Adding a metabolic layer of root clock regulation

Abstract

As important structures for water and nutrient absorption, lateral roots are formed at regular time points along with root growth. The sites of lateral root initiation are pre-patterned by an oscillatory mechanism known as the root clock, which is regulated by carotenoid metabolism. Blocking carotenoid metabolism by D15, a chemical inhibitor, reduces root clock oscillations and lateral root formation. However, the exact nature of carotenoid metabolites that function during this process remains unclear. A recent study by Dickinson et al., 2021Dickinson A. Zhang J. Luciano M. Wachsman G. Sandoval E. Schnermann M. Dinneny J. Benfey P. A plant lipocalin promotes retinal-mediated oscillatory lateral root initiation.Science. 2021; https://doi.org/10.1126/science.abf7461Crossref Scopus (12) Google Scholar identified retinal and its binding protein as potential regulators of the root clock in Arabidopsis. The authors used a chemical reporter of vertebrate retinoid binding protein activity, named MCA, and firstly demonstrated the presence of proteins that interact with retinal in the roots. Interestingly, they found that MCA fluorescence displays an oscillatory pattern similar to the root clock in the early differentiation zone where lateral roots initiate. Through time-lapse imaging, MCA oscillation was determined to precede the root clock, as indicated by a DR5:LUC reporter, in growing roots. Moreover, MCA oscillation was found to predict the pre-branch sites of further lateral root initiation (Figure 1) and to be impaired under D15 treatment, suggesting that retinoids may play a role in lateral root formation and that their binding activities rely on carotenoid metabolites. Using a HPLC-MS screen, the authors identified retinal and three other apo-carotenals with a reduced level after D15 treatment. They discovered that only retinal and 14′-apo-β-carotenal (apo14) are able to rescue both D15-induced inhibition of root clock oscillation and lateral root formation. Experiments further demonstrated that application of either retinal or apo14 is sufficient to induce ectopic lateral root formation in wild-type plants. Considering that apo14 can generate retinal when oxidized, retinal may be the active signaling molecule during these processes. Next, the authors identified a type of lipocalin, termed TIL, as the potential retinal-binding protein in Arabidopsis based on its sequence homology to the vertebrate RETINOL-BINDING PROTEIN 4 (RPB4). The authors demonstrated that TIL interacts with the MCA reporter and binds to retinal in Escherichia coli, suggesting that this type of lipocalin may promote retinal-mediated lateral root formation. Consistently, TIL expression overlaps with the oscillatory pattern of MCA fluorescence in the root and is required for lateral root initiation. The til mutants exhibit reduction in lateral root number, root clock amplitude, and retinal sensitivity. Retinoid is known to play pivotal roles in multiple processes during vertebrate development. This study shows that retinal is also important as an endogenous regulator in plants and reveals an intriguing metabolic layer that regulates the root clock. Other known regulators of the root clock include auxin (Dubrovsky et al., 2008Dubrovsky J. Sauer M. Napsucialy-Mendivil S. Ivanchenko M. Friml J. Shishkova S. Celenza J. Benková E. Auxin acts as a local morphogenetic trigger to specify lateral root founder cells.Proc. Natl. Acad. Sci. U S A. 2008; 105: 8790-8794Crossref PubMed Scopus (429) Google Scholar) and cell-wall modification (Wachsman et al., 2020Wachsman G. Zhang J. Moreno-Risueno M. Anderson C. Benfey P. Cell wall remodeling and vesicle trafficking mediate the root clock in Arabidopsis.Science. 2020; 370: 819-823Crossref PubMed Scopus (29) Google Scholar). Whether and how these different regulators interplay in the root clock remain to be addressed in future studies. F.D. was supported by the Young Scientists Fund of NSFC ( 32000507 ). No conflict of interest declared.