Type II Toxin–Antitoxin Systems in the Unicellular Cyanobacterium Synechocystis sp. PCC 6803

Abstract

Bacterial toxin–antitoxin (TA) systems are genetic elements, which are encoded by plasmid as well as chromosomal loci. They mediate plasmid and genomic island maintenance through post-segregational killing mechanisms but may also have milder effects, acting as mobile stress response systems that help certain cells of a population in persisting adverse growth conditions. Very few cyanobacterial TA system have been characterized thus far. In this work, we focus on the cyanobacterium Synechocystis 6803, a widely used model organism. We expand the number of putative Type II TA systems from 36 to 69 plus seven stand-alone components. Forty-seven TA pairs are located on the chromosome and 22 are plasmid-located. Different types of toxins are associated with various antitoxins in a mix and match principle. According to protein domains and experimental data, 81% of all toxins in Synechocystis 6803 likely exhibit RNase activity, suggesting extensive potential for toxicity-related RNA degradation and toxin-mediated transcriptome remodeling. Of particular interest is the Ssr8013–Slr8014 system encoded on plasmid pSYSG, which is part of a larger defense island or the pSYSX system Slr6056–Slr6057, which is linked to a bacterial ubiquitin-like system. Consequently, Synechocystis 6803 is one of the most prolific sources of new information about these genetic elements.

Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq)

“…In the case of Type II TA systems, both of these components are small proteins (Schuster & Bertram, 2013). Previously, 69 Type II TA systems were predicted for Synechocystis (Kopfmann et al, 2016). While the majority of these proteins are plasmid-localized, consistent with their function in plasmid maintenance, 22 predicted TA systems are encoded in the main chromosome.…”

Integrity and stability of virulence plasmids fromPseudomonas syringaeare modulated by mobile genetic elements and multiple toxin-antitoxin systems

“…To inactivate functionally the TA systems [43] and facilitate plasmid loss, we constructed pRK3C, containing the three antitoxin genes from pPsv48C cloned in pRK415 ( Table 2), and introduced it into UPN827 to neutralise the three corresponding toxins.…”

“…To evaluate the role of TA systems on plasmid maintenance, we proceeded to their functional inactivation, by supplying in trans the cognate antitoxins cloned in the broad-host range vector pRK415; resulting in the neutralization of the toxin by the cloned antitoxin, as described [43]. Antitoxin genes PSPSV_A0043, PSPSV_A0032 and PSPSV_A0020 from pPsv48A were amplified by PCR with their own promoters, cloned into pGEM-T Easy, excised as BamHI or NcoI-SacI (for PSPSV_A0032) fragments, and sequentially cloned into the BamHI, NcoI-SacI and BglII sites of vector pME6041, respectively.…”

Advances in bacterial transcriptome understanding: From overlapping transcription to the excludon concept

“…Therefore, SigB‐activated long mRNA has a dual function by ensuring the repression of motility genes at both transcriptional and post‐transcriptional levels. Additional genomic configurations involving the overlapping of 5′ UTRs from genes with opposite or related functions have been described in several bacteria, indicating that the regulatory mechanism involving overlapping between the long 5′ UTRs of contiguous genes is widespread in bacteria (Cohen et al, ; Kopfmann, Roesch, & Hess, ; Lasa, Toledo‐Arana, & Gingeras, ; Wurtzel et al, ).…”

“…Therefore, SigBactivated long mRNA has a dual function by ensuring the repression of motility genes at both transcriptional and post-transcriptional levels. Additional genomic configurations involving the overlapping of 5′ UTRs from genes with opposite or related functions have been described in several bacteria, indicating that the regulatory mechanism involving overlapping between the long 5′ UTRs of contiguous genes is widespread in bacteria(Cohen et al, 2016;Kopfmann, Roesch, & Hess, 2016;Lasa, Toledo-Arana, & Gingeras, 2012;Wurtzel et al, 2012).The next breakthrough in the field came from the transcriptome analysis of another Gram-positive bacteria, Staphylococcus aureus, which demonstrated that overlapping RNA transcripts are digested genome-wide by the action of the double-stranded endoribonuclease RNase III(Lasa et al, 2011). High-resolution transcriptome mapping was performed by combining the analysis of the total RNA fraction and the RNA fraction shorter than 50 nt.This methodological innovation turned out to be extremely useful for identifying the regions of the genome where overlapping transcription was taking place.…”