Persistence is a transient and non-inheritable tolerance to antibiotics by a small fraction of a bacterial population. One of the proposed determinants of bacterial persistence is Toxin-Antitoxin systems (TAS) which are also implicated in a wide range of stress-related phenomena. In a report (Maisonneuve E, Castro-Camargo M, Gerdes K. 2013. Cell 154:1140-1150) an interesting link between ppGpp mediated stringent response, TAS and persistence is proposed. It is proposed that accumulation of ppGpp enhances the accumulation of inorganic polyphosphate which modulates Lon protease to degrade antitoxins. The decrease in the concentration of antitoxins supposedly activated the toxin to increase in the number of persisters during antibiotic treatment. In this study, we show that inorganic polyphosphate is not required for Lon-dependent degradation of YefM, the antitoxin of YefM/YoeB TAS. The Δ10 strain, an Escherichia coli MG1655 derivative in which the ten TAS are deleted, is more sensitive to Ciprofloxacin and Ampicillin compared to wild-type MG1655. Furthermore, we show that the Δ10 strain has relatively lower fitness compared to the wild type and hence, we argue that the implications based on this strain are void. We conclude that there is no direct and specific link between stringent response and the regulation of TAS. The link between TAS and persistence is inconclusive due to altered fitness of Δ10 strain and hence requires thorough inspection and debate.