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Computational Molecular Biology – Analytical Genomics

    Comparative in silico meta - Genomics: Annotation analyses, comparative gene regulators and gene evolution analyses, motive conservation pattern, codon usage
    Genome Mining - identification of new genes, regulators and metabolic pathways
    Functional Genomics - Data Mining - functional analyses, predictions
      •   Metabolomics and metabolic reconstructions
      •   Transcriptomics and conceptual expression optimization, RNAseq analyses
      •   Analytical and synthetic proteomics and structural molecular biology

Synthetic Molecular Biology – Gene Function Oriented Computation

    Gene sequence analyses of expression relevant functional sequence parameters on different molecular levels (DNA, RNA, Protein, Interaction level)
    In silico simultaneous multi-parameter calculations for expression optimization on different molecular levels
      •   Transcriptional and translational initiation optimization
      •   Translational elongation optimization
      •   mRNA stability, internal secondary structures, motives (e.g.internal SD, splicingsites etc.)
    Identification and selection of regulatory genetic elements based on genomic analyses and data mining
    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
    Sequence calculations for functional substitution of sequence building blocks
      •   Promoter Libraries
      •   Leader Libraries (TIR)
      •   CDS - libraries

We at ATG:biosynthetics over time and with support of governmental funding money developed and improved our in house knowledge and proprietary computer programs like EvoMAG and myBioDesign along with the requirements of our customers. We are supporting our customers not only with genomic annotations, data mining, information generation, condensation and handling. In addition we are computing optimal sequence compositions for constructive and functional gene and gene cluster designs. In silico gene evolution with multi-target parametric are Pareto optimized. Please inquire for any problem you have in constructive and designing multi-gene applications in gene clusters for metabolic pathways (anabolic and catabolic), hetero-protein complexes and multiple constructive elements like for metabolic channeling etc.

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Examples processed by ATG

Bioproduction Product Pathway in kb Application Constructional Design Expression Optimization Leader-Library Specific Vector: Design & Syntheses
Epothilone 65 Cytostatic yes yes yes/no yes
ω-3-PUFA 31,4 Essent. Fatty Acid yes yes yes yes
Argyrin 37,2 Antibiotic yes yes yes yes
MethylMalonylCoA 18,8 Metabolic yes yes no yes
MyxoChromid 32 Antibiotic yes yes no yes
Coronatin 36 Phytotoxin yes no no yes
Bottromyicin 20 Antibiotic yes no no yes
Myxopyronin 53,4 Antibiotic yes no no yes
Glumicin 35,2 Antibiotic yes no no yes
Magnetit 8,9 Geotropism yes no no yes
5-Hetero-Proteins Complex 10,4 Regulation on Protein Level yes no no yes
Multiple Glycosyl-transferase Genes 9,5 Glycosyl-ation yes no no yes

Decoupling of DNA - syntheses from constructional and functional gene design was anticipated as early as SB2.0 in Berkeley 2006. This process, which is in a direct analogy to the manufacturing of hard discs and memory sticks now seems to approach its finalization. On the other side of the coin is the very interesting topic of predictive functional programming of genes for desired application purposes. It accumulated high levels of knowledge over the time frame of the last years not only in the scene of protagonists like Mutalik VK et al. (2013), Goler et al. (2008) and Andrianantoandro E. (2006) but Rössger K et al. (2013) and Arkin AP and Fussenegger M. (2013) even on very high impact. But also in company environments with academic and company clients many projects are realized straight along to the customers desires and ideas without the high visibility on the list of authors of publications.

Arkin AP, Fussenegger M. (2013) Curr Opin Chem Biol. Dec;17(6):869-70. doi: 10.1016/j.cbpa.2013.11.005. Epub 2013 Nov 20. Synthetic biology.
Rössger K et al. (2013) A closed-loop synthetic gene circuit for the treatment of diet-induced obesity in mice. Nat Commun. Nov 26;4:2825. doi: 10.1038/ncomms3825.
Mutalik VK et al. (2013) Precise and reliable gene expression via standard transcription and translation initiation elements. Nature Methods, doi:10.1038/nmeth.2404.
Andrianantoandro E et al. (2006) Synthetic biology: new engineering rules for an emerging discipline Molecular Systems Biology doi:10.1038/msb4100073.
Goler et al. (2008) Genetic design: rising above the Sequence, Trends Biotechnol., 26:538-44