Javier Brumos

Research Associate


Plants are sessile organisms with an extraordinary phenotypic plasticity. Responses of plants to stimuli take place in a dynamic and ever changing environment. Plants thrive in these constantly changing conditions due to their ability to integrate all these external cues with their internal growth-and-development programs. Therefore, understanding how this integration process works is critical for coping with the consequences of global environmental changes facing our planet, as well as with the growing agricultural demand for food, raw materials, and energy.

Hormones play a central role in the signal integration process modifying the organism’s internal programs according to the surrounding conditions. Throughout my entire career, since I was an undergraduate student up to my present research associate position, I have been focusing on understanding the connections between genetics, environmental changes, and phenotypic plasticity. Currently one of my projects focuses on deciphering how plants make auxin, where this auxin is produced, and how the biosynthesis is regulated. The other project aims to unravel how ethylene regulates translation of specific genes and what the physiological significance of such regulation is. The objective of my research is to understand the nature of hormone-regulated gene networks controlling plant growth and development with the ultimate goal to modify them in a predictable way to enable the rational improvement and generation of new, more resilient crop varieties as well as improved agricultural practices.


Auxin is an essential plant hormone involved in nearly every aspect of a plant’s life, from embryo development to fruit ripening and abscission. The main pool of auxin, indole-3-acetic acid (IAA), is synthesized from the amino acid tryptophan via a simple two-step pathway catalyzed by aminotransferases TAA1/TARs and flavin monooxygenases YUCs. The TAA1/TARs and YUCs gene families have been shown to exhibit very specific and dynamic spatiotemporal expression patterns, disproving former views supporting the idea that IAA is primarily produced in shoot meristems and is then distributed to the rest of the plant establishing the auxin gradients.

To define the role of local auxin biosynthesis and its contribution in the regulation of plant growth and development in Arabidopsis, we utilized an array of experimental approaches, including pharmacological treatments with chemical inhibitors of auxin biosynthesis and transport, a set of auxin transport and production mutants, ectopic expression of auxin biosynthetic genes under the control of tissue-specific promoters, inducible Cre-Lox systems, recombineering-based whole-gene fusions with protein reporters, and grafting.

Our results indicate that local auxin biosynthesis and auxin transport act redundantly in the establishment and maintenance of robust morphogenic auxin gradients essential for proper root meristem activity and flower development.

The results of this project thoroughly describe how and where auxin is produced and precisely define auxin sources and sinks. Thereby, a more refined picture of the polar auxin transport system has been established and our understanding of how auxin gradients are generated and maintained in the root has been improved. This novel knowledge can now be utilized as the foundation of applied studies to modify in a predictable way the plant responses to diverse environmental cues improving the root architecture of future crop varieties.

Regulation of translation in tomato fruit ripening:

One of the major challenges of modern agricultural production is to minimize crop losses caused by over-ripening and senescence. A better understanding of how the ripening process is regulated has the potential to reduce spoilage and avoid food waste.

Gene expression changes during fruit ripening have been extensively studied at the transcriptional level, but little is known about ripening-associated shifts in the efficiency of transcript translation. We hypothesize that a subset of transcripts displays ripening-associated changes in their translational efficiencies.

The Ribo-seq technology will be employed to monitor changes in transcript translation at a whole-genome scale and single-codon resolution. We will optimize our protocols for polysomal RNA isolation and RNase digestion to enable Ribo-seq on different-stage tomato fruits. Ribo-seq and RNA-seq will be carried out to identify transcripts that change in their translation efficiency during fruit ripening.

In parallel, previously characterized cis-regulatory elements that are required and sufficient for the translational inhibition of gene expression in the presence of the ripening hormone ethylene will be tested for their ability to control the timing of fruit softening.

This study will serve as a foundation for (1) future in-depth analyses of novel translation regulation mechanisms involved in fruit ripening and (2) the potential implementation of these regulatory modules as a promising biotechnological tool. The project will pave a new path to developing novel approaches for controlling fruit and vegetable spoilage.