Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use

Atkins, John F.; Loughran, Gary; Bhatt, Pramod R.; Firth, Andrew E.; Baranov, Pavel V.

ICE (Bacterial Integrative and Conjugative Elements) are the most abundant conjugative DNA elements in bacteria. Naturally occurring non-symbiotic mesorhizobia that receive one of the well-studied elements, 502 kb ICE-MlSymR7A, via conjugation can communicate interactively with the pasture legume commonly known as bird'sfoot trefoil or deervetch (Lotus corniculatus), leading to the formation of bacteroids that fix atmospheric nitrogen into ammonia (200) . Countervailing the potential population benefit of new endosymbiont formation is selection against disadvantageous occurrence to the original host of the element excision. Excision results in circularization and rolling circle replication. The element can be maintained in the multi-copy extrachromosomal state at energetic cost to the host, and in this state it has greater transfer propensity. For the vast majority of cells carrying the ICE element, this cost does not arise since in WT laboratory M. loti strain R7A, the excised state is only observed in 0.06% of log-phase and 6% of stationary phase cells with only ∼3 in 10 million cells acting as transfer donor. A quorum sensing system keeps the process at a very low level but when derepressed excision can occur in 40-100% of cells and the transfer rate can increase 1000-fold. The ICE element encodes components responsible for a complex system of activators and repressors for quorum sensing and also components of the excision system responsive to it (201) . Crucial for excision is a product expressed from genes msi172 and msi171. Plus one ribosomal frameshifting near the 3 end of the msi172 coding sequence causes ribosomes to enter the msi171 ORF and synthesize Frameshifted excision activator, FseA, a master transcriptional activator of the excision system. Perhaps to modulate leaky expression, FseA itself is subject to binding and inhibition by a quorum-sensing antiactivator (202) . This antiactivator's own expression is bimodal so that individual cells are either 'on' of 'off' for propensity for ICE excision. This has been proposed to be part of a 'bet-hedging' strategy in which only a small proportion of cells in a population are sensitive to induction of excision, with potentially deleterious consequences for those cells but potentially beneficial cell population benefits. In this scenario frameshift utilization is part of the scheme for dampening biological noise present in a quorum-sensing auroinduction circuit and ensuring that excision is not spuriously induced. Ramsay, Ronson and colleagues who discovered the frameshifting involved, anticipate that nutrient availability likely contributes to the proportion of cells that enter the 'on' state, with frameshift efficiency being a sensor (201, 202) . Identification of the potential for frameshifting in similar genes in other elements suggests more widespread utilization (202) but the extent of this awaits investigation.