How does a tomato obtain the huge amount of energy and substrates needed to transition from green to red? Tomatoes are the universal model of climacteric fruit, meaning they undergo a respiratory burst at the onset of ripening. This metabolic peak is essential for producing ethylene, the hormone giving the signal to ripen, and the carotenoid pigments responsible for colour. However, details are now emerging as to how the fruit manages to bring about this significant metabolic change.

The team, led by IRTA researcher at CRAG Igor Florez-Sarasa with Ariadna Iglesias-Sanchez as first author, published in Plant Physiology the discovery that a specific mitochondrial route, known as the alternative oxidase pathway (AOX), is the main engine enabling this transformation.

Precision technology to measure fruit respiration

Measuring how a fruit breathes internally, as well as the contribution of the AOX pathway, is particularly difficult due to the fruit’s size and thickness. To overcome this, the scientists used a high‑precision technique based on oxygen isotopes (¹⁸O). They discovered that AOX pathway activity spikes exactly when the tomato starts changing colour, becoming the main support of fruit respiration.

To prove this pathway is essential, the team used CRISPR‑Cas9 gene editing to deactivate the AOX1a gene in tomato plants. The resulting mutant tomatoes took much longer to ripen. Through comprehensive metabolic and molecular profiling, the researchers observed altered ripening-related metabolites in the mutants. Specifically, fruit with a deficiency in the AOX pathway was unable to accumulate key amino acids, such as aspartate and methionine, which are essential for the synthesis of ethylene. Moreover, the mutants showed a limitation in carbon skeletons required for carotenoid biosynthesis, causing unusually low levels of pigments like phytoene and lycopene in the early ripening stages.

A new perspective on fruit quality and agricultural breeding

This discovery provides a completely new context for how fruits manage energy: as plant sugars break down at the onset of ripening, the resulting metabolic intermediates allosterically activate the AOX pathway. In other words, the AOX route acts as an extra engine that allows the tomato to burn sugars to build ripening compounds without being restricted by the cell’s usual energetic brakes.

The broader relevance of these alternative respiratory pathways in fruit development has also been highlighted in a recent comprehensive review published in New Phytologist by the same CRAG team, consolidating the centre’s leadership in deciphering plant energy metabolism.

Understanding this metabolic engine opens new possibilities for agriculture by enabling the modulation of alternative respiratory pathways to develop varieties with greater nutritional value, improved quality, and traits beyond those achievable through traditional ethylene‑based strategies.

Reference Article

Ariadna Iglesias-Sanchez, Nestor Fernandez Del-Saz, Miguel Ezquerro, Elisenda Feixes-Prats, Miquel Ribas-Carbo, Alisdair R Fernie, Manuel Rodríguez-Concepción, Igor Florez-Sarasa. Activation of alternative oxidase ensures carbon supply for ethylene and carotenoid biosynthesis during tomato fruit ripening. Plant Physiology (2025), https://doi.org/10.1093/plphys/kiaf516

Iglesias-Sanchez, A., García-Carbonell, S., Fernie, A.R., Pujol, M. and Florez-Sarasa, I. Fruit respiration: putting alternative pathways into perspective. New Phytolgist (2026), https://doi.org/10.1111/nph.70882

About the authors and funding of the study

This work was supported by grants PID2020-120229RA-I00 and PID2024-163099NB-I00 to IF-S, and PID2021-125998OB-C21 to MP, all funded by MICIU/AEI/10.13039/501100011033 and by ‘ERDF/EU’, Ministerio de Ciencia, Innovación y Universidades–Agencia Estatal de Investigación (MCIU/AEI, Spain). We also thank the support of grants Plant Genetics-2021SGR00756 funded by Generalitat de Catalunya, RedoxPlant-RED2022-134072-T funded by MICIU/AEI/10.13039/501100011033 (MCIU/AEI, Spain), as well as CEX2019-000902-S funded by MICIU/AEI/10.13039/501100011033 (MCIU/AEI, Spain) and CERCA Programme (Generalitat de Catalunya) to CRAG. AI-S received a predoctoral fellowship (PRE2018-083610) funded by MICIU/AEI/10.13039/501100011033 and by ‘ESF Investing in your future’. SG-C received a predoctoral fellowship (PRE2021-097127) funded by MICIU/AEI/10.13039/501100011033 and by ‘ESF Investing in your future’. IF-S received funding from the ‘Ramon y Cajal’ contract RYC2019-028030-I funded by MCIN/AEI/10.13039/501100011033 and by ‘ESF Investing in your future’.