August 29, 2020 Feature, Protocols, Results

Analyzing the del Gene Cluster

By Lauren Ramilo

Analyzing the del Gene Cluster for Gold Biomineralization across Delftia spp.

Presenter: Rose Krebs

NC State Undergraduate Research and Creativity Symposium

Abstract

Delftia acidovorans produces delftibactin, a non-ribosomal peptide to protect itself from the toxic effects of gold ions in its environment. Delftibactin removes gold ions from solution and forms them into nontoxic gold nanoparticles. A series of genes called the del cluster are responsible for the production of delftibactin. This project set out to determine if the del cluster was present across the Delftia genus and develop tools for students to use to assemble novel Delftia genomes from metagenomic data. The Department of Energy’s Systems Biology Knowledgebase, KBase, was used to identify and compare the del cluster within different published Delftia genomes. KBase was further used to develop a narrative for students to assemble publicly available metagenomic data and search for novel Delftia metagenomic assembled genomes (MAGs).

The del cluster was identified in D. tsuruhatensis, D. lacustris and many other Delftia spp. The cluster was highly similar at the protein level across the genus. A narrative guide was created to teach students the basics of using KBase. This guide was supplemented with a template for students to copy and walk through this process themselves. Further research will search metagenomic data for the del cluster itself and investigate the conditions under which this cluster is the most active or repressed.