Journal of Plant Research

, Volume 130, Issue 4, pp 625–634 | Cite as

Phylogenetic analysis of proteins involved in the stringent response in plant cells

  • Doshun Ito
  • Yuta Ihara
  • Hidenori Nishihara
  • Shinji Masuda
Regular Paper


The nucleotide (p)ppGpp is a second messenger that controls the stringent response in bacteria. The stringent response modifies expression of a large number of genes and metabolic processes and allows bacteria to survive under fluctuating environmental conditions. Recent genome sequencing analyses have revealed that genes responsible for the stringent response are also found in plants. These include (p)ppGpp synthases and hydrolases, RelA/SpoT homologs (RSHs), and the pppGpp-specific phosphatase GppA/Ppx. However, phylogenetic relationship between enzymes involved in bacterial and plant stringent responses is as yet generally unclear. Here, we investigated the origin and evolution of genes involved in the stringent response in plants. Phylogenetic analysis and primary structures of RSH homologs from different plant phyla (including Embryophyta, Charophyta, Chlorophyta, Rhodophyta and Glaucophyta) indicate that RSH gene families were introduced into plant cells by at least two independent lateral gene transfers from the bacterial Deinococcus-Thermus phylum and an unidentified bacterial phylum; alternatively, they were introduced into a proto-plant cell by a lateral gene transfer from the endosymbiotic cyanobacterium followed by gene loss of an ancestral RSH gene in the cyanobacterial linage. Phylogenetic analysis of gppA/ppx families indicated that plant gppA/ppx homologs form an individual cluster in the phylogenetic tree, and show a sister relationship with some bacterial gppA/ppx homologs. Although RSHs contain a plastidial transit peptide at the N terminus, GppA/Ppx homologs do not, suggesting that plant GppA/Ppx homologs function in the cytosol. These results reveal that a proto-plant cell obtained genes for the stringent response by lateral gene transfer events from different bacterial phyla and have utilized them to control metabolism in plastids and the cytosol.


Chloroplast GppA ppGpp pppGpp Ppx RelA/SpoT homolog 



This work was supported in part by JSPS KAKENHI Grant Nos. 16H03280 and 16K14694 to SM.

Supplementary material

10265_2017_922_MOESM1_ESM.pdf (343 kb)
Supplementary material 1 (PDF 342 KB) (110 kb)
Supplementary material 2 (ZIP 110 KB)


  1. Adachi J, Hesegawa M (1996) MOLPHY version 2.3: programs for molecular phylogenetics based on maximum likelihood. Comput Sci Monogr 28:1–150Google Scholar
  2. Albi T, Serrano A (2014) Two exopolyphosphatases with distinct molecular architectures and substrate specificities from the thermophilic green-sulfur bacterium Chlorobium tepidum TLS. Microbiology 160:2067–2078CrossRefPubMedGoogle Scholar
  3. Aravind L, Koonin EV (1998) The HD domain defines a new superfamily of metal-dependent phosphohydrolases. Trends Biochem Sci 23:469–472CrossRefPubMedGoogle Scholar
  4. Atkinson GC, 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:e23479CrossRefPubMedPubMedCentralGoogle Scholar
  5. Brown A, Fernandez IS, Gordiyenko Y, Ramakrishnan V (2016) Ribosome-dependent activation of stringent control. Nature 534:277–280PubMedPubMedCentralGoogle Scholar
  6. Cashel M, Gentry DR, Hernandez VJ, Vinella D (1996) The stringent response. In: Neidhardt FC, Curtiss IR, Ingraham JL et al (eds) Escherichia coli and Salmonella: cellular and molecular biology, 2nd edn. ASM Press, Washington DC, pp 1458–1496Google Scholar
  7. Choi MY, Wang Y, Wong LLY et al (2012) The two PPX-GppA homologues from Mycobacterium tuberculosis have distinct biochemical activities. PLoS One 7:e42561CrossRefPubMedPubMedCentralGoogle Scholar
  8. Dalebroux ZD, Swanson MS (2012) ppGpp: magic beyond RNA polymerase. Nat Rev Microbiol 10:203–212CrossRefPubMedGoogle Scholar
  9. Darriba D, Taboada GL, Doallo R, Posada D (2011) ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27:1164–1165CrossRefPubMedPubMedCentralGoogle Scholar
  10. Givens RM, Lin M-H, Taylor DJ et al (2004) Inducible expression, enzymatic activity, and origin of higher plant homologues of bacterial RelA/SpoT stress proteins in Nicotiana tabacum. J Biol Chem 279:7495–7504CrossRefPubMedGoogle Scholar
  11. Gupta RS, Johari V (1998) Signature sequences in diverse proteins provide evidence of a close evolutionary relationship between the Deinococcus-Thermus group and cyanobacteria. J Mol Evol 46:716–720CrossRefPubMedGoogle Scholar
  12. Hara A, Sy J (1983) Guanosine 5′-triphosphate, 3′-diphosphate 5′-phosphohydrolase. Purification and substrate specificity. J Biol Chem 258:1678–1683PubMedGoogle Scholar
  13. Hauryliuk V, Atkinson GC, Murakami KS et al (2015) Recent functional insights into the role of (p)ppGpp in bacterial physiology. Nat Rev Microbiol 13:298–309CrossRefPubMedPubMedCentralGoogle Scholar
  14. Hogg T, Mechold U, Malke H et al (2004) Conformational antagonism between opposing active sites in a bifunctional RelA/SpoT homolog modulates (p)ppGpp metabolism during the stringent response. Cell 117:57–68CrossRefPubMedGoogle Scholar
  15. Hori K, Maruyama F, Fujisawa T et al (2014) Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation. Nat Commun 5:3978CrossRefPubMedPubMedCentralGoogle Scholar
  16. Ihara Y, Masuda S (2016) Cytosolic ppGpp accumulation induces retarded plant growth and development. Plant Signal Behav 11:e1132966CrossRefPubMedPubMedCentralGoogle Scholar
  17. Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780CrossRefPubMedPubMedCentralGoogle Scholar
  18. Keasling JD, Bertsch L, Kornberg A (1993) Guanosine pentaphosphate phosphohydrolase of Escherichia coli is a long-chain exopolyphosphatase. Proc Natl Acad Sci USA 90:7029–7033CrossRefPubMedPubMedCentralGoogle Scholar
  19. Le SQ, Gascuel O (2008) An improved general amino acid replacement matrix. Mol Biol Evol 25:1307–1320CrossRefPubMedGoogle Scholar
  20. Loveland AB, Bah E, Madireddy R, et al (2016) Ribosome-RelA structures reveal the mechanism of stringent response activation. Elife 5:e17029CrossRefPubMedPubMedCentralGoogle Scholar
  21. Maekawa M, Honoki R, Ihara Y, et al (2015) Impact of the plastidial stringent response in plant growth and stress responses. Nat Plants 1:15167CrossRefPubMedGoogle Scholar
  22. Masuda S (2012) The stringent response in phototrophs. In: Najafpour M (ed) Advances in photosynthesis. In Tech, Rijeka, pp 487–500Google Scholar
  23. Masuda S, Mizusawa K, Narisawa T et al (2008) The bacterial stringent response, conserved in chloroplasts, controls plant fertilization. Plant Cell Physiol 49:135–141CrossRefPubMedGoogle Scholar
  24. Mechold U, Potrykus K, Murphy H et al (2013) Differential regulation by ppGpp versus pppGpp in Escherichia coli. Nucleic Acids Res 41:6175–6189CrossRefPubMedPubMedCentralGoogle Scholar
  25. Mitchell A, Chang H-Y, Daugherty L et al (2014) The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res 43:D213–D221CrossRefPubMedPubMedCentralGoogle Scholar
  26. Mittenhuber G (2001) Comparative genomics and evolution of genes encoding bacterial (p)ppGpp synthetases/hydrolases (the Rel, RelA and SpoT proteins). J Mol Microbiol Biotechnol 3:585–600PubMedGoogle Scholar
  27. Mizusawa K, Masuda S, Ohta H (2008) Expression profiling of four RelA/SpoT-like proteins, homologues of bacterial stringent factors, in Arabidopsis thaliana. Planta 228:553–562CrossRefPubMedGoogle Scholar
  28. Potrykus K, Cashel M (2008) (p)ppGpp: still magical? Annu Rev Microbiol 62:35–51CrossRefPubMedGoogle Scholar
  29. Price DC, Chan CX, Yoon HS et al (2012) Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. Science 335:843–847CrossRefPubMedGoogle Scholar
  30. Rambaut A, Suchard M, Drummond A (2013) Tracer v1.6. Accessed 14 Mar 2017
  31. Ronquist F, Teslenko M, van der Mark P, et al (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61:539–542CrossRefPubMedPubMedCentralGoogle Scholar
  32. Shimodaira H, Hasegawa M (2001) CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246–1247CrossRefPubMedGoogle Scholar
  33. Stamatakis A (2014) RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313CrossRefPubMedPubMedCentralGoogle Scholar
  34. Suzuki K, Miyagishima S (2010) Eukaryotic and eubacterial contributions to the establishment of plastid proteome estimated by large-scale phylogenetic analyses. Mol Biol Evol 27:581–590CrossRefPubMedGoogle Scholar
  35. Tozawa Y, Nomura Y (2011) Signalling by the global regulatory molecule ppGpp in bacteria and chloroplasts of land plants. Plant Biol (Stuttg) 13:699–709CrossRefGoogle Scholar
  36. Tozawa Y, Nozawa A, Kanno T et al (2007) Calcium-activated (p)ppGpp synthetase in chloroplasts of land plants. J Biol Chem 282:35536–35545CrossRefPubMedGoogle Scholar
  37. van der Biezen EA, Sun J, Coleman MJ, et al (2000) Arabidopsis RelA/SpoT homologs implicate (p)ppGpp in plant signaling. Proc Natl Acad Sci 97:3747–3752CrossRefPubMedPubMedCentralGoogle Scholar
  38. Wendrich TM, Marahiel MA (1997) Cloning and characterization of a relA/spoT homologue from Bacillus subtilis. Mol Microbiol 26:65–79CrossRefPubMedGoogle Scholar

Copyright information

© The Botanical Society of Japan and Springer Japan 2017

Authors and Affiliations

  • Doshun Ito
    • 1
  • Yuta Ihara
    • 1
  • Hidenori Nishihara
    • 1
  • Shinji Masuda
    • 2
    • 3
  1. 1.Graduate School of Bioscience and BiotechnologyTokyo Institute of TechnologyYokohamaJapan
  2. 2.Center for Biological Resources and InformaticsTokyo Institute of TechnologyYokohamaJapan
  3. 3.Earth-Life Science InstituteTokyo Institute of TechnologyTokyoJapan

Personalised recommendations