Comparing Proteomes of Cupriavidus basilensis 4G11 and Cupriavidus necator H16

Authors

Kyle Sander^1,2, Anthony J. Abel^1,3, Skyler Friedline^1,2,*, William Sharpless^1,&, Jeffrey Skerker^1,2,4,%, Adam Deutschbauer⁴, Douglas S. Clark^1,3, Adam P. Arkin^1,2,4

Affiliations

1. Center for the Utilization of Biological Engineering in Space, Berkeley, CA
2. Department of Bioengineering, University of California, Berkeley. Berkeley, CA
3. Department of Chemical & Biomolecular Engineering, University of California, Berkeley. Berkeley, CA
4. Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA

& - Current Affiliation: Department of Bioengineering, University of San Diego, San Diego, CA
* - Current Affiliation: Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, BC, Canada
% - Current Affiliation: Zymergen, Emeryville, CA

Introduction

Species of Cupriavidus are among the best bioplastic producing microorganisms known, though intracellular poly-hydroxybutyrate (PHB) is made exclusively during unbalanced growth (e.g. nitrogen limitation), a state characterized by poor growth and cellular stress. Much work has been done studying bioplastic production in the model/type strain C. necator H16. We use an RB-TnSeq library of the closely related C. basilensis 4G11 to assess for genes which decouple PHB production from growth state. In this narrative we compute genome-wide protein homology between these two organisms, and generate a synteny plot across the genomes as well.

Methods

1. Import publically available genome of C. necator H16 (RefSeq assembly accession GCF_000009285.1)
2. Import publically available genome of C. basilensis 4G11 (RefSeq assembly accession GCF_000832305.1)
3. Use app 'Compare Two Proteomes' to comupte protein synteny and generate synteny plot