Identification and DNA annotation of a plasmid isolated from Chromobacterium violaceum

Daniel C Lima,Lena K Nyberg,Silvia R Batistuzzo De Medeiros,Fredrik Westerlund

doi:10.1038/s41598-018-23708-5

Abstract

Chromobacterium violaceum is a ß-proteobacterium found widely worldwide with important biotechnological properties and is associated to lethal sepsis in immune-depressed individuals. In this work, we report the discover, complete sequence and annotation of a plasmid detected in C. violaceum that has been unnoticed until now. We used DNA single-molecule analysis to confirm that the episome found was a circular molecule and then proceeded with NGS sequencing. After DNA annotation, we found that this extra-chromosomal DNA is probably a defective bacteriophage of approximately 44 kilobases, with 39 ORFs comprising, mostly hypothetical proteins. We also found DNA sequences that ensure proper plasmid replication and partitioning as well as a toxin addiction system. This report sheds light on the biology of this important species, helping us to understand the mechanisms by which C. violaceum endures to several harsh conditions. This discovery could also be a first step in the development of a DNA manipulation tool in this bacterium.

Highlights

Chromobacterium violaceum is a Gram-negative facultative anaerobe bacillus belonging to the Neisseriaceae family[1]
We used single DNA molecule analysis and next-generation sequencing to identify a plasmid in C. violaceum strain ATCC 12472
From C. violaceum strain ATCC 12472 to construct a genomic library, we noticed after agarose gel electrophoresis the recurrence of a DNA species smaller than expected for high molecular weight genomic DNA in our preparations

Summary

Introduction

Chromobacterium violaceum is a Gram-negative facultative anaerobe bacillus belonging to the Neisseriaceae family[1]. We used single DNA molecule analysis and next-generation sequencing to identify a plasmid in C. violaceum strain ATCC 12472. As can be seen in lane 2 of Fig. 1, the preparation contained contaminating high molecular weight genomic DNA trapped in the well and a species with mobility much greater than 10 kb, our putative episome An abundant number of genes related to phage structure are present in the sequence of the plasmid.

Results

Conclusion