Genome rearrangements and megaplasmid loss in the filamentous bacterium Kitasatospora viridifaciens are associated with protoplast formation and regeneration

Karina Ramijan,Zheren Zhang,Gilles P Van Wezel,Dennis Claessen

doi:10.1007/s10482-020-01393-7

Abstract

Filamentous Actinobacteria are multicellular bacteria with linear replicons. Kitasatospora viridifaciens DSM 40239 contains a linear 7.8 Mb chromosome and an autonomously replicating plasmid KVP1 of 1.7 Mb. Here we show that lysozyme-induced protoplast formation of the multinucleated mycelium of K. viridifaciens drives morphological diversity. Characterisation and sequencing of an individual revertant colony that had lost the ability to differentiate revealed that the strain had not only lost most of KVP1 but also carried deletions in the right arm of the chromosome. Strikingly, the deletion sites were preceded by insertion sequence elements, suggesting that the rearrangements may have been caused by replicative transposition and homologous recombination between both replicons. These data indicate that protoplast formation is a stressful process that can lead to profound genetic changes.

Highlights

Filamentous Actinobacteria are prolific producers of bioactive compounds
We provide evidence that protoplast formation and regeneration in K. viridifaciens can lead to profound genomic rearrangements in the chromosome as well as loss of the megaplasmid KVP1
Given that these genomic rearrangements translate into major phenotypic variations, caution should be taken when using protoplasts for creating mutants, in particular when using strains that carry natural plasmids

Summary

Introduction

Filamentous Actinobacteria are prolific producers of bioactive compounds These metabolites are mostly used as weapons that provide protection against other microorganisms and phages in the environment (Abrudan et al 2015; Kronheim et al 2018; van der Heul et al 2018). This is useful for filamentous organisms, given that they generally lack the ability to make flagella for escaping dangerous situations. These bacteria are able to generate resistant spores that can invade new environments after their dispersal. Stressful conditions (such as nutrient depletion) induce program cell death (PCD) of the mycelium, which in turn triggers morphological and chemical differentiation (Claessen et al 2014)

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