New Traits Discovery

Data mining has proven to be highly useful for commercial purposes, especially in identifying enzymes with unique or exceptional characteristics that can be utilized in various industrial processes or in the development of genetically modified organisms. With the help of genomics and data mining, researchers can now search for hypothetical proteins with homology with known proteins or enzymes. Through the use of bioinformatic tools and statistical models, TAXON can analyze large amounts of genomic or transcriptomic data to identify enzymes with specific properties. 

TAXON provides services that involve the identification of enzymes suitable for commercial use through in-silico methods. Our approach involves the use of bioinformatics tools and statistical models to search protein databases with precision and specificity for specific purposes. The company performs ad hoc procedures that combine data mining and genomics to search for hypothetical protein homologs of known proteins or enzymes. To achieve this, we utilize BLASTP/PHMMER search methods at public or custom databases to identify enzymes of interest. Afterward, we select representative homologs and construct a hidden Markov model (HMM) to further screen and identify homologs codified in genomes of organisms adapted to specific niches, such as high salt or temperature. Finally, we use the HMM to identify proteins or enzymes with exceptional properties that are applicable in the industrial, agronomical, or pharmaceutical sectors.

Deliverables of Enzyme discovery service:

  • Found enzyme sequences (in FASTA format)
  • When possible, the annotated region at the gene discovery location (Genbank format)
  • A complete report describing methods and supporting data for enzyme discovery (in PDF format)

See Our Services in Practice

The search for thermostable phospholipase C enzyme (PC-PLC) candidates involved constructing specific profiles using the sequence of BcPLC and divergent homologs. This profile was then used to identify putative PLC sequences from available genomes of thermophilic bacteria or archaea. Among the identified candidates, a putative PC-PLC from Thermococcus kodakarensis (TkPLC) was found to have low identity with BcPLC but conserved catalytic residues involved in Zn(II) binding. TkPLC's demonstrated thermostability and catalytic properties make it an excellent candidate for high-temperature enzymatic degumming, providing significant industrial, economic, and environmental benefits. The Case emphasizes the importance of searching for sequences with low identity but conserved catalytic residues.

Reference: Marchisio, F., Di Nardo, L., Val, D.S. et al. Characterization of a novel thermostable phospholipase C from T. kodakarensis suitable for oil degumming. Appl Microbiol Biotechnol 106, 5081–5091 (2022).

Genomic Characterization

Identify genes responsible for desirable traits and ensure the absence of undesirable characteristics, enabling the development of safer and more efficient microorganisms.

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Comparative Genomics

The whole genomic sequences of various organisms are analyzed and compared through comparative genomics. This helps in determining the uniqueness of the trait of interest.

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Experience comprehensive transcriptome analysis with TAXON, ensuring precise quality control, accurate alignment, and reliable gene expression quantification.

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Dive into the depths of metatranscriptomics with TAXON's comprehensive analysis, revealing the hidden dynamics of microbial gene expression within complex communities.

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