Literature DB >> 30988512

Evolution of buffering in a genetic circuit controlling plant stem cell proliferation.

Daniel Rodriguez-Leal1,2, Cao Xu1,3, Choon-Tak Kwon1, Cara Soyars4, Edgar Demesa-Arevalo1, Jarrett Man5, Lei Liu1, Zachary H Lemmon1,2, Daniel S Jones4, Joyce Van Eck6,7, David P Jackson8, Madelaine E Bartlett9, Zachary L Nimchuk10, Zachary B Lippman11,12.   

Abstract

Precise control of plant stem cell proliferation is necessary for the continuous and reproducible development of plant organs1,2. The peptide ligand CLAVATA3 (CLV3) and its receptor protein kinase CLAVATA1 (CLV1) maintain stem cell homeostasis within a deeply conserved negative feedback circuit1,2. In Arabidopsis, CLV1 paralogs also contribute to homeostasis, by compensating for the loss of CLV1 through transcriptional upregulation3. Here, we show that compensation4,5 operates in diverse lineages for both ligands and receptors, but while the core CLV signaling module is conserved, compensation mechanisms have diversified. Transcriptional compensation between ligand paralogs operates in tomato, facilitated by an ancient gene duplication that impacted the domestication of fruit size. In contrast, we found little evidence for transcriptional compensation between ligands in Arabidopsis and maize, and receptor compensation differs between tomato and Arabidopsis. Our findings show that compensation among ligand and receptor paralogs is critical for stem cell homeostasis, but that diverse genetic mechanisms buffer conserved developmental programs.

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Year:  2019        PMID: 30988512      PMCID: PMC7274162          DOI: 10.1038/s41588-019-0389-8

Source DB:  PubMed          Journal:  Nat Genet        ISSN: 1061-4036            Impact factor:   38.330


  50 in total

1.  Rate of meristem maturation determines inflorescence architecture in tomato.

Authors:  Soon Ju Park; Ke Jiang; Michael C Schatz; Zachary B Lippman
Journal:  Proc Natl Acad Sci U S A       Date:  2011-12-27       Impact factor: 11.205

2.  Efficient gene editing in tomato in the first generation using the clustered regularly interspaced short palindromic repeats/CRISPR-associated9 system.

Authors:  Christopher Brooks; Vladimir Nekrasov; Zachary B Lippman; Joyce Van Eck
Journal:  Plant Physiol       Date:  2014-09-15       Impact factor: 8.340

3.  Functional divergence for every paralog.

Authors:  Patricia S Soria; Kriston L McGary; Antonis Rokas
Journal:  Mol Biol Evol       Date:  2014-01-21       Impact factor: 16.240

4.  Signaling from maize organ primordia via FASCIATED EAR3 regulates stem cell proliferation and yield traits.

Authors:  Byoung Il Je; Jeremy Gruel; Young Koung Lee; Peter Bommert; Edgar Demesa Arevalo; Andrea L Eveland; Qingyu Wu; Alexander Goldshmidt; Robert Meeley; Madelaine Bartlett; Mai Komatsu; Hajime Sakai; Henrik Jönsson; David Jackson
Journal:  Nat Genet       Date:  2016-05-16       Impact factor: 38.330

5.  The tomato genome sequence provides insights into fleshy fruit evolution.

Authors: 
Journal:  Nature       Date:  2012-05-30       Impact factor: 49.962

6.  HTSeq--a Python framework to work with high-throughput sequencing data.

Authors:  Simon Anders; Paul Theodor Pyl; Wolfgang Huber
Journal:  Bioinformatics       Date:  2014-09-25       Impact factor: 6.937

7.  Differential regulation of meristem size, morphology and organization by the ERECTA, CLAVATA and class III HD-ZIP pathways.

Authors:  Tali Mandel; Héctor Candela; Udi Landau; Lior Asis; Einat Zelinger; Cristel C Carles; Leor Eshed Williams
Journal:  Development       Date:  2016-03-17       Impact factor: 6.868

8.  The evolution of inflorescence diversity in the nightshades and heterochrony during meristem maturation.

Authors:  Zachary H Lemmon; Soon Ju Park; Ke Jiang; Joyce Van Eck; Michael C Schatz; Zachary B Lippman
Journal:  Genome Res       Date:  2016-11-07       Impact factor: 9.043

9.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.

Authors:  Daehwan Kim; Geo Pertea; Cole Trapnell; Harold Pimentel; Ryan Kelley; Steven L Salzberg
Journal:  Genome Biol       Date:  2013-04-25       Impact factor: 13.583

10.  An Agrobacterium-delivered CRISPR/Cas9 system for high-frequency targeted mutagenesis in maize.

Authors:  Si Nian Char; Anjanasree K Neelakandan; Hartinio Nahampun; Bronwyn Frame; Marcy Main; Martin H Spalding; Philip W Becraft; Blake C Meyers; Virginia Walbot; Kan Wang; Bing Yang
Journal:  Plant Biotechnol J       Date:  2016-09-05       Impact factor: 9.803

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  41 in total

1.  Enhancing grain-yield-related traits by CRISPR-Cas9 promoter editing of maize CLE genes.

Authors:  Lei Liu; Joseph Gallagher; Edgar Demesa Arevalo; Richelle Chen; Tara Skopelitis; Qingyu Wu; Madelaine Bartlett; David Jackson
Journal:  Nat Plants       Date:  2021-02-22       Impact factor: 15.793

Review 2.  Paired Receptor and Coreceptor Kinases Perceive Extracellular Signals to Control Plant Development.

Authors:  Xiaoping Gou; Jia Li
Journal:  Plant Physiol       Date:  2020-03-06       Impact factor: 8.340

Review 3.  Genetic dissection of the auxin response network.

Authors:  Alon Israeli; Jason W Reed; Naomi Ori
Journal:  Nat Plants       Date:  2020-08-17       Impact factor: 15.793

4.  The maize heterotrimeric G protein β subunit controls shoot meristem development and immune responses.

Authors:  Qingyu Wu; Fang Xu; Lei Liu; Si Nian Char; Yezhang Ding; Byoung Il Je; Eric Schmelz; Bing Yang; David Jackson
Journal:  Proc Natl Acad Sci U S A       Date:  2019-12-18       Impact factor: 11.205

5.  Variation burst during dedifferentiation and increased CHH-type DNA methylation after 30 years of in vitro culture of sweet orange.

Authors:  Xia Wang; Lili Ke; Shuting Wang; Jialing Fu; Jidi Xu; Yujin Hao; Chunying Kang; Wenwu Guo; Xiuxin Deng; Qiang Xu
Journal:  Hortic Res       Date:  2022-01-18       Impact factor: 6.793

Review 6.  CLE peptides: critical regulators for stem cell maintenance in plants.

Authors:  Xiu-Fen Song; Xiu-Li Hou; Chun-Ming Liu
Journal:  Planta       Date:  2021-11-29       Impact factor: 4.116

7.  Shoot meristem maintenance and immune response signaling converge at the G protein β subunit.

Authors:  Kevin Rodriguez; G Venugopala Reddy
Journal:  Proc Natl Acad Sci U S A       Date:  2020-01-14       Impact factor: 11.205

8.  Dissecting cis-regulatory control of quantitative trait variation in a plant stem cell circuit.

Authors:  Xingang Wang; Lyndsey Aguirre; Daniel Rodríguez-Leal; Anat Hendelman; Matthias Benoit; Zachary B Lippman
Journal:  Nat Plants       Date:  2021-04-12       Impact factor: 15.793

9.  CLAVATA Signaling Ensures Reproductive Development in Plants across Thermal Environments.

Authors:  Daniel S Jones; Amala John; Kylie R VanDerMolen; Zachary L Nimchuk
Journal:  Curr Biol       Date:  2020-11-05       Impact factor: 10.834

Review 10.  Next Generation Cereal Crop Yield Enhancement: From Knowledge of Inflorescence Development to Practical Engineering by Genome Editing.

Authors:  Lei Liu; Penelope L Lindsay; David Jackson
Journal:  Int J Mol Sci       Date:  2021-05-13       Impact factor: 5.923

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