Insights into the strategies used by related group II introns to adapt successfully for the colonisation of a bacterial genome

Abstract

Abbreviations: IEP, intron encoded protein; RNP, ribonucleoprotein; EBS, exon binding site; IBS, intron binding site;RT, reverse transcriptaseGroup II introns are self-splicing RNAs and site-specific mobile retroelements found in bacterial and organellar genomes. The group II intron RmInt1 is present at high copy number in Sinorhizobium meliloti species, and has a multifunctional intron-encoded protein (IEP) with reverse transcriptase/maturase activities, but lacking the DNA-binding and endonuclease domains. We characterized two RmInt1-related group II introns RmInt2 from S. meliloti strain GR4 and Sr.md.I1 from S. medicae strain WSM419 in terms of splicing and mobility activities. We used both wild-type and engineered intron-donor constructs based on ribozyme DORF-coding sequence derivatives, and we determined the DNA target requirements for RmInt2, the element most distantly related to RmInt1. The excision and mobility patterns of intron-donor constructs expressing different combinations of IEP and intron RNA provided experimental evidence for the co-operation of IEPs and intron RNAs from related elements in intron splicing and, in some cases, in intron homing. We were also able to identify the DNA target regions recognized by these IEPs lacking the DNA endonuclease domain. Our results provide new insight into the versatility of related group II introns and the possible co-operation between these elements to facilitate the colonization of bacterial genomes.

The mitochondrial genome of Endoconidiophora resinifera is intron rich

“…Another category of introns is represented by those that appear to have invaded new sites within the same genome 60 , a temporary means of escaping the Goddard and Burt 27 HEG lifecycle of invasion, decay and eventual loss. Related introns present within the same genome may still interact in trans in some collaborative fashion rendering them less prone to extinction 61 , 62 . Some intron encoded proteins (IEPs) can also act as maturases that facilitate the intron RNA to fold into a splicing-competent configuration 29 .…”

DNA cleavage and reverse splicing of ribonucleoprotein particles reconstitutedin vitrowith linear RmInt1 RNA

“…The RmInt1 RNP complex containing the lariat intron recognizes the DNA target site via both its RNA and protein components [36,37]. In particular, the RNA component base-pairs via its EBS sequences to nucleotide residues in the 5´and 3´exons (mostly at positions −13 to +1 relative to the intron insertion site), whereas the IEP interacts with distal positions in the 5´exon (T −15 nucleotide).…”

Contribution of Mobile Group II Introns to Sinorhizobium meliloti Genome Evolution

“…RmInt1 is widespread in S. meliloti ( Muñoz et al, 2001 ) and was first described in the GR4 strain ( Martínez-Abarca et al, 1998 ), which contains 10 copies of RmInt1 ( Martínez-Abarca et al, 2013 ) distributed between the different replicons [four copies on the chromosome, five copies on pRmeGR4c (pSymA), and one copy on the accessory plasmid pRmeGR4b]. This bacterial strain also harbors a closely related mobile intron called RmInt2 ( Martínez-Rodríguez et al, 2014 ). RmInt2 also belongs to class D, it has a nucleotide sequence 72% identical to that of RmInt1, and it is present in seven copies (four copies on pSymA and three on pSymB).…”

“…Group II introns are highly flexible in terms of their ability to colonize the S. meliloti genome ( Nisa-Martínez et al, 2007 ). For example, RmInt2 has a lower retrohoming efficiency than RmInt1, and a greater probability of survival and spread in the genome through the relaxation of target-site specificity using the left and right inverted repeats of IS Rm17 as DNA targets ( Figure 2 ), thereby ensuring that at least one of its targets is on the template of the lagging strand during DNA replication ( Martínez-Rodríguez et al, 2014 ). The spread, gain, and losses of these IS elements not carrying adaptive traits likely impose costs on their hosts in the short term, particularly when their copy number increases, generating a source of genetic instability and a burden for the cell replication machinery ( Rankin et al, 2011 ).…”