Author: watersmt

Brachy paper finally out

It was back in 2014 when I first thought it would be worthwhile looking into KAI2 signalling in a monocot – and Brachypodium seemed like a decent model that was easier to grow here in Oz than rice! Well finally – actually on Christmas Day 2021 – our findings from characterising two kai2 alleles in Brachypodium were published in The Plant Journal. You can read all about it there, in glorious Open Access format funded by a handy agreement between the publisher Wiley and German universities – but here I thought I might reflect on the process, to update the website and procrastinate over writing a grant application.

This work was a huge collaborative effort with first authors Yongjie Frank Meng from my lab, and Kartikye Varshney from Caroline Gutjahr’s lab, and substantial contributions in bioinformatics from Norbi and Eszter in Vilmos Sóos’ lab in Hungary. Identifying the mutants in the first place was only feasible thanks to hard work by many members of the Brachypodium research community, who established mutant populations and high-throughput screening methods. These people included co-authors Marion Dálmais, Richard Sibout, John Vogel and Debbie Laudencia-Chingcuanco.

Why did it take so long? In part it was because it was always a bit of a “side” project (kicked off by undergrad Lara!) that was not really prioritised until Frank joined the lab in 2018. Once an interesting phenotype emerged, of course we realised that a second mutant allele was essential to make a compelling set of results, so we had to scour the Brachy germplasm and screen a few more. Thankfully by this time HTP sequencing of the mutant populations meant that putative mutants could be identified from the desktop, rather than by TILLING screens as was the case for the first allele we found. And we got lucky with another strong allele, so we had our pair. Time to re-do everything, this time with both mutants. Then it was the briefest, Covid-19-cut-short visit to my lab by Eszter Badics that prompted us to do some RNA-seq and gain a little more insight into the basis for the mutant phenotypes – followed by a fair bit of tidying up loose ends by Muhammad, Sabrina and myself to wrangle the manuscript into a publishable state.

I wouldn’t say I was burned by Brachy, and I am absolutely glad that we undertook the work, but it was certainly a learning experience. It is not like growing Arabidopsis! Even getting the seeds to germinate was a challenge, which is a pain when you are supposedly working on germination stimulants (who knew you had to remove the glume first? And then they all germinate, synchronously!). The very different growth habits and architecture of monocots vs dicots brought me back to my very first research days working on photosynthetic mutants in maize – what’s that flappy-bendy bit at the bottom of the leaf blade again? can we use that as the node to determine internode length? Fun times. But of course, if you stick to Arabidopsis, with its insistent refusal to support arbuscular mycorrhizal associations, well you are missing out. Monocots just do it differently, and with style.

Thank you to all co-authors, and the ARC (Australia), DFG (Germany) and NKFIH (Hungary) for funding the work. Happy 2022 everyone!


Desmethyl butenolides – the new frontier?

I have been a bit remiss in updating the website but thought I would mention this one while I’m on here: the latest publication from the lab is recently published in New Phytologist, Hugh Yao as first author with valuable contributions from Frank and Kim as well. We think KAI2 proteins prefer to work with butenolide compounds that lack a methyl group, versus D14 proteins that require a methyl group. We used a couple of different compounds – GR24 and nitrile debranones – and showed that if you remove their respective methyl groups, they become much more active through KAI2. And most importantly, they become *specific* for KAI2 – they do not activate D14. So now we have a specific molecular feature that can be used to manipulate KAI2-dependent signalling. Most excellent.

2020 is the year that will be remembered.. for SMAX1

It was a behemoth, but Aashima Khosla, Dave Nelson and team at UC Riverside have published a tour de force analysing the functional domains of SMAX1, and showing how it is degraded in response to Karrikins and GR24. Jiaren (Hugh) and I contributed by showing that KAI2 degradation was dependent on SMAX1 and SMXL2, suggesting that the receptor and downstream repressor proteins form a complex and are possibly degraded together.

It was a pleasure to be part of this work – and congratulations to Aashima, Dave and others for an enormous effort that finally paid off. It’s rare to see such an admission in a manuscript, but I quote verbatim from the final paragraph of the introduction: “This proved to be an unexpectedly difficult undertaking”. Indeed it was.

Read the paper in The Plant Cell here. Here’s the full citation:

Khosla, A., Morffy, N., Li, Q., Faure, L., Chang, S., Yao, J., Zheng, J., Cai, M., Stanga, JP., Flematti, GR., Waters, MT., Nelson, DC. (2020). Structure-Function Analysis of SMAX1 Reveals Domains that Mediate its Karrikin-Induced Proteolysis and Interaction with the Receptor KAI2. The Plant cell


Our manuscript comes at a time of a veritable flurry of SMAX1 and SMXL-related publications from other groups, namely:

Wang, L., Xu, Q., Yu, H., Ma, H., Li, X., Yang, J., Chu, J., Xie, Q., Wang, Y., Smith, S., Li, J., Xiong, G., Wang, B. (2020). Strigolactone and Karrikin Signaling Pathways Elicit Ubiquitination and Proteolysis of SMXL2 to Regulate Hypocotyl Elongation in Arabidopsis thaliana. The Plant Cell

Bunsick, M., Toh, S., Wong, C., Xu, Z., Ly, G., McErlean, C., Pescetto, G., Nemrish, K., Sung, P., Li, J., Scholes, J., Lumba, S. (2020). SMAX1-dependent seed germination bypasses GA signalling in Arabidopsis and Striga Nature Plants

Wang, L., Wang, B., Yu, H., Guo, H., Lin, T., Kou, L., Wang, A., Shao, N., Ma, H., Xiong, G., Li, X., Yang, J., Chu, J., Li, J.(2020). Transcriptional regulation of strigolactone signalling in Arabidopsis Nature

Choi, J., Lee, T., Cho, J., Servante, E., Pucker, B., Summers, W., Bowden, S., Rahimi, M., An, K., An, G., Bouwmeester, H., Wallington, E., Oldroyd, G., Paszkowski, U. (2020). The negative regulator SMAX1 controls mycorrhizal symbiosis and strigolactone biosynthesis in rice. Nature Communications 11(1), 2114.

This corpus of work represents one of the biggest leaps forward in this field for some time, and constitutes a considerable collective achievement. Congratulations to everyone!