Atkinson G C, Tenson T, Hauryliuk V. 2011. The RelA/SpoT homolog (RSH) superfamily: Distribution and functional evolution of ppGpp synthetases and hydrolases across the tree of life. PLoS ONE, 6, e23479.

Barahona E, Navazo A, Gartinez-Granero F, Zea-Bonilla T, Perez-Jimenez R M, Martin M, Rivilla R. 2011. Pseudomonas fluorescens F113 mutant with enhanced competitive colonization ability and improved biocontrol activity against fungal root pathogens. Applied and Environmental Microbiology, 77, 5412–5419.

Belitsky B R, Sonenshein A L. 2011. Roadblock repression of transcription by Bacillus subtilis CodY. Journal of Molecular Biology, 411, 729–743.

Chatnaparat T, Li Z, Korban S S, Zhao Y. 2015. The stringent response mediated by (p)ppGpp is required for virulence of Pseudomonas syringae pv. tomato and its survival on tomato. Molecular Plant-Microbe Interactions, 28, 776–789.

Chilton M D, Currier T C, Farrand S K, Bendich A J, Gordon M P, Nester E W. 1974. Agrobacterium tumefaciens DNA and PS8 bacteriophage DNA not detected in crown gall tumors. Proceedings of the National Academy of Sciences of the United States of America, 71, 3672–3676.

Dalebroux Z D, Svensson S L, Gaynor E C, Swanson M S. 2010. ppGpp conjures bacterial virulence. Microbiology and Molecular Biology Reviews, 74, 171–199.

Dalebroux Z D, Swanson M S. 2012. ppGpp: Magic beyond RNA polymerase. Nature Reviews Microbiology, 10, 203–212.

Dekkers L C, Bloemendaal C J P, De Weger L A, Wijffelman C A, Spaink H P, Lugtenberg B J J. 1998. A two-component system plays an important role in the root-colonizing ability of Pseudomonas fluorescens strain WCS365. Molecular Plant-Microbe Interactions, 11, 45–56.

Huang C, Meng J, Li W, Chen J. 2022. Similar and divergent role of stringent regulator (p)ppGpp and DksA on pleiotropic phenotype of Yersinia enterocolitica. Microbiology Spectrum, 6, e02055–22.

Irving S E, Choudhurg N R, Corrigan R M. 2021. The stringent response and physiological role of (pp)pGpp in bacteria. Nature Reviews Microbiology, 19, 256–271.

Kang H, Lumactud R, Li N, Bell T H, Kim H S, Park S Y, Lee Y H. 2021. Harnessing chemical ecology for environment-friendly crop protection. Phytopathology, 111, 1697–1710.

Keen N T, Tamaki S, Kobayashi D, Trollinger D. 1988. Improved broad-host-range plasmids for DNA cloning in gram-negative bacteria. Gene, 70, 191–197.

King E O, Ward M K, Raney D E. 1954. Two simple media for the demonstration of pyocyanin and fluorescein. Journal of Laboratory and Clinical Medicine, 44, 301–307.

Kuiper I, Bloemberg G V, Noreen S, Thomas-Oates J E, Lugtenberg B J J. 2001. Increased uptake of putrescine in the rhizosphere inhibits competitive root colonization by Pseudomonas fluorescens strain WCS365. Molecular Plant-Microbe Interactions, 14, 1096–1104.

Lemke J J, Durfee T, Gourse R L. 2009. DksA and ppGpp directly regulate transcription of the Escherichia coli flagellar cascade. Molecular Microbiology, 74, 1368–1379.

Liang F, Zhang B, Yang Q, Zhang Y, Zheng D, Zhang L Q, Yan Q, Wu X. 2020. Cyclic-di-GMP regulates the quorum-sensing system and biocontrol activity of Pseudomonas fluorescens 2P24 through the RsmA and RsmE proteins. Applied and Environmental Microbiology, 86, e02016–20.

Magnusson L U, Farewell A, Nyström T. 2005. ppGpp: A global regulator in Escherichia coli. Trends in Microbiology, 13, 236–242.

Mavrodi O V, Mavrodi D V, Weller D M, Thomashow L S. 2006. Role of ptsP, orfT, and sss recombinase genes in root colonization by Pseudomonas fluorescens Q8r1-96. Applied and Environmental Microbiology, 72, 7111–7122.

Miller J H. 1972. Experiments in Molecular Genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

Milon P, Tischenko E, Tomšic J, Caserta E, Folkers G, Teana A L, Rodnima M V, Pon C L, Boelens R, Gualerzi C O. 2006. The nucleotide-binding site of bacterial translation initiation factor 2 (IF2) as a metabolic sensor. Proceeding of the National Academy of Sciences of the United States of America, 103, 13962–13967.

Mitkevich V A, Ermakov A, Kulikova A A, Tankov S, Shyp V, Soosaar A, Tenson T, Makarov A A, Ehrenberg M, Hauryliuk V. 2010. Thermodynamic characterization of ppGpp binding to EF-G or IF2 and of initiator tRNA binding to free IF2 in the presence of GDP, GTP, or ppGpp. Journal of Molecular Biology, 402, 838–846.

Pacios O, Blasco L, Bleriot L, Fernandez-Garcia L, Ambroa A, López M, Bou G, Cantón R, Garcia-Contreras R, Wood T K, Tomás M. 2020. (p)ppGpp and its role in bacterial persistence: New challenges. Antimicrobial Agents and Chemotherapy, 64, e01283–20.

Pomerleau M, Charrron-Lamoureux V, Léonard L, Grenier F, Rodrigue S, Beauregard P B. 2024. Adaptive laboratory evolution reveals regulators involved in repressing biofilm development as key players in Bacillus subtilis root colonization. mSystems, 9, e00843–23.

Ross W, Sanchez-Vazquez P, Chen A Y, Lee J H, Burgos H L, Gourse R L. 2016. ppGpp binding to a site at the RNAP-DksA interface accounts for its dramatic effects on transcription initiation during the stringent response. Molecular Cell, 62, 811–823.

Santoyo G, Urtis-Flores C A, Loeza-Lara P D, Orozco-Mosqueda M C, Glick B R. 2021. Rhizosphere colonization determinants by plant growth-promoting rhizobacteria (PGPR). Biology, 10, 475.

Schneider C A, Rasband W S, Eliceiri K W. 2012. NIH image to ImageJ: 25 years of image analysis. Nature Methods, 9, 671–675.

Schnider-Keel U, Seematter A, Maurhofer M, Blumer C, Duffy B, Gigot-Bonnefoy C, Reimmann C, Notz R, Défago G, Haas D, Keel C. 2000. Autoinduction of 2,4-diacetylphloroglucinol biosynthesis in the biocontrol agent Pseudomonas fluorescens CHA0 and repression by the bacterial metabolites salicylate and pyoluteorin. Journal of Bacteriology, 182, 1215–1225.

Scrima A, Vetter I R, Armengod M E, Wittinghofer A. 2005. The structure of the TrmE GTP-binding protein and its implications for tRNA modification. The EMBO Journal, 24, 23–33.

Sherlock M E, Sudarsan N, Breaker R R. 2018. Riboswitches for the alarmone ppGpp expand the collection of RNA-based signaling systems. Proceedings of the National Academy of Sciences of the United States of America, 115, 6052–6057.

Simons M, Permentire H P, De Weger L A, Wijffelman C A, Lugtenberg B J J. 1997. Amino acid synthesis is necessary for tomato root colonization by Pseudomonas fluorescens strain WCS365. Molecular Plant-Microbe Interactions, 10, 102–106.

Takeuchi K, Yamada K, Haas D. 2012. ppGpp controlled by the Gac/Rsm regulatory pathway sustains biocontrol activity in Pseudomonas fluorescens CHA0. Molecular Plant-Microbe Interactions, 11, 1440–1449.

Wang B, Dai P, Ding D, Rosario A D, Grant R A, Pentelute B L, Laub M T. 2019. Affinity-based capture and identification of protein effectors of the growth regulator ppGpp. Nature Chemical Biology, 15, 141–150.

Wang J, Atolia E, Hua B, Savir Y, Escalante-Chong R, Springer M. 2015. Natural variation in preparation for nutrient depletion reveals a cost-benefit tradeoff. Plos Biology, 13, e1002042.

Wei H L, Wang Y, Zhang L Q, Tang W H. 2004. Identification and characterization of biocontrol bacterial strain 2P24 and CPF-10. Acta Phytopathologica Sinica, 34, 80–85. (in Chinese)

Wei H L, Zhang L Q. 2006. Quorum-sensing system influences root colonization and biological control ability in Pseudomonas fluorescens 2P24. Antonie Van Leeuwenhoek, 89, 267–280.

Weller D M. 1983. Colonization of wheat roots by a fluorescent pseudomonad suppressive to take-all. Phytopathology, 73, 1548–1553.

Yan Q, Wu X G, Wei H L, Wang H M, Zhang L Q. 2009. Differential control of the PcoI/PcoR quorum-sensing system in Pseudomonas fluorescens 2P24 by sigma factor RpoS and the GacS/GacA two-component regulatory system. Microbiological Research, 164, 18–26.

Yang Q, Yan Q, Zhang B, Zhang L Q, Wu X. 2023. Citrate synthase GltA modulates the 2,4-diacetylphloroglucinol biosynthesis of Pseudomonas fluorescens 2P24 and is essential for the biocontrol capacity. Journal of Agricultural and Food Chemistry, 71, 11892–11902.

Yu X, Zhang B, Zhang L Q, Wu, X. 2022. The regulatory network involving PcoR, RsaL, and MvaT coordinates the quorum-sensing system in Pseudomonas fluorescens 2P24. Applied and Environmental Microbiology, 88, e00625–22.

Zhang W, Zhao Z, Zhang B, Wu X G, Ren Z G, Zhang L Q. 2014. Posttranscriptional regulation of 2,4-diacetylphloroglucinol production by GidA and TrmE in Pseudomonas fluorescens 2P24. Applied and Environmental Microbiology, 80, 3972–3981.

Zhang Y, Zborníková E, Rejman D, Gerdes K. 2018a. Novel (p)ppGpp binding and metabolizing proteins of Escherichia coli. mBio, 9, e02188017.

Zhang Y, Zhang B, Wu X, Zhang L Q. 2020. Characterization the role of GacA-dependent small RNAs and RsmA family proteins on 2,4-diacetylphloroglucinol production in Pseudomonas fluorescens 2P24. Microbiological Research, 233, 126391.

Zhang Y, Zhang Y, Zhang B, Wu X, Zhang L Q. 2018b. Effect of carbon sources on production of 2,4-diacetylphloroglucinol in Pseudomonas fluorescens 2P24. Acta Microbiologica Sinica, 58, 1202–1212. (in Chinese)

Zhu M, Dai X. 2023. Stringent response ensures the timely adaptation of bacterial growth to nutrient downshift. Nature Communications, 14, 467.