Archives of Microbiology

, Volume 201, Issue 2, pp 171–183 | Cite as

Revealing the roles of y4wF and tidC genes in Rhizobium tropici CIAT 899: biosynthesis of indolic compounds and impact on symbiotic properties

  • Leandro Datola Tullio
  • André Shigueyoshi Nakatani
  • Douglas Fabiano Gomes
  • Francisco Javier Ollero
  • Manuel Megías
  • Mariangela HungriaEmail author
Original Paper


Rhizobium tropici CIAT 899 is a strain known by its ability to nodulate a broad range of legume species, to synthesize a variety of Nod factors, its tolerance of abiotic stresses, and its high capacity to fix atmospheric N2, especially in symbiosis with common bean (Phaseolus vulgaris L.). Genes putatively related to the synthesis of indole acetic acid (IAA) have been found in the symbiotic plasmid of CIAT 899, in the vicinity of the regulatory nodulation gene nodD5, and, in this study, we obtained mutants for two of these genes, y4wF and tidC (R. tropiciindole-3-pyruvic acid decarboxylase), and investigated their expression in the absence and presence of tryptophan (TRP) and apigenin (API). In general, mutations of both genes increased exopolysaccharide (EPS) synthesis and did not affect swimming or surface motility; mutations also delayed nodule formation, but increased competitiveness. We found that the indole-3-acetamide (IAM) pathway was active in CIAT 899 and not affected by the mutations, and—noteworthy—that API was required to activate the tryptamine (TAM) and the indol-3-pyruvic acid (IPyA) pathways in all strains, particularly in the mutants. High up-regulation of y4wF and tidC genes was observed in both the wild-type and the mutant strains in the presence of API. The results obtained revealed an intriguing relationship between IAA metabolism and nod-gene-inducing activity in R. tropici CIAT 899. We discuss the IAA pathways, and, based on our results, we attribute functions to the y4wF and tidC genes of R. tropici.


Biological nitrogen fixation Nodulation genes Phytohormones IAA IPyA Exopolysaccharides 







Indole acetic acid






Indol-3-pyruvic acid








Yeast-extract mannitol medium



Authors thank João Alves Filho, Dr. Estela de Oliveira Nunes and Dr. Clara Beatriz Hoffman-Campo (Embrapa Soja) for help in the UPLC analysis, and to Dr. Allan R. J. Eaglesham for English review. L.D. Tullio acknowledges a PhD fellow and D.F. Gomes a post-doc fellow from CAPES-Embrapa (Edital 15/2014); A.S. Nakatani acknowledges a post-doc fellowship from Fundação Araucária (Edital 14/2012), F.J. Ollero a research project of the Spanish Government (AGL2016-77163-R), and M. Hungria a research fellow from CNPq (300878/2015-0).

Authors contributions

Conceived and designed the experiments: All authors. Performed the experiments: LDT, ASN, DFG. Analyzed the data: All authors. Contributed reagents/materials/analysis tools: FJO, MM, MH. Wrote the paper: All authors. All authors read and approved the final manuscript.


Funded by INCT-Plant-Growth Promoting Microorganisms for Agricultural Sustainability and Environmental Responsibility (CNPq 465133/2014-2, Fundação Araucária-STI, CAPES), Embrapa (, CNPq-Universal (400468/2016-6), and Ministerio de Economía y Competitividad (MINECO, AGL2016-77163-R).

Compliance with ethical standards

Ethics approval and consent to participate

The authors declare no ethical conflicts; authors declare that they have consented to contribute to the manuscript.

Consent to publish

The authors declare consent to publish the manuscript.

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

203_2018_1607_MOESM1_ESM.docx (604 kb)
Supplementary material 1 (DOCX 604 KB)


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© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Embrapa SojaLondrinaBrazil
  2. 2.Department of Biochemistry and BiotechnologyUniversidade Estadual de LondrinaLondrinaBrazil
  3. 3.Departamento de Microbiología, Facultad de BiologíaUniversidad de SevillaSevilleSpain

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