< Back to previous page
Project
A systems biology approach for the ethylene synthesis during climactericripening of tomato fruit.
Tomato is an important commodity in Belgium, as it is the most producedvegetable and greenhouse crop and is a common ingredient for a healthy diet. Tomatoes are produced for local consumption and
international trade. Color, taste, aroma, firmness are all decisive quality attributes that determine the purchasing behavior of cusumers and wholesalers. Overall fruit quality is highly dependent on the climacteric ripening process, which is induced and coordinated by the plant hormone ethylene. A better understanding on how ethylene regulates fruit ripening is crucial tomanage tomato fruit quality throughout the postharvest quality chain.
We have conducted a targeted systems biology investigation of the ethylene biosynthesis pathway during tomato fruit development, climacteric ripening and postharvest storage. This approach requires advanced analytical and molecular techniques in order to combine transcriptomics, proteomics and metabolomics data. First, we have optimized a capillary electrophoresis technique for the fast quantification of
S-adenosyl-L-methionine (SAM), a general precursor of ethylene. This technique allowed us to study the behavior of SAM in relation to fruit ripening and other SAM-demanding pathways like polyamine biosynthesis and transmethylation reactions. We found that the cellular SAM pool is tightly regulated to match the demand of all pathways. A more in depth characterization of ethylene biosynthesis revealed that when fruits have completed their ripening process, ethylene biosynthesis is shut down. This post-climacteric decline in ethylene production is achieved through the regulation of 1-aminocyclopropane-1-carboxilic acid (ACC) oxidase, the ethylene forming enzyme. We also found that the associated Yang cycle, responsible for recycling of an ethylene biosynthesis by-product towards SAM, is coordinated during ripening and is highly active in the post-climacteric stage. In a tissue
specific investigation we found that different tissues of a tomato fruit all show the climacteric pattern in ethylene biosynthesis, yet with a different amplitude. This result suggests that each tissue has its own specific strict regulation of ethylene biosynthesis.
In order to cope with the diverse amount of data from systems biology studies, mathematical models are constructed, that allow a more in-depth interpretation of the data. First, we have constructed a
model that describes fruit maturity in terms of biological age to take into account biological variability between individual tomatoes. This allows a time dependent classification of fruit of different ripening stages. Having incorporated time, we were able to develop a kinetic network model that
predicts the fruit ethylene production and the underlying changes of metabolites and proteins solely based upon gene expression data. This model was subsequently validated against some well characterized ripening mutants. The model was also used to evaluate in silico the role of 1-(malonylamino)cyclopropane-1-carboxylic acid (MACC), an important derivate in ethylene synthesis. It was found that MACC formation potentially may control fruitethylene biosynthesis.
All in all, our systems biology study revealed many new aspects about ethylene biology in tomato fruit. We have provide new data at the cellular and tissue level. We have shown how ethylene
biosynthesis operates together with some adjacent pathways like theYang cycle, polyamine biosynthesis and transmethylations. Furthermore, a kinetic model was constructed that described the data well and was able to predict in silico fruit ethylene production. We can conclude that this targeted systems biology study has contributed to the fundamental understanding of ethylene biosynthesis and fruit ripening, out of
whichhopefully in future new biotechnological applications can arise.
international trade. Color, taste, aroma, firmness are all decisive quality attributes that determine the purchasing behavior of cusumers and wholesalers. Overall fruit quality is highly dependent on the climacteric ripening process, which is induced and coordinated by the plant hormone ethylene. A better understanding on how ethylene regulates fruit ripening is crucial tomanage tomato fruit quality throughout the postharvest quality chain.
We have conducted a targeted systems biology investigation of the ethylene biosynthesis pathway during tomato fruit development, climacteric ripening and postharvest storage. This approach requires advanced analytical and molecular techniques in order to combine transcriptomics, proteomics and metabolomics data. First, we have optimized a capillary electrophoresis technique for the fast quantification of
S-adenosyl-L-methionine (SAM), a general precursor of ethylene. This technique allowed us to study the behavior of SAM in relation to fruit ripening and other SAM-demanding pathways like polyamine biosynthesis and transmethylation reactions. We found that the cellular SAM pool is tightly regulated to match the demand of all pathways. A more in depth characterization of ethylene biosynthesis revealed that when fruits have completed their ripening process, ethylene biosynthesis is shut down. This post-climacteric decline in ethylene production is achieved through the regulation of 1-aminocyclopropane-1-carboxilic acid (ACC) oxidase, the ethylene forming enzyme. We also found that the associated Yang cycle, responsible for recycling of an ethylene biosynthesis by-product towards SAM, is coordinated during ripening and is highly active in the post-climacteric stage. In a tissue
specific investigation we found that different tissues of a tomato fruit all show the climacteric pattern in ethylene biosynthesis, yet with a different amplitude. This result suggests that each tissue has its own specific strict regulation of ethylene biosynthesis.
In order to cope with the diverse amount of data from systems biology studies, mathematical models are constructed, that allow a more in-depth interpretation of the data. First, we have constructed a
model that describes fruit maturity in terms of biological age to take into account biological variability between individual tomatoes. This allows a time dependent classification of fruit of different ripening stages. Having incorporated time, we were able to develop a kinetic network model that
predicts the fruit ethylene production and the underlying changes of metabolites and proteins solely based upon gene expression data. This model was subsequently validated against some well characterized ripening mutants. The model was also used to evaluate in silico the role of 1-(malonylamino)cyclopropane-1-carboxylic acid (MACC), an important derivate in ethylene synthesis. It was found that MACC formation potentially may control fruitethylene biosynthesis.
All in all, our systems biology study revealed many new aspects about ethylene biology in tomato fruit. We have provide new data at the cellular and tissue level. We have shown how ethylene
biosynthesis operates together with some adjacent pathways like theYang cycle, polyamine biosynthesis and transmethylations. Furthermore, a kinetic model was constructed that described the data well and was able to predict in silico fruit ethylene production. We can conclude that this targeted systems biology study has contributed to the fundamental understanding of ethylene biosynthesis and fruit ripening, out of
whichhopefully in future new biotechnological applications can arise.
Date:11 Aug 2008 → 24 Jan 2013
Keywords:BIOSYNTHESIS, Systems biology
Disciplines:Food sciences and (bio)technology, Agriculture, land and farm management, Biotechnology for agriculture, forestry, fisheries and allied sciences, Fisheries sciences, Analytical chemistry, Macromolecular and materials chemistry, Other chemical sciences, Nutrition and dietetics, Agricultural animal production, Plant biology, Agricultural plant production, Horticultural production
Project type:PhD project