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Members of the Arabidopsis auxin receptor gene family are essential early in embryogenesis and have broadly overlapping functions

Michael J Prigge, Nikita Kadakia, Kathleen Greenham, Mark Estelle

Preprint posted on January 23, 2019 https://www.biorxiv.org/content/10.1101/529248v1

Auxin receptor TIR1/AFB is a happy family of genes that work together in plant embryogenesis.

Selected by Chandra Shekhar Misra

Introduction

Auxin is one of the most important phytohormones involved in cell differentiation, root and shoot development; it mediates plant responses to both abiotic and biotic stresses [1]. Auxin regulation of gene expression is dependent on three families of proteins: Auxin Response Factors (ARF), Aux/IAA transcriptional repressors and Transport Inhibitor Response 1 (TIR1)/Auxin signalling F-Box (AFB) proteins [1-2].

The Arabidopsis genome encodes six TIR1/AFB proteins that arise out of whole-genome duplication and each of these proteins contain an amino-terminal F-Box followed by Leucine-rich repeats (LRRs) (Fig. 1). The authors argue that duplication and diversification of these three gene families might be the reason auxin acquired a new possible role in vascular development, lateral root formation, and organ polarity. Though previous studies have revealed functions of individual members of this gene family, a comprehensive study about this auxin gene family has been lacking. Authors in this study have tried to unravel the role of the TIR1/AFB gene family in Arabidopsis that led them to uncover the functional redundancy of this family in their genetic analysis. The authors also identified a previously unknown function of this gene family in early embryogenesis.

Fig 1: Role of six TIR1/AFB gene family in Arabidopsis (With due permission from Prigge et al., 2019, bioRxiv 529248)

Key findings

The authors did a phylogenetic analysis and found that the TIR1/AFB gene family had diversified before ferns-seeds-plants, over 400 million years ago. However, it was astonishing that despite this long divergence, TIR/AFB proteins retained largely similar functions. Though the authors found TIR1 to be the most important member of this family, AFB5, AFB2 followed by AFB3 and AFB4 also played a significant role.

The authors also identified tissue-specific expression patterns of different members of this gene family. For instance, they found TIR1 and AFB2 to be expressed more in the root, compared to AFB5 which was expressed at high level in the inflorescence. The authors found no to little expression of the AFB4 gene in all tissues, concluding that it played a very minor role in the gene family.

The authors also found that AFB1 uniquely differs from the rest of the TIR1/AFB members. Unlike all other members, AFB1 is expressed at a very high level in the root epidermis and vascular tissues and is absent from any other tissue. Genetic studies further revealed that AFB1 had no effect on root elongation, but surprisingly it was found to be a negative regulator of lateral root formation.

The authors found that most members of this family from TIR1 to AFB2 to AFB5 are all localized to the nucleus, but some proteins were also found to be present in the cytoplasm, for reasons which remain unknown.

The authors finally explored the importance of auxin in embryo patterning, a function lately well described in the literature [3]. The authors found that in a tir1afb235 quadruple mutant, apical cells and hypophysis suffered cell division errors (Fig. 2). Embryos from tir1afb235 quadruple and tir1afb12345 sextuple mutants were fully lethal.

Fig 2: Representation of embryo-lethal phenotypes of tir1/afb sextuple mutant characterised by absence of cotyledon primordia and over-proliferated suspensors in some of the embryo development stages. The embryo stages are 2-cell (A–D), 16- cell (dermatogen) (E-F), late transition (G–H), torpedo (I-–J), and bent cotyledon (K–L). Upper panel shows the mutants with absence of mCitrine signal (Yellow) while those in the lower panel are complemented siblings showing the presence of citrine signal. (With due permission from Prigge et al., 2019, bioRxiv 529248)

 

The authors also noted that no embryonic markers were expressed in the quadruple and sextuple mutant which led to the defects in embryo patterning. Although tir1afb235 quadruple mutant formed a normal hypophysis, they never showed the expression of embryonic markers such as NTT (NO TRANSMITTING TRACT) or WOX5. Suspensor marker PIN7 was found to have reduced expression in the suspensor which led to its proliferation, however, it was also found to be expressed in the basal half of the embryo which led the authors to hypothesize that PIN7 expression in the embryo might be linked to the TIR1/AFB pathway.

What I liked about this preprint

Auxin is an important plant hormone responsible for plant growth and development. This hormone regulates gene expression which is dependent on three families of proteins as described above [4]. While some studies have described the role of this gene regulatory network on auxin-mediated responses, detailed analysis of this gene family was lacking. The authors have very clearly identified the role of six TIR1/AFB proteins and established that they share overlapping functions. However, what was most interesting was the role of this gene family in embryogenesis. Though several auxin mutants have been reported before with varying defects, the authors in this study found the embryos to be completely lethal in quadruple and sextuple mutants.

Questions for the authors

  1. The authors have alluded to the role of TIR1/AFBs under specific conditions. Since auxin is known to play an important role in various abiotic and biotic stress responses, did they check the function of these genes in other environmental conditions?
  2. It would be also interesting to know whether the authors have checked what is the effect of exogenous IAA specifically in the sextuple mutant tir1afb12345?
  3. Can the authors explain the possible underlying mechanism of this complex, as it is clear that although the gene family has overlapping functions, it looks like TIR1 or AFB2 alone is enough to rescue the growth. Can they be called a master regulator of this complex ?

References

  1. Zhao, Y., 2010. Auxin biosynthesis and its role in plant development. Annual review of plant biology61, pp.49-64.
  2. Lavy, M. and Estelle, M., 2016. Mechanisms of auxin signaling. Development143(18), pp.3226-3229.
  3. Palovaara, J., de Zeeuw, T. and Weijers, D., 2016. Tissue and organ initiation in the plant embryo: a first time for everything. Annual review of cell and developmental biology32, pp.47-75.
  4. Dindas, J., Scherzer, S., Roelfsema, M.R.G., Meyer, K., Müller, H.M., Al-Rasheid, K.A.S., Palme, K., Dietrich, P., Becker, D., Bennett, M.J. and Hedrich, R., 2018. AUX1-mediated root hair auxin influx governs SCF TIR1/AFB-type Ca 2+ signaling. Nature communications9(1), p.1174.

Tags: arabidopsis, auxin, embryogenesis

Posted on: 4th April 2019

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  • Author's response

    Mark Estelle shared

    Q. The authors have alluded to the role of TIR1/AFBs under specific conditions. Since auxin is known to play an important role in various abiotic and biotic stress response, did they check the function of these genes in other environmental conditions?

    A. We have examined this question with respect to drought response and have a manuscript on bioRxiv. See Salehin et al. (https://www.biorxiv.org/content/10.1101/572305v2)

    Q. It would be also interesting to know whether authors have checked what is the effect of exogenous IAA specially in sextuple mutant tir1afb12345?

    A. We have not done this experiment.

    Q. Can the authors explain the possible underlying mechanism of this complex as it is clear that although the gene family has overlapping functions, it looks like TIR1 or AFB2 alone is enough to rescue the growth. Can they be called a master regulator of this complex.

    A. No, they are not master regulators. Each of the TIR1/AFB proteins is assembled into a ubiquitin protein ligase called an SCFTIR1/AFB complex that is responsible for degradation of the Aux/IAA transcriptional repressors. As far as we know, each of the SCFTIR1/AFB­ complexes has a similar biochemical function. The fact that TIR1 and AFB2 are sufficient for viability, while the others are not, is probably related to their expression level and broad distribution. It is important to note that our plants are grown under controlled and ideal conditions. Under natural conditions, I would not expect the quintuple mutants to survive.

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