Search bioRxiv⌕ Search

Biology subjects

Moss, B. L.

Publications and source records attributed to Moss, B. L..

2 recordsLinked to original sources

A synthetic approach reveals a highly sensitive maize auxin response circuit

Auxin plays a key role across all land plants in growth and developmental processes. Although auxin signaling function has diverged and expanded, differences in the molecular functions of signaling components have largely been characterized in Arabidopsis thaliana. Here, we used the Auxin Response Circuit recapitulated in Saccharomyces cerevisiae (ARCSc) system to functionally annotate maize auxin signaling components, focusing on genes expressed during development of ear and tassel inflorescences. All 16 maize Auxin (Aux)/Indole-3-Acetic Acid (IAA) repressor proteins are degraded in response to auxin, with rates that depended on both receptor and repressor identity. When fused to the maize TOPLESS (TPL) homolog RAMOSA1 ENHANCER LOCUS2 (REL2), maize Aux/IAAs were able to repress AUXIN RESPONSE FACTOR (ARF) transcriptional activity. A complete auxin response circuit comprised of all maize components, including ZmAFB2/3 b1 maize AUXIN SIGNALING F-BOX (AFB) receptor, was found to be fully functional. The ZmAFB2/3 b1 auxin receptor was found to be more sensitive to hormone than AtAFB2 and allowed for rapid circuit activation upon auxin addition. These results validate the conserved role of predicted auxin response genes in maize, as well as provide evidence that a synthetic approach can facilitate broader comparative studies across the wide range of species with sequenced genomes. A synthetic maize auxin response circuit is recapitulated in Saccharomyces cerevisiae, revealing a highly sensitive auxin signaling network with functional homology to the Arabidopsis circuit.

plant biology↗

Accelerating structure-function mapping using the ViVa webtool to mine natural variation

Thousands of sequenced genomes are now publicly available capturing a significant amount of natural variation within plant species; yet, much of this data remains inaccessible to researchers without significant bioinformatics experience. Here, we present a webtool called ViVa (Visualizing Variation) which aims to empower any researcher to take advantage of the amazing genetic resource collected in the Arabidopsis thaliana 1001 Genomes Project (http://1001genomes.org). ViVa facilitates data mining on the gene, gene family or gene network level. To test the utility and accessibility of ViVa, we assembled a team with a range of expertise within biology and bioinformatics to analyze the natural variation within the well-studied nuclear auxin signaling pathway. Our analysis has provided further confirmation of existing knowledge and has also helped generate new hypotheses regarding this well studied pathway. These results highlight how natural variation could be used to generate and test hypotheses about less studied gene families and networks, especially when paired with biochemical and genetic characterization. ViVa is also readily extensible to databases of interspecific genetic variation in plants as well as other organisms, such as the 3,000 Rice Genomes Project (http://snp-seek.irri.org/) and human genetic variation (https://www.ncbi.nlm.nih.gov/clinvar/).

bioinformatics↗