Fructooligosaccharides (FOS) are compounds possessing various health properties and are added to functional foods as prebiotics. The commercial production of FOS is done through the enzymatic transfructolysation of sucrose by β-fructofuranosidases which is found in various organisms of which Aureobasidium pullulans and Aspergillus niger are the most well known. This study overexpressed two differently codon-optimized variations of the Aspergillus fijiensis β-fructofuranosidase-encoding gene (fopA) under the transcriptional control of either the alcohol oxidase (AOX1) or glyceraldehyde-3-phosphate dehydrogenase (GAP) promoters. When cultivated in shake flasks, the two codon-optimized variants displayed similar volumetric enzyme activities when expressed under control of the same promoter with the GAP strains producing 11.7 U/ml and 12.7 U/ml, respectively, and the AOX1 strains 95.8 U/ml and 98.6 U/ml, respectively. However, the highest production levels were achieved for both codon-optimized genes when expressed under control of the AOX1 promoter. The AOX1 promoter was superior to the GAP promoter in bioreactor cultivations for both codon-optimized genes with 13,702 U/ml and 2718 U/ml for the AOX1 promoter for ATUM and GeneArt®, respectively, and 6057 U/ml and 1790 U/ml for the GAP promoter for ATUM and GeneArt®, respectively. The ATUM-optimized gene produced higher enzyme activities when compared to the one from GeneArt®, under the control of both promoters.
Translation is divided into initiation, elongation, termination and ribosome recycling. Earlier work implicated several eukaryotic initiation factors (eIFs) in ribosomal recycling in vitro. Here, we uncover roles for HCR1 and eIF3 in translation termination in vivo. A substantial proportion of eIF3, HCR1 and eukaryotic release factor 3 (eRF3) but not eIF5 (a well-defined "initiation-specific" binding partner of eIF3) specifically co-sediments with 80S couples isolated from RNase-treated heavy polysomes in an eRF1-dependent manner, indicating the presence of eIF3 and HCR1 on terminating ribosomes. eIF3 and HCR1 also occur in ribosome- and RNA-free complexes with both eRFs and the recycling factor ABCE1/RLI1. Several eIF3 mutations reduce rates of stop codon read-through and genetically interact with mutant eRFs. In contrast, a slow growing deletion of hcr1 increases read-through and accumulates eRF3 in heavy polysomes in a manner suppressible by overexpressed ABCE1/RLI1. Based on these and other findings we propose that upon stop codon recognition, HCR1 promotes eRF3·GDP ejection from the post-termination complexes to allow binding of its interacting partner ABCE1/RLI1. Furthermore, the fact that high dosage of ABCE1/RLI1 fully suppresses the slow growth phenotype of hcr1Δ as well as its termination but not initiation defects implies that the termination function of HCR1 is more critical for optimal proliferation than its function in translation initiation. Based on these and other observations we suggest that the assignment of HCR1 as a bona fide eIF3 subunit should be reconsidered. Together our work characterizes novel roles of eIF3 and HCR1 in stop codon recognition, defining a communication bridge between the initiation and termination/recycling phases of translation.
- MeSH
- ATP-Binding Cassette Transporters genetics MeSH
- Eukaryotic Initiation Factor-3 genetics MeSH
- Peptide Initiation Factors genetics MeSH
- Mutation MeSH
- Protein Biosynthesis * MeSH
- Saccharomyces cerevisiae Proteins genetics MeSH
- Saccharomyces cerevisiae genetics MeSH
- Amino Acid Sequence MeSH
- Peptide Chain Termination, Translational * MeSH
- Codon, Terminator genetics MeSH
- Protein Binding MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Expression and purification of whole and nuclear localization signal (NLS) deleted ORF2 capsid protein of porcine circovirus 2 (PCV2) is demonstrated in the present study. Gene coding for both protein forms were cloned into pDest17 vector and expressed in BL21 (DE3)AI cells and in BL21-CodonPlus (DE3)-RIPL E. coli cells. The later cells were used to overcome difficulties with the heterologous expression of viral proteins in prokaryotic systems. Whole 30 kDa recombinant ORF2 protein was successfully expressed in BL21-CodonPlus (DE3)-RIPL cells only, 3 mg of pure protein was consistently obtained per liter of bacterial culture. NLS deleted ORF2 protein was expressed in both cell types. Resulting proteins reacted with PCV2 positive swine serum in immunofluorescent test and immunoblot.
Here we present an optimized procedure to generate amino acid variations at specific site(s) of proteins, followed by a simple one-step screen for mutants with the desired β-glucosidase activity. The procedure was evaluated by introducing sequence variation into a codon specifying a non-functional variant of the catalytic nucleophile (E401) of the maize β-glucosidase Zm-p60.1. Observed and theoretically expected frequencies of the four possible variants of the codon and the two possible phenotypes (functional and non-functional) were investigated. Deviations in codon and phenotype frequencies were expressed as a coefficient. This coefficient was then used to estimate the extent of oversampling, of the mutant library, which would be necessary to compensate for the underrepresentation of some sequences. This evaluation of the overall performance of the method allows experimentally derived parameters to be incorporated into mutant library design. This method combines the application of a well-defined distribution of variability with a reliable screening process. Thus, it facilitates the production of novel functional variants of β-glucosidases for either fundamental studies or potential biotechnological applications.
- MeSH
- Amino Acids chemistry genetics MeSH
- Cellulases chemistry genetics isolation & purification MeSH
- Escherichia coli genetics MeSH
- Codon chemistry genetics MeSH
- Zea mays enzymology MeSH
- Mutagenesis MeSH
- Directed Molecular Evolution methods MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Protein engineering is the discipline of developing useful proteins for applications in research, therapeutic, and industrial processes by modification of naturally occurring proteins or by invention of de novo proteins. Modern protein engineering relies on the ability to rapidly generate and screen diverse libraries of mutant proteins. However, design of mutant libraries is typically hampered by scale and complexity, necessitating development of advanced automation and optimization tools that can improve efficiency and accuracy. At present, automated library design tools are functionally limited or not freely available. To address these issues, we developed Mutation Maker, an open source mutagenic oligo design software for large-scale protein engineering experiments. Mutation Maker is not only specifically tailored to multisite random and directed mutagenesis protocols, but also pioneers bespoke mutagenic oligo design for de novo gene synthesis workflows. Enabled by a novel bundle of orchestrated heuristics, optimization, constraint-satisfaction and backtracking algorithms, Mutation Maker offers a versatile toolbox for gene diversification design at industrial scale. Supported by in silico simulations and compelling experimental validation data, Mutation Maker oligos produce diverse gene libraries at high success rates irrespective of genes or vectors used. Finally, Mutation Maker was created as an extensible platform on the notion that directed evolution techniques will continue to evolve and revolutionize current and future-oriented applications.
- MeSH
- Algorithms MeSH
- Escherichia coli genetics MeSH
- Gene Library MeSH
- Codon genetics MeSH
- Mutation * MeSH
- Mutagenesis, Site-Directed methods MeSH
- Mutagenesis * MeSH
- Mutant Proteins MeSH
- Oligonucleotides genetics MeSH
- Computer Simulation MeSH
- Proteins genetics MeSH
- Directed Molecular Evolution methods MeSH
- Software * MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Using a codon-optimized gene fragment, we report remarkable yields for extracellular domain of human NK cell receptor (NKp30ex) when produced on M9 minimal medium, even with low (2g/L) glucose concentration. The yields were identical using media containing (15)NH(4)Cl or (15)NH(4)Cl in combination with all-(13)C-d-glucose allowing to produce homogenous soluble monomeric NKp30 in several formats needed for advanced NMR studies. Our optimized protocol now allows to produce routinely 10mg batches of these NKp30ex proteins per 1L of M9 production medium in four working days. The purity and identity of the produced proteins were checked by SDS-PAGE, MALDI MS peptide mapping, and high resolution ion cyclotron resonance MS. Analytical ultracentrifugation confirmed the monomeric status of the produced proteins. Long-term stability of the produced protein proved to be very good allowing its use for NMR studies using elevated temperatures. These studies should reveal further details of the interaction of NKp30 with several of its ligands including target cell surface proteins and heparin-derived oligosaccharides.
- MeSH
- Bioreactors MeSH
- Ammonium Chloride chemistry MeSH
- Electrophoresis, Polyacrylamide Gel MeSH
- Escherichia coli chemistry genetics metabolism MeSH
- Codon MeSH
- Humans MeSH
- Molecular Sequence Data MeSH
- Nuclear Magnetic Resonance, Biomolecular methods MeSH
- Natural Cytotoxicity Triggering Receptor 3 biosynthesis chemistry genetics metabolism MeSH
- Recombinant Proteins chemistry genetics metabolism MeSH
- Solubility MeSH
- Protein Folding MeSH
- Amino Acid Sequence MeSH
- Base Sequence MeSH
- Ultracentrifugation MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Due to the fast global spreading of the Severe Acute Respiratory Syndrome Coronavirus - 2 (SARS-CoV-2), prevention and treatment options are direly needed in order to control infection-related morbidity, mortality, and economic losses. Although drug and inactivated and attenuated virus vaccine development can require significant amounts of time and resources, DNA and RNA vaccines offer a quick, simple, and cheap treatment alternative, even when produced on a large scale. The spike protein, which has been shown as the most antigenic SARS-CoV-2 protein, has been widely selected as the target of choice for DNA/RNA vaccines. Vaccination campaigns have reported high vaccination rates and protection, but numerous unintended effects, ranging from muscle pain to death, have led to concerns about the safety of RNA/DNA vaccines. In parallel to these studies, several open reading frames (ORFs) have been found to be overlapping SARS-CoV-2 accessory genes, two of which, ORF2b and ORF-Sh, overlap the spike protein sequence. Thus, the presence of these, and potentially other ORFs on SARS-CoV-2 DNA/RNA vaccines, could lead to the translation of undesired proteins during vaccination. Herein, we discuss the translation of overlapping genes in connection with DNA/RNA vaccines. Two mRNA vaccine spike protein sequences, which have been made publicly-available, were compared to the wild-type sequence in order to uncover possible differences in putative overlapping ORFs. Notably, the Moderna mRNA-1273 vaccine sequence is predicted to contain no frameshifted ORFs on the positive sense strand, which highlights the utility of codon optimization in DNA/RNA vaccine design to remove undesired overlapping ORFs. Since little information is available on ORF2b or ORF-Sh, we use structural bioinformatics techniques to investigate the structure-function relationship of these proteins. The presence of putative ORFs on DNA/RNA vaccine candidates implies that overlapping genes may contribute to the translation of smaller peptides, potentially leading to unintended clinical outcomes, and that the protein-coding potential of DNA/RNA vaccines should be rigorously examined prior to administration.
- MeSH
- Vaccines, DNA adverse effects genetics MeSH
- Spike Glycoprotein, Coronavirus genetics MeSH
- Codon MeSH
- Nucleic Acid Conformation MeSH
- Humans MeSH
- RNA, Messenger MeSH
- mRNA Vaccines adverse effects genetics MeSH
- Open Reading Frames MeSH
- Genes, Overlapping * MeSH
- Protein Domains MeSH
- Protein Biosynthesis MeSH
- COVID-19 Vaccines adverse effects genetics MeSH
- Genes, Viral * MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Východiska: V současné době bylo popsáno již více než 200 nádorových syndromů. Ve většině populací jsou však dostupné pouze informace o mutačním spektru ve vysoce rizikových genech limitované počtem vyšetřených jedinců. Metody: V rámci retrospektivní NGS studie v Masarykově onkologickém ústavu bylo provedeno vyšetření TruSight Cancer panelem zahrnujícím 94 genů u 50 vysoce rizikových jedinců se závažnou osobní i rodinnou anamnézou onkologického onemocnění bez detekované kauzální mutace v genech BRCA1, BRCA2, MLH1, MSH2, MSH6, TP53 nebo APC dle indikace. Všechny patogenní nebo pravděpodobně patogenní mutace detekované pomocí NGS technologie byly potvrzeny Sangerovým sekvenováním. Výsledky: Ztrátové (frame-shift, nonsense) mutace byly detekovány v genech ATM, BAP1, FANCC, FANCI, PMS2, SBDS, ERCC2, RECQL4. Několik patogenních nebo pravděpodobně patogenních mutací (missense, predikované sestřihové mutace, in-frame delece/inzerce) bylo zachyceno v genech ATM, BRIP1, CDH1, CHEK2, ERCC2, ERCC3, ERCC4, FANCA, MC1R, MEN1, MRE11A, MUTYH, PALB2, RAD51C, RET, SDHB, STK11. Nacházejí se ve vysoce konzervovaných funkčních doménách proteinů a některé z nich již byly prokázány jako patogenní mutace pomocí funkčních testů nebo u závažných autozomálně recesivních syndromů (Ataxia telangiectasia, Fanconiho anémie). Většina z detekovaných missense variant v řadě dalších genů je nejasného klinického významu a determinace jejich významnosti zůstává otevřená do budoucna. Závěr: Detekce variant se střední nebo nízkou penetrancí má pouze limitovanou klinickou využitelnost. Panelové testování u vysoce rizikových osob s nádorovým onemocněním může poskytnout důležitou informaci o příčině nádorové predispozice a může pomoci s výběrem optimální léčby a v preventivní personalizované onkologii.
Background: Currently, more than 200 hereditary cancer syndromes have been described, yet, in most countries genetic testing is restricted to a narrow spectrum of genes within a limited group of people tested. Methods: For this retrospective study we used the TruSight cancer panel (Illumina) – NGS panel targeting 94 cancer predisposition genes in order to analyze 50 high-risk cancer patients with significant personal and family history of cancer who did not carry mutations in BRCA1, BRCA2, MLH1, MSH2, MSH6, TP53 or APC genes. All pathogenic and potentially pathogenic mutations detected by NGS technology have been confirmed by Sanger sequencing. Results: There were several deleterious (frame-shift/nonsense) mutations detected in ATM, BAP1, FANCC, FANCI, PMS2, SBDS, ERCC2, RECQL4 genes. Various pathogenic or potentially pathogenic (missense, predicted splice site, in-frame insertion/deletion) mutations were detected in ATM, BRIP1, CDH1, CHEK2, ERCC2, ERCC3, ERCC4, FANCA, MC1R, MEN1, MRE11A, MUTYH, PALB2, RAD51C, RET, SDHB, STK11. These mutations affect highly conserved protein domains and affect their function as proved by the available functional assays. They were confirmed to be pathogenic as an „Parent No2 “ in serious recessive diseases such as Ataxia telangiectasia or Fanconi anemia. The clinical significance of the majority of detected missense variants still remains to be identified. Conclusion: Moderate or low penetrance variants are of limited clinical importance. Panel genetic testing in high-risk individuals with cancer provides important information concerning the cause of the investigated cancer, and may assist in the risk assesment and optimal management of the cancer, as well as in further preventive care. Key words: hereditary cancer syndromes – hereditary breast and ovarian cancer syndrome – hereditary nonpolyposis colorectal cancer – high-throughput DNA sequencing – TruSight cancer panel – MiSeq This work was supported by MH CZ – DRO (MMCI, 00209805) and by the State budget project of CR (OP VaVpI – RECAMO CZ.1.05/2.1.00/03.0101). The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study. The Editorial Board declares that the manuscript met the ICMJE recommendation for biomedical papers. Submitted: 20. 8. 2015 Accepted: 22. 9. 2015
- Keywords
- hereditární nádorové syndromy, TruSight cancer panel, sekvenování nové generace, ATM mutace, BAP1, PMS2, FANCI, RAD51C, BRIP1, ztrátové mutace,
- MeSH
- Adenosine Triphosphatases genetics MeSH
- Medical History Taking MeSH
- Ataxia Telangiectasia Mutated Proteins genetics MeSH
- Neoplastic Syndromes, Hereditary * diagnosis genetics MeSH
- Colorectal Neoplasms, Hereditary Nonpolyposis genetics MeSH
- Hereditary Breast and Ovarian Cancer Syndrome genetics MeSH
- DNA-Binding Proteins genetics MeSH
- Adult MeSH
- DNA Repair Enzymes genetics MeSH
- Genetic Predisposition to Disease MeSH
- Genetic Testing MeSH
- Risk Assessment MeSH
- Middle Aged MeSH
- Humans MeSH
- Mutation, Missense MeSH
- Adolescent MeSH
- Tumor Suppressor Proteins genetics MeSH
- Kidney Neoplasms genetics MeSH
- Breast Neoplasms genetics MeSH
- Pancreatic Neoplasms genetics MeSH
- Colonic Neoplasms genetics MeSH
- Codon, Nonsense MeSH
- Pilot Projects MeSH
- Fanconi Anemia Complementation Group Proteins genetics MeSH
- Retrospective Studies MeSH
- Rhabdomyosarcoma genetics MeSH
- RNA Helicases genetics MeSH
- Pedigree MeSH
- Sequence Analysis, DNA * methods utilization MeSH
- Ubiquitin Thiolesterase genetics MeSH
- Check Tag
- Adult MeSH
- Middle Aged MeSH
- Humans MeSH
- Adolescent MeSH
- Male MeSH
- Female MeSH
- Publication type
- Case Reports MeSH
- Research Support, Non-U.S. Gov't MeSH
BACKGROUND: The DNA released into the bloodstream by malignant tumours· called circulating tumour DNA (ctDNA), is often a small fraction of total cell-free DNA shed predominantly by hematopoietic cells and is therefore challenging to detect. Understanding the biological properties of ctDNA is key to the investigation of its clinical relevance as a non-invasive marker for cancer detection and monitoring. METHODS: We selected 40 plasma DNA samples of pancreatic cancer cases previously reported to carry a KRAS mutation at the 'hotspot' codon 12 and re-screened the cell-free DNA using a 4-size amplicons strategy (57 bp, 79 bp, 167 bp and 218 bp) combined with ultra-deep sequencing in order to investigate whether amplicon lengths could impact on the capacity of detection of ctDNA, which in turn could provide inference of ctDNA and non-malignant cell-free DNA size distribution. FINDINGS: Higher KRAS amplicon size (167 bp and 218 bp) was associated with lower detectable cell-free DNA mutant allelic fractions (p < 0·0001), with up to 4·6-fold (95% CI: 2·6-8·1) difference on average when comparing the 218bp- and the 57bp-amplicons. The proportion of cases with detectable KRAS mutations was also hampered with increased amplicon lengths, with only half of the cases having detectable ctDNA using the 218 bp assay relative to those detected with amplicons less than 80 bp. INTERPRETATION: Tumour-derived mutations are carried by shorter cell-free DNA fragments than fragments of wild-type allele. Targeting short amplicons increases the sensitivity of cell-free DNA assays for pancreatic cancer and should be taken into account for optimized assay design and for evaluating their clinical performance. FUNDING: IARC; MH CZ - DRO; MH SK; exchange program between IARC and Sao Paulo medical Sciences; French Cancer League.
- MeSH
- Alleles MeSH
- Pancreatitis, Chronic blood diagnosis genetics pathology MeSH
- Circulating Tumor DNA blood genetics MeSH
- Gene Expression MeSH
- Gene Frequency MeSH
- Codon MeSH
- Humans MeSH
- Mutation MeSH
- Biomarkers, Tumor blood genetics MeSH
- Pancreatic Neoplasms blood diagnosis genetics pathology MeSH
- Proto-Oncogene Proteins p21(ras) blood genetics MeSH
- Base Sequence MeSH
- Sensitivity and Specificity MeSH
- Case-Control Studies MeSH
- Computational Biology MeSH
- High-Throughput Nucleotide Sequencing methods MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Multicenter Study MeSH
