Synthetic Biology and Bioengineering
Zylacta develops new tools and methods for the synthetic generation and manipulation of genetically encoded microbial pathways. These can be used in a variety of applications, including:
• Rebuilding and then manipulating biosynthetic pathways from difficult-to-access organisms, enabling access to new diversity and lowering cost of goods.
• Expressing and isolating biocatalytic enzymes from eukaryotic and prokaryotic organisms.
• Generating and testing diverse variants of target proteins, for example through manipulation of substrate specificity.
To enable this we have a suite of host organisms, including Gram-positive and -negative bacteria and those based on industrial scale multi-gram natural product producers, each with a suite of vectors and methods which enable facile manipulation and regeneration of pathways.
Genomics of PGN synthesis, maturation and "shedding"
Our primary interest in LAB genomics is the synthesis and metabolism of peptidoglycans. To achieve this goal, we are creating a genomic database that relates genes and the specific type of peptidoglycan synthesized by LAB.
There are many gaps in the current knowledge surrounding the PG genes and their specificities. Using the Rosetta Stone approach, we have identified a new class of genes responsible for the incorporation of D-amino acids into the interpeptide crosslinks; we found critical sequence features responsible for the selection of the third amino acid in the stem peptide and selected gene candidates responsible for chemical modifications of peptidoglycans. The work on the gene classes responsible for selecting specific amino acids into each position in interpeptide crosslinks and their modifications is in progress. A preliminary example showcasing the utility of Zylacta's PG Dictionary is our discovery of a potentially novel peptidoglycan type in a cheese bacterium.
A long-term goal of this project is to create an enabling technology for the synthesis of a wide variety of compounds (as it is done in the chemical synthesis of oligonucleotides and peptides). The compounds will be released from peptidoglycans of proprietary strains using our proprietary enzymes. We expect that chemical synthesis of analogous compounds with branching peptides and sugar moieties will be unrealistic in the foreseeable future.
A mid-term practical utility of this database will be to help creating production-friendly strains with a desired structure of peptidoglycan, using genes borrowed from the production-unfriendly strains. Selecting or engineering bacterial strains with a desired pattern of secondary modifications of glycopeptides is a near-term priority.