ppGpp Ribosome Dimerization Model for Bacterial Persister Formation and Resuscitation

Abstract

Stress is ubiquitous for bacteria and converts a subpopulation of cells into a dormant state known as persistence, in which cells are tolerant to antimicrobials. These cells revive rapidly when the stress is removed and are likely the cause of many recurring infections such as those associated with tuberculosis, cystic fibrosis, and Lyme disease. However, how persister cells are formed is not understood well. Here we 5 propose the ppGpp ribosome dimerization persister (PRDP) model in which the alarmone guanosine pentaphosphate/tetraphosphate (henceforth ppGpp) generates persister cells directly by inactivating ribosomes via the ribosome modulation factor (RMF) and the hibernation promoting factor (Hpf). We demonstrate both RMF and HpF increase persistence and reduce single-cell persister resuscitation and that ppGpp has no effect on single-cell persister resuscitation. Hence, a direct connection between ppGpp and 10 persistence is shown.

Phenol-Soluble Modulins Modulate Persister Cell Formation in Staphylococcus aureus

“…Persister cells are a subpopulation of cells that in a state of dormancy have been characterized by low ATP levels ( Conlon et al, 2016 ), reduced membrane potential ( Wang et al, 2018 ), and can be triggered by, for example, toxins ( Wilmaerts et al, 2018 ) or ribosome inactivation ( Song and Wood, 2020 ). We previously demonstrated that persister cells are susceptible to PSMα toxins ( Bojer et al, 2018 ) and, here, this observation has been investigated further.…”

“…Persister cells are subpopulations of cells that, in the absence of mutations, are highly tolerant to antibiotics at concentrations often 100 times greater than the minimum inhibitory concentration (MIC; Fisher et al, 2017 ; Balaban et al, 2019 ). These cells are generally thought to be in a state of dormancy ( Song and Wood, 2020 ) and upon the removal of the antibiotic pressure will revert back to an antibiotic sensitive state. Persister cells may be generated spontaneously or due to environmental stress, such as starvation or drug exposure, and they are formed in both exponential and stationary phase ( Balaban et al, 2019 ).…”

Combatting Persister Cells With Substituted Indoles

“…Instead, we have proposed the simpler ribosome dimerization persister (PRDP) model ( Figure 1A) in which ppGpp generates persister cells directly; i.e., without TA systems, by inactivating ribosomes by converting 70S ribosomes into inactive 100S ribosomes (Song and Wood, 2020b;Wood and Song, 2020). In support of this model, we found (Song and Wood, 2020b) that (i) most ribosomes in persister cells are inactive as 100S ribosomes, (ii) inactivation of RMF, Hpf, and RaiA leads to the formation of fewer persister cells and increases single-cell persister resuscitation substantially, and (iii) single-cell persister resuscitation is not affected by ppGpp levels. This model does not rely on TA systems for persister cell formation as their link to persistence is unconvincing (Conlon, 2016;Goormaghtigh et al, 2018;Pontes and Groisman, 2019).…”

“…Critically, the PRDP model suggests the "phenotypic switch" for persistence is predicated on the number of ribosomes inactivated; hence, only a small subpopulation of stressed cells become persistent since they are the cells with a threshold level of ribosomes inactivated (Song and Wood, 2020a;Wood and Song, 2020); i.e., not all stationary cells are persisters since not all of these cells have a large enough percentage of ribosomes inactivated. The PRDP model is general in that it is applicable to how persister cells form from various stresses since RMF has been shown to increase persistence dramatically in E. coli for myriad stresses including (i) ampicillin (Song and Wood, 2020b), ciprofloxacin (Song and Wood, 2020b), netilmicin (Tkachenko et al, 2017), gentamicin (McKay and Portnoy, 2015), acid (El-Sharoud and Niven, 2007), osmotic stress (Shcherbakova et al, 2015), and nutrient limitation (Yamagishi et al, 1993;Bubunenko et al, 2007). Furthermore, since RMF (Prossliner et al, 2018) and HflX (Basu and Yap, 2017) are conserved in bacteria, and Hpf is distributed in several kingdoms (i.e., prokaryotes and plants) (Akiyama et al, 2018), the PRDP model is probably applicable for the formation of the persister cells of many species.…”

Persister cells resuscitate via ribosome modification by 23S rRNA pseudouridine synthase RluD

“…However, as nutrient deprivation also results in persistence (Kim et al ., ), the subpopulation of cells may become dormant simply by running out of food. In addition, we have proposed a model whereby the alarmone ppGpp (synthesized as a result of myriad stress conditions) directly creates persister cells via ribosome dimerization, without the need of TA systems (Song and Wood, ). Regardless of the mechanism, persistence appears to be primarily an elegantly regulated response to an unfavourable environment (Wood et al ., ).…”