Plant Biology

Computational modeling of cambium activity provides a regulatory framework for simulating radial plant growth

1. Ivan Lebovka
2. Bruno Hay Mele
3. Xiaomin Liu
4. Alexandra Zakieva
5. Theresa Schlamp
6. Nial Rau Gursanscky
7. Roeland MH Merks
8. Ruth Großeholz
9. Thomas Greb

• Curated by eLife

  Evaluation Summary:

  The paper presents a sequence of models, simulating with increasing accuracy the production of phloem and xylem in a cross-section of a generalized circularly symmetric plant organ. The results may serve as a stepping stone for the construction of predictive models.

  (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 #2 agreed to share their name with the authors.)

Reviewed by eLife

Production of ORF8 protein from SARS-CoV-2 using an inducible virus-mediated expression system in suspension-cultured tobacco BY-2 cells

1. Tomohiro Imamura
2. Noriyoshi Isozumi
3. Yasuki Higashimura
4. Shinya Ohki
5. Masashi Mori

Reviewed by ScreenIT

Rapid expression of COVID-19 proteins by transient expression in tobacco

1. Penelope Lindsay
2. Amanda Ackerman
3. Yinan Jian
4. Oliver Artz
5. Daniele Rosado
6. Tara Skopelitis
7. Munenori Kitagawa
8. Ullas V. Pedmale
9. David Jackson

Reviewed by ScreenIT

Genomic basis of drought resistance in Fagus sylvatica

1. Markus Pfenninger
2. Friederike Reuss
3. Angelika Kiebler
4. Philipp Schönnenbeck
5. Cosima Caliendo
6. Susanne Gerber
7. Berardino Cocchiararo
8. Sabrina Reuter
9. Nico Blüthgen
10. Karsten Mody
11. Bagdevi Mishra
12. Miklós Bálint
13. Marco Thines
14. Barbara Feldmeyer

• Curated by eLife

  Evaluation Summary:

  This study uses a genome-wide association approach combining pool-seq data with whole-genome resequencing, which provides a cost-effective means to scale genome-wide association studies to a larger number of individuals, to dissect the genetic basis of drought resistance in several German populations of European beech. European beech is an ecologically important forest tree species and drought resistance is a trait that is likely to be becoming increasingly relevant to the survival of these trees as climate change leads to more frequent and prolonged periods of drought. Knowledge of the genetic basis of such variation existing within current populations can help with management of those populations in the face of increasing threats, especially when such information is used to develop tools for predicting individuals that are likely to have the highest chances of survival, and to suggest hypotheses regarding traits and genetic material which will be important for the future of forests.

  (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.)

Reviewed by eLife

Repression by the Arabidopsis TOPLESS corepressor requires association with the core Mediator complex

1. Alexander R. Leydon
2. Wei Wang
3. Hardik P. Gala
4. Sabrina Gilmour
5. Samuel Juarez-Solis
6. Mollye L. Zahler
7. Joseph E. Zemke
8. Ning Zheng
9. Jennifer L. Nemhauser

• Curated by eLife

  Evaluation Summary:

  In this study, Leydon et al. use an elegant multi-component genetic system to address the mechanisms of repression by the Arabadopsis TOPLESS (Tpl) protein. Taking advantage of the genetic tools and knowledge of the structure of the Tpl protein, the authors determine two short alpha helical regions that act as independent repression domains, with the target of one of these domains being the N-terminal region of the Med21 subunit of the mediator complex. Experiments are presented that indicate that Tpl mediated repression involves formation of a promoter complex comprising the mediator complex along with several general transcription factors, but lacking RNA polymerase II. The experimental data comes from both heterologous experimental systems in yeast and the native plant setting and involves diverse but complementary experimental approaches that converge towards a model for gene repression. This paper will be of interest to researchers investigating the mechanisms regulating gene expression, in particular how specific protein-protein interactions repress gene expression.

  (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.)

Reviewed by eLife

Organ geometry channels cell fate in the Arabidopsis ovule primordium

1. Elvira Hernandez-Lagana
2. Gabriella Mosca
3. Ethel Mendocilla Sato
4. Nuno Pires
5. Anja Frey
6. Alejandro Giraldo-Fonseca
7. Ueli Grossniklaus
8. Olivier Hamant
9. Christophe Godin
10. Arezki Boudaoud
11. Daniel Grimanelli
12. Daphné Autran
13. Célia Baroux

• Curated by eLife

  Evaluation Summary:

  The authors use imaging analysis of Arabidopsis developing ovule primordia until the onset of meiosis to clarify the importance of organ morphogenesis in cell fate. They first document the growth of ovule cells in three dimensions, then use computational modelling to predict factors underlying ovule growth, shape and spore mother cell (SMC) differentiation. They test this model through analysis of a mutant of Katanin, encoding a microtubule-severing protein. Overall, this work is elegant, adds new information and confirms previous hypotheses for the field. A well appreciated feature of this paper is OvuleViz, an R-based software tool that they developed, which will provide a consistent way for others to analyze mutants with similar phenotypic abnormalities.

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

Reviewed by eLife

Multi-dimensional leaf phenotypes reflect root system genotype in grafted grapevine over the growing season

1. Zachary N Harris
2. Mani Awale
3. Niyati Bhakta
4. Daniel H Chitwood
5. Anne Fennell
6. Emma Frawley
7. Laura L Klein
8. Laszlo G Kovacs
9. Misha Kwasniewski
10. Jason P Londo
11. Qin Ma
12. Zoë Migicovsky
13. Joel F Swift
14. Allison J Miller

• Curated by eLife

  Summary: Experimentally, this is a very solid and nicely replicated experimental design that provides a strong ability to interrogate the questions at hand. Both reviewers had a concern that the use of PCs was underpowering the analysis to test the key questions that were the goal of the experiment. The manuscript could also be improved by working to interleave the different omics datasets to develop a deeper insight.

Reviewed by eLife

A spatial model of the plant circadian clock reveals design principles for coordinated timing

1. Mark Greenwood
2. Isao T Tokuda
3. James C W Locke

Reviewed by Review Commons

Expansin-controlled cell wall stiffness regulates root growth in Arabidopsis

1. Marketa Samalova
2. Kareem Elsayad
3. Alesia Melnikava
4. Alexis Peaucelle
5. Evelina Gahurova
6. Jaromir Gumulec
7. Ioannis Spyroglou
8. Elena V. Zemlyanskaya
9. Elena V. Ubogoeva
10. Jan Hejatko

• Curated by eLife

  Summary: The reviewers felt that this is important work because in vivo characterization of expansins has lagged far behind their in vitro characterization. However, both reviewers also made important points about additional controls and statistical comparisons that are required to fully interpret and appreciate the results that are presented here. It seems that the role of expansins in the plant cell wall may be complex and nuanced. However, it is clear from the author's discussion of their results that significant further experimentation is required to bring new insight to the function of expansins in mediating plant root growth.

Reviewed by eLife

A multifaceted analysis reveals two distinct phases of chloroplast biogenesis during de-etiolation in Arabidopsis

1. Rosa Pipitone
2. Simona Eicke
3. Barbara Pfister
4. Gaetan Glauser
5. Denis Falconet
6. Clarisse Uwizeye
7. Thibaut Pralon
8. Samuel C Zeeman
9. Felix Kessler
10. Emilie Demarsy

• Curated by eLife

  Summary: All three reviewers as well as myself are impressed by the in depth and multi-method analysis of chloroplast and thylakoid membrane development provided in your study, including time courses of 3D imaging combining TEM, SBF-SEM and confocal microscopy, lipidomics and proteomics. However, some analyses need to be improved and/or better explained.

  • There is a concern about the proteomics analysis, as the low number of proteins changing in abundance upon de-etiolation is unexpected. It is not clear how the samples were harvested. Were they harvested in the light and could that have influenced protein abundance? The harvesting procedure needs to be better explained. Or is the proteomics method not sensitive enough? The proteomics should be validated, for example by Western Blots with well-established marker proteins such as phyA and HY5.

  • Please also add loading controls to Fig 6 and the associated supplemental figure.

  • Please explain better how the volume of dividing chloroplasts was determined.

Reviewed by eLife