported a two-plasmid system for single locus modification in Escherichia coli and an improved method for simultaneous multiple-loci modification is needed.

Results: An intermediate bacterial strain was generated with different resistance marker genes flanked by I-SceI recognition sites at multiple target loci. Then a donor plasmid carrying several alleles with desired modifications was transformed into the intermediate strain together with a bifunctional helper plasmid encoding λ-Red recombinase and I-SceI endonuclease.

I-SceI-mediated scarless gene modification via allelic exchange in Clostridium.

Although gene disruption in Clostridium spp. with the TargeTron technology is much more effective than single-crossover integration, it cannot achieve gene modification via allelic exchange. Here, we developed a targeted, nonpolar, scarless gene modification system based on the I-SceI endonuclease.

Utilization of economical substrate-derived carbohydrates by solventogenic clostridia: pathway dissection, regulation and engineering.

Solventogenic clostridia can produce acetone, butanol and ethanol (ABE) by using different carbohydrates. For economical reasons, the utilization of cheap and renewable biomass in clostridia-based ABE fermentation has recently attracted increasing interests. With the study of molecular microbiology and development of genetic tools, the understanding of carbohydrate metabolism in clostridia has increased in recent years.

High-efficiency scarless genetic modification in Escherichia coli by using lambda red recombination and I-SceI cleavage.

Genetic modifications of bacterial chromosomes are important for both fundamental and applied research. In this study, we developed an efficient, easy-to-use system for genetic modification of the Escherichia coli chromosome, a two-plasmid method involving lambda Red (λ-Red) recombination and I-SceI cleavage. An intermediate strain is generated by integration of a resistance marker gene(s) and I-SceI recognition sites in or near the target gene locus, using λ-Red PCR targeting.