journal
Journals Metabolic Engineering Communic...

Metabolic Engineering Communications

https://read.qxmd.com/read/36311477/biosynthesis-of-value-added-bioproducts-from-hemicellulose-of-biomass-through-microbial-metabolic-engineering
#21
REVIEW
Biao Geng, Xiaojing Jia, Xiaowei Peng, Yejun Han
Hemicellulose is the second most abundant carbohydrate in lignocellulosic biomass and has extensive applications. In conventional biomass refinery, hemicellulose is easily converted to unwanted by-products in pretreatment and therefore can't be fully utilized. The present study aims to summarize the most recent development of lignocellulosic polysaccharide degradation and fully convert it to value-added bioproducts through microbial and enzymatic catalysis. Firstly, bioprocess and microbial metabolic engineering for enhanced utilization of lignocellulosic carbohydrates were discussed...
December 2022: Metabolic Engineering Communications
https://read.qxmd.com/read/36281261/metabolomics-and-modelling-approaches-for-systems-metabolic-engineering
#22
REVIEW
Jasmeet Kaur Khanijou, Hanna Kulyk, Cécilia Bergès, Leng Wei Khoo, Pnelope Ng, Hock Chuan Yeo, Mohamed Helmy, Floriant Bellvert, Wee Chew, Kumar Selvarajoo
Metabolic engineering involves the manipulation of microbes to produce desirable compounds through genetic engineering or synthetic biology approaches. Metabolomics involves the quantitation of intracellular and extracellular metabolites, where mass spectrometry and nuclear magnetic resonance based analytical instrumentation are often used. Here, the experimental designs, sample preparations, metabolite quenching and extraction are essential to the quantitative metabolomics workflow. The resultant metabolomics data can then be used with computational modelling approaches, such as kinetic and constraint-based modelling, to better understand underlying mechanisms and bottlenecks in the synthesis of desired compounds, thereby accelerating research through systems metabolic engineering...
December 2022: Metabolic Engineering Communications
https://read.qxmd.com/read/36249306/rna-polymerase-ii-driven-crispr-cas9-system-for-efficient-non-growth-biased-metabolic-engineering-of-kluyveromyces-marxianus
#23
JOURNAL ARTICLE
Danielle Bever, Ian Wheeldon, Nancy Da Silva
The thermotolerant yeast Kluyveromyces marxianus has gained significant attention in recent years as a promising microbial candidate for industrial biomanufacturing. Despite several contributions to the expanding molecular toolbox for gene expression and metabolic engineering of K. marxianus , there remains a need for a more efficient and versatile genome editing platform. To address this, we developed a CRISPR-based editing system that enables high efficiency marker-less gene disruptions and integrations using only 40 bp homology arms in NHEJ functional and non-functional K...
December 2022: Metabolic Engineering Communications
https://read.qxmd.com/read/36188638/engineering-sorghum-for-higher-4-hydroxybenzoic-acid-content
#24
JOURNAL ARTICLE
Chien-Yuan Lin, Yang Tian, Kimberly Nelson-Vasilchik, Joel Hague, Ramu Kakumanu, Mi Yeon Lee, Venkataramana R Pidatala, Jessica Trinh, Christopher M De Ben, Jutta Dalton, Trent R Northen, Edward E K Baidoo, Blake A Simmons, John M Gladden, Corinne D Scown, Daniel H Putnam, Albert P Kausch, Henrik V Scheller, Aymerick Eudes
Engineering bioenergy crops to accumulate coproducts in planta can increase the value of lignocellulosic biomass and enable a sustainable bioeconomy. In this study, we engineered sorghum with a bacterial gene encoding a chorismate pyruvate-lyase ( ubiC ) to reroute the plastidial pool of chorismate from the shikimate pathway into the valuable compound 4-hydroxybenzoic acid (4-HBA). A gene encoding a feedback-resistant version of 3-deoxy-d-arabino-heptulonate-7-phosphate synthase ( aroG ) was also introduced in an attempt to increase the carbon flux through the shikimate pathway...
December 2022: Metabolic Engineering Communications
https://read.qxmd.com/read/36158112/tuning-a-high-performing-multiplexed-crispri-pseudomonas-putida-strain-to-further-enhance-indigoidine-production
#25
JOURNAL ARTICLE
Jeffrey J Czajka, Deepanwita Banerjee, Thomas Eng, Javier Menasalvas, Chunsheng Yan, Nathalie Munoz Munoz, Brenton C Poirier, Young-Mo Kim, Scott E Baker, Yinjie J Tang, Aindrila Mukhopadhyay
In this study, a 14-gene edited Pseudomonas putida KT2440 strain for heterologous indigoidine production was examined using three distinct omic datasets. Transcriptomic data indicated that CRISPR/dCpf1-interference (CRISPRi) mediated multiplex repression caused global gene expression changes, implying potential undesirable changes in metabolic flux. 13 C-metabolic flux analysis (13 C-MFA) revealed that the core P. putida flux network after CRISPRi repression was conserved, with moderate reduction of TCA cycle and pyruvate shunt activity along with glyoxylate shunt activation during glucose catabolism...
December 2022: Metabolic Engineering Communications
https://read.qxmd.com/read/36119807/a-targeted-metabolomics-method-for-extra-and-intracellular-metabolite-quantification-covering-the-complete-monolignol-and-lignan-synthesis-pathway
#26
JOURNAL ARTICLE
Andrea Steinmann, Katrin Schullehner, Anna Kohl, Christina Dickmeis, Maurice Finger, Georg Hubmann, Guido Jach, Ulrich Commandeur, Marco Girhard, Vlada B Urlacher, Stephan Lütz
Microbial synthesis of monolignols and lignans from simple substrates is a promising alternative to plant extraction. Bottlenecks and byproduct formation during heterologous production require targeted metabolomics tools for pathway optimization. In contrast to available fractional methods, we established a comprehensive targeted metabolomics method. It enables the quantification of 17 extra- and intracellular metabolites of the monolignol and lignan pathway, ranging from amino acids to pluviatolide. Several cell disruption methods were compared...
December 2022: Metabolic Engineering Communications
https://read.qxmd.com/read/36093381/dynamic-and-single-cell-characterization-of-a-crispr-interference-toolset-in-pseudomonas-putida-kt2440-for-%C3%AE-ketoadipate-production-from-p-coumarate
#27
JOURNAL ARTICLE
Jacob A Fenster, Allison Z Werner, Jian Wei Tay, Matthew Gillen, Leo Schirokauer, Nicholas C Hill, Audrey Watson, Kelsey J Ramirez, Christopher W Johnson, Gregg T Beckham, Jeffrey C Cameron, Carrie A Eckert
Pseudomonas putida KT2440 is a well-studied bacterium for the conversion of lignin-derived aromatic compounds to bioproducts. The development of advanced genetic tools in P. putida has reduced the turnaround time for hypothesis testing and enabled the construction of strains capable of producing various products of interest. Here, we evaluate an inducible CRISPR-interference (CRISPRi) toolset on fluorescent, essential, and metabolic targets. Nuclease-deficient Cas9 (dCas9) expressed with the arabinose (8K)-inducible promoter was shown to be tightly regulated across various media conditions and when targeting essential genes...
December 2022: Metabolic Engineering Communications
https://read.qxmd.com/read/36065328/itaconic-acid-production-is-regulated-by-laea-in-aspergillus-pseudoterreus
#28
JOURNAL ARTICLE
Kyle R Pomraning, Ziyu Dai, Nathalie Munoz, Young-Mo Kim, Yuqian Gao, Shuang Deng, Teresa Lemmon, Marie S Swita, Jeremy D Zucker, Joonhoon Kim, Stephen J Mondo, Ellen Panisko, Meagan C Burnet, Bobbie-Jo M Webb-Robertson, Beth Hofstad, Scott E Baker, Kristin E Burnum-Johnson, Jon K Magnuson
The global regulator LaeA controls secondary metabolism in diverse Aspergillus species. Here we explored its role in regulation of itaconic acid production in Aspergillus pseudoterreus . To understand its role in regulating metabolism, we deleted and overexpressed laeA, and assessed the transcriptome, proteome, and secreted metabolome prior to and during initiation of phosphate limitation induced itaconic acid production. We found that secondary metabolite clusters, including the itaconic acid biosynthetic gene cluster, are regulated by laeA and that laeA is required for high yield production of itaconic acid...
December 2022: Metabolic Engineering Communications
https://read.qxmd.com/read/36017490/metabolic-engineering-of-pseudomonas-taiwanensis-vlb120-for-rhamnolipid-biosynthesis-from-biomass-derived-aromatics
#29
JOURNAL ARTICLE
Vaishnavi Sivapuratharasan, Christoph Lenzen, Carina Michel, Anantha Barathi Muthukrishnan, Guhan Jayaraman, Lars M Blank
Lignin is a ubiquitously available and sustainable feedstock that is underused as its depolymerization yields a range of aromatic monomers that are challenging substrates for microbes. In this study, we investigated the growth of Pseudomonas taiwanensis VLB120 on biomass-derived aromatics, namely, 4-coumarate, ferulate, 4-hydroxybenzoate, and vanillate. The wild type strain was not able to grow on 4-coumarate and ferulate. After integration of catabolic genes for breakdown of 4-coumarate and ferulate, the metabolically engineered strain was able to grow on these aromatics...
December 2022: Metabolic Engineering Communications
https://read.qxmd.com/read/35662893/development-of-a-dedicated-golden-gate-assembly-platform-rtgga-for-rhodotorula-toruloides
#30
JOURNAL ARTICLE
Nemailla Bonturi, Marina Julio Pinheiro, Paola Monteiro de Oliveira, Eka Rusadze, Tobias Eichinger, Gintare Liudžiūtė, Juliano Sabedotti De Biaggi, Age Brauer, Maido Remm, Everson Alves Miranda, Rodrigo Ledesma-Amaro, Petri-Jaan Lahtvee
Rhodotorula toruloides is a potential chassis for microbial cell factories as this yeast can metabolise different substrates into a diverse range of natural products, but the lack of efficient synthetic biology tools hinders its applicability. In this study, the modular, versatile and efficient Golden Gate DNA assembly system (RtGGA) was adapted to the first basidiomycete, an oleaginous yeast R. toruloides . R. toruloides CCT 0783 was sequenced, and used for the GGA design. The DNA fragments were assembled with predesigned 4-nt overhangs and a library of standardized parts was created containing promoters, genes, terminators, insertional regions, and resistance genes...
December 2022: Metabolic Engineering Communications
https://read.qxmd.com/read/35571351/control-of-d-lactic-acid-content-in-p-la-3hb-copolymer-in-the-yeast-saccharomyces-cerevisiae-using-a-synthetic-gene-expression-system
#31
JOURNAL ARTICLE
Anna Ylinen, Laura Salusjärvi, Mervi Toivari, Merja Penttilä
The fully biobased polyhydroxyalkanoate (PHA) polymers provide interesting alternatives for petrochemical derived plastic materials. The mechanical properties of some PHAs, including the common poly(3-hydroxybutyrate) (PHB), are limited, but tunable by addition of other monomers into the polymer chain. In this study we present a precise synthetic biology method to adjust lactate monomer fraction of a polymer by controlling the monomer formation in vivo at gene expression level, independent of cultivation conditions...
June 2022: Metabolic Engineering Communications
https://read.qxmd.com/read/35517715/-in-vivo-production-of-pederin-by-labrenzin-pathway-expansion
#32
JOURNAL ARTICLE
Dina Kačar, Carmen Schleissner, Librada M Cañedo, Pilar Rodríguez, Fernando de la Calle, Carmen Cuevas, Beatriz Galán, José Luis García
Pederin is a potent polyketide toxin that causes severe skin lesions in humans after contact with insects of genus Paederus. Due to its potent anticancer activities, pederin family compounds have raised the interest of pharmaceutical industry. Despite the extensive studies on the cluster of biosynthetic genes responsible for the production of pederin, it has not yet been possible to isolate and cultivate its bacterial endosymbiont producer. However, the marine bacterium Labrenzia sp. PHM005 was recently reported to produce labrenzin, the closest pederin analog...
June 2022: Metabolic Engineering Communications
https://read.qxmd.com/read/35433265/engineering-of-yarrowia-lipolytica-for-the-production-of-plant-triterpenoids-asiatic-madecassic-and-arjunolic-acids
#33
JOURNAL ARTICLE
Jonathan Asmund Arnesen, Arian Belmonte Del Ama, Sidharth Jayachandran, Jonathan Dahlin, Daniela Rago, Aaron John Christian Andersen, Irina Borodina
Several plant triterpenoids have valuable pharmaceutical properties, but their production and usage is limited since extraction from plants can burden natural resources, and result in low yields and purity. Here, we engineered oleaginous yeast Yarrowia lipolytica to produce three valuable plant triterpenoids (asiatic, madecassic, and arjunolic acids) by fermentation. First, we established the recombinant production of precursors, ursolic and oleanolic acids, by expressing plant enzymes in free or fused versions in a Y...
June 2022: Metabolic Engineering Communications
https://read.qxmd.com/read/35310468/development-of-an-e-coli-based-norbaeocystin-production-platform-and-evaluation-of-behavioral-effects-in-rats
#34
JOURNAL ARTICLE
Alexandra M Adams, Nicholas A Anas, Abhishek K Sen, Jordan D Hinegardner-Hendricks, Philip J O'Dell, William J Gibbons, Jessica E Flower, Matthew S McMurray, J Andrew Jones
Interest in the potential therapeutic efficacy of psilocybin and other psychedelic compounds has escalated significantly in recent years. To date, little is known regarding the biological activity of the psilocybin pathway intermediate, norbaeocystin, due to limitations around sourcing the phosphorylated tryptamine metabolite for in vivo testing. To address this limitation, we first developed a novel E. coli platform for the rapid and scalable production of gram-scale amounts of norbaeocystin. Through this process we compare the genetic and fermentation optimization strategies to that of a similarly constructed and previously reported psilocybin producing strain, uncovering the need for reoptimization and balancing upon even minor genetic modifications to the production host...
June 2022: Metabolic Engineering Communications
https://read.qxmd.com/read/35287355/-de-novo-biosynthesis-of-diverse-plant-derived-styrylpyrones-in-saccharomyces-cerevisiae
#35
JOURNAL ARTICLE
Yinan Wu, Maple N Chen, Sijin Li
Plant styrylpyrones exerting well-established neuroprotective properties have attracted increasing attention in recent years. The ability to synthesize each individual styrylpyrone in engineered microorganisms is important to understanding the biological activity of medicinal plants and the complex mixtures they produce. Microbial biomanufacturing of diverse plant-derived styrylpyrones also provides a sustainable and efficient approach for the production of valuable plant styrylpyrones as daily supplements or potential drugs complementary to the prevalent agriculture-based approach...
June 2022: Metabolic Engineering Communications
https://read.qxmd.com/read/35242556/application-of-metabolic-engineering-to-enhance-the-content-of-alkaloids-in-medicinal-plants
#36
REVIEW
Soledad Mora-Vásquez, Guillermo Gael Wells-Abascal, Claudia Espinosa-Leal, Guy A Cardineau, Silverio García-Lara
Plants are a rich source of bioactive compounds, many of which have been exploited for cosmetic, nutritional, and medicinal purposes. Through the characterization of metabolic pathways, as well as the mechanisms responsible for the accumulation of secondary metabolites, researchers have been able to increase the production of bioactive compounds in different plant species for research and commercial applications. The intent of the current review is to describe the metabolic engineering methods that have been used to transform in vitro or field-grown medicinal plants over the last decade and to identify the most effective approaches to increase the production of alkaloids...
June 2022: Metabolic Engineering Communications
https://read.qxmd.com/read/35145855/thermodynamics-contributes-to-high-limonene-productivity-in-cyanobacteria
#37
JOURNAL ARTICLE
Shrameeta Shinde, Sonali Singapuri, Zhenxiong Jiang, Bin Long, Danielle Wilcox, Camille Klatt, J Andrew Jones, Joshua S Yuan, Xin Wang
Terpenoids are a large group of secondary metabolites with broad industrial applications. Engineering cyanobacteria is an attractive route for the sustainable production of commodity terpenoids. Currently, a major obstacle lies in the low productivity attained in engineered cyanobacterial strains. Traditional metabolic engineering to improve pathway kinetics has led to limited success in enhancing terpenoid productivity. In this study, we reveal thermodynamics as the main determinant for high limonene productivity in cyanobacteria...
June 2022: Metabolic Engineering Communications
https://read.qxmd.com/read/35036316/production-of-human-milk-fat-substitute-by-engineered-strains-of-yarrowia-lipolytica
#38
JOURNAL ARTICLE
Govindprasad Bhutada, Guillaume Menard, Rupam Kumar Bhunia, Piotr P Hapeta, Rodrigo Ledesma-Amaro, Peter J Eastmond
Human milk fat has a distinctive stereoisomeric structure where palmitic acid is esterified to the middle (sn-2) position on the glycerol backbone of the triacylglycerol and unsaturated fatty acids to the outer (sn-1/3) positions. This configuration allows for more efficient nutrient absorption in the infant gut. However, the fat used in most infant formulas originates from plants, which exclude palmitic acid from the sn-2 position. Oleaginous yeasts provide an alternative source of lipids for human nutrition...
June 2022: Metabolic Engineering Communications
https://read.qxmd.com/read/35028290/heterologous-phasin-expression-in-rhodopseudomonas-palustris-cga009-for-bioplastic-production-from-lignocellulosic-biomass
#39
JOURNAL ARTICLE
Brandi Brown, Cheryl Immethun, Adil Alsiyabi, Dianna Long, Mark Wilkins, Rajib Saha
Rhodopseudomonas palustris CGA009 is a metabolically robust microbe that can utilize lignin breakdown products to produce polyhydroxyalkanoates (PHAs), biopolymers with the potential to replace conventional plastics. Our recent efforts suggest PHA granule formation is a limiting factor for maximum production of the bioplastic poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) by R. palustris. The Phap1 phasin ( phaP1 ) from the PHB-producing model bacterium Cupriavidus necator H16 was expressed in R. palustris with the aim of overproducing PHBV from the lignin breakdown product p- coumarate by fostering smaller and more abundant granules...
June 2022: Metabolic Engineering Communications
https://read.qxmd.com/read/34934621/overcoming-glutamate-auxotrophy-in-escherichia-coli-itaconate-overproducer-by-the-weimberg-pathway
#40
JOURNAL ARTICLE
Ken W Lu, Chris T Wang, Hengray Chang, Ryan S Wang, Claire R Shen
Biosynthesis of itaconic acid occurs through decarboxylation of the TCA cycle intermediate cis-aconitate. Engineering of efficient itaconate producers often requires elimination of the highly active isocitrate dehydrogenase to conserve cis-aconitate, leading to 2-ketoglutarate auxotrophy in the producing strains. Supplementation of glutamate or complex protein hydrolysate then becomes necessary, often in large quantities, to support the high cell density desired during itaconate fermentation and adds to the production cost...
December 2021: Metabolic Engineering Communications
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