CodoNewsletter 97 | September. 2019    

Comparative Genome Analytics and the Bioinformatics of Gene Function

ATG:biosynthetic Bioinformatics team is always YOUR reliable and trustworthy partner for all issues in Comparative Explorative Genomics - for Genomic Data Mining.

Precise genomic data are leading especially to high functional level molecular BioDesigns, Molecular Engineering of Synthetic Genes and Clusters thereof in Constructional and Artificial Applications of Synthetic Biology.

Based on Synthetic Genes ATG is specialized in planning and realization of bioproduction processes from proof of principle up to the requirements of pilot scales.

Design & Analysis - "codon harmonization" of Synthetic Genes

Core-CDS variants consisting of optimized sequences targting varying codon bias in accordance with the expression host's preferences but showing similar estimated velocity profile shapes can be useful library building blocks for new experimental designs. Provided that other important sequence requirements are considered simultanously in the couse of bioinformatic strategies related to related to "Codon Harmonization" gene function can be influenced towards desired traits. By harmonizing the Codon Usage Frequencies of the Target Gene with those of the Expression Host, Heterologous Protein Expression can be enhanced Fig1.

Fig1.(A)Possible strategy related to "codon harmonization": Signals 1-3 are obtained using different but correlated codon scores based on data-analysis of the native producer. The red line reflects the estimated local translation velocity in the expression host. Velocity indices can be tRNA, codon-bias or codon-enrichment based, preferably combined and crosschecked with insights from mechanistic modeling, or strictly defined according to the customers proposal and specialized knowledge. In the shown example CAI-scores were used and suspected to be problematic codons were avoided. (B,C)Variants of the translation initiation site and in the case of bacterial operons also the translational coupling regions of adjacent orfs should be parametrized and controlled accordingly. The general idea is: When slowing down translational speed, then lower the translation rate according to the pattern in the native host (similar to "codon harmonization") without risking translational arrest, no-go-decay or ribosomal drop-off. (D)Simultaneous control of the synonymous codon frequency distribution following preferences of the eukaryotic expression host for the bacterial NRPS sequence depicted in (A). Codon usage cluster analyses, more detailed tRNA-adaptation analyses and evolutionary-distance based investigations that connect synonymous codon conservation, pausing signals and predicted protein structure have been used to decipher translational regulation (E-G). Data-mining the often highly conserved relative protein expression levels or translational efficiencies of orthologous genes, for which reliable measurements have been performed in the community, is also a promising method to gain insights and estimations.

Complementary it could be desireable to target a standardized, flat profile with built-in assumed to be either slower or faster than average translated regions at selected positions. On the protein-level identical sequences with varying strengths and positions of such "slow(fast) codon clusters" can be manufatured cost efficently by reusing the invariable parts of the CDS during gene synthesis, or possibly, depending on the configuration, via engineered restriction sites and standard cloning techniques.

Controlled gradual attenuation of the mean elongtion rate across the library (by) simulaneously preserving "more sccurate" (usually faster) single codons or codon-pairs, suspected to be important within conserved/functional protein domains, is another example.

In combination with diverse TIR (Translation initiation region including the 5'CDS) - Elements, characterized according to predefined key-parameters, combinatorial experimental designs which enable iterative improvement towards the goals of our customers can be performed.

Optimization projects involving difficult-to-express proteins, which have the tendency to aggregate and form inclusion bodies because the host translation rate may be too high for proper co-translational folding, are possible applications. Especially in cases when other measures such as for example downregulation of the mRNA expression level or co-expression strategies are not sufficient.

Regardless of whether you have a clear imagination for of Active Learning and DoE (Design of Experiments), want to cooperate with us in the development of your experimental setup or simply let us analyze and propose. ATG will provide you the design simultaneously considering constructional constraints of the building-blocks for most cost efficient performance.

Examples processed by ATG

Bioproduction Product Pathway in kb Application Constructional Design Expression Optimization Leader-Library Specific Vector: Design & Syntheses
ω-3-PUFA31Essent. Fatty Acidyesyesyesyes
5-Hetero-Proteins Complex10Regulation on Protein Levelyesnonoyes
Multiple Glycosyl-transferase Genes10Glycosylationyesnonoyes
Disciformycin36Macrolid-Glycoside Antibioticyesnonoyes
AstX22NRPS Antibioticnoyesnoyes

Explorative and Comparative OMICS-Analyses

  • Annotation analyses and corrections, comparative gene regulators and gene evolution analyses, motif conservation pattern, codon usage bias.
  • Genome annotations in detail by comparative evolutionary analyses.
  • Genome mining - identification of new genes, regulators and metabolic pathways.
  • Gene/pathway mining and information evaluation.
  • Pathway discovery and identification (operons of unidentified traits - biosynthetic gene clusters).
  • Analyses of evolutionary genomic data in terms of orthologs, paralogs and xenologs of the target host genomes.
  • Multi-OMICS data analyses for conceptual expression optimization.
    • Extraction of host-specific natural design rules for artificial genes, operons and gene clusters.
    • Idenifying formal molecular parameters relevant for functionally recoding synthetic genes in the context of refactoring pathway systems.
    • Gene sequence analyses of expression relevant functional sequence parameters on different molecular levels (DNA, RNA, Protein, Interaction level).
    • Analyses based on available data from the public domain or supplied by the customer to gain insights about preferences and peculiarities of the expression host and source organism.
    • Extracting information from draft genome sequences of unexplored organisms.

Recoding auto– and heterologous genes and operons for the improvement of expression

  • Transcriptional and translational initiation and termination optimization.
  • Protein function specific translation elongation optimization; polysome formation.
  • Efficiency and fidelity of the translational elongation process.
  • Reconstruction or enhancement of co-translational folding for heterologous expression especially for multiple-domain-proteins.
  • Improving specific activity of protein function by avoiding the formation of inclusion bodies and non-functional protein debris.
  • mRNA stability, control of local secondary structures, motifs (e.g.internal SD-ASD interactions, splicing-sites).
  • Operon optimization including coupling regions and inter-orf interactions.
  • Optimizing coding sequences and regulator regions of pathway genes.
  • Insertion of regulatory genetic elements on DNA- and RNA-level.
  • Assessment of functional optimization strategies for proteins e.g. enzymes.

Constructional DNA - Design Projects

  • Constructional design and realization of functional gene clusters (artificial biochemical pathways, hetero-protein complexes).
  • Sequence calculations for different types of gene cluster assembly strategies.
  • Context-dependent functional substitution of sequence building blocks.
    • Promoter Libraries.
    • TIR(Translation initiation region including 5'-CDS) - Libraries with SD or Kozak - Sequence.
    • CDS Libraries, diversified or pareto optimized on sequence feature level.
    • Interchangeable artficial slow codon clusters or slow / fast translated coding regions.
    • Libraries of Termination-re-initiation coupling regions (Operon).
    • Terminators and (3'CDS-3'UTR) - variants.
    • Sequence context dependent optimization of genetic elements (TIR, RBS, coupling, trans-termination).
    • Taking into account interactions between parts (protein-coding / UTR).

Gene Cluster Expression Engineering - Consulting and Project Realization

  • muliple target gene parameter calculations.
  • pathway expression optimization.
  • Molecular Engineering, Synthetic, Constructional and Artificial Molecular Biology Applications.
  • High production yield of natural compounds by the deployment of cellular factories with heterologous expression systems.

Refactoring of Biosynthetic Gene Clusters

  • Balanced metabolic flux on the highest possible educt versus product levels by means of tuning promoters, spacers, TIRs, coding sequences and coupling regions of adjacent CDSs.
  • Different genetically modified variants with different strength of expression on single protein level.
  • Designing sequence variants which are best suitable for the objectives of improving the yield of the pathway.
  • Refactoring of natural existing biochemical pathway systems and retro-engineering of desired output traits.
  • Design of Experiments – DoE in pathway engineering
  • Exploring the experimental space of the pathway engineering problem in order to find advantageous parameter constellations.

Design of experiments (DoE)

  • Small scale comparison of the native gene with few adapted alternatives diversified on sequence feature level.
  • Coding sequence variant libraries for controlled experiments (e.g. keeping one or several sequence parameters fixed).
  • In regard to predefined key parameters pareto-optimal variant libraries.
  • Example: Fast ribosome clearance of the start codon versus ribosomal accessibility (often conflicting).
  • Full- or fractional-factorial designs based on controlled sequence features.
  • Optimal simultaneous diversification on sequence-feature- and nucleotide-level.
  • Model prediction- or genetic algorithm based iterative optimization if suited.
  • Transferring target parameter sets calculated for the native producer to the expression host to up- or downregulate expression and activity.

ATG's list of publications:-

Co-authored Publications

  • Gemperlein, K., Dietrich, D., Kohlstedt, M., Zipf, G., Bernauer, H., Wittmann, C., Wenzel, S., Müller, R., 2019.
    Polyunsaturated fatty acid production by Yarrowia lipolytica employing designed myxobacterial PUFA synthases. Nat. Comm. In press.
  • Pogorevc, D., Tang, Y., Hoffmann, M.G., Zipf, G., Bernauer, H.S., Popoff, A., Steinmetz, H. and Wenzel, S.C., 2019.
    Biosynthesis and heterologous production of argyrins. ACS synthetic biology, 8(5), pp.1121-1133.
  • Yan, F., Burgard, C., Popoff, A., Zaburannyi, N., Zipf, G., Maier, J., Bernauer, H.S., Wenzel, S.C. and Müller, R., 2018.
    Synthetic biology approaches and combinatorial biosynthesis towards heterologous lipopeptide production. Chemical science, 9(38), pp.7510-7519.
  • Burgard, C., Zaburannyi, N., Nadmid, S., Maier, J., Jenke-Kodama, H., Luxenburger, E., Bernauer, H.S. and Wenzel, S.C., 2017.
    Genomics-guided exploitation of lipopeptide diversity in myxobacteria. ACS chemical biology, 12(3), pp.779-786.
  • Gemperlein, K., Zipf, G., Bernauer, H.S., Müller, R. and Wenzel, S.C., 2016.
    Metabolic engineering of Pseudomonas putida for production of docosahexaenoic acid based on a myxobacterial PUFA synthase. Metabolic engineering, 33, pp.98-108.
  • Zaburannyi, N., Bunk, B., Maier, J., Overmann, J. and Müller, R., 2016.
    Genome analysis of the fruiting body-forming myxobacterium Chondromyces crocatus reveals high potential for natural product biosynthesis. Appl. Environ. Microbiol., 82(6), pp.1945-1957.
  • Oßwald, C., Zipf, G., Schmidt, G., Maier, J., Bernauer, H.S., Müller, R. and Wenzel, S.C., 2012.
    Modular construction of a functional artificial epothilone polyketide pathway. ACS synthetic biology, 3(10), pp.759-772.
  • Gaisser, S., Reiss, T., Lunkes, A., Müller, K.M. and Bernauer, H., 2009.
    Making the most of synthetic biology. EMBO reports, 10(S1), pp.S5-S8.
  • Maurer, S.M., Fischer, M., Schwer, H., Stähler, C., Stähler, P. and Bernauer, H.S., 2009.
    Making commercial biology safer: What the gene synthesis industry has learned about screening customers and orders. Working Paper.
  • Bernauer, H., Christopher, J., Deininger, W., Fischer, M., Habermeier, P., Heumann, K., Maurer, S., Schwer, H., Stähler, P. and Wagner, T., 2008.
    Technical Solutions for Biosecurity in Synthetic Biology. IASB Workshop Report.
  • Müller, K.M., Stebel, S.C., Knall, S., Zipf, G., Bernauer, H.S. and Arndt, K.M., 2005.
    Nucleotide exchange and excision technology (NExT) DNA shuffling: a robust method for DNA fragmentation and directed evolution. Nucleic acids research, 33(13), pp.e117-e117.

Tribute to Customers

  • da Silva, E.S., Huber, S., Alcantara-Neves, N.M., Asam, C., Silveira, E.F., de Andrade Belitardo, E.M.M., Aglas, L., Wallner, M., Gadermaier, G., Briza, P. and Karner, I., 2020.
    N-terminal peptide deletion influences immunological and structural features of Blo t 5. Allergy, 75(6), pp.1503-1507.
  • Grabarczyk, D.B., 2020.
    Crystal structure and interactions of the Tof1–Csm3 (Timeless–Tipin) fork protection complex. Nucleic Acids Research.
  • Janke, C., Gaida, S. and Jennewein, S., 2020.
    The production of isoprene from cellulose using recombinant Clostridium cellulolyticum strains expressing isoprene synthase. MicrobiologyOpen, 9(4), p.e1008.
  • González-Benjumea, A., Carro, J., Renau-Mínguez, C., Linde, D., Fernández-Fueyo, E., Gutiérrez, A. and Martínez, A.T., 2020.
    Fatty acid epoxidation by Collariella virescens peroxygenase and heme-channel variants. Catalysis Science & Technology, 10(3), pp.717-725.
  • Viegas, A., Yin, D.M., Borggräfe, J., Viennet, T., Falke, M., Schmitz, A., Famulok, M. and Etzkorn, M., 2020.
    Molecular Architecture of a Network of Potential Intracellular EGFR Modulators: ARNO, CaM, Phospholipids, and the Juxtamembrane Segment. Structure, 28(1), pp.54-62.
  • Kracher, D., Forsberg, Z., Bissaro, B., Gangl, S., Preims, M., Sygmund, C., Eijsink, V.G. and Ludwig, R., 2020.
    Polysaccharide oxidation by lytic polysaccharide monooxygenase is enhanced by engineered cellobiose dehydrogenase. The FEBS Journal, 287(5), pp.897-908.
  • Gomez-Fernandez, B.J., Risso, V.A., Rueda, A., Sanchez-Ruiz, J.M. and Alcalde, M., 2020.
    Ancestral Resurrection and Directed Evolution of Fungal Mesozoic Laccases. Applied and Environmental Microbiology.
  • Viñambres, M., Espada, M., Martínez, A.T. and Serrano, A., 2020.
    Screening and Evaluation of New Hydroxymethylfurfural Oxidases for Furandicarboxylic Acid Production. Applied and Environmental Microbiology.
  • Mickoleit, F., Lanzloth, C. and Schüler, D., 2020.
    A Versatile Toolkit for Controllable and Highly Selective Multifunctionalization of Bacterial Magnetic Nanoparticles. Small, 16(16), p.1906922.
  • Linde, D., Olmedo, A., González-Benjumea, A., Estévez, M., Renau-Mínguez, C., Carro, J., Fernández-Fueyo, E., Gutiérrez, A. and Martínez, A.T., 2020.
    Two new unspecific peroxygenases from heterologous expression of fungal genes in Escherichia coli. Applied and environmental microbiology, 86(7).
  • Pinar, M. and Peñalva, M.A., 2020.
    En bloc TGN recruitment of Aspergillus TRAPPII reveals TRAPP maturation as unlikely to drive RAB1-to-RAB11 transition. Journal of Cell Science, 133(10).
  • Białopiotrowicz, E., Noyszewska-Kania, M., Kachamakova-Trojanowska, N., Łoboda, A., Cybulska, M., Grochowska, A., Kopczyński, M., Mikula, M., Prochorec-Sobieszek, M., Firczuk, M. and Graczyk-Jarzynka, A., 2020.
    Serine Biosynthesis Pathway Supports MYC-miR-494-EZH2 Feed-Forward Circuit Necessary to Maintain Metabolic and Epigenetic Reprogramming of Burkitt Lymphoma Cells. Cancers, 12(3).
  • Imai, S., Yokomizo, T., Kofuku, Y., Shiraishi, Y., Ueda, T. and Shimada, I., 2020.
    Structural equilibrium underlying ligand-dependent activation of β 2-adrenoreceptor. Nature Chemical Biology, 16(4), pp.430-439.
  • Tobias, J., Battin, C., Linhares, A.D.S., Lebens, M., Baier, K., Ambroz, K., Drinić, M., Högler, S., Inic-Kanada, A., Garner-Spitzer, E. and Preusser, M., 2020.
    A New Strategy Toward B Cell-Based Cancer Vaccines by Active Immunization With Mimotopes of Immune Checkpoint Inhibitors. Frontiers in Immunology, 11.
  • Wei, Q., Hargett, A.A., Knoppova, B., Duverger, A., Rawi, R., Shen, C.H., Farney, S.K., Hall, S., Brown, R., Keele, B.F. and Heath, S.L., 2020.
    Impact of glycan positioning on HIV-1 Env glycan shield density, function, and antibody recognition.
  • Foley, G., Mora, A., Ross, C.M., Bottoms, S., Sützl, L., Lamprecht, M.L., Zaugg, J., Essebier, A., Balderson, B., Newell, R. and Thomson, R.E., 2020.
    Identifying and engineering ancient variants of enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP). bioRxiv, pp.2019-12.
  • Alcolea, P.J., Alonso, A., Esteban, A., Peris, P., Cortés, A., Castillo, J.A. and Larraga, V., 2019.
    IL12 p35 and p40 subunit genes administered as pPAL plasmid constructs do not improve protection of pPAL-LACK vaccine against canine leishmaniasis. PloS one, 14(2), p.e0212136.
  • Dorofeeva, Y., Colombo, P., Blanca, M., Mari, A., Khanferyan, R., Valenta, R. and Focke-Tejkl, M., 2019.
    Expression and characterization of recombinant Par j 1 and Par j 2 resembling the allergenic epitopes of Parietaria judaica pollen. Scientific reports, 9(1), pp.1-12.
  • Giraldo, R., 2019.
    Optogenetic navigation of routes leading to protein amyloidogenesis in bacteria. Journal of molecular biology, 431(6), pp.1186-1202.
  • Tarazona, N.A., Maestro, B., Revelles, O., Sanz, J.M. and Prieto, M.A., 2019.
    Role of leucine zipper-like motifs in the oligomerization of Pseudomonas putida phasins. Biochimica et Biophysica Acta (BBA)-General Subjects, 1863(2), pp.362-370.
  • Sánchez-Osuna, M., Cortés, P., Barbé, J. and Erill, I., 2019.
    Origin of the mobile di-hydro-pteroate synthase gene determining sulfonamide resistance in clinical isolates. Frontiers in microbiology, 9, p.3332.
  • Pogorevc, D., Popoff, A., Abou Fayad, A., Wenzel, S.C. and Müller, R., 2019.
    Production profile engineering and precursor directed biosynthesis for production of novel argyrin derivatives. Establishing and engineering heterologous production systems for argyrin and α-pyrone antibiotics, p.209.
  • Hofmann, R., Akimoto, G., Wucherpfennig, T.G., Zeymer, C. and Bode, J., 2019.
    Lysine acylation using conjugating enzymes (LACE) for site-specific modification and ubiquitination of native proteins.
  • Hargett, A.A., Wei, Q., Knoppova, B., Hall, S., Huang, Z.Q., Prakash, A., Green, T.J., Moldoveanu, Z., Raska, M., Novak, J. and Renfrow, M.B., 2019.
    Defining HIV-1 envelope N-glycan microdomains through site-specific heterogeneity profiles. Journal of virology, 93(1), pp.e01177-18.
  • Gattinger, P., Mittermann, I., Lupinek, C., Hofer, G., Keller, W., Stojkovic, U.B., Korosec, P., Koessler, C., Novak, N. and Valenta, R., 2019.
    Recombinant glycoproteins resembling carbohydrate-specific IgE epitopes from plants, venoms and mites. EBioMedicine, 39, pp.33-43.
  • Ivanusic, D., Pietsch, H., König, J. and Denner, J., 2018.
    Absence of IL-10 production by human PBMCs co-cultivated with human cells expressing or secreting retroviral immunosuppressive domains. PloS one, 13(7), p.e0200570.
  • Liau, N.P., Laktyushin, A., Lucet, I.S., Murphy, J.M., Yao, S., Whitlock, E., Callaghan, K., Nicola, N.A., Kershaw, N.J. and Babon, J.J., 2018.
    The molecular basis of JAK/STAT inhibition by SOCS1. Nature communications, 9(1), p.1558.
  • White, C.J. and Bode, J.W., 2018.
    PEGylation and dimerization of expressed proteins under near equimolar conditions with potassium 2-pyridyl acyltrifluoroborates. ACS central science, 4(2), pp.197-206.
  • Korp, J., Winand, L., Sester, A. and Nett, M., 2018.
    Engineering pseudochelin production in Myxococcus xanthus. Appl. Environ. Microbiol., 84(22), pp.e01789-18.
  • Gemperlein, K., Hoffmann, M., Huo, L., Pilak, P., Petzke, L., Müller, R. and Wenzel, S.C., 2017.
    Synthetic biology approaches to establish a heterologous production system for coronatines. Metabolic engineering, 44, p.213.
  • de Sousa, M., Manzo, R., García, J., Mammarella, E., Gonçalves, L. and Pessela, B., 2017.
    Engineering the L-arabinose isomerase from Enterococcus Faecium for D-tagatose synthesis. Molecules, 22(12), p.2164.
  • Kosler, S., Strukelj, B. and Berlec, A., 2017.
    Lactic Acid Bacteria with Concomitant IL-17, IL-23 and TNFα-Binding Ability for the Treatment of Inflammatory Bowel Disease. Current pharmaceutical biotechnology, 18(4), p.318.
  • Ayuso-Fernández, I., Martínez, A.T. and Ruiz-Dueñas, F.J., 2017.
    Experimental recreation of the evolution of lignin-degrading enzymes from the Jurassic to date. Biotechnology for biofuels, 10(1), p.67.
  • Pinar, M. and Peñalva, M.A., 2017.
    Aspergillus nidulans BapH is a RAB11 effector that connects membranes in the Spitzenkörper with basal autophagy. Molecular microbiology, 106(3), pp.452-468.
  • Bomblies, R., Luitz, M.P., Scanu, S., Madl, T. and Zacharias, M., 2017.
    Transient helicity in intrinsically disordered Axin-1 studied by NMR spectroscopy and molecular dynamics simulations. PloS one, 12(3), p.e0174337.
  • Bustamante, N., Iglesias-Bexiga, M., Bernardo-García, N., Silva-Martín, N., García, G., Campanero-Rhodes, M.A., García, E., Usón, I., Buey, R.M., García, P. and Hermoso, J.A., 2017.
    Deciphering how Cpl-7 cell wall-binding repeats recognize the bacterial peptidoglycan. Scientific reports, 7(1), p.16494.
  • Martínez, I., Mohamed, M.E.S., Rozas, D., García, J.L. and Díaz, E., 2016.
    Engineering synthetic bacterial consortia for enhanced desulfurization and revalorization of oil sulfur compounds. Metabolic engineering, 35, pp.46-54.
  • Acebes, S., Fernandez-Fueyo, E., Monza, E., Lucas, M.F., Almendral, D., Ruiz-Dueñas, F.J., Lund, H., Martinez, A.T. and Guallar, V., 2016.
    Rational enzyme engineering through biophysical and biochemical modeling. ACS Catalysis, 6(3), pp.1624-1629.
  • Gieras, A., Linhart, B., Roux, K.H., Dutta, M., Khodoun, M., Zafred, D., Cabauatan, C.R., Lupinek, C., Weber, M., Focke-Tejkl, M. and Keller, W., 2016.
    IgE epitope proximity determines immune complex shape and effector cell activation capacity. Journal of Allergy and Clinical Immunology, 137(5), pp.1557-1565.
  • Wan, L.C., Maisonneuve, P., Szilard, R.K., Lambert, J.P., Ng, T.F., Manczyk, N., Huang, H., Laister, R., Caudy, A.A., Gingras, A.C. and Durocher, D., 2016.
    Proteomic analysis of the human KEOPS complex identifies C14ORF142 as a core subunit homologous to yeast Gon7. Nucleic acids research, 45(2), pp.805-817.
  • Bire, S., Casteret, S., Piégu, B., Beauclair, L., Moiré, N., Arensbuger, P. and Bigot, Y., 2016.
    Mariner transposons contain a silencer: possible role of the polycomb repressive complex 2. PLoS genetics, 12(3), p.e1005902.
  • Navas-Navarro, P., Rojo-Ruiz, J., Rodriguez-Prados, M., Ganfornina, M.D., Looger, L.L., Alonso, M.T. and García-Sancho, J., 2016.
    GFP-aequorin protein sensor for ex vivo and in vivo imaging of Ca2+ dynamics in high-Ca2+ organelles. Cell chemical biology, 23(6), pp.738-745.
  • Zalem, D., Ribeiro, J.P., Varrot, A., Lebens, M., Imberty, A. and Teneberg, S., 2016.
    Biochemical and structural characterization of the novel sialic acid-binding site of Escherichia coli heat-labile enterotoxin LT-IIb. Biochemical Journal, 473(21), pp.3923-3936.
  • Janowski, R., Scanu, S., Niessing, D. and Madl, T., 2016.
    Crystal and solution structural studies of mouse phospholipid hydroperoxide glutathione peroxidase 4. Acta Crystallographica. Section F, Structural Biology Communications, 72(Pt 10), p.743.
  • Fernández-Fueyo, E., Linde, D., Almendral, D., López-Lucendo, M.F., Ruiz-Dueñas, F.J. and Martínez, A.T., 2015.
    Description of the first fungal dye-decolorizing peroxidase oxidizing manganese (II). Applied microbiology and biotechnology, 99(21), pp.8927-8942.
  • Staudacher, J.J., Naarmann-de Vries, I.S., Ujvari, S.J., Klinger, B., Kasim, M., Benko, E., Ostareck-Lederer, A., Ostareck, D.H., Bondke Persson, A., Lorenzen, S. and Meier, J.C., 2015.
    Hypoxia-induced gene expression results from selective mRNA partitioning to the endoplasmic reticulum. Nucleic Acids Research, 43(6), pp.3219-3236.
  • Kries, H., Niquille, D.L. and Hilvert, D., 2015.
    A subdomain swap strategy for reengineering nonribosomal peptides. Chemistry & biology, 22(5), pp.640-648.
  • Linhart, B., Focke-Tejkl, M., Weber, M., Narayanan, M., Neubauer, A., Mayrhofer, H., Blatt, K., Lupinek, C., Valent, P. and Valenta, R., 2015.
    Molecular evolution of hypoallergenic hybrid proteins for vaccination against grass pollen allergy. The Journal of Immunology, 194(8), pp.4008-4018.
  • McKinley, K.L., Sekulic, N., Guo, L.Y., Tsinman, T., Black, B.E. and Cheeseman, I.M., 2015.
    The CENP-LN complex forms a critical node in an integrated meshwork of interactions at the centromere-kinetochore interface. Molecular cell, 60(6), pp.886-898.
  • Borg, S., Popp, F., Hofmann, J., Leonhardt, H., Rothbauer, U. and Schüler, D., 2015.
    An intracellular nanotrap redirects proteins and organelles in live bacteria. MBio, 6(1), pp.e02117-14.
  • Fernández-Fueyo, E., Ruiz-Dueñas, F.J., Martínez, M.J., Romero, A., Hammel, K.E., Medrano, F.J. and Martínez, A.T., 2014.
    Ligninolytic peroxidase genes in the oyster mushroom genome: heterologous expression, molecular structure, catalytic and stability properties, and lignin-degrading ability. Biotechnology for biofuels, 7(1), p.2.
  • Pahr, S., Selb, R., Weber, M., Focke-Tejkl, M., Hofer, G., Dordić, A., Keller, W., Papadopoulos, N.G., Giavi, S., Mäkelä, M. and Pelkonen, A., 2014.
    Biochemical, biophysical and IgE-epitope characterization of the wheat food allergen, Tri a 37. PloS one, 9(11), p.e111483.
  • Bösken, C.A., Farnung, L., Hintermair, C., Schachter, M.M., Vogel-Bachmayr, K., Blazek, D., Anand, K., Fisher, R.P., Eick, D. and Geyer, M., 2014.
    The structure and substrate specificity of human Cdk12/Cyclin K. Nature communications, 5, p.3505.
  • Hsia, K.C., Wilson-Kubalek, E.M., Dottore, A., Hao, Q., Tsai, K.L., Forth, S., Shimamoto, Y., Milligan, R.A. and Kapoor, T.M., 2014.
    Reconstitution of the augmin complex provides insights into its architecture and function. Nature cell biology, 16(9), p.852.
  • Curin, M., Weber, M., Thalhamer, T., Swoboda, I., Focke‐Tejkl, M., Blatt, K., Valent, P., Marth, K., Garmatiuk, T., Grönlund, H. and Thalhamer, J., 2014.
    Hypoallergenic derivatives of Fel d 1 obtained by rational reassembly for allergy vaccination and tolerance induction. Clinical & Experimental Allergy, 44(6), pp.882-894.
  • Díez-Martínez, R., de Paz, H., Bustamante, N., García, E., Menéndez, M. and García, P., 2013.
    Improving the Lethal Effect of Cpl-7, a Pneumococcal Phage Lysozyme with Broad Bactericidal Activity, by Inverting the Net Charge of Its Cell Wall-Binding Module. Antimicrobial Agents and Chemotherapy, 57(11), p.5355.
  • Kershaw, N.J., Murphy, J.M., Liau, N.P., Varghese, L.N., Laktyushin, A., Whitlock, E.L., Lucet, I.S., Nicola, N.A. and Babon, J.J., 2013.
    SOCS3 binds specific receptor–JAK complexes to control cytokine signaling by direct kinase inhibition. Nature structural & molecular biology, 20(4), p.469.
  • Berlec, A., Malovrh, T., Zadravec, P., Steyer, A., Ravnikar, M., Sabotič, J., Poljšak-Prijatelj, M. and Štrukelj, B., 2013.
    Expression of a hepatitis A virus antigen in Lactococcus lactis and Escherichia coli and evaluation of its immunogenicity. Applied microbiology and biotechnology, 97(10), pp.4333-4342.
  • Thaa, B., Sinhadri, B.C., Tielesch, C., Krause, E. and Veit, M., 2013.
    Signal peptide cleavage from GP5 of PRRSV: a minor fraction of molecules retains the decoy epitope, a presumed molecular cause for viral persistence. PLoS One, 8(6), p.e65548.
  • Guerrero, F., Carbonell, V., Cossu, M., Correddu, D. and Jones, P.R., 2012.
    Ethylene Synthesis and Regulated Expression of Recombinant Protein in Synechocystis sp. PCC 6803. PloS one, 7(11), p.e50470.
  • Fernández-Fueyo, E., Ruiz-Dueñas, F.J., Miki, Y., Martínez, M.J., Hammel, K.E. and Martínez, A.T., 2012.
    Lignin-degrading peroxidases from genome of selective ligninolytic fungus Ceriporiopsis subvermispora. Journal of Biological Chemistry, 287(20), pp.16903-16916.
  • Chen, K.W., Blatt, K., Thomas, W.R., Swoboda, I., Valent, P., Valenta, R. and Vrtala, S., 2012.
    Hypoallergenic Der p 1/Der p 2 combination vaccines for immunotherapy of house dust mite allergy. The Journal of allergy and clinical immunology, 130(2), pp.435-43.
  • Salinas, T., Duby, F., Larosa, V., Coosemans, N., Bonnefoy, N., Motte, P., Maréchal-Drouard, L. and Remacle, C., 2012.
    Co-evolution of mitochondrial tRNA import and codon usage determines translational efficiency in the green alga Chlamydomonas. PLoS genetics, 8(9), p.e1002946.
  • Loveridge, E.J. and Allemann, R.K., 2011.
    Effect of pH on hydride transfer by Escherichia coli dihydrofolate reductase. ChemBioChem, 12(8), pp.1258-1262.
  • Ferrari, E., Darios, F., Zhang, F., Niranjan, D., Bailes, J., Soloviev, M. and Davletov, B., 2010.
    Binary polypeptide system for permanent and oriented protein immobilization. Journal of nanobiotechnology, 8(1), p.9.
  • Hernández, P., Heimann, M., Riera, C., Solano, M., Santalla, J., Luquetti, A.O. and Beck, E., 2010.
    Highly effective serodiagnosis for Chagas' disease. Clin. Vaccine Immunol., 17(10), pp.1598-1604.
  • Noto, T., Kurth, H.M., Kataoka, K., Aronica, L., DeSouza, L.V., Siu, K.M., Pearlman, R.E., Gorovsky, M.A. and Mochizuki, K., 2010.
    The Tetrahymena argonaute-binding protein Giw1p directs a mature argonaute-siRNA complex to the nucleus. Cell, 140(5), pp.692-703.

ATG's Services and Projects

With extensive experience accumulated over decades, scientists in ATG:biosynthetics could provide our worldwide clients with the multi-gene and multi-peptide expression products and services along with bioinformatics analysis and work-up for academic and industrial R&D in the fields of drug discovery, industrial and medical biotechnology, molecular diagnostics, and bioengineering.

ATG:Types of Services and Projects-
    Analytical-, Comparative-, Differential-, Functional-, Immune-, Evolutionary - Genetics and Genomics
  • Mono- to Multi-Gene Syntheses (45 bp – 17 Kbp), GeneChecks, Expression Optimization
  • Minimal Function – (e.g. bioComputing Assisted Epitope Screening)
  • Administration of Multiple Gene Variants (Combinatorial Vaccines)
  • Provision of ISO-Quality Assured – Application Vectors (Gene Therapy)
  • GeneCluster Integrated Expression
  • Multiple Gene Variant Calculations
  • BioDesigns Biochemical GeneCluster - Prokaryotes
  • Gene Engineering - Eukaryotes (Gene Therapy)

We also provide Transfection reagents which can efficiently transfect a variety of cells with minimal cytoxicity and very good viability even in complex cell culture media.

Sincerely yours,

Dr. Hubert S. Bernauer

Dr. Hubert S. Bernauer

ATG:biosynthetics GmbH


Finding the best solution for you!