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Table 4 Some examples of less-reported entities (namely in recent reviews), which are relevant in the E. coli stringent response.

From: Stringent response of Escherichia coli: revisiting the bibliome using literature mining

Biological entities Freq (%) Details References
DnaJ - chaperone with DnaK 3.11 Chaperone protein that assists the DnaJ/DnaK/GrpE system of E. coli. The overproduction of ppGpp has shown to induce the accumulation of these chaperones. [68]
ClpB chaperone 1.55 ClpB, together with the DnaJ/DnaK/GrpE chaperone system, is able to resolubilize aggregated proteins. [69]
GroEL-GroES chaperonin complex 0.52 GroEL and GroES are both induced by heat and when ppGpp is overproduced in E. coli. [68]
RuvB - branch migration of Holliday structures; repair helicase 1.55 Component of the RuvABC enzymatic complex that promotes the rescue of stalled (often formed by ppGpp) or broken DNA replication forks in E. coli. [70]
CsrA - carbon storage regulator 1.04 Regulator of carbohydrate metabolism, which activates UvrY, responsible for the transcription of csrB that, in turn, inhibits the CsrA activity. [71]
uvrY 0.52 Encodes the UvrY protein that has been shown to be the cognate response regulator for the BarA sensor protein. This regulator participates in controlling several genes involved in the DNA repair system (e.g. CsrA) and carbon metabolism. [72]
cstA 0.52 Gene encoding the CstA peptide transporter, which expression is induced by carbon starvation and requires the CRP-cAMP transcriptional regulator. The CstA translation is regulated by the CsrA that occludes ribosome binding to the cstA mRNA. [73]
CspD - DNA replication inhibitor 0.52 CspD is a toxin that appears to inhibit the DNA replication. ppGpp is one of the positive factors for the expression of cspD. [74]
FabH - β-ketoacyl-ACP synthase III 0.52 A key enzyme in the initiation of fatty acids biosynthesis that is stringently regulated by ppGpp. [75]
FadR transcriptional dual regulator 1.55 Regulates the fatty acid biosynthesis and fatty acid degradation at the level of transcription. ppGpp has been shown to be also involved in the regulation of these pathways [75]
NtrC-Phosphorylated transcriptional dual regulator 1.04 Regulatory protein involved in the assimilation of nitrogen and in slow growth caused by N-limited condition. It was reported that ppGpp levels increase upon nitrogen starvation. [76]
dps 2.59 Gene encoding the Dps protein that is highly abundant in the stationary-phase and is required for the starvation responses. It was found to be regulated by ppGpp and RpoS. [77, 78]
psiF 2.07 Gene induced during phosphate starvation that has been associated with the accumulation of ppGpp. [41]
chpR 2.07 Encodes the MazE antitoxin, a component of the MazE-MazF system that causes a "programmed cell death" in response to stresses, including starvation. Genes mazE and mazF are located in the E. coli rel operon and are regulated by ppGpp. [79]
mazG 0.52 Encodes the MazG nucleoside pyrophosphohydrolase that limits the detrimental effects of the MazF toxin under nutritional stress conditions. Overexpression of mazG inhibits cell growth and negatively affects accumulation of ppGpp. [80]