Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Plant commensal type VII secretion system causes iron leakage from roots to promote colonization

Nature Microbiology volume 8, pages 1434–1449 (2023)Cite this article

Subjects

Abstract

Competition for iron is an important factor for microbial niche establishment in the rhizosphere. Pathogenic and beneficial symbiotic bacteria use various secretion systems to interact with their hosts and acquire limited resources from the environment. Bacillus spp. are important plant commensals that encode a type VII secretion system (T7SS). However, the function of this secretion system in rhizobacteria–plant interactions is unclear. Here we use the beneficial rhizobacterium Bacillus velezensis SQR9 to show that the T7SS and the major secreted protein YukE are critical for root colonization. In planta experiments and liposome-based experiments demonstrate that secreted YukE inserts into the plant plasma membrane and causes root iron leakage in the early stage of inoculation. The increased availability of iron promotes root colonization by SQR9. Overall, our work reveals a previously undescribed role of the T7SS in a beneficial rhizobacterium to promote colonization and thus plant–microbe interactions.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Contribution of the B. velezensis SQR9 tT7SS to root colonization.
Fig. 2: Effect of the SQR9-derived strain and YukE on plant iron content.
Fig. 3: YukE-mediated root iron leakage contributes to root colonization by SQR9.
Fig. 4: YukE function and location on the surface of 15-day-old Arabidopsis cells.
Fig. 5: Insertion of YukE into the plant plasma membrane.
Fig. 6: Comparison of the function of the T7SS and the siderophore-Feu system in B. velezensis SQR9.

Similar content being viewed by others

Data availability

Raw data for the plant RNA-seq have been deposited in the Sequence Read Archive (SRA) with the accession number PRJNA649312. Summary data for strains, plasmids and oligonucleotides used in this study can be found in Supplementary Tables 4 and 5. The crystal form of Geobacillus thermodenitrificans EsxA could be download with PDB identifier: 3ZBH (https://www.rcsb.org/structure/3ZBH). Other data supporting the findings of the present study are available within the paper, in Extended Data and the Supplementary Information. Source data are provided with this paper.

References

  1. Arnaouteli, S., Bamford, N. C., Stanley-Wall, N. R. & Kovács, Á. T. Bacillus subtilis biofilm formation and social interactions. Nat. Rev. Microbiol. 19, 600–614 (2021).

    CAS  PubMed  Google Scholar 

  2. De Coninck, B., Timmermans, P., Vos, C., Cammue, B. P. A. & Kazan, K. What lies beneath: belowground defense strategies in plants. Trends Plant Sci. 20, 91–101 (2015).

    PubMed  Google Scholar 

  3. Haas, D. & Défago, G. Biological control of soil-borne pathogens by fluorescent pseudomonads. Nat. Rev. Microbiol. 3, 307–319 (2005).

    CAS  PubMed  Google Scholar 

  4. Lugtenberg, B. J. J. J., Dekkers, L. & Bloemberg, G. V. Molecular determinants of rhizosphere colonization by Pseudomonas. Annu. Rev. Phytopathol. 39, 461–490 (2001).

    CAS  PubMed  Google Scholar 

  5. Bulgarelli, D., Schlaeppi, K., Spaepen, S., van Themaat, E. V. L. & Schulze-Lefert, P. Structure and functions of the bacterial microbiota of plants. Annu. Rev. Plant Biol. 64, 807–838 (2013).

    CAS  PubMed  Google Scholar 

  6. Siddiqui, Z. A. (Ed) in PGPR: Biocontrol and Biofertilization 111–142 (Springer, 2006).

  7. Philippot, L., Raaijmakers, J. M., Lemanceau, P. & van der Putten, W. H. Going back to the roots: the microbial ecology of the rhizosphere. Nat. Rev. Microbiol. 11, 789–799 (2013).

    CAS  PubMed  Google Scholar 

  8. Pieterse, C. M. J. et al. Induced systemic resistance by beneficial microbes. Annu. Rev. Phytopathol. 52, 347–375 (2014).

    CAS  PubMed  Google Scholar 

  9. Harbort, C. J. et al. Root-secreted coumarins and the microbiota interact to improve iron nutrition in Arabidopsis. Cell Host Microbe 28, 825–837 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Verbon, E. H. et al. Iron and immunity. Annu. Rev. Phytopathol. 55, 355–375 (2017).

    CAS  PubMed  Google Scholar 

  11. Herlihy, J. H., Long, T. A. & McDowell, J. M. Iron homeostasis and plant immune responses: recent insights and translational implications. J. Biol. Chem. 295, 13444–13457 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Xu, Z. et al. Antibiotic bacillomycin D affects iron acquisition and biofilm formation in Bacillus velezensis through a Btr-mediated FeuABC-dependent pathway. Cell Rep. 29, 1192–1202.e5 (2019).

    CAS  PubMed  Google Scholar 

  13. Chang, J. H., Desveaux, D. & Creason, A. L. The ABCs and 123s of bacterial secretion systems in plant pathogenesis. Annu. Rev. Phytopathol. 52, 317–345 (2014).

    CAS  PubMed  Google Scholar 

  14. Costa, T. R. D. et al. Secretion systems in Gram-negative bacteria: structural and mechanistic insights. Nat. Rev. Microbiol. 13, 343–359 (2015).

    CAS  PubMed  Google Scholar 

  15. Abdallah, A. M. et al. Type VII secretion — Mycobacteria show the way. Nat. Rev. Microbiol. 5, 883–891 (2007).

    CAS  PubMed  Google Scholar 

  16. Conrad, W. H. et al. Mycobacterial ESX-1 secretion system mediates host cell lysis through bacterium contact-dependent gross membrane disruptions. Proc. Natl Acad. Sci. USA 114, 1371–1376 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. De Leon, J. et al. Mycobacterium tuberculosis ESAT-6 exhibits a unique membrane-interacting activity that is not found in its ortholog from non-pathogenic Mycobacterium smegmatis. J. Biol. Chem. 287, 44184–44191 (2012).

    PubMed  PubMed Central  Google Scholar 

  18. Zhang, Q., Aguilera, J., Reyes, S. V. & Sun, J. Membrane insertion of Mycobacterium tuberculosis EsxA in cultured lung epithelial cells. Preprint at bioRxiv https://doi.org/10.1101/2020.04.09.035238 (2020).

  19. Baptista, C., Barreto, H. C. & São-José, C. High levels of DegU-P activate an Esat-6-like secretion system in Bacillus subtilis. PLoS ONE 8, e67840 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Huppert, L. A. et al. The ESX system in Bacillus subtilis mediates protein secretion. PLoS ONE 9, e96267 (2014).

    PubMed  PubMed Central  Google Scholar 

  21. Sysoeva, T. A., Zepeda-Rivera, M. A., Huppert, L. A. & Burton, B. M. Dimer recognition and secretion by the ESX secretion system in Bacillus subtilis. Proc. Natl Acad. Sci. USA 111, 7653–7658 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Li, Y. et al. Volatile compounds from beneficial rhizobacteria Bacillus spp. promote periodic lateral root development in Arabidopsis. Plant Cell Environ. 44, 1663–1678 (2021).

    CAS  PubMed  Google Scholar 

  23. Liu, Y. et al. Identification of root-secreted compounds involved in the communication between cucumber, the beneficial Bacillus amyloliquefaciens, and the soil-borne pathogen Fusarium oxysporum. Mol. Plant Microbe Interact. 30, 53–62 (2017).

    CAS  PubMed  Google Scholar 

  24. Zhang, H. et al. Bacillus velezensis tolerance to the induced oxidative stress in root colonization contributed by the two-component regulatory system sensor ResE. Plant Cell Environ. 44, 3094–3102 (2021).

    CAS  PubMed  Google Scholar 

  25. Xiong, Q. et al. Quorum sensing signal autoinducer-2 promotes root colonization of Bacillus velezensis SQR9 by affecting biofilm formation and motility. Appl. Microbiol. Biotechnol. 104, 7177–7185 (2020).

    CAS  PubMed  Google Scholar 

  26. Liu, Y. et al. Induced root-secreted d-galactose functions as a chemoattractant and enhances the biofilm formation of Bacillus velezensis SQR9 in an McpA-dependent manner. Appl. Microbiol. Biotechnol. 104, 785–797 (2020).

    CAS  PubMed  Google Scholar 

  27. Dong, X. et al. Synthesis and detoxification of nitric oxide in the plant beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 and its effect on biofilm formation. Biochem. Biophys. Res. Commun. 503, 784–790 (2018).

    CAS  PubMed  Google Scholar 

  28. Liu, Y. et al. Root-secreted spermine binds to Bacillus amyloliquefaciens SQR9 histidine kinase KinD and modulates biofilm formation. Mol. Plant Microbe Interact. 33, 423–432 (2020).

    CAS  PubMed  Google Scholar 

  29. Colangelo, E. P. & Guerinot, M. L. The essential basic helix-loop-helix protein FIT1 is required for the iron deficiency response. Plant Cell 16, 3400–3412 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Trapet, P. L. et al. Mechanisms underlying iron deficiency-induced resistance against pathogens with different lifestyles. J. Exp. Bot. 72, 2231–2241 (2021).

    CAS  PubMed  Google Scholar 

  31. Hsiao, P. Y., Cheng, C. P., Koh, K. W. & Chan, M. T. The Arabidopsis defensin gene, AtPDF1.1, mediates defence against Pectobacterium carotovorum subsp. carotovorum via an iron-withholding defence system. Sci. Rep. 7, 9175 (2017).

  32. Xing, Y. et al. Bacterial effector targeting of a plant iron sensor facilitates iron acquisition and pathogen colonization. Plant Cell 33, 2015–2031 (2021).

    PubMed  PubMed Central  Google Scholar 

  33. Dangol, S., Chen, Y., Hwang, B. K. & Jwa, N. S. Iron- and reactive oxygen species-dependent ferroptotic cell death in rice–Magnaporthe oryzae interactions. Plant Cell 31, 189–209 (2019).

    CAS  PubMed  Google Scholar 

  34. Sun, L. et al. Restriction of iron loading into developing seeds by a YABBY transcription factor safeguards successful reproduction in Arabidopsis. Mol. Plant 14, 1624–1639 (2021).

    CAS  PubMed  Google Scholar 

  35. Pescador, L. et al. Nitric oxide signalling in roots is required for MYB72-dependent systemic resistance induced by Trichoderma volatile compounds in Arabidopsis. J. Exp. Bot. 73, 584–595 (2022).

    CAS  PubMed  Google Scholar 

  36. Yu, K. et al. Rhizosphere-associated Pseudomonas suppress local root immune responses by gluconic acid-mediated lowering of environmental pH. Curr. Biol. 29, 3913–3920.e4 (2019).

    CAS  PubMed  Google Scholar 

  37. Zamioudis, C., Hanson, J. & Pieterse, C. M. J. ß-glucosidase BGLU42 is a MYB72-dependent key regulator of rhizobacteria-induced systemic resistance and modulates iron deficiency responses in Arabidopsis roots. New Phytol. 204, 368–379 (2014).

    CAS  PubMed  Google Scholar 

  38. Zamioudis, C. et al. Rhizobacterial volatiles and photosynthesis-related signals coordinate MYB72 expression in Arabidopsis roots during onset of induced systemic resistance and iron-deficiency responses. Plant J. 84, 309–322 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Ma, Y., Keil, V. & Sun, J. Characterization of Mycobacterium tuberculosis EsxA membrane insertion: roles of N- and C-terminal flexible arms and central helix-turn-helix motif. J. Biol. Chem. 290, 7314–7322 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Gröschel, M. I., Sayes, F., Simeone, R., Majlessi, L. & Brosch, R. ESX secretion systems: mycobacterial evolution to counter host immunity. Nat. Rev. Microbiol. 14, 677–691 (2016).

    PubMed  Google Scholar 

  41. Refai, A. et al. Two distinct conformational states of Mycobacterium tuberculosis virulent factor early secreted antigenic target 6 kDa are behind the discrepancy around its biological functions. FEBS J. 282, 4114–4129 (2015).

    CAS  PubMed  Google Scholar 

  42. Casabona, M. G. et al. Functional analysis of the EsaB component of the Staphylococcus aureus type VII secretion system. Microbiology 163, 1851–1863 (2017).

    PubMed  PubMed Central  Google Scholar 

  43. Isaac, D. T., Laguna, R. K., Valtz, N. & Isberg, R. R. MavN is a Legionella pneumophila vacuole-associated protein required for efficient iron acquisition during intracellular growth. Proc. Natl Acad. Sci. USA 112, E5208–E5217 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Ravet, K. et al. Ferritins control interaction between iron homeostasis and oxidative stress in Arabidopsis. Plant J. 57, 400–412 (2009).

    CAS  PubMed  Google Scholar 

  45. Khan, A., Singh, P. & Srivastava, A. Synthesis, nature and utility of universal iron chelator – siderophore: a review. Microbiol. Res. 212–213, 103–111 (2018).

    PubMed  Google Scholar 

  46. Kremer, J. M. et al. Peat-based gnotobiotic plant growth systems for Arabidopsis microbiome research. Nat. Protoc. 16, 2450–2470 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Feng, H. et al. Identification of chemotaxis compounds in root exudates and their sensing chemoreceptors in plant-growth-promoting rhizobacteria Bacillus amyloliquefaciens SQR9. Mol. Plant Microbe Interact. 31, 995–1005 (2018).

    CAS  PubMed  Google Scholar 

  48. Bulgarelli, D. et al. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488, 91–95 (2012).

    CAS  PubMed  Google Scholar 

  49. Qiu, M. et al. De-coupling of root–microbiome associations followed by antagonist inoculation improves rhizosphere soil suppressiveness. Biol. Fertil. Soils 50, 217–224 (2014).

    CAS  Google Scholar 

  50. Inoue, T. et al. Genome-wide screening of genes required for swarming motility in Escherichia coli K-12. J. Bacteriol. 189, 950–957 (2007).

    CAS  PubMed  Google Scholar 

  51. De Meutter, J. & Goormaghtigh, E. Protein structural denaturation evaluated by MCR-ALS of protein microarray FTIR spectra. Anal. Chem. 93, 13441–13449 (2021).

    PubMed  Google Scholar 

  52. Liu, F., Shah, D. S. & Gadd, G. M. Role of protein in fungal biomineralization of copper carbonate nanoparticles. Curr. Biol. 31, 358–368.e3 (2021).

    PubMed  Google Scholar 

  53. Cai, S. & Singh, B. R. A distinct utility of the amide III infrared band for secondary structure estimation of aqueous protein solutions using partial least squares methods. Biochemistry 43, 2541–2549 (2004).

    CAS  PubMed  Google Scholar 

  54. Lei, G. J. et al. Abscisic acid alleviates iron deficiency by promoting root iron reutilization and transport from root to shoot in Arabidopsis. Plant Cell Environ. 37, 852–863 (2014).

    CAS  PubMed  Google Scholar 

  55. Huang, D. W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44–57 (2009).

    CAS  PubMed  Google Scholar 

  56. Sherman, B. T. et al. DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update). Nucleic Acids Res. 50, W216–W221 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  57. Wei, H. L., Chakravarthy, S., Worley, J. N. & Collmer, A. Consequences of flagellin export through the type III secretion system of Pseudomonas syringae reveal a major difference in the innate immune systems of mammals and the model plant Nicotiana benthamiana. Cell. Microbiol. 15, 601–618 (2013).

    CAS  PubMed  Google Scholar 

  58. Emonet, A. et al. Spatially restricted immune responses are required for maintaining root meristematic activity upon detection of bacteria. Curr. Biol. 31, 1012–1028.e7 (2021).

    CAS  PubMed  Google Scholar 

  59. Oroz, J. et al. Structure and pro-toxic mechanism of the human Hsp90/PPIase/Tau complex. Nat. Commun. 9, 4532 (2018).

    PubMed  PubMed Central  Google Scholar 

  60. Yavlovich, A., Singh, A., Blumenthal, R. & Puri, A. A novel class of photo-triggerable liposomes containing DPPC:DC 8,9PC as vehicles for delivery of doxorubcin to cells. Biochim. Biophys. Acta 1808, 117–126 (2011).

    CAS  PubMed  Google Scholar 

  61. Chen, D. et al. S-acylation of P2K1 mediates extracellular ATP-induced immune signaling in Arabidopsis. Nat. Commun. 12, 2750 (2021).

  62. Atakpa, P., Thillaiappan, N. B., Mataragka, S., Prole, D. L. & Taylor, C. W. IP3 receptors preferentially associate with ER-lysosome contact sites and selectively deliver Ca2+ to lysosomes. Cell Rep. 25, 3180–3193.e7 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. Cao, Z., Casabona, M. G., Kneuper, H., Chalmers, J. D. & Palmer, T. The type VII secretion system of Staphylococcus aureus secretes a nuclease toxin that targets competitor bacteria. Nat. Microbiol. 2, 16183 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This work was funded by the National Natural Science Foundation of China (32070104, Y.L.), the National Natural Science Foundation of China (32172661, R.Z.), the National Key Research and Development Programme (2022YFF1001804, R.Z.), the National Key Research and Development Program (2021YFF1000400, Y.L. and R.Z.), the Central Public-interest Scientific Institution Basal Research Fund (No. Y2022QC15, Y.L.), and the Agricultural Science and Technology Innovation Program (CAAS-ZDRW202308, Y.L.). We thank H. Wei and J. Li of the Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, for providing the strains and plasmid used in the Agrobacterium-mediated transient expression experiment; and X. Shen of the College of Life Sciences, Northwest A&F University, for help with editing the manuscript.

Author information

Author notes

  1. These authors contributed equally to this study: Yunpeng Liu, Xia Shu, Lin Chen.

Authors and Affiliations

  1. State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China (the Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China

    Yunpeng Liu, Xia Shu, Xiting Sun, Qin Xiong, Guangqi Li & Ruifu Zhang

  2. Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, P.R. China

    Xia Shu, Huihui Zhang, Haichao Feng, Weibing Xun, Zhihui Xu, Nan Zhang, Qirong Shen & Ruifu Zhang

  3. State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China

    Xia Shu

  4. Experimental Center of Forestry in North China, Chinese Academy of Forestry, Beijing, P. R. China

    Lin Chen

  5. Plant-Microbe Interactions, Department of Biology, Utrecht University, Utrecht, the Netherlands

    Corné M. J. Pieterse

Authors
  1. Yunpeng Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xia Shu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Lin Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Huihui Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Haichao Feng
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Xiting Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Qin Xiong
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Guangqi Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Weibing Xun
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Zhihui Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Nan Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Corné M. J. Pieterse
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Qirong Shen
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Ruifu Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Y.L. and R.Z. conceptualized the project; X. Shu, L.C. and G.L conducted formal analysis; Y.L., X. Shu, L.C., H.Z. and X. Sun conducted the investigation; H.F. and Q.X. performed verification; Y.L. and L.C. wrote the original draft; L.C., C.M.J.P. and R.Z. reviewed and edited the paper; X. Shu, W.X. and Z.X. performed visualization; Y.L., C.M.J.P. and R.Z. supervised the work; N.Z. and Q.S. administered the project; Y.L. and R.Z acquired funding. All authors read and approved the submitted version.

Corresponding authors

Correspondence to Yunpeng Liu or Ruifu Zhang.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Microbiology thanks Edith Houben and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 Colonization of roots of Arabidopsis and cucumber grown in soil.

WT and the derived strains were introduced with gfp fragments in their genomes for specific detection by qPCR in soil. Bacteria were inoculated to a final concentration of 107 cells/mL. DNA of the rhizosphere soil was extracted at 2 days post-inoculation. qRT‒PCR was used to measure the copies of the gfp fragment. (A) The gnotobiotic FlowPot device was used to grow Arabidopsis in soil. (B-D) Root colonization of Arabidopsis grown in sterile soil (B), in sterile soil with a microbial community extracted from natural soil (C) and in natural soil (D). Ferrozine and excess iron were supplied at the mean time of inoculation at final concentrations of 300 μM and 180 μM, respectively, when necessary. (E) Root colonization of cucumber grown in natural soil. Fifteen-day-old Arabidopsis Col-0 plants and 21-day-old cucumber plants were used for the colonization assay. Error bars indicate the standard errors. Three replicates were included for each strain. Different letters above the column indicate significant differences (two-side one-way ANOVA or two-way ANOVA with Duncan’s multiple-range tests, α = 0.05, for (B C and E): P < 0.001, P < 0.001, P < 0.001, for the two-way ANOVA in (D), P < 0.001, for the one-way ANOVA in (D), from left to right, P < 0.001, P < 0.001, P < 0.001).

Source data

Extended Data Fig. 2 Effect of the B. velezensis SQR9 type VII secretion system (T7SS) on the transcription of iron acquisition genes in 15-day-old Arabidopsis.

(A) Functional enrichment of the DEGs in the YukE treatment but not in the heat-treated YukE treatment. Briefly, 5 μM purified YukE or heat-treated YukE was added to the plant medium, and RNA-seq was performed at 1 h, 3 h, 6 h and 24 h post-treatment. The FPKM value of each gene in the YukE or heat-treated YukE treatment was compared with that of untreated plants to identify the DEGs. Then, DEGs in the YukE and heat-treated YukE treatments were compared to identify the DEGs present in the YukE treatment but not in the heat-treated YukE treatment. These DEGs were then subjected to functional enrichment analysis using DAVID (https://david.ncifcrf.gov). (B) The iron acquisition pathway in Arabidopsis. (C-E) Relative expression of FIT (C), IRT1 (D), and FRO2 (E) in 15-day-old Arabidopsis roots in response to wild-type B. velezensis SQR9 and the mutants DT7, DyukE and DT7E measured by qRT–PCR. CK indicates the untreated plant. Roots were harvested at 3, 6 and 24 h post-inoculation, respectively. Actin served as a reference. Data are presented as mean values +/- SEM (n = 3). Different letters above the column indicate significant differences (two-side one-way ANOVA or two-way ANOVA with Duncan’s multiple-range tests, α = 0.05, for one-way ANOVA in (C-E), P = 0.258, P = 0.001, P < 0.001, P = 0.560, P = 0.003, P = 0.008, P = 0.307, P = 0.009, P < 0.001, for all the two-way ANOVA in (C-E), P < 0.001). This experiment was repeated three times with similar results.

Source data

Extended Data Fig. 3 YukE enhances the growth-promoting effect of B. velezensis SQR9 on cucumber.

CK indicates the untreated plant. Cucumber was inoculated by dipping the root into a cell suspension (107 cells/mL) with or without 5 μM YukE for 1 day before transplanting into soil. Data are presented as mean values +/- SEM (n = 10). Different letters above the column indicate significant differences (two-side one-way ANOVA with Duncan’s multiple-range tests, α = 0.05, P < 0.001). This experiment was repeated twice with similar results.

Source data

Extended Data Fig. 4 Model for the role of YukE in the decrease in root iron content.

The predicted structure of YukE consists of two helices with a helix-turn-helix motif (WXG motif). The protein was structured as a dimer in vivo and in vitro. The length of the protein is 10.1 Å. The thickness of the phospholipid bilayer is approximately 10 Å. YukE may be inserted into the phospholipid bilayer to cause iron leakage from root cells.

Extended Data Fig. 5

Model of T7SS function in the interaction of B. velezensis SQR9 and plant cells.

Extended Data Fig. 6 Protein structures of YukE and EsxA.

(A-C) Structure of the YukE homodimer built by Swiss-model using EsxA of M. tuberculosis as the template. The polarity of the residues is colored. Red indicates a higher polarity calculated by PyMOL (V. 2.4.1). (D-F) Asymmetric unit of EsxA from Geobacillus thermodenitrificans. Different colors indicate different molecules.

Supplementary information

Supplementary information

Supplementary Figs. 1–19.

Reporting Summary

Supplementary Table

Supplementary Tables 1–5.

Source data

Source Data Fig. 1

Statistical source data and unprocessed western blots.

Source Data Fig. 1

Statistical source data and unprocessed western blots.

Source Data Fig. 2

Statistical source data.

Source Data Fig. 3

Statistical source data.

Source Data Fig. 5

Statistical source data.

Source Data Fig. 6

Statistical source data.

Source Data Extended Data Fig. 1

Statistical source data.

Source Data Extended Data Fig. 2

Statistical source data.

Source Data Extended Data Fig. 3

Statistical source data.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Liu, Y., Shu, X., Chen, L. et al. Plant commensal type VII secretion system causes iron leakage from roots to promote colonization. Nat Microbiol 8, 1434–1449 (2023). https://doi.org/10.1038/s41564-023-01402-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41564-023-01402-1

This article is cited by

Search

Advanced search

Quick links

Nature Briefing Microbiology

Sign up for the Nature Briefing: Microbiology newsletter — what matters in microbiology research, free to your inbox weekly.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing: Microbiology