1
|
LaFountain AM, Lin Q, McMahon HE, Min Y, Ding B, Gurung V, Seemann JR, Yuan YW. A distinct foliar pigmentation pattern formed by activator-repressor gradients upstream of an anthocyanin-activating R2R3-MYB. Cell Rep 2024; 43:114444. [PMID: 38990723 DOI: 10.1016/j.celrep.2024.114444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 05/24/2024] [Accepted: 06/20/2024] [Indexed: 07/13/2024] Open
Abstract
The emergence of novel traits is often preceded by a potentiation phase, when all the genetic components necessary for producing the trait are assembled. However, elucidating these potentiating factors is challenging. We have previously shown that an anthocyanin-activating R2R3-MYB, STRIPY, triggers the emergence of a distinct foliar pigmentation pattern in the monkeyflower Mimulus verbenaceus. Here, using forward and reverse genetics approaches, we identify three potentiating factors that pattern STRIPY expression: MvHY5, a master regulator of light signaling that activates STRIPY and is expressed throughout the leaf, and two leaf developmental regulators, MvALOG1 and MvTCP5, that are expressed in opposing gradients along the leaf proximodistal axis and negatively regulate STRIPY. These results provide strong empirical evidence that phenotypic novelties can be potentiated through incorporation into preexisting genetic regulatory networks and highlight the importance of positional information in patterning the novel foliar stripe.
Collapse
Affiliation(s)
- Amy M LaFountain
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Storrs, CT 06269-3043, USA.
| | - Qiaoshan Lin
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Storrs, CT 06269-3043, USA
| | - Hayley E McMahon
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Storrs, CT 06269-3043, USA
| | - Ya Min
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Storrs, CT 06269-3043, USA
| | - Baoqing Ding
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Storrs, CT 06269-3043, USA
| | - Vandana Gurung
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Storrs, CT 06269-3043, USA
| | - Jeffrey R Seemann
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Storrs, CT 06269-3043, USA
| | - Yao-Wu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Storrs, CT 06269-3043, USA; Institute for Systems Genomics, University of Connecticut, 67 North Eagleville Road, Storrs, CT 06269, USA.
| |
Collapse
|
2
|
Kim DS, Li Y, Ahn HK, Woods-Tör A, Cevik V, Furzer OJ, Ma W, Tör M, Jones JDG. ATR2 C ala2 from Arabidopsis-infecting downy mildew requires 4 TIR-NLR immune receptors for full recognition. THE NEW PHYTOLOGIST 2024; 243:330-344. [PMID: 38742296 DOI: 10.1111/nph.19790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 04/17/2024] [Indexed: 05/16/2024]
Abstract
Arabidopsis Col-0 RPP2A and RPP2B confer recognition of Arabidopsis downy mildew (Hyaloperonospora arabidopsidis [Hpa]) isolate Cala2, but the identity of the recognized ATR2Cala2 effector was unknown. To reveal ATR2Cala2, an F2 population was generated from a cross between Hpa-Cala2 and Hpa-Noks1. We identified ATR2Cala2 as a non-canonical RxLR-type effector that carries a signal peptide, a dEER motif, and WY domains but no RxLR motif. Recognition of ATR2Cala2 and its effector function were verified by biolistic bombardment, ectopic expression and Hpa infection. ATR2Cala2 is recognized in accession Col-0 but not in Ler-0 in which RPP2A and RPP2B are absent. In ATR2Emoy2 and ATR2Noks1 alleles, a frameshift results in an early stop codon. RPP2A and RPP2B are essential for the recognition of ATR2Cala2. Stable and transient expression of ATR2Cala2 under 35S promoter in Arabidopsis and Nicotiana benthamiana enhances disease susceptibility. Two additional Col-0 TIR-NLR (TNL) genes (RPP2C and RPP2D) adjacent to RPP2A and RPP2B are quantitatively required for full resistance to Hpa-Cala2. We compared RPP2 haplotypes in multiple Arabidopsis accessions and showed that all four genes are present in all ATR2Cala2-recognizing accessions.
Collapse
Affiliation(s)
- Dae Sung Kim
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, 430062, China
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Yufei Li
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Hee-Kyung Ahn
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Alison Woods-Tör
- Department of Biological Sciences, School of Science and the Environment, University of Worcester, Worcester, WR2 6AJ, UK
| | - Volkan Cevik
- Department of Life Sciences, The Milner Centre for Evolution, University of Bath, Bath, BA2 7AY, UK
| | - Oliver J Furzer
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Wenbo Ma
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Mahmut Tör
- Department of Biological Sciences, School of Science and the Environment, University of Worcester, Worcester, WR2 6AJ, UK
| | | |
Collapse
|
3
|
Wang Z, Wang R, Yuan H, Fan F, Li S, Cheng M, Tian Z. Comprehensive identification and analysis of DUF640 genes associated with rice growth. Gene 2024; 914:148404. [PMID: 38521113 DOI: 10.1016/j.gene.2024.148404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/13/2024] [Accepted: 03/20/2024] [Indexed: 03/25/2024]
Abstract
Protein domains with conserved amino acid sequences and uncharacterized functions are called domains of unknown function (DUF). The DUF640 gene family plays a crucial role in plant growth, particularly in light regulation, floral organ development, and fruit development. However, there exists a lack of systematic understanding of the evolutionary relationships and functional differentiation of DUF640 within the Oryza genus. In this study, 61 DUF640 genes were identified in the Oryza genus. The expression of DUF640s is induced by multiple hormonal stressors including abscisic acid (ABA), cytokinin (CK), ethylene (ETH), and indole-3-acetic acid (IAA). Specifically, OiDUF640-10 expression significantly increased after ETH treatment. Transgenic experiments showed that overexpressing OiDUF640-10 lines were sensitive to ETH, and seedling length was obstructed. Evolutionary analysis revealed differentiation of the OiDUF640-10 gene in O. sativa ssp. indica and japonica varieties, likely driven by natural selection during the domestication of cultivated rice. These results indicate that OiDUF640-10 plays a vital role in the regulation of rice seedling length.
Collapse
Affiliation(s)
- Zhikai Wang
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, College of Life Science, Yangtze University, Jingzhou, China
| | - Ruihua Wang
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China
| | - Huanran Yuan
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Fengfeng Fan
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Mingxing Cheng
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China.
| | - Zhihong Tian
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, College of Life Science, Yangtze University, Jingzhou, China.
| |
Collapse
|
4
|
Gauley A, Pasquariello M, Yoshikawa GV, Alabdullah AK, Hayta S, Smedley MA, Dixon LE, Boden SA. Photoperiod-1 regulates the wheat inflorescence transcriptome to influence spikelet architecture and flowering time. Curr Biol 2024; 34:2330-2343.e4. [PMID: 38781956 PMCID: PMC11149547 DOI: 10.1016/j.cub.2024.04.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/08/2024] [Accepted: 04/11/2024] [Indexed: 05/25/2024]
Abstract
Photoperiod insensitivity has been selected by breeders to help adapt crops to diverse environments and farming practices. In wheat, insensitive alleles of Photoperiod-1 (Ppd-1) relieve the requirement of long daylengths to flower by promoting expression of floral promoting genes early in the season; however, these alleles also limit yield by reducing the number and fertility of grain-producing florets through processes that are poorly understood. Here, we performed transcriptome analysis of the developing inflorescence using near-isogenic lines that contain either photoperiod-insensitive or null alleles of Ppd-1, during stages when spikelet number is determined and floret development initiates. We report that Ppd-1 influences the stage-specific expression of genes with roles in auxin signaling, meristem identity, and protein turnover, and analysis of differentially expressed transcripts identified bZIP and ALOG transcription factors, namely PDB1 and ALOG1, which regulate flowering time and spikelet architecture. These findings enhance our understanding of genes that regulate inflorescence development and introduce new targets for improving yield potential.
Collapse
Affiliation(s)
- Adam Gauley
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK; Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Marianna Pasquariello
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Guilherme V Yoshikawa
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Hartley Grove, Glen Osmond, SA 5064, Australia
| | - Abdul Kader Alabdullah
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Sadiye Hayta
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Mark A Smedley
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Laura E Dixon
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK; Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Scott A Boden
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK; School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Hartley Grove, Glen Osmond, SA 5064, Australia.
| |
Collapse
|
5
|
Li M, Jiao Y. Cereal genetics: Novel modulators of spikelet number and flowering time. Curr Biol 2024; 34:R528-R530. [PMID: 38834023 DOI: 10.1016/j.cub.2024.04.071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
The spikelet is the unit component of the spike and the site of grain production in Triticeae crops. Two new studies revealed that plant-specific transcription factors ALOG1 and PDB1 participate in modulating spikelet number and flowering time in barley and wheat.
Collapse
Affiliation(s)
- Mingjiu Li
- Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Peking University Institute of Advanced Agricultural Sciences, Shandong, China.
| | - Yuling Jiao
- Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Peking University Institute of Advanced Agricultural Sciences, Shandong, China; School of Life Sciences, State Key Laboratory for Protein and Plant Gene Research, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
| |
Collapse
|
6
|
Jiang G, Koppolu R, Rutten T, Hensel G, Lundqvist U, Tandron Moya YA, Huang Y, Rajaraman J, Poursarebani N, von Wirén N, Kumlehn J, Mascher M, Schnurbusch T. Non-cell-autonomous signaling associated with barley ALOG1 specifies spikelet meristem determinacy. Curr Biol 2024; 34:2344-2358.e5. [PMID: 38781954 DOI: 10.1016/j.cub.2024.04.083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/18/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
Inflorescence architecture and crop productivity are often tightly coupled in our major cereal crops. However, the underlying genetic mechanisms controlling cereal inflorescence development remain poorly understood. Here, we identified recessive alleles of barley (Hordeum vulgare L.) HvALOG1 (Arabidopsis thaliana LSH1 and Oryza G1) that produce non-canonical extra spikelets and fused glumes abaxially to the central spikelet from the upper-mid portion until the tip of the inflorescence. Notably, we found that HvALOG1 exhibits a boundary-specific expression pattern that specifically excludes reproductive meristems, implying the involvement of previously proposed localized signaling centers for branch regulation. Importantly, during early spikelet formation, non-cell-autonomous signals associated with HvALOG1 expression may specify spikelet meristem determinacy, while boundary formation of floret organs appears to be coordinated in a cell-autonomous manner. Moreover, barley ALOG family members synergistically modulate inflorescence morphology, with HvALOG1 predominantly governing meristem maintenance and floral organ development. We further propose that spatiotemporal redundancies of expressed HvALOG members specifically in the basal inflorescence may be accountable for proper patterning of spikelet formation in mutant plants. Our research offers new perspectives on regulatory signaling roles of ALOG transcription factors during the development of reproductive meristems in cereal inflorescences.
Collapse
Affiliation(s)
- Guojing Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Ravi Koppolu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Goetz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | | | - Yudelsy Antonia Tandron Moya
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Yongyu Huang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Jeyaraman Rajaraman
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Naser Poursarebani
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Nicolaus von Wirén
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany; Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany.
| |
Collapse
|
7
|
Liu Z, Fan Z, Wang L, Zhang S, Xu W, Zhao S, Fang S, Liu M, Kofi SM, Zhang S, Kang N, Ai H, Li R, Feng T, Wei S, Zhao H. Expression profiling of ALOG family genes during inflorescence development and abiotic stress responses in rice ( Oryza sativa L.). Front Genet 2024; 15:1381690. [PMID: 38650857 PMCID: PMC11033443 DOI: 10.3389/fgene.2024.1381690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 03/25/2024] [Indexed: 04/25/2024] Open
Abstract
The ALOG (Arabidopsis LSH1 and Oryza G1) family proteins, namely, DUF640 domain-containing proteins, have been reported to function as transcription factors in various plants. However, the understanding of the response and function of ALOG family genes during reproductive development and under abiotic stress is still largely limited. In this study, we comprehensively analyzed the structural characteristics of ALOG family proteins and their expression profiles during inflorescence development and under abiotic stress in rice. The results showed that OsG1/OsG1L1/2/3/4/5/6/7/8/9 all had four conserved helical structures and an inserted Zinc-Ribbon (ZnR), the other four proteins OsG1L10/11/12/13 lacked complete Helix-1 and Helix-2. In the ALOG gene promoters, there were abundant cis-acting elements, including ABA, MeJA, and drought-responsive elements. Most ALOG genes show a decrease in expression levels within 24 h under ABA and drought treatments, while OsG1L2 expression levels show an upregulated trend under ABA and drought treatments. The expression analysis at different stages of inflorescence development indicated that OsG1L1/2/3/8/11 were mainly expressed in the P1 stage; in the P4 stage, OsG1/OsG1L4/5/9/12 had a higher expression level. These results lay a good foundation for further studying the expression of rice ALOG family genes under abiotic stresses, and provide important experimental support for their functional research.
Collapse
Affiliation(s)
- Zhiyuan Liu
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Zhenjiang Fan
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Lei Wang
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Siyue Zhang
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Weichen Xu
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Sijie Zhao
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Sijia Fang
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Mei Liu
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Sackitey Mark Kofi
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Shuangxi Zhang
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Ningning Kang
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Hao Ai
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Ruining Li
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Tingting Feng
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Shuya Wei
- College of Bioengineering, Wuhan Polytechnic University, Wuhan, China
| | - Heming Zhao
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, China
| |
Collapse
|
8
|
Rieu P, Beretta VM, Caselli F, Thévénon E, Lucas J, Rizk M, Franchini E, Caporali E, Paleni C, Nanao MH, Kater MM, Dumas R, Zubieta C, Parcy F, Gregis V. The ALOG domain defines a family of plant-specific transcription factors acting during Arabidopsis flower development. Proc Natl Acad Sci U S A 2024; 121:e2310464121. [PMID: 38412122 PMCID: PMC10927535 DOI: 10.1073/pnas.2310464121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/05/2023] [Indexed: 02/29/2024] Open
Abstract
The ALOG (Arabidopsis LIGHT-DEPENDENT SHORT HYPOCOTYLS 1 (LSH1) and Oryza G1) proteins are conserved plant-specific Transcription Factors (TFs). They play critical roles in the development of various plant organs (meristems, inflorescences, floral organs, and nodules) from bryophytes to higher flowering plants. Despite the fact that the first members of this family were originally discovered in Arabidopsis, their role in this model plant has remained poorly characterized. Moreover, how these transcriptional regulators work at the molecular level is unknown. Here, we study the redundant function of the ALOG proteins LSH1,3,4 from Arabidopsis. We uncover their role in the repression of bract development and position them within a gene regulatory network controlling this process and involving the floral regulators LEAFY, BLADE-ON-PETIOLE, and PUCHI. Next, using in vitro genome-wide studies, we identified the conserved DNA motif bound by ALOG proteins from evolutionarily distant species (the liverwort Marchantia polymorpha and the flowering plants Arabidopsis, tomato, and rice). Resolution of the crystallographic structure of the ALOG DNA-binding domain in complex with DNA revealed the domain is a four-helix bundle with a disordered NLS and a zinc ribbon insertion between helices 2 and 3. The majority of DNA interactions are mediated by specific contacts made by the third alpha helix and the NLS. Taken together, this work provides the biochemical and structural basis for DNA-binding specificity of an evolutionarily conserved TF family and reveals its role as a key player in Arabidopsis flower development.
Collapse
Affiliation(s)
- Philippe Rieu
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre national de la recherche scientifique, Commissariat à l’énergie atomique et aux énergies alternatives, Institut national de recherche pour l’agriculture, l’alimentation et l’environnement, Département de Biologie Structurale et Cellulaire intégrée, GrenobleF-38054, France
| | | | - Francesca Caselli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano20133, Italy
| | - Emmanuel Thévénon
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre national de la recherche scientifique, Commissariat à l’énergie atomique et aux énergies alternatives, Institut national de recherche pour l’agriculture, l’alimentation et l’environnement, Département de Biologie Structurale et Cellulaire intégrée, GrenobleF-38054, France
| | - Jérémy Lucas
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre national de la recherche scientifique, Commissariat à l’énergie atomique et aux énergies alternatives, Institut national de recherche pour l’agriculture, l’alimentation et l’environnement, Département de Biologie Structurale et Cellulaire intégrée, GrenobleF-38054, France
| | - Mahmoud Rizk
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble38000, France
| | - Emanuela Franchini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano20133, Italy
| | - Elisabetta Caporali
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano20133, Italy
| | - Chiara Paleni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano20133, Italy
| | - Max H. Nanao
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble38000, France
| | - Martin M. Kater
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano20133, Italy
| | - Renaud Dumas
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre national de la recherche scientifique, Commissariat à l’énergie atomique et aux énergies alternatives, Institut national de recherche pour l’agriculture, l’alimentation et l’environnement, Département de Biologie Structurale et Cellulaire intégrée, GrenobleF-38054, France
| | - Chloe Zubieta
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre national de la recherche scientifique, Commissariat à l’énergie atomique et aux énergies alternatives, Institut national de recherche pour l’agriculture, l’alimentation et l’environnement, Département de Biologie Structurale et Cellulaire intégrée, GrenobleF-38054, France
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre national de la recherche scientifique, Commissariat à l’énergie atomique et aux énergies alternatives, Institut national de recherche pour l’agriculture, l’alimentation et l’environnement, Département de Biologie Structurale et Cellulaire intégrée, GrenobleF-38054, France
| | - Veronica Gregis
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano20133, Italy
| |
Collapse
|
9
|
Turchetto C, Silvério ADC, Waschburger EL, Lacerda MEG, Quintana IV, Turchetto-Zolet AC. Genome-wide identification and evolutionary view of ALOG gene family in Solanaceae. Genet Mol Biol 2023; 46:e20230142. [PMID: 38048778 PMCID: PMC10695626 DOI: 10.1590/1415-4757-gmb-2023-0142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/10/2023] [Indexed: 12/06/2023] Open
Abstract
The ALOG gene family, which was named after its earliest identified members ( Arabidopsis LSH1 and Oryza G1), encodes a class of transcription factors (TF) characterized by the presence of a highly conserved ALOG domain. These proteins are found in various plant species playing regulatory roles in plant growth, development, and morphological diversification of inflorescence. The functional characterization of these genes in some plant species has demonstrated their involvement in floral architecture. In this study, we used a genome-wide and phylogenetic approach to gain insights into plants' origin, diversification, and functional aspects of the ALOG gene family. In total, 648 ALOG homologous genes were identified in 77 Viridiplantae species, and their evolutionary relationships were inferred using maximum likelihood phylogenetic analyses. Our results suggested that the ALOG gene family underwent several rounds of gene duplication and diversification during angiosperm evolution. Furthermore, we found three functional orthologous groups in Solanaceae species. The study provides insights into the evolutionary history and functional diversification of the ALOG gene family, which could aid in understanding the mechanisms underlying floral architecture in angiosperms.
Collapse
Affiliation(s)
- Caroline Turchetto
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Botânica (PPGBOT), Departamento de Botânica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Porto Alegre, RS, Brazil
| | - Ariadne de Castro Silvério
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Botânica (PPGBOT), Departamento de Botânica, Porto Alegre, RS, Brazil
| | - Edgar Luis Waschburger
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Porto Alegre, RS, Brazil
| | - Maria Eduarda Gonçalves Lacerda
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Porto Alegre, RS, Brazil
| | - Isadora Vieira Quintana
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Porto Alegre, RS, Brazil
| | - Andreia Carina Turchetto-Zolet
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Porto Alegre, RS, Brazil
| |
Collapse
|
10
|
Adam H, Gutiérrez A, Couderc M, Sabot F, Ntakirutimana F, Serret J, Orjuela J, Tregear J, Jouannic S, Lorieux M. Genomic introgressions from African rice (Oryza glaberrima) in Asian rice (O. sativa) lead to the identification of key QTLs for panicle architecture. BMC Genomics 2023; 24:587. [PMID: 37794325 PMCID: PMC10548634 DOI: 10.1186/s12864-023-09695-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Developing high yielding varieties is a major challenge for breeders tackling the challenges of climate change in agriculture. The panicle (inflorescence) architecture of rice is one of the key components of yield potential and displays high inter- and intra-specific variability. The genus Oryza features two different crop species: Asian rice (Oryza sativa L.) and the African rice (O. glaberrima Steud.). One of the main morphological differences between the two independently domesticated species is the structure (or complexity) of the panicle, with O. sativa displaying a highly branched panicle, which in turn produces a larger number of grains than that of O. glaberrima. The gene regulatory network that governs intra- and interspecific panicle diversity is still under-studied. RESULTS To identify genetic factors linked to panicle architecture diversity in the two species, we used a set of 60 Chromosome Segment Substitution Lines (CSSLs) issued from third generation backcross (BC3DH) and carrying genomic segments from O. glaberrima cv. MG12 in the genetic background of O. sativa Tropical Japonica cv. Caiapó. Phenotypic data were collected for rachis and primary branch length, primary, secondary and tertiary branch number and spikelet number. A total of 15 QTLs were localized on chromosomes 1, 2, 3, 7, 11 and 12, QTLs associated with enhanced secondary and tertiary branch numbers were detected in two CSSLs. Furthermore, BC4F3:5 lines carrying different combinations of substituted segments were produced to decipher the effects of the identified QTL regions on variations in panicle architecture. A detailed analysis of phenotypes versus genotypes was carried out between the two parental genomes within these regions in order to understand how O. glaberrima introgression events may lead to alterations in panicle traits. CONCLUSION Our analysis led to the detection of genomic variations between O. sativa cv. Caiapó and O. glaberrima cv. MG12 in regions associated with enhanced panicle traits in specific CSSLs. These regions contain a number of key genes that regulate panicle development in O. sativa and their interspecific genomic variations may explain the phenotypic effects observed.
Collapse
Affiliation(s)
- Hélène Adam
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France.
| | | | - Marie Couderc
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | - François Sabot
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | | | - Julien Serret
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | - Julie Orjuela
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | - James Tregear
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France
| | - Stefan Jouannic
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France.
| | - Mathias Lorieux
- UMR DIADE, University of Montpellier, IRD, Cirad, Montpellier, France.
- Agrobiodiversity Unit, Alliance Bioversity-CIAT, Cali, Colombia.
| |
Collapse
|