A systems model of vesicle trafficking in Arabidopsis pollen tubes.

Naohiro Kato,Alexander P Steger,Hongyu He

doi:10.1104/pp.109.148700

Abstract

A systems model that describes vesicle trafficking during pollen tube growth in Arabidopsis (Arabidopsis thaliana) was constructed. The model is composed of ordinary differential equations that connect the molecular functions of genes expressed in pollen. The current model requires soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptors (SNAREs) and small GTPases, Arf or Rab, to reasonably predict tube growth as a function of time. Tube growth depends on vesicle trafficking that transports phospholipid and pectin to the tube tip. The vesicle trafficking genes identified by analyzing publicly available transcriptome data comprised 328 genes. Fourteen of them are up-regulated by the gibberellin signaling pathway during pollen development, which includes the SNARE genes SYP124 and SYP125 and the Rab GTPase gene RABA4D. The model results adequately fit the pollen tube growth of both previously reported wild-type and raba4d knockout lines. Furthermore, the difference of pollen tube growth in syp124/syp125 single and double mutations was quantitatively predicted based on the model analysis. In general, a systems model approach to vesicle trafficking arguably demonstrated the importance of the functional connections in pollen tube growth and can help guide future research directions.

Highlights

A systems model that describes vesicle trafficking during pollen tube growth in Arabidopsis (Arabidopsis thaliana) was constructed
Because the closest yeast homologs of AtRabA4d, Ypt31/ 32, are known to initiate vesicle budding from the trans-Golgi network and direct the vesicles to the plasma membrane (Benli et al, 1996; Jedd et al, 1997), we used the raba4d knockout data to compare the function of GTPase B, which initiates vesicle transport from the Golgi apparatus to the tube tip in the mathematical model
The computational results showed that the average growth rate of the pollen tubes is 0.84 6 0.34 mm min21 when we measured the same time window as in wild-type pollen (Supplemental Program S1). This suggests that the growth rate would be reduced to 26% (0.84 of 3.12) of the wild-type pollen rate (Table V). This number reasonably agrees with the observation of the Arabidopsis raba4d knockout line, in which the pollen tube growth rate is reduced to about 18% of that of wild-type pollen (Szumlanski and Nielsen, 2009)

Summary

Introduction

A systems model that describes vesicle trafficking during pollen tube growth in Arabidopsis (Arabidopsis thaliana) was constructed. To study the function of vesicle trafficking machinery at a systems level, we constructed a mathematical model that connects the functions of molecules expressed in pollen tubes, which includes gene products elucidated by the transcriptome analysis, using a set of ordinary differential equations (for details, see “Materials and Methods” and Supplemental Proof S1).

Results

Conclusion