Retrotransposon-induced Tomato Evolution

Krishna Amin (St Catharine’s). September 21, 2019.

Cambridge researchers have shown that genetic elements activated by drought can induce positive changes in major crops: a potential method for future crop improvement and a valuable tool against world hunger.

The paper published in PLOS Genetics last week focusses on the transposon family Rider in tomatoes, the world’s most grown fruit.

Transposons play a large part in plant genomes and are a major source of genetic instability, threatening deleterious mutations, to the extent that they are often silenced by epigenetic mechanisms. These usually involve hypermethylation at cytosine residues, association with nucleosomes containing methylated histones and targeting by small interfering RNAs that guide RNA-dependent DNA methylation. Interference with these mechanisms can result in transposon activation, giving potential for genetic and epigenetic variation, especially when one finds itself near a gene. Rider is consequently responsible for many beneficial traits of agronomical interest in tomatoes, including fruit shape and plant architecture.

Transposons can also be activated by environmental stresses. Described examples include a cold-responsive transposon family in citrus and heat-responsive retrotransposons in rice. Once activated, transposons represent significant sources of genetic and epigenetic variation, such as the jointless pedicel Rider-induced phenotype selected for during tomato breeding, which reduces fruit dropping and eases mechanical harvesting.

The researchers showed that an increase in Rider expression, and an increase in extra-chromosomal DNA, can be caused by dehydration stress; this mechanism relies on the signalling pathway of the phytohormone abscisic acid. Evidence that RNA-dependent DNA methylation controls Rider activity through small-interfering RNAs and DNA methylation may point towards a possible explanation for the influence of drought on Rider, and a cross-species examination revealed Rider-like elements in major crop plants such as rapeseed, beetroot and quinoa.

Overall, their findings suggest that Rider is a drought-induced retrotransposon family found in many important modern crops that may have contributed to phenotypic changes as a result of past drought periods. They postulate that Rider could be deliberately activated to generate further variation for crop improvement, highlighting the potential of transposon-directed mutagenesis for the future of agriculture.

Authors: Matthias Benoit, Hajk-Georg Drost, Marco Catoni and Jerzy Paszkowski from the Sainsbury Laboratory. Quentin Guoil, Sara Lopez-Gomolion and David Baulcombe from the Department of Plant Sciences.

Their paper:
Benoit M, Drost H-G, Catoni M, Gouil Q, Lopez-Gomollon S, Baulcombe D, et al. (2019) Environmental and epigenetic regulation of Rider retrotransposons in tomato. PLoS Genet 15(9): e1008370.

Predicting Organic Syntheses

Krishna Amin (St Catharine’s). September 10, 2019.

Although we may be somewhat late to the party, we would like to extend our congratulations to Dr Alpha Lee, one of last year’s speakers, and his co-researchers, which included Dr Phillipe Schwaller, at the Cavendish Laboratory with Dr Alpha Lee, and Dr Christopher A. Hunterford and PhD student Peter Bolgar at the Department of Chemistry, for their two remarkable papers reporting on the development of a new model which predicts, with over 90% accuracy, the outcomes of various organic synthesis reactions, the sort that might be involved in medicinal drug discovery. Importantly, this novel model does away with handcrafted rules, which means that the team’s method can be scaled up to cope with the ever-increasing volume of reported organic reactions without significant manhour investment. Furthermore, their method can accurately predict subtle and selective chemical transformations, such as those regarding chemoselectivity and regioselectivity, as well as estimate its own uncertainty.

Their papers:
Lee, A. A.; Yang, Q., Sresht, V.; Bolgar, P., Hou, X.; Klug-McLeod, J. L.; Butler, C. R.. Molecular Transformer Unifies Reaction Prediction and Retrosynthesis across Pharma Chemical Space. Chem. Commun.. 2019, 55, 12152-12155.
Schwaller, P.; Laino, T.; Gaudin, T.; Bolgar, P.; Hunter, C. A.; Bekas, C.; Lee, A. A.. Molecular Transformer: A Model for Uncertainty-Calibrated Chemical Reaction Prediction. ACS Central Science. 2019, 5(9), 1572-1583


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