What makes a megaplasmid?

Abstract

Naturally occurring plasmids come in different sizes. The smallest are less than a kilobase of DNA, while the largest can be over three orders of magnitude larger. Historically, research has tended to focus on smaller plasmids that are usually easier to isolate, manipulate and sequence, but with improved genome assemblies made possible by long-read sequencing, there is increased appreciation that very large plasmids—known as megaplasmids—are widespread, diverse, complex, and often encode key traits in the biology of their host microorganisms. Why are megaplasmids so big? What other features come with large plasmid size that could affect bacterial ecology and evolution? Are megaplasmids 'just' big plasmids, or do they have distinct characteristics? In this perspective, we reflect on the distribution, diversity, biology, and gene content of megaplasmids, providing an overview to these large, yet often overlooked, mobile genetic elements. This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.

Diversity and distribution of Type VI Secretion System gene clusters in bacterial plasmids

“…Even so, some sequences containing ribosomal genes remained in our analysis, as they have other elements that characterize them as plasmids (for example, the presence of the rep gene). In fact, some of the genera identified here were associated with secondary essential replicons (secondary chromosomes and chromids), such as Burkholderia , Cupriavidus , Ensifer / Sinorhizobium , Pantoea , Ralstonia , Rhizobium , Vibrio 27 , 28 . It can be speculated that this could explain the large number of elements with T6SS predicted as non-mobilizable, since chromids, for example, tend to lose the ability to transmit horizontally, thus becoming "stuck" to a particular genome.…”

“…It can be speculated that this could explain the large number of elements with T6SS predicted as non-mobilizable, since chromids, for example, tend to lose the ability to transmit horizontally, thus becoming "stuck" to a particular genome. In fact, non-mobilizable megaplasmids can undergo processes to become chromids 28 . Thus, the identity of these replicons of these organisms is still under debate (megaplasmid, chromid, or secondary chromosome).…”

“…Some replicons of some genera presented sizes in megabases (e.g., Ralstonia solanacearum strain RS10 plasmid unnamed with ~ 2 Mb; Rhizobium phaseoli strain BS3 plasmid pBS3d with ~ 1.1 Mb). The identity of these replicons of these organisms is still under debate (megaplasmid, chromid, or secondary chromosome) 28 , but as they were assigned as plasmids by the authors and they are present in a curated plasmid database (PLSDB), we considered them for the analysis.…”

Introduction: the secret lives of microbial mobile genetic elements

“…With plasmid size spanning three orders of magnitude, what factors drive megaplasmids to become so large, and what are the consequences for microbial genome evolution? In their review of the field, Hall et al [58] suggest that while there is no meaningful size threshold for assigning megaplasmid status, distinct selective pressures can favour and stabilize larger plasmids and their magnified capacity for HGT.…”

“…In their review of the field, Hall et al . [ 58 ] suggest that while there is no meaningful size threshold for assigning megaplasmid status, distinct selective pressures can favour and stabilize larger plasmids and their magnified capacity for HGT.…”