Plant Biology

eLife assessment

In this important article, the authors characterize ancient DNA from maize unearthed in archaeological contexts from Paredones and Huaca Prieta in the Chicama river valley of Peru, recovered by painstakingly controlled excavation. The genetic evidence is compelling, albeit from a small sample size, but the dating evidence, despite the excellent archaeological context, is inadequate. Since the age of the samples is so important for the inferences, the individual radiocarbon determinations should be subject to further scrutiny.

eLife assessment

This important paper advances the understanding, in the model plant Arabidopsis thaliana, of the molecular basis of the promotion of flowering in the spring by exposure to winter cold through a process known as vernalization. In Arabidopsis, there are two classes of long non-coding RNAs produced only when plants are in the cold, and this work provides compelling evidence that the cold-induced expression of one of these (COOLAIR) involves C-repeat binding factor proteins that bind to cognate binding elements in the COOLAIR promoter, but also that COOLAIR is not required for the vernalization-mediated promotion of flowering under standard laboratory conditions in which the vernalization response is measured.

eLife assessment

The work of Caspy and coworkers resolves the cryo-EM structures of stacked and unstacked PSII supercomplexes of Dunaliella, revealing unexpected connectivity and conformational flexibility, with intriguing implications for the function and regulation of photosynthesis.

eLife assessment

This boundary-crossing work on dandelion diaspore flight is an excellent demonstration of how to address fundamental questions about wind dispersal of plant seeds from biophysical and ecological perspectives. Both wind-tunnel experiments and models provide compelling evidence that the aerodynamics of dandelion diaspores change with the environment. Addition of local climate data enables the authors to make a convincing case about how the biophysical properties can scale up to affect dispersal across the landscape under different environmental conditions. In addition to the strong data, this is a clear, accessible, and very enjoyable read.

eLife assessment

This is a valuable study of Arabidopsis shoot apical meristem maintenance and organ initiation, defining the expression, interactions and functions of four transcription factors (SHR, SCR, JKD, and SCL23) whose roles were initially described in the root apical meristem. The imaging, genetics and FRET-FLIM evidence supporting the claims of the authors is comprehensive, extensive, and solid, although similar mechanisms, protein interactions, and gene regulatory interactions were previously reported in the root. The work will be of interest and importance for plant developmental biologists.

Evaluation Summary:

The chemical sensing mechanisms of plants, which are largely unknown, are a topic of broad interest. The authors hypothesise that plant chemical receptors may be transporter proteins or odorant binding proteins analogous to those found in animals. The authors have identified a list of plant proteins with possible odorant binding activity and they predict binding constants for relevant odorants. The calculated binding constants are generally very weak in comparison to known animal odorant binding proteins (i.e., would require much higher concentrations of odor for detection). The in silico investigation, while inspiring, leaves many open questions, for example whether or not there is evidence for functional analogy between plant and animal odorant binding proteins.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript.The reviewers remained anonymous to the authors.)

eLife assessment

This manuscript characterizes the localization and function of two proteins promoting division asymmetry in developing stomata of the grass Brachypodium distachyon. The authors demonstrate that the opposing polarity domains of these proteins are linked to cell division orientation. While both proteins have been studied previously in other systems, there was no prior evidence of cooperative functions in a single cell type, as shown here. With further clarification of some of the localization findings, this study will be of strong interest to plant cell biologists and those interested in asymmetric cell division generally.

eLife assessment

This paper, of relevance to a broad range of plant biologists and colleagues in the circandian field, reports important results that demonstrate circadian coordination of characteristic floral development in sunflower. The current manuscript includes convincing observations and possible hypotheses, but the ecological relevance of the temporally-controlled flower development is incompletely shown.

Evaluation Summary:

Engineering NLR proteins to improve disease resistance in crop plants is a major goal of the field. This study applies knowledge from structural and evolutionary studies of the rice NLR protein Pik-1 and cognate effector protein AVR-Pik to engineering of new disease resistance genes. The authors nicely demonstrate that it is indeed possible to engineer resistance proteins with broad recognition specificity for the rice blast fungus. The work is of interest to colleagues in synthetic biology, protein engineering and plant-pathogen interactions.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript, of interest to those studying the evolution of immunity, investigates the evolutionary history of a recently described herbivore-associated molecular pattern (HAMP) receptor, INR, which perceives the caterpillar-derived peptide HAMP, In11. The authors compare INR homologs to identify evolutionarily conserved residues and use chimeric fusion proteins to investigate specificity. The findings presented are valuable and supported by convincing experiments and analysis.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

eLife assessment

This work, which will be of interest to all who study plant-microbe interactions as well as plant cell biology, addresses a fundamental question in symbiosis, placing a classic nodulation defective mutant (rpg) into a plausible protein complex and establishing a hierarchy of "infectosome" assembly. Evidence includes convincing genetics and subcellular localization of components during establishment and maintenance of infection. The study also includes compelling new FLIM-based imaging techniques to distinguish signals from closely associated domains in plant cells.

Evaluation Summary:

The study is of interest to researchers in the field of cell biology, especially mechanosensing. The work identifies a new context to evaluate the activity of MSL proteins in mechanosensing by identifying two novel suppressors of MSL10 as components of the ER-PM contact sites (EPCS). The work has significance for both the plant and the animal science community providing the basics for various avenues of further research in the area of mechanobiology.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

Presented here is a study on the role of cation chloride cotransporter CCC1 as a key regulator of the plant Trans-Golgi/Early Endosome trafficking network. While the work is well controlled and presented overall, the reviewers judged the data supporting localization of CCC1 to TGN/EE as not being sufficiently clear, as was the role of CCC1 in endocytosis, which is one of the main conclusions. These points can be clarified with future careful experimentation.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript.The reviewers remained anonymous to the authors.)

Evaluation Summary:

The authors make an important contribution to our understanding of the universal mechanism of unloading of sugars from the phloem (the vascular tissue dedicated to long-distance sugar transport in plants) into root tip cells. Specifically, the authors investigate the pores (called plasmodesmata) present in the cell wall separating phloem cells from those cells into which sugars get unloaded in roots, which they found to have the same characteristic structure in all plant species investigated. The physical properties of these particular plasmodesmata suggest that they are especially suited for efficient and selective phloem unloading. The paper is relevant for audiences studying plant physiology and development. There are a few criticisms of the modelling work.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

The work describes the energetic constraints and preferred operating conditions of these "strategies" in particular on how nature has solved the problem of low energy "headroom'" required to prevent deleterious back reactions while maintaining efficient energy storage. The differences between the species are quite interesting and show that nature has evolved multiple solutions to fundamental limitations. Given the importance of understanding and improving the efficiency of photosynthesis, and the new insights revealed, the work will be of interest to a broad audience.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)

Evaluation Summary:

Beginning with transcriptome data, Rhodes et al. identify a new family of peptides with signalling function called CTNIP in the model plant Arabidopsis thaliana. They use an elegant biochemical capture approach to pinpoint the SERK-dependent LRR receptor kinase HSL3 as the only receptor for these peptides. They provide convincing genetic and biochemical evidence that HSL3 binds CTNIP and that CTNIP perception triggers HSL3-dependent cytoplasmic calcium influx, ROS production and transcriptional changes. Furthermore, they provide initial evidence that the CTNIP-HSL3 module may participate in regulating root growth.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

The study provides evidence that PEN1 and SYP122 regulate defense structures against filamentous pathogen infection including papillae formation and encasement of haustoria; this appears to be an ancient defense mechanism in land plants. If the findings that PEN1 and its close homolog SYP122 play an overlapping role in pre- and post-invasive immunity against cell-wall penetrating filamentous pathogens could be further validated, this would advance our understanding of callosic papilla/encasement-based nonhost defense mechanisms.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This study addresses the effect of brassinosteroid hormones on acidification of the apoplast. The authors characterize a novel ionic channel involved in this process as well as a gradient of H+-ATPase activity, providing evidence for a fast brassinosteroid response that has so far received little attention. A combination of computational modeling and quantitative cell physiology is used to explain the regulation of proton pumping into Arabidopsis root cell walls. The authors show that regulation of AHA proton pump activity by the activated brassinosteroid receptor complex could potentially explain the experimentally determined zonation of root cell wall pH and growth. The work will be of interest to plant biologists as well as cell biologists in general.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

Plant cells can grow to extraordinarily large volumes; Arabidopsis root cells, for example, can expand beyond 50um long. Vacuole expansion is correlated with cell elongation, presumably to "fill up" the volume of the cell without requiring a tremendous volume of cytoplasm. Here, the authors carefully characterize a new small molecule inhibitor of endocytic trafficking to the vacuole. This new tool will be valuable to researchers studying endocytic trafficking and vacuole biogenesis in plants.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

The authors present an automated system for phenotyping root system architecture based on bioluminescent roots resulting from a constitutively expressed luciferase transgene (GLO-Root). They have developed a robotics-assisted phenotyping platform and an automated image analysis pipeline for high throughput analysis. An impressive array of 93 luciferase expressing Arabidopsis thaliana accessions provides a major resource for understanding the genetic basis for root system architecture variation in response to a range of environmental conditions. The work will be of interest to plant biologists and all those studying genetic variation in plants.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #3 agreed to share their names with the authors.)