Plasmid localization of sole rrn operon in genomes of Oecophyllibacter saccharovorans (Acetobacteraceae)

Highlights

• The genome architecture of three Oecophyllibacter saccharovorans strains was studied.

• The strains harboured their sole ribosomal RNA (rrn) operon on a 6.6 kb plasmid instead of the main chromosome.

• The rrn operon-containing plasmid was characterized and its importance is discussed.

Abstract

The bacterium Oecophyllibacter saccharovorans of family Acetobacteraceae is a symbiont of weaver ant Oecophylla smaragdina. In our previous study, we published the finding of novel O. saccharovorans strains Ha5^T, Ta1 and Jb2 (Chua et al. 2020) but their plasmid sequences have not been reported before. Here, we demonstrate for the first time that the sole rrn operon of their genomes was detected on a 6.6 kb circular replicon. This replicon occurred in high copy number, much smaller size and lower G + C content than the main chromosome. Based on these features, the 6.6 kb circular replicon was regarded as rrn operon-containing plasmid. Further restriction analysis on the plasmids confirmed their circular conformation. A Southern hybridization analysis also corroborated the presence of 16S rRNA gene and thus the rrn operon on a single locus in the genome of the O. saccharovorans strains. However, similar genome architecture was not observed in other closely related bacterial strains. Additional survey also detected no plasmid-borne rrn operon in available genomes of validly described taxa of family Acetobacteraceae. To date, plasmid localization of rrn operon is rarely documented. This study reports the occurrence of rrn operon on the smallest bacterial plasmid in three O. saccharovorans strains and discusses its possible importance in enhancing their competitive fitness as bacterial symbiont of O. smaragdina.

Introduction

Bacterial genomes are commonly multipartite and split into chromosomal and non-chromosomal DNA molecules. The main chromosomes, including second chromosomes are the largest replicons in bacterial genomes which contain majority of the core genes with essential functions. In contrast, smaller replicons that harbour nonessential genes are considered as plasmids (diCenzo and Finan, 2017). The multipartite genome architecture of bacteria does not occur stochastically and variations in genome organization are often driven by evolutionary forces to attain functional or regulatory purpose (Rocha, 2008).

The rrn operon of bacteria consists of ribosomal RNA (rRNA) genes that are separated by internal transcribed spacers (ITS) and transfer RNA (tRNA) genes (Espejo and Plaza, 2018). The 5S, 16S and 23S rRNAs encoded by rRNA genes of the operon are important ribosomal components that are involved in mRNA-dependent polymerization of amino acids during cellular protein synthesis (Stoddard et al., 2014). Due to its essential function, it was a generally accepted view that rrn operon contains the core genes that bacteria harbour on their chromosomes. It was so until the discovery of a unique clade of strains in genus Aureimonas that had the sole rrn operon in their genomes borne on small and high copy number plasmids of 9.4 to 10 kb (Anda et al., 2015). Genomic analysis on the group of Aureimonas sp. with rrn operon-lacking chromosomes revealed a novel genome organization and presented evidence of plasmid-borne core genes in bacteria.

The Oecophyllibacter saccharovorans strains Ha5^T, Ta1 and Jb2 were isolated from the guts of weaver ant Oecophylla smaragdina (Chua et al., 2020). These strains were identified as one of the persistent and dominant Acetobacteraceae taxa in bacterial microbiome of O. smaragdina (Chua et al., 2018). We sequenced the genomes of these strains to incorporate their genomic data in a previous polyphasic taxonomic analysis but their plasmid sequences have not been explored (Chua et al., 2020). In this work, we determined that these O. saccharovorans strains were lacking of chromosomal rrn operon but the sole rrn operon detected in these strains was plasmid-borne. As closely related bacteria exhibit similar traits, we included closely related bacterial strains of the O. saccharovorans strains in most analyses and conducted a survey for similar genome organization on validly described family Acetobacteraceae taxa with genomes publicly available. Here, we report the genome architecture of the O. saccharovorans strains and demonstrate that their rrn operon-containing plasmids are the smallest to date.