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codon optimality

Sung Don Lim, Won Cheol Yim, Degao Liu, Rongbin Hu, Xiaohan Yang, John C Cushman
Strategies for improving plant size are critical targets for plant biotechnology to increase vegetative biomass or reproductive yield. To improve biomass production, a codon-optimized helix-loop-helix transcription factor (VvCEB1opt ) from wine grape was overexpressed in Arabidopsis thaliana resulting in significantly increased leaf number, leaf and rosette area, fresh weight, and dry weight. Cell size, but typically not cell number, was increased in all tissues resulting in increased vegetative biomass and reproductive organ size, number, and seed yield...
March 9, 2018: Plant Biotechnology Journal
Wen Zhu, Guihua Gong, Jie Pan, Shu Han, Wei Zhang, Youjia Hu, Liping Xie
Human serum albumin (HSA) has been extensively used in a series of clinical care settings for nearly seven decades. However, the broad application of this protein is seriously limited by its short supply. In this work, the codon sequence of HSA was cloned under the control of the alcohol oxidase 1 promoter (AOX1) and expressed as a secretory protein in Pichia pastoris. A recombinant strain displaying the highest HSA yield was selected by screening for resistance to the highest concentration of antibiotic G418...
March 5, 2018: Protein Expression and Purification
Xinwei Yang, Chongrong Ke, Jiangming Zhu, Yan Wang, Wenchao Zeng, Jianzhong Huang
We previously developed a gamma-amino butyric acid (GABA)-producing strain of Escherichia coli, leading to production of 614.15 g/L GABA at 45 °C from L-glutamic acid (L-Glu) with a productivity of 40.94 g/L/h by three successive whole-cell conversion cycles. However, the increase in pH caused by the accumulation of GABA resulted in inactivation of the biocatalyst and consequently led to relatively lower productivity. In this study, by overcoming the major problem associated with the increase in pH during the production process, a more efficient biocatalyst was obtained through cascade modifications of the previously reported E...
March 7, 2018: Applied Microbiology and Biotechnology
Kati Thiel, Edita Mulaku, Hariharan Dandapani, Csaba Nagy, Eva-Mari Aro, Pauli Kallio
BACKGROUND: Photosynthetic cyanobacteria have been studied as potential host organisms for direct solar-driven production of different carbon-based chemicals from CO2 and water, as part of the development of sustainable future biotechnological applications. The engineering approaches, however, are still limited by the lack of comprehensive information on most optimal expression strategies and validated species-specific genetic elements which are essential for increasing the intricacy, predictability and efficiency of the systems...
March 2, 2018: Microbial Cell Factories
Lara Ajamian, Luca Melnychuk, Patrick Jean-Pierre, Gerasimos J Zaharatos
Flagellin's potential as a vaccine adjuvant has been increasingly explored over the last three decades. Monomeric flagellin proteins are the only known agonists of Toll-like receptor 5 (TLR5). This interaction evokes a pro-inflammatory state that impacts upon both innate and adaptive immunity. While pathogen associated molecular patterns (PAMPs) like flagellin have been used as stand-alone adjuvants that are co-delivered with antigen, some investigators have demonstrated a distinct advantage to incorporating antigen epitopes within the structure of flagellin itself...
February 27, 2018: Viruses
Jung-Ho Park, Jae-Woo Lee, Hoonsung Choi, Sun Keun Jung, Jeom Sun Kim, Kyung-Woon Kim, Keon Bong Oh, Hyeon Yang, Sung June Byun
Previously, Escherichia coli harboring the codon-optimized 3D8scFv gene (E. coli 3D8scFv) was developed as a feed additive for use in preventing norovirus infection. Here, we evaluated whether the 3D8scFv gene affects the colonization of E coli when E. coli 3D8scFv passes through the mouse gastrointestinal tract. To determine the colonization ability of E. coli 3D8scFv, E. coli cells with or without the 3D8scFv gene were fed to mice. Total DNA was extracted from the animals' stools, stomach, small intestine and colon...
February 24, 2018: Regulatory Toxicology and Pharmacology: RTP
Hao Zhang, Jian Li, Ruixue Wang, Junkai Zhi, Peng Yin, Jichen Xu
Expansins are essential components of plant cell wall and play an important role in plant growth, development, and stress resistance via loosening function. To understand the codon usage pattern of expansin genes, we gained the sequence data of expansin genes from eight plant species. Statistics analysis showed obvious codon characteristics between monocot and dicot plants. Comparably, expansin genes in monocot plants had really higher GC content, more high frequency codons, and more optimal codons than that in dicot plants...
February 26, 2018: Journal of Biomolecular Structure & Dynamics
Bin Zhang, Miao Yu, Ying Zhou, Bang-Ce Ye
L-Ornithine, a non-essential amino acid, has enormous industrial applications in food, pharmaceutical, and chemical industries. Currently, L-ornithine production is focused on microorganism fermentation using Escherichia coli or Corynebacterium glutamicum. In C. glutamicum, development of high L-ornithine producing C. glutamicum was achieved by deletion of argF, but was accompanied by growth deficiency and arginine auxotrophy. L-Arginine has been routinely added to solve this problem; however, this increases production cost and causes feedback inhibition of N-acetyl-L-glutamate kinase activity...
February 24, 2018: AMB Express
Cindy Jazmín Delgado-Galván, Felipe Padilla-Vaca, Fátima Berenice Ramírez Montiel, Ángeles Rangel-Serrano, Itzel Paramo-Pérez, Fernando Anaya Velázquez, B Franco
Entamoeba histolytica genetic organization and genome structure is complex and under intense research. The genome is fully sequenced, and several tools have been developed for the molecular study of this organism. Nevertheless, good protein tracking tags that are easy to measure and image, like the fluorescent proteins are lacking. In this report, we codon-optimized the red fluorescent protein from the coral Discosoma striata (DsRFP) for its use in E. histolytica and demonstrated functionality in vivo. We envision that this protein can be widely used for the development of transcriptional reporter systems and protein-tagging applications...
February 21, 2018: Experimental Parasitology
Zhimin Huang, Juan Liu, Kaka Ng, Xuesi Wan, Lijuan Xu, Xiaoying He, Zhihong Liao, Yanbing Li
AIMS: Glimepiride is a sulfonylurea known to have unique insulin mimetic and sensitizing effect. We aimed to study the efficacy of glimepiride in a patient with type A insulin resistance syndrome. METHODS: A 15-year-old female with type A insulin resistance syndrome was treated with glimpiride for 6 months. Self-monitoring of blood glucose was recorded, OGTTs on glucose and insulin were measured during the treatment. Hyperinsulinemic euglycemic clamp was used to evaluate whole body insulin sensitivity before and after the treatment...
February 22, 2018: Journal of Diabetes Investigation
Hao Yang, Alan M Swartz, Hyun June Park, Poonam Srivastava, Ken Ellis-Guardiola, David M Upp, Gihoon Lee, Ketaki Belsare, Yifan Gu, Chen Zhang, Raymond E Moellering, Jared C Lewis
Random mutagenesis has the potential to optimize the efficiency and selectivity of protein catalysts without requiring detailed knowledge of protein structure; however, introducing synthetic metal cofactors complicates the expression and screening of enzyme libraries, and activity arising from free cofactor must be eliminated. Here we report an efficient platform to create and screen libraries of artificial metalloenzymes (ArMs) via random mutagenesis, which we use to evolve highly selective dirhodium cyclopropanases...
March 2018: Nature Chemistry
Drew S Tack, Austin C Cole, Raghav Shroff, Barrett R Morrow, Andrew D Ellington
Since the fixation of the genetic code, evolution has largely been confined to 20 proteinogenic amino acids. The development of orthogonal translation systems that allow for the codon-specific incorporation of noncanonical amino acids may provide a means to expand the code, but these translation systems cannot be simply superimposed on cells that have spent billions of years optimizing their genomes with the canonical code. We have therefore carried out directed evolution experiments with an orthogonal translation system that inserts 3-nitro-L-tyrosine across from amber codons, creating a 21 amino acid genetic code in which the amber stop codon ambiguously encodes either 3-nitro-L-tyrosine or stop...
February 19, 2018: Scientific Reports
Zhiliang Yang, Zisheng Zhang
Background: 2,3-butanediol (2,3-BD) is a bulk platform chemical with various potential applications such as aviation fuel. 2,3-BD has three optical isomers: (2R, 3R)-, (2S, 3S)- and meso-2,3-BD. Optically pure 2,3-BD is a crucial precursor for the chiral synthesis and it can also be used as anti-freeze agent due to its low freezing point. 2,3-BD has been produced in both native and non-native hosts. Several pathogenic bacteria were reported to produce 2,3-BD in mixture of its optical isomers including Klebsiella pneumoniae and Klebsiella oxytoca ...
2018: Biotechnology for Biofuels
Jenny A Greig, Jayme M L Nordin, Christine Draper, Peter Bell, James M Wilson
Adeno-associated viral (AAV) vectors can target the liver, making them an attractive platform for gene therapy approaches that require the correction of hepatocytes. Crigler-Najjar syndrome is an autosomal recessive disorder of bilirubin metabolism that occurs when the liver's uridine diphosphate glucuronosyl transferase 1A1 (UGT1A1) enzyme activity is partially or completely absent. This syndrome is characterized by elevated bilirubin levels in the blood. We developed an AAV8 vector expressing a codon-optimized human version of UGT1A1 from a liver-specific promoter...
February 16, 2018: Human Gene Therapy
E Carlos Rodriguez-Merchan
BACKGROUND: Several methods have been investigated to effectively and safely transmit genes that stimulate cells to release therapeutic factor VIII (FVIII) and factor IX (FIX) into the circulation of people with hemophilia (PWH). OBJECTIVE: To review the role of gene therapy (GT) in PWH. METHODS: A Cochrane Library and PubMed (MEDLINE) search related to the role of GT in hemophilia was analyzed. RESULTS: The most promising vectors for hemophilia GT are adeno-associated virus (AAV) and lentivirus...
February 14, 2018: Current Gene Therapy
Dianhui Wu, Guolin Cai, Xiaomin Li, Bing Li, Jian Lu
OBJECTIVES: To optimize the expression of type A ferulic acid esterase (FaeA) from Aspergillus niger in Pichia pastoris X-33 using codon optimization. RESULTS: Recombinant FaeA was purified from the fermentation broth, with the maximum specific activity of 48.4 ± 0.1 U mg-1. Adding it during mashing process for beer brewing raised the filtration rate by 14.5% while the turbidity and viscosity declined by 22 and 6.9%, respectively. Addition of FaeA increased the concentrations of free ferulic acid (FA) and arabinoxylan (AX) in the wort, while the polymeric arabinoxylans content declined significantly...
February 12, 2018: Biotechnology Letters
Gokul Kesavan, Juliane Hammer, Stefan Hans, Michael Brand
New genome-editing approaches, such as the CRISPR/Cas system, have opened up great opportunities to insert or delete genes at targeted loci and have revolutionized genetics in model organisms like the zebrafish. The Cre-loxp recombination system is widely used to activate or inactivate genes with high spatial and temporal specificity. Using a CRISPR/Cas9-mediated knock-in strategy, we inserted a zebrafish codon-optimized CreER T2 transgene at the otx2 gene locus to generate a conditional Cre-driver line. We chose otx2 as it is a patterning gene of the anterior neural plate that is expressed during early development...
February 12, 2018: Cell and Tissue Research
Luiza Cesca Piva, Janice Lisboa De Marco, Lidia Maria Pepe de Moraes, Viviane Castelo Branco Reis, Fernando Araripe Gonçalves Torres
We have investigated the use of the gene coding for acetamidase (amdS) as a recyclable dominant marker for the methylotrophic yeast Komagataella phaffii in order to broaden its genetic toolbox. First, the endogenous constitutive AMD2 gene (a putative acetamidase) was deleted generating strain LA1. A cassette (amdSloxP) was constructed bearing a codon-optimized version of the Aspergillus nidulans amdS gene flanked by loxP sites for marker excision with Cre recombinase. This cassette was successfully tested as a dominant selection marker for transformation of the LA1 strain after selection on plates containing acetamide as a sole nitrogen source...
February 12, 2018: Applied Microbiology and Biotechnology
Changqing Liu, Xiao Men, Hailin Chen, Meijie Li, Zhaorui Ding, Guoqiang Chen, Fan Wang, Haobao Liu, Qian Wang, Youshuang Zhu, Haibo Zhang, Mo Xian
Background: Styrene is a versatile commodity petrochemical used as a monomer building-block for the synthesis of many useful polymers. Although achievements have been made on styrene biosynthesis in microorganisms, several bottleneck problems limit factors for further improvement in styrene production. Results: A two-step styrene biosynthesis pathway was developed and introduced into Escherichia coli BL21(DE3). Systematic optimization of styrene biosynthesis, such as enzyme screening, codon and plasmid optimization, metabolic flow balance, and in situ fermentation was performed...
2018: Biotechnology for Biofuels
Xin Min Qin, Yu Zhang, Yu Jie Liu, Dan Ni Guo, Hui Min Li
The RIB (ribonuclease T2) of Citrus grandis var. Shatianyu Hort involved in self-incompatibility (SI) mechanism was identified by prokaryotic expression. RT-qPCR results showed that the expression level of RIB in self pollinated stigma is significantly higher than that in cross pollinated stigma. A vector for prokaryotic expression of RIB was constructed after codon-optimization, and the recombinant protein was induced and purified. In vitro pollen germination test indicated that the RIB protein markedly inhibited pollen germination and pollen tube growth...
January 31, 2018: Cellular and Molecular Biology
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