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codon optimality

Orion S Rivers, Silvia Beurmann, Allexa Dow, Loralyn M Cozy, Patrick Videau
Multicellular organisms must carefully regulate the timing, number, and location of specialized cellular development. In the filamentous cyanobacterium Anabaena sp. strain PCC 7120, nitrogen-fixing heterocysts are interspersed between vegetative cells in a periodic pattern to achieve optimal exchange of bioavailable nitrogen and reduced carbon. The spacing between heterocysts is regulated by the activity of two developmental inhibitors: PatS and HetN. PatS functions to create a de novo pattern from a homogenous field of undifferentiated cells, while HetN maintains the pattern throughout subsequent growth...
May 21, 2018: Journal of Bacteriology
Jared Weaver, Steven G Boxer
Photosynthetic reaction centers (RCs) are the membrane proteins responsible for the initial charge separation steps central to photosynthesis. As a complex and spectroscopically complicated membrane protein, the RC (and other associated photosynthetic proteins) would benefit greatly from the insight offered by site-specifically encoded non-canonical amino acids in the form of probes and an increased chemical range in key amino acid analogues. Towards that goal, we developed a method to transfer amber codon suppression machinery developed for E...
May 15, 2018: ACS Synthetic Biology
Josefine Liljeruhm, Saskia K Funk, Sandra Tietscher, Anders D Edlund, Sabri Jamal, Pikkei Wistrand-Yuen, Karl Dyrhage, Arvid Gynnå, Katarina Ivermark, Jessica Lövgren, Viktor Törnblom, Anders Virtanen, Erik R Lundin, Erik Wistrand-Yuen, Anthony C Forster
Background: Coral reefs are colored by eukaryotic chromoproteins (CPs) that are homologous to green fluorescent protein. CPs differ from fluorescent proteins (FPs) by intensely absorbing visible light to give strong colors in ambient light. This endows CPs with certain advantages over FPs, such as instrument-free detection uncomplicated by ultra-violet light damage or background fluorescence, efficient Förster resonance energy transfer (FRET) quenching, and photoacoustic imaging. Thus, CPs have found utility as genetic markers and in teaching, and are attractive for potential cell biosensor applications in the field...
2018: Journal of Biological Engineering
Haifeng Li, Shuling Wang, Yunyi Zhang, Liehuan Chen
An alginate lyase encoding gene sagl from Flavobacterium sp. H63 was codon optimized and recombinantly expressed at high level in P.pastoris through high cell-density fermentation. The highest yield of recombinant enzyme of sagl (rSAGL) in yeast culture supernatant reached 226.4 μg/mL (915.5 U/mL). This was the highest yield record of recombinant expression of alginate lyase so far. The rSAGL was confirmed as a partially glycosylated protein through EndoH digestion. The optimal reaction temperature and pH of this enzyme were 45 °C and 7...
May 11, 2018: Marine Drugs
Meng-Ze Du, Shuo Liu, Zhi Zeng, Labena Abraham Alemayehu, Wen Wei, Feng-Biao Guo
Inconsistent results on the association between evolutionary rates and amino acid composition of proteins have been reported in eukaryotes. However, there are few studies of how amino acid composition can influence evolutionary rates in bacteria. Thus, we constructed linear regression models between composition frequencies of amino acids and evolutionary rates for bacteria. Compositions of all amino acids can on average explain 21.5% of the variation in evolutionary rates among 273 investigated bacterial organisms...
May 9, 2018: Scientific Reports
Min You, Yi Yang, Chuanqi Zhong, Fentian Chen, Xin Wang, Tianrong Jia, Yuanzhi Chen, Bing Zhou, Qingyu Mi, Qinjian Zhao, Zhiqiang An, Wenxin Luo, Ningshao Xia
Antibody drugs have been used to treat a number of diseases successfully. Producing antibodies with high yield and quality is necessary for clinical applications of antibodies. For a candidate molecule, optimization of a vector to produce sufficient yield and an accurate primary structure is indispensable in the early stage of the production process development. It is especially important to maintain the fidelity of N-terminal sequence. In order to produce antibodies with a high yield and accurate N-terminal, the expression vector was systematically optimized in this study...
May 8, 2018: Applied Microbiology and Biotechnology
Tsukasa Ohmori, Hiroaki Mizukami, Yuko Katakai, Sho Kawai, Hitoyasu Nakamura, Makoto Inoue, Tsugumine Shu, Hideharu Sugimoto, Yoichi Sakata
Joint bleeding and resultant arthropathy are major determinants of quality of life in haemophilia patients. We previously developed a mesenchymal stromal cell (MSC)-based treatment approach for haemophilic arthropathy in a mouse model of haemophilia A. Here, we evaluated the long-term safety of intra-articular injection of lentivirally transduced autologous MSCs in non-human primates. Autologous bone-marrow-derived MSCs transduced with a lentiviral vector expressing coagulation factor VIII (FVIII) were injected into the left knee joint of cynomolgus monkeys...
May 8, 2018: International Journal of Hematology
Qian Du, Xiangdong Yang, Jinhua Zhang, Xiaofang Zhong, Kyung Seok Kim, Jing Yang, Guojie Xing, Xiaoyu Li, Zhaoyuan Jiang, Qiyun Li, Yingshan Dong, Hongyu Pan
Phytophthora root and stem rot (PRR) caused by Phytophthora sojae is one of the most devastating diseases reducing soybean (Glycine max) production all over the world. Harpin proteins in many plant pathogenic bacteria were confirmed to enhance disease and insect resistance in crop plants. Here, a harpin protein-encoding gene hrpZpsta from the P. syringae pv. tabaci strain Psta218 was codon-optimized (renamed hrpZm) and introduced into soybean cultivars Williams 82 and Shennong 9 by Agrobacterium-mediated transformation...
May 4, 2018: Transgenic Research
Veeranarayanan Surya Aathmanathan, Nattarsingam Jothi, Vijay Kumar Prajapati, Muthukalingan Krishnan
Infectious diseases are the major cause of high mortality among infants and geriatric patients. Vaccines are the only weapon in our arsenal to defend us ourselves against innumerable infectious diseases. Though myriad of vaccines are available, still countless people die due to microbial infections. Subunit vaccine is an effective strategy of vaccine development, combining a highly immunogenic carrier protein with highly antigenic but non-immunogenic antigen (haptens). In this study we have made an attempt to utilize the immunoinformatic tool for carrier protein development...
May 3, 2018: Scientific Reports
Mohammad M Pourseif, Gholamali Moghaddam, Hossein Daghighkia, Ahmad Nematollahi, Yadollah Omidi
Introduction: In this study, we targeted the worm stage of Echinococcus granulosus to design a novel multi-epitope B- and helper T-cell based vaccine construct for immunization of dogs against this multi-host parasite. Methods: The vaccine was designed based on the local Eg14-3-3 antigen (Ag). DNA samples were extracted from the protoscoleces of the infected sheep's liver, and then subjected to the polymerase chain reaction (PCR) with 14-3-3 specific forward and reverse primers. For the vaccine designing, several in silico steps were undertaken...
2018: BioImpacts: BI
Valentina Poletti, Sabine Charrier, Guillaume Corre, Bernard Gjata, Alban Vignaud, Fang Zhang, Michael Rothe, Axel Schambach, H Bobby Gaspar, Adrian J Thrasher, Fulvio Mavilio
X-linked severe combined immunodeficiency (SCID-X1) is caused by mutations in the interleukin-2 receptor γ chain gene (IL2RG), and it is characterized by profound defects in T, B, and natural killer (NK) cell functions. Transplantation of hematopoietic stem/progenitor cells (HSPCs) genetically corrected with early murine leukemia retrovirus (MLV)-derived gammaretroviral vectors showed restoration of T cell immunity in patients, but it resulted in vector-induced insertional oncogenesis. We developed a self-inactivating (SIN) lentiviral vector carrying a codon-optimized human IL2RG cDNA driven by the EF1α short promoter (EFS-IL2RG), and we tested its efficacy and safety in vivo by transplanting transduced Il2rg-deficient Lin- HSPCs in an Il2rg -/- / Rag2 -/- mouse model...
June 15, 2018: Molecular Therapy. Methods & Clinical Development
Siya Zhou, Shixin Guan, Zuowen Duan, Xiao Han, Xin Zhang, Wenli Fan, Haoge Li, Lijing Chen, Hui Ma, Hangmei Liu, Yanye Ruan, Jingwei Lin
Fungal immunomodulatory proteins (FIPs) have been identified from a series of fungi, especially in Ganoderma species. However, little is known about the FIPs from G. applanatum. In this study, two novel FIP genes, termed as FIP-gap1 and FIP-gap2, were cloned from G. applanatum, characterized and functionally expressed after codon optimization in Pichia pastoris GS115. Results showed that FIP-gap1 and FIP-gap2 comprised 342-bp encoding peptides of 113 amino acids, which shared a high homology with other Ganoderma FIPs...
April 28, 2018: Applied Microbiology and Biotechnology
Ting Fang, Zhenghong Tao, Yanhong Liu, Changming Yu, Ruizhi Zhi, Rui Yu
CRM197 (cross-reacting material 197), a non-toxic mutant of diphtheria toxin, has wide application potential in biopharmaceuticals. However, it is difficult to express CRM197 in bacteria other than Corynebacterium diphtheriae. Here we proposed a new alternative method to produce soluble CRM197 without label in Escherichia coli. In particular, a synthetic gene coding for CRM197, optimized for E. coli codon usage, was cloned in the pET32a (+) vector. Accordingly, the over-expression of the protein was simply induced with IPTG in E...
April 25, 2018: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
E S Starodubova, Y V Kuzmenko, E O Pankova, A A Latanova, O V Preobrazhenskaya, V L Karpov
Safe and effective anti-rabies vaccines are intensely sought worldwide. DNA vaccines have already shown their efficacy and safety and have occupied a special place in the field. Two prototype anti-rabies DNA vaccines were compared for the potential to induce virus-specific antibody production. One vector contained a codon-optimized gene with a territory-adapted consensus sequence of the rabies virus glycoprotein. The other one expressed the same glycoprotein in fusion with a c-CD63 lysosome targeting motif at the C terminus...
March 2018: Molekuliarnaia Biologiia
Vidya Pradeep Kumar, Atul P Kolte, Arindam Dhali, Chandrashekar Naik, Manpal Sridhar
Utilization of energy-rich crop residues by ruminants is restricted by the presence of lignin, which is recalcitrant to digestion. Application of lignin degrading enzymes on the lignocellulosic biomass exposes the cellulose for easy digestion by ruminants. Laccases have been found to be considerably effective in improving the digestibility by way of delignification. However, laccase yields from natural hosts are not sufficient for industrial scale applications, which restricts their use. A viable option would be to express the laccase gene in compatible hosts to achieve higher production yields...
April 25, 2018: Journal of General and Applied Microbiology
Qi Gao, Xuan Cao, Yuying Huang, Jinglin Yang, Jun Chen, Liujing Wei, Qiang Hua
Recent advances in the production of biofuels by microbes have attracted attention due to increasingly-limited fossil fuels. Biodiesels, especially fatty acid ethyl esters (FAEEs), are considered a potentially fully-sustainable fuel in the near future due to similarities with petrodiesels and compatibility with existing infrastructure. However, biosynthesis of FAEEs is limited by the supply of precursor lipids and acetyl-CoA. In the present study, we explored the production potential of an engineered biosynthetic pathway coupled to the addition of ethanol in the oleaginous yeast Yarrowia lipolytica...
April 25, 2018: ACS Synthetic Biology
Robert Serfling, Lisa Seidel, Thore Böttke, Irene Coin
The genetic incorporation of non-canonical amino acids (ncAAs) via amber stop codon suppression is a powerful technique to install artificial probes and reactive moieties onto proteins directly in the live cell. Each ncAA is incorporated by a dedicated orthogonal suppressor-tRNA/amino-acyl-tRNA-synthetase (AARS) pair that is imported into the host organism. The incorporation efficiency of different ncAAs can greatly differ, and be unsatisfactory in some cases. Orthogonal pairs can be improved by manipulating either the AARS or the tRNA...
April 9, 2018: Journal of Visualized Experiments: JoVE
Feng Shi, Mingyue Luan, Yongfu Li
Glutamate decarboxylase (GAD) converts L-glutamate (Glu) into γ-aminobutyric acid (GABA). Corynebacterium glutamicum that expresses exogenous GAD gene, gadB2 or gadB1, can synthesize GABA from its own produced Glu. To enhance GABA production in C. glutamicum, ribosomal binding site (RBS) sequence and promoter were searched and optimized for increasing the expression efficiency of gadB2. R4 exhibited the highest strength among RBS sequences tested, with 6 nt the optimal aligned spacing (AS) between RBS and start codon...
April 18, 2018: AMB Express
Jing Wu, Xiangchen Fan, Jia Liu, Qiuling Luo, Jisi Xu, Xiulai Chen
Enzymatic transformation is now an attractive alternative for α-ketoglutaric acid (α-KG) production, but the oxidative deamination from L-glutamic acid to α-KG is along with H2 O2 accumulation. To remove the effect of H2 O2 on α-KG production, in vitro cascade biocatalysis was designed using the purified L-glutamate oxidase (LGOX) from Streptomyces ghanaensis and catalase (KatG) from Escherichia coli W3110, and the optimal ratio of LGOX:KatG (2.0:1250) was detected in this system. To achieve this ratio, in vivo cascade biocatalysis was constructed by varying promoters and ribosome binding sites (RBSs), and optimized by promoter engineering, such as adjusting the junctions between the SD sequence and start codon ATG and tuning the strengths of RBSs...
April 16, 2018: Applied Microbiology and Biotechnology
Kolja N Eckermann, Hassan M M Ahmed, Mohammad KaramiNejadRanjbar, Stefan Dippel, Christian E Ogaugwu, Peter Kitzmann, Musa D Isah, Ernst A Wimmer
Even in times of advanced site-specific genome editing tools, the improvement of DNA transposases is still on high demand in the field of transgenesis: especially in emerging model systems where evaluated integrase landing sites have not yet been created and more importantly in non-model organisms such as agricultural pests and disease vectors, in which reliable sequence information and genome annotations are still pending. In fact, random insertional mutagenesis is essential to identify new genomic locations that are not influenced by position effects and thus can serve as future stable transgene integration sites...
April 10, 2018: Insect Biochemistry and Molecular Biology
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