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codon optimality

Nour Rashwan, Marilyn Scott, Roger Prichard
BACKGROUND: The benzimidazole (BZ) anthelmintics, albendazole (ABZ) and mebendazole (MBZ) are the most common drugs used for treatment of soil-transmitted helminths (STHs). Their intensive use increases the possibility that BZ resistance may develop. In veterinary nematodes, BZ resistance is caused by a single nucleotide polymorphism (SNP) in the β-tubulin isotype 1 gene at codon position 200, 167 or 198, and these SNPs have also been correlated with poor response of human Trichuris trichiura to BZ treatment...
January 2017: PLoS Neglected Tropical Diseases
Tabata P Cardoso, Larissa A de Sá, Priscila Dos S Bury, Sair M Chavez-Pacheco, Marcio V B Dias
Glycopeptides are an important class of antibiotics used in the treatment of several infections, including those caused by methicillin resistant Staphylococcus aureus. Glycopeptides are biosynthesized by a Non Ribosomal Peptide Synthase (NRPS) and the resulting peptide precursors are decorated by several tailoring enzymes, such as halogenases and glycosyltransferases. These enzymes are important targets of protein engineering to produce new derivatives of known antibiotics. Herein we show the production of two putative halogenases, denominated StaI and StaK, involved in the biosynthesis of the glycopeptide A47,934 in Streptomyces toyocaensis NRRL 15,009...
January 5, 2017: Protein Expression and Purification
Kuniaki Nerome, Sayaka Matsuda, Kenichi Maegawa, Shigeo Sugita, Kazumichi Kuroda, Kazunori Kawasaki, Reiko Nerome
In this study, we aimed to quantitatively compare the increased production of three H7 influenza virus-like particle (VLP) haemagglutinin (HA) with the use of a codon-optimized single HA gene in silkworm pupae. Recombinant baculovirus (Korea H7-BmNPV) could produce 0.40 million HA units per pupa, corresponding to 1832μg protein. The yield of the HA produced in larva was estimated to be approximately 0.31 million HA units per larva, and there were no significant differences between the three HA proteins. We could establish efficient recovery system of HA production in larvae and pupae with the use of three cycles sonication methods...
January 5, 2017: Vaccine
Thea Bursac, Jeffrey A Gralnick, Johannes Gescher
This study describes the realization of an anoxic acetoin production process using the proteobacterium Shewanella oneidensis. Fermentative processes are of high biotechnological relevance since they offer high productivity and a low percentage of substrate consumption for anabolic processes. Nevertheless, the range of compounds that can be produced as sole end product of a fermentative process is limited, since the average oxidation state of substrate and products has to be identical in the absence of an external electron acceptor...
January 6, 2017: Biotechnology and Bioengineering
Jenny A Greig, Qiang Wang, Amanda L Reicherter, Shu-Jen Chen, Alexandra L Hanlon, Christopher H Tipper, K Reed Clark, Samuel Wadsworth, Lili Wang, James M Wilson
Adeno-associated viral (AAV) vectors are promising vehicles for hemophilia gene therapy, with favorable clinical trial data seen in the treatment of hemophilia B. In an effort to optimize the expression of human coagulation factor VIII (hFVIII) for the treatment of hemophilia A, we performed an extensive study with numerous combinations of liver-specific promoter and enhancer elements with a codon-optimized hFVIII transgene. After generating 42 variants of three reduced-size promoters and three small enhancers, transgene cassettes were packaged within a single AAV capsid, AAVrh10, to eliminate performance differences due to the capsid type...
January 5, 2017: Human Gene Therapy
Yelin Zhu, Yan Hua, Biao Zhang, Lianhong Sun, Wenjie Li, Xin Kong, Jiong Hong
BACKGROUND: Indole pyruvic acid (IPA) is a versatile platform intermediate and building block for a number of high-value products in the pharmaceutical and food industries. It also has a wide range of applications, such as drugs for the nervous system, cosmetics, and luminophores. Chemical synthesis of IPA is a complicated and costly process. Moreover, through the biosynthesis route employing L-amino acid oxidase, the byproduct hydrogen peroxide leads the degradation of IPA. TdiD, identified as a specific tryptophan aminotransferase, could be an alternative solution for efficient IPA biosynthesis...
January 3, 2017: Microbial Cell Factories
Tobias C Wagner, Jochen Bodem
Nucleotide sequences are the fundamental basis for work on molecular mechanisms and for phylogenetic analysis. Recently, we identified sequence errors in all of the LTR sequences of the prototypic foamy virus stored in the GenBank database. Here, we report the resequencing of the proviral plasmids pHSRV13 and pHSRV2. Sequence comparisons revealed an error rate for the foamy virus sequences stored in the database of up to 10 errors per 1000 bp. Even the newest sequences of the codon-optimized foamy virus synthetic Gag, Pol, and Env amino acid sequences showed exchanges compared to the new proviral pHSRV13n sequence...
December 31, 2016: Archives of Virology
Ketaki D Belsare, Mary C Andorfer, Frida S Cardenas, Julia R Chael, Hyun June Park, Jared C Lewis
Directed evolution is a powerful tool for optimizing enzymes, and mutagenesis methods that improve enzyme library quality can significantly expedite the evolution process. Here, we report a simple method for targeted combinatorial codon mutagenesis (CCM). To demonstrate the utility of this method for protein engineering, CCM libraries were constructed for cytochrome P450BM3, pfu prolyl oligopeptidase, and the flavin-dependent halogenase RebH; 10-26 sites were targeted for codon mutagenesis in each of these enzymes, and libraries with a tunable average of 1-7 codon mutations per gene were generated...
January 4, 2017: ACS Synthetic Biology
Alex C Stabell, John Hawkins, Manqing Li, Xia Gao, Michael David, William H Press, Sara L Sawyer
Schlafen11 (encoded by the SLFN11 gene) has been shown to inhibit the accumulation of HIV-1 proteins. We show that the SLFN11 gene is under positive selection in simian primates and is species-specific in its activity against HIV-1. The activity of human Schlafen11 is relatively weak compared to that of some other primate versions of this protein, with the versions encoded by chimpanzee, orangutan, gibbon, and marmoset being particularly potent inhibitors of HIV-1 protein production. Interestingly, we find that Schlafen11 is functional in the absence of infection and reduces protein production from certain non-viral (GFP) and even host (Vinculin and GAPDH) transcripts...
December 2016: PLoS Pathogens
June Y Hou, Caitlin Baptiste, Radhika Bangalore Hombalegowda, Ana I Tergas, Rebecca Feldman, Nathaniel L Jones, Sudeshna Chatterjee-Paer, Ama Bus-Kwolfski, Jason D Wright, William M Burke
BACKGROUND: Optimal treatments for vulvar and vaginal melanomas (VVMs) have not been identified. Herein, the authors compare molecular profiles between VVM and nongynecologic melanoma (NGM) subtypes with the objective of identifying novel, targetable biomarkers. METHODS: In total, 2304 samples of malignant melanoma that were submitted to Caris Life Sciences between 2009 and 2015 were reviewed. In situ hybridization and immunohistochemistry were used to assess copy numbers and protein expression of selected genes...
December 27, 2016: Cancer
Jung-Hun Kim, Chonglong Wang, Hui-Jung Jang, Myeong-Seok Cha, Ju-Eon Park, Seon-Yeong Jo, Eui-Sung Choi, Seon-Won Kim
BACKGROUND: Isoprene, a volatile C5 hydrocarbon, is an important platform chemical used in the manufacturing of synthetic rubber for tires and various other applications, such as elastomers and adhesives. RESULTS: In this study, Escherichia coli MG1655 harboring Populus trichocarpa isoprene synthase (PtispS) and the exogenous mevalonate (MVA) pathway produced 80 mg/L isoprene. Codon optimization and optimal expression of the ispS gene via adjustment of the RBS strength and inducer concentration increased isoprene production to 199 and 337 mg/L, respectively...
December 23, 2016: Microbial Cell Factories
Eric D Kelsic, Hattie Chung, Niv Cohen, Jimin Park, Harris H Wang, Roy Kishony
Synonymous codon choices at the beginning of genes optimize 5' RNA structures for enhanced translation initiation, but less is known about mechanisms that drive codon optimization downstream within the gene. To understand what determines codon choices across a gene, we generated 12,726 in situ codon mutants in the Escherichia coli essential gene infA and measured their fitness by combining multiplex automated genome engineering mutagenesis with amplicon deep sequencing (MAGE-seq). Correlating predicted 5' RNA structure with fitness revealed that codons even far from the start of the gene are deleterious if they disrupt the native 5' RNA conformation...
December 21, 2016: Cell Systems
Giovanni Magistrelli, Yves Poitevin, Florence Schlosser, Guillemette Pontini, Pauline Malinge, Soheila Josserand, Marie Corbier, Nicolas Fischer
When production of bispecific antibodies requires the co-expression and assembly of three or four polypeptide chains, low expression of one chain can significantly limit assembly and yield. κλ bodies, fully human bispecific antibodies with native IgG structure, are composed of a common heavy chain and two different light chains, one kappa and one lambda. No engineering is applied to force pairing of the chains, thus both monospecific and bispecific antibodies are secreted in the supernatant. In this context, stoichiometric expression of the two light chains allows for maximal assembly of the bispecific antibody...
December 21, 2016: MAbs
Hasnain Hussain, Nikson Fatt-Ming Chong
The combined overlap extension PCR (COE-PCR) method developed in this work combines the strengths of the overlap extension PCR (OE-PCR) method with the speed and ease of the asymmetrical overlap extension (AOE-PCR) method. This combined method allows up to 6 base pairs to be mutated at a time and requires a total of 40-45 PCR cycles. A total of eight mutagenesis experiments were successfully carried out, with each experiment mutating between two to six base pairs. Up to four adjacent codons were changed in a single experiment...
2016: BioMed Research International
Wenjing Cui, Jintao Cheng, Shengnan Miao, Li Zhou, Zhongmei Liu, Junling Guo, Zhemin Zhou
Tuneable gene expression controlled by synthetic biological elements is of great importance to biotechnology and synthetic biology. The synthetic riboswitch is a pivotal type of elements that can easily control the heterologous gene expression in diverse bacteria. In this study, the theophylline-dependent synthetic riboswitch and the corresponding variants with varied spacings between Shine-Dalgarno (SD) sequence and start codon were employed to comprehensively characterize the induction and regulation properties through combining a strong promoter aprE in Bacillus subtilis...
December 16, 2016: Applied Microbiology and Biotechnology
Taketo Otsuka, Aimee L Brauer, Charmaine Kirkham, Erin K Sully, Melinda M Pettigrew, Yong Kong, Bruce L Geller, Timothy F Murphy
BACKGROUND: Antisense peptide nucleic acids (PNAs) are synthetic polymers that mimic DNA/RNA and inhibit bacterial gene expression in a sequence-specific manner. METHODS: To assess activity against non-typeable Haemophilus influenzae (NTHi), we designed six PNA-peptides that target acpP, encoding an acyl carrier protein. MICs and minimum biofilm eradication concentrations (MBECs) were determined. Resistant strains were selected by serial passages on media with a sub-MIC concentration of acpP-PNA...
January 2017: Journal of Antimicrobial Chemotherapy
Valerie Matagne, Yann Ehinger, Lydia Saidi, Ana Borges-Correia, Martine Barkats, Marc Bartoli, Laurent Villard, Jean-Christophe Roux
Rett syndrome (RTT) is a severe X-linked neurodevelopmental disorder that is primarily caused by mutations in the methyl CpG binding protein 2 gene (MECP2). RTT is the second most prevalent cause of intellectual disability in girls and there is currently no cure for the disease. The finding that the deficits caused by the loss of Mecp2 are reversible in the mouse has bolstered interest in gene therapy as a cure for RTT. In order to assess the feasibility of gene therapy in a RTT mouse model, and in keeping with translational goals, we investigated the efficacy of a self-complementary AAV9 vector expressing a codon-optimized version of Mecp2 (AAV9-MCO) delivered via a systemic approach in early symptomatic Mecp2-deficient (KO) mice...
December 11, 2016: Neurobiology of Disease
Chao Zhong, Ping Wei, Yi-Heng Percival Zhang
Rare codon in a heterologous gene may cause premature termination of protein synthesis, misincorporation of amino acids, and/or slow translation of mRNA, decreasing the heterologous protein expression. However, its hypothetical function pertaining to functional protein folding has been barely reported. Here, we investigated the effects of selective introduction of synonymous rare codons (SRCs) to two codon-optimized (i.e., rare codon-free) genes sucrose phosphorylase (SP) gene from Thermoanaerobacterium thermosaccharolyticum and amidohydrolase gene from Streptomyces caatingaensis on their expression levels in Escherichia coli BL21(DE3)...
December 12, 2016: Biotechnology and Bioengineering
Derrick White, Raghuveer Singh, Deepak Rudrappa, Jackie Mateo, Levi Kramer, Laura Freese, Paul Blum
: Thermotoga maritima ferments a broad range of sugars to form acetate, carbon dioxide, traces of lactate and near theoretic yields of molecular hydrogen (H2). In this organism, the catabolism of pentose sugars such as arabinose depends on the interaction between the pentose phosphate pathway along with the Embden Myerhoff and Entner Doudoroff pathways. While values for H2 yield have been determined using pentose supplemented complex media (CM) and predicted by metabolic pathway reconstruction, the actual effect of pathway elimination on hydrogen production has not been reported due to the lack of a genetic method for the creation of targeted mutations...
December 9, 2016: Applied and Environmental Microbiology
Lingqia Su, Dening Ji, Xiumei Tao, Lingang Yu, Jing Wu, Yongmei Xia
In this study, a gene encoding a putative lipase from Fusarium oxysporum was optimized via codon optimization and expressed in Pichia pastoris KM71. The gene product was identified as a phospholipase B (PLB). The engineered P. pastoris was further cultured in a 3.6-L bioreactor. After optimization of the induction conditions, this system produced 6.6mgmL(-1) protein and 6503.8UmL(-1) PLB activity in the culture medium. Efficient expression of this PLB in P. pastoris should reduce the costs of production and application...
January 20, 2017: Journal of Biotechnology
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