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Cenci A, Rouard M. Evolutionary Analyses of GRAS Transcription Factors in Angiosperms. FRONTIERS IN PLANT SCIENCE 2017; 8:273. [PMID: 28303145 PMCID: PMC5332381 DOI: 10.3389/fpls.2017.00273] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 02/14/2017] [Indexed: 05/21/2023]
Abstract
GRAS transcription factors (TFs) play critical roles in plant growth and development such as gibberellin and mycorrhizal signaling. Proteins belonging to this gene family contain a typical GRAS domain in the C-terminal sequence, whereas the N-terminal region is highly variable. Although, GRAS genes have been characterized in a number of plant species, their classification is still not completely resolved. Based on a panel of eight representative species of angiosperms, we identified 29 orthologous groups or orthogroups (OGs) for the GRAS gene family, suggesting that at least 29 ancestor genes were present in the angiosperm lineage before the "Amborella" evolutionary split. Interestingly, some taxonomic groups were missing members of one or more OGs. The gene number expansion usually observed in transcription factors was not observed in GRAS while the genome triplication ancestral to the eudicots (γ hexaploidization event) was detectable in a limited number of GRAS orthogroups. We also found conserved OG-specific motifs in the variable N-terminal region. Finally, we could regroup OGs in 17 subfamilies for which names were homogenized based on a literature review and described 5 new subfamilies (DLT, RAD1, RAM1, SCLA, and SCLB). This study establishes a consistent framework for the classification of GRAS members in angiosperm species, and thereby a tool to correctly establish the orthologous relationships of GRAS genes in most of the food crops in order to facilitate any subsequent functional analyses in the GRAS gene family. The multi-fasta file containing all the sequences used in our study could be used as database to perform diagnostic BLASTp to classify GRAS genes from other non-model species.
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Affiliation(s)
- Alberto Cenci
- Bioversity InternationalMontpellier, France
- CGIAR Research Programme on Roots, Tubers and BananasMontpellier, France
- *Correspondence: Alberto Cenci
| | - Mathieu Rouard
- Bioversity InternationalMontpellier, France
- CGIAR Research Programme on Roots, Tubers and BananasMontpellier, France
- Mathieu Rouard
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Cai H, Chen Y, Zhang M, Cai R, Cheng B, Ma Q, Zhao Y. A novel GRAS transcription factor, ZmGRAS20, regulates starch biosynthesis in rice endosperm. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:143-154. [PMID: 28250591 PMCID: PMC5313408 DOI: 10.1007/s12298-016-0404-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/29/2016] [Indexed: 05/07/2023]
Abstract
Starch occupies the maximal component of cereal grains and is pivotal for maize yield and quality. However, the regulatory mechanism of starch synthesis is still poorly understand. In this study, a GRAS transcription factor, ZmGRAS20, was isolated from maize inbred line B73 based on transcriptome sequencing. Quantitative real-time PCR indicated that ZmGRAS20 is specifically expressed in maize endosperm. Transient expression of ZmGRAS20-green fluorescent protein fusion protein in tobacco cells showed a nucleus and membrane localization of the protein. Transactivation assay of ZmGRAS20 demonstrated that it has no transactivation activity in yeast cells. Overexpression of ZmGRAS20 led to a chalky region of ventral endosperm with decreased starch content and defective agronomic characters in transgenic seeds. Moreover, ZmGRAS20-overexpression plants had fewer fractions of long-branched starch chains. Further scanning electron microscopy observation of ZmGRAS20 transgenic seeds exhibited altered starch granules morphology compared with wide type plants. Taken together, these results suggested that ZmGRAS20 may function as a starch synthesis regulatory factor in rice endosperm.
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Affiliation(s)
- Huilin Cai
- National Engineering Laboratory of Crop Stress Resistance/Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
| | - Yulong Chen
- National Engineering Laboratory of Crop Stress Resistance/Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
| | - Min Zhang
- National Engineering Laboratory of Crop Stress Resistance/Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
| | - Ronghao Cai
- National Engineering Laboratory of Crop Stress Resistance/Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
| | - Beijiu Cheng
- National Engineering Laboratory of Crop Stress Resistance/Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
| | - Qing Ma
- National Engineering Laboratory of Crop Stress Resistance/Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
| | - Yang Zhao
- National Engineering Laboratory of Crop Stress Resistance/Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
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Molecular cloning, phylogenetic analysis, and expression patterns of LATERAL SUPPRESSOR-LIKE and REGULATOR OF AXILLARY MERISTEM FORMATION-LIKE genes in sunflower (Helianthus annuus L.). Dev Genes Evol 2016; 227:159-170. [PMID: 28035495 DOI: 10.1007/s00427-016-0571-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 12/21/2016] [Indexed: 10/20/2022]
Abstract
The wild sunflower (Helianthus annuus) plants develop a highly branched form with numerous small flowering heads. The origin of a no branched sunflower, producing a single large head, has been a key event in the domestication process of this species. The interaction between hormonal factors and several genes organizes the initiation and outgrowth of axillary meristems (AMs). From sunflower, we have isolated two genes putatively involved in this process, LATERAL SUPPRESSOR (LS)-LIKE (Ha-LSL) and REGULATOR OF AXILLARY MERISTEM FORMATION (ROX)-LIKE (Ha-ROXL), encoding for a GRAS and a bHLH transcription factor (TF), respectively. Typical amino acid residues and phylogenetic analyses suggest that Ha-LSL and Ha-ROXL are the orthologs of the branching regulator LS and ROX/LAX1, involved in the growth habit of both dicot and monocot species. qRT-PCR analyses revealed a high accumulation of Ha-LSL transcripts in roots, vegetative shoots, and inflorescence shoots. By contrast, in internodal stems and young leaves, a lower amount of Ha-LSL transcripts was observed. A comparison of transcription patterns between Ha-LSL and Ha-ROXL revealed some analogies but also remarkable differences; in fact, the gene Ha-ROXL displayed a low expression level in all organs analyzed. In situ hybridization (ISH) analysis showed that Ha-ROXL transcription was strongly restricted to a small domain within the boundary zone separating the shoot apical meristem (SAM) and the leaf primordia and in restricted regions of the inflorescence meristem, beforehand the separation of floral bracts from disc flower primordia. These results suggested that Ha-ROXL may be involved to establish a cell niche for the initiation of AMs as well as flower primordia. The accumulation of Ha-LSL transcripts was not restricted to the boundary zones in vegetative and inflorescence shoots, but the mRNA activity was expanded in other cellular domains of primary shoot apical meristem as well as AMs. In addition, Ha-LSL transcript accumulation was also detected in leaves and floral primordia at early stages of development. These results were corroborated by qRT-PCR analyses that evidenced high levels of Ha-LSL transcripts in very young leaves and disc flowers, suggesting a role of Ha-LSL for the early outgrowth of lateral primordia.
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54
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Wang Y, Shi S, Zhou Y, Zhou Y, Yang J, Tang X. Genome-wide identification and characterization of GRAS transcription factors in sacred lotus (Nelumbo nucifera). PeerJ 2016; 4:e2388. [PMID: 27635351 PMCID: PMC5012262 DOI: 10.7717/peerj.2388] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 07/29/2016] [Indexed: 11/20/2022] Open
Abstract
The GRAS gene family is one of the most important plant-specific gene families, which encodes transcriptional regulators and plays an essential role in plant development and physiological processes. The GRAS gene family has been well characterized in many higher plants such as Arabidopsis, rice, Chinese cabbage, tomato and tobacco. In this study, we identified 38 GRAS genes in sacred lotus (Nelumbo nucifera), analyzed their physical and chemical characteristics and performed phylogenetic analysis using the GRAS genes from eight representative plant species to show the evolution of GRAS genes in Planta. In addition, the gene structures and motifs of the sacred lotus GRAS proteins were characterized in detail. Comparative analysis identified 42 orthologous and 9 co-orthologous gene pairs between sacred lotus and Arabidopsis, and 35 orthologous and 22 co-orthologous gene pairs between sacred lotus and rice. Based on publically available RNA-seq data generated from leaf, petiole, rhizome and root, we found that most of the sacred lotus GRAS genes exhibited a tissue-specific expression pattern. Eight of the ten PAT1-clade GRAS genes, particularly NnuGRAS-05, NnuGRAS-10 and NnuGRAS-25, were preferentially expressed in rhizome and root. In summary, this is the first in silico analysis of the GRAS gene family in sacred lotus, which will provide valuable information for further molecular and biological analyses of this important gene family.
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Affiliation(s)
- Yu Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Shenglu Shi
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Ying Zhou
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yu Zhou
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jie Yang
- Institute of Food Crops, Jiangsu Academy Agricultural Sciences, Nanjing, Jiangsu, China
| | - Xiaoqing Tang
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
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Lehti-Shiu MD, Panchy N, Wang P, Uygun S, Shiu SH. Diversity, expansion, and evolutionary novelty of plant DNA-binding transcription factor families. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:3-20. [PMID: 27522016 DOI: 10.1016/j.bbagrm.2016.08.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/21/2016] [Accepted: 08/06/2016] [Indexed: 12/19/2022]
Abstract
Plant transcription factors (TFs) that interact with specific sequences via DNA-binding domains are crucial for regulating transcriptional initiation and are fundamental to plant development and environmental response. In addition, expansion of TF families has allowed functional divergence of duplicate copies, which has contributed to novel, and in some cases adaptive, traits in plants. Thus, TFs are central to the generation of the diverse plant species that we see today. Major plant agronomic traits, including those relevant to domestication, have also frequently arisen through changes in TF coding sequence or expression patterns. Here our goal is to provide an overview of plant TF evolution by first comparing the diversity of DNA-binding domains and the sizes of these domain families in plants and other eukaryotes. Because TFs are among the most highly expanded gene families in plants, the birth and death process of TFs as well as the mechanisms contributing to their retention are discussed. We also provide recent examples of how TFs have contributed to novel traits that are important in plant evolution and in agriculture.This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
| | - Nicholas Panchy
- The Genetics Graduate Program, Michigan State University, East Lansing, MI 48824, USA
| | - Peipei Wang
- Department of Plant Biology, East Lansing, MI 48824, USA
| | - Sahra Uygun
- The Genetics Graduate Program, Michigan State University, East Lansing, MI 48824, USA
| | - Shin-Han Shiu
- Department of Plant Biology, East Lansing, MI 48824, USA; The Genetics Graduate Program, Michigan State University, East Lansing, MI 48824, USA.
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56
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Xu W, Chen Z, Ahmed N, Han B, Cui Q, Liu A. Genome-Wide Identification, Evolutionary Analysis, and Stress Responses of the GRAS Gene Family in Castor Beans. Int J Mol Sci 2016; 17:ijms17071004. [PMID: 27347937 PMCID: PMC4964380 DOI: 10.3390/ijms17071004] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/17/2016] [Accepted: 06/20/2016] [Indexed: 12/01/2022] Open
Abstract
Plant-specific GRAS transcription factors play important roles in regulating growth, development, and stress responses. Castor beans (Ricinus communis) are important non-edible oilseed plants, cultivated worldwide for its seed oils and its adaptability to growth conditions. In this study, we identified and characterized a total of 48 GRAS genes based on the castor bean genome. Combined with phylogenetic analysis, the castor bean GRAS members were divided into 13 distinct groups. Functional divergence analysis revealed the presence of mostly Type-I functional divergence. The gene structures and conserved motifs, both within and outside the GRAS domain, were characterized. Gene expression analysis, performed in various tissues and under a range of abiotic stress conditions, uncovered the potential functions of GRAS members in regulating plant growth development and stress responses. The results obtained from this study provide valuable information toward understanding the potential molecular mechanisms of GRAS proteins in castor beans. These findings also serve as a resource for identifying the genes that allow castor beans to grow in stressful conditions and to enable further breeding and genetic improvements in agriculture.
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Affiliation(s)
- Wei Xu
- College of Life Sciences, Yunnan University, Kunming 650091, China.
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China.
- University of the Chinese Academy of Sciences, Beijing 100049, China.
| | - Zexi Chen
- College of Life Sciences, Yunnan University, Kunming 650091, China.
| | - Naeem Ahmed
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China.
- Department of Botany, University of Karachi, Karachi-75270, Pakistan.
| | - Bing Han
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China.
- University of the Chinese Academy of Sciences, Beijing 100049, China.
| | - Qinghua Cui
- College of Life Sciences, Yunnan University, Kunming 650091, China.
| | - Aizhong Liu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China.
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57
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Li S, Zhao Y, Zhao Z, Wu X, Sun L, Liu Q, Wu Y. Crystal Structure of the GRAS Domain of SCARECROW-LIKE7 in Oryza sativa. THE PLANT CELL 2016; 28:1025-34. [PMID: 27081181 PMCID: PMC4904676 DOI: 10.1105/tpc.16.00018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/13/2016] [Indexed: 05/04/2023]
Abstract
GRAS proteins belong to a plant-specific protein family with many members and play essential roles in plant growth and development, functioning primarily in transcriptional regulation. Proteins in the family are minimally defined as containing the conserved GRAS domain. Here, we determined the structure of the GRAS domain of Os-SCL7 from rice (Oryza sativa) to 1.82 Å. The structure includes cap and core subdomains and elucidates the features of the conserved GRAS LRI, VHIID, LRII, PFYRE, and SAW motifs. The structure is a dimer, with a clear groove to accommodate double-stranded DNA. Docking a DNA segment into the groove to generate an Os-SCL7/DNA complex provides insight into the DNA binding mechanism of GRAS proteins. Furthermore, the in vitro DNA binding property of Os-SCL7 and model-defined recognition residues are assessed by electrophoretic mobility shift analysis and mutagenesis assays. These studies reveal the structure and preliminary DNA interaction mechanisms of GRAS proteins and open the door to in-depth investigation and understanding of the individual pathways in which they play important roles.
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Affiliation(s)
- Shengping Li
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Yanhe Zhao
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Zheng Zhao
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda 20894, Maryland
| | - Xiuling Wu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Lifang Sun
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
| | - Qingsong Liu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
| | - Yunkun Wu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
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58
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Hofmann NR. A Structure for Plant-Specific Transcription Factors: The GRAS Domain Revealed. THE PLANT CELL 2016; 28:993-4. [PMID: 27095838 PMCID: PMC4904681 DOI: 10.1105/tpc.16.00309] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
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59
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Grimplet J, Agudelo-Romero P, Teixeira RT, Martinez-Zapater JM, Fortes AM. Structural and Functional Analysis of the GRAS Gene Family in Grapevine Indicates a Role of GRAS Proteins in the Control of Development and Stress Responses. FRONTIERS IN PLANT SCIENCE 2016; 7:353. [PMID: 27065316 PMCID: PMC4811876 DOI: 10.3389/fpls.2016.00353] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/07/2016] [Indexed: 05/18/2023]
Abstract
GRAS transcription factors are involved in many processes of plant growth and development (e.g., axillary shoot meristem formation, root radial patterning, nodule morphogenesis, arbuscular development) as well as in plant disease resistance and abiotic stress responses. However, little information is available concerning this gene family in grapevine (Vitis vinifera L.), an economically important woody crop. We performed a model curation of GRAS genes identified in the latest genome annotation leading to the identification of 52 genes. Gene models were improved and three new genes were identified that could be grapevine- or woody-plant specific. Phylogenetic analysis showed that GRAS genes could be classified into 13 groups that mapped on the 19 V. vinifera chromosomes. Five new subfamilies, previously not characterized in other species, were identified. Multiple sequence alignment showed typical GRAS domain in the proteins and new motifs were also described. As observed in other species, both segmental and tandem duplications contributed significantly to the expansion and evolution of the GRAS gene family in grapevine. Expression patterns across a variety of tissues and upon abiotic and biotic conditions revealed possible divergent functions of GRAS genes in grapevine development and stress responses. By comparing the information available for tomato and grapevine GRAS genes, we identified candidate genes that might constitute conserved transcriptional regulators of both climacteric and non-climacteric fruit ripening. Altogether this study provides valuable information and robust candidate genes for future functional analysis aiming at improving the quality of fleshy fruits.
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Affiliation(s)
- Jérôme Grimplet
- Instituto de Ciencias de la Vid y del Vino (Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja)Logroño, Spain
| | | | - Rita T. Teixeira
- Faculdade de Ciências de Lisboa, BioISI, Universidade de LisboaLisboa, Portugal
| | - Jose M. Martinez-Zapater
- Instituto de Ciencias de la Vid y del Vino (Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja)Logroño, Spain
| | - Ana M. Fortes
- Faculdade de Ciências de Lisboa, BioISI, Universidade de LisboaLisboa, Portugal
- Instituto de Tecnologia de Química Biológica, Biotecnologia de Células VegetaisOeiras, Portugal
- *Correspondence: Ana M. Fortes
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60
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Fambrini M, Mariotti L, Parlanti S, Salvini M, Pugliesi C. A GRAS-like gene of sunflower (Helianthus annuus L.) alters the gibberellin content and axillary meristem outgrowth in transgenic Arabidopsis plants. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:1123-34. [PMID: 26081041 DOI: 10.1111/plb.12358] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 06/11/2015] [Indexed: 05/03/2023]
Abstract
The GRAS proteins belong to a plant transcriptional regulator family that function in the regulation of plant growth and development. Despite their important roles, in sunflower only one GRAS gene (HaDella1) with the DELLA domain has been reported. Here, we provide a functional characterisation of a GRAS-like gene from Helianthus annuus (Ha-GRASL) lacking the DELLA motif. The Ha-GRASL gene contains an intronless open reading frame of 1,743 bp encoding 580 amino acids. Conserved motifs in the GRAS domain are detected, including VHIID, PFYRE, SAW and two LHR motifs. Within the VHII motif, the P-H-N-D-Q-L residues are entirely maintained. Phylogenetic analysis reveals that Ha-GRASL belongs to the SCARECROW LIKE4/7 (SCL4/7) subfamily of the GRAS consensus tree. Accumulation of Ha-GRASL mRNA at the adaxial boundaries from P6/P7 leaf primordia suggests a role of Ha-GRASL in the initiation of median and basal axillary meristems (AMs) of sunflower. When Ha-GRASL is over-expressed in Arabidopsis wild-type plants, the number of lateral bolts increases differently from untransformed plants. However, Ha-GRASL slightly affects the lateral suppressor (las-4-) mutation. Therefore, we hypothesise that Ha-GRASL and LAS are not functionally equivalent. The over-expression of Ha-GRASL reduces metabolic flow of gibberellins (GAs) in Arabidopsis and this modification could be relevant in AM development. Phylogenetic analysis includes LAS and SCL4/7 in the same major clade, suggesting a more recent separation of these genes with respect to other GRAS members. We propose that some features of their ancestor, as well as AM initiation and outgrowth, are partially retained in both LAS and SCL4/7.
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Affiliation(s)
- M Fambrini
- Dipartimento di Scienze Agrarie, Alimentari ed Agro-ambientali, Università degli Studi di Pisa, Pisa, Italy
| | - L Mariotti
- Dipartimento di Biologia, Università degli Studi di Pisa, Pisa, Italy
| | - S Parlanti
- PlantLab, Scuola Superiore Sant'Anna, Pisa, Italy
| | - M Salvini
- Dipartimento di Scienze Agrarie, Alimentari ed Agro-ambientali, Università degli Studi di Pisa, Pisa, Italy
- Scuola Normale Superiore, Pisa, Italy
| | - C Pugliesi
- Dipartimento di Scienze Agrarie, Alimentari ed Agro-ambientali, Università degli Studi di Pisa, Pisa, Italy
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61
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Fox NK, Brenner SE, Chandonia JM. The value of protein structure classification information-Surveying the scientific literature. Proteins 2015; 83:2025-38. [PMID: 26313554 PMCID: PMC4609302 DOI: 10.1002/prot.24915] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 08/06/2015] [Accepted: 08/18/2015] [Indexed: 11/08/2022]
Abstract
The Structural Classification of Proteins (SCOP) and Class, Architecture, Topology, Homology (CATH) databases have been valuable resources for protein structure classification for over 20 years. Development of SCOP (version 1) concluded in June 2009 with SCOP 1.75. The SCOPe (SCOP-extended) database offers continued development of the classic SCOP hierarchy, adding over 33,000 structures. We have attempted to assess the impact of these two decade old resources and guide future development. To this end, we surveyed recent articles to learn how structure classification data are used. Of 571 articles published in 2012-2013 that cite SCOP, 439 actually use data from the resource. We found that the type of use was fairly evenly distributed among four top categories: A) study protein structure or evolution (27% of articles), B) train and/or benchmark algorithms (28% of articles), C) augment non-SCOP datasets with SCOP classification (21% of articles), and D) examine the classification of one protein/a small set of proteins (22% of articles). Most articles described computational research, although 11% described purely experimental research, and a further 9% included both. We examined how CATH and SCOP were used in 158 articles that cited both databases: while some studies used only one dataset, the majority used data from both resources. Protein structure classification remains highly relevant for a diverse range of problems and settings.
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Affiliation(s)
- Naomi K Fox
- Lawrence Berkeley National Laboratory, Physical Biosciences Division, Berkeley, California, 94720
| | - Steven E Brenner
- Lawrence Berkeley National Laboratory, Physical Biosciences Division, Berkeley, California, 94720.,Department of Plant and Microbial Biology, University of California, Berkeley, California, 94720
| | - John-Marc Chandonia
- Lawrence Berkeley National Laboratory, Physical Biosciences Division, Berkeley, California, 94720
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62
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Huang W, Xian Z, Kang X, Tang N, Li Z. Genome-wide identification, phylogeny and expression analysis of GRAS gene family in tomato. BMC PLANT BIOLOGY 2015; 15:209. [PMID: 26302743 PMCID: PMC4549011 DOI: 10.1186/s12870-015-0590-6] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 08/11/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND GRAS transcription factors usually act as integrators of multiple growth regulatory and environmental signals, including axillary shoot meristem formation, root radial pattering, phytohormones, light signaling, and abiotic/biotic stress. However, little is known about this gene family in tomato (Solanum lycopersicum), the most important model plant for crop species with fleshy fruits. RESULTS In this study, 53 GRAS genes were identified and renamed based on tomato whole-genome sequence and their respective chromosome distribution except 19 members were kept as their already existed name. Multiple sequence alignment showed typical GRAS domain in these proteins. Phylogenetic analysis of GRAS proteins from tomato, Arabidopsis, Populus, P.mume, and Rice revealed that SlGRAS proteins could be divided into at least 13 subfamilies. SlGRAS24 and SlGRAS40 were identified as target genes of miR171 using5'-RACE (Rapid amplification of cDNA ends). qRT-PCR analysis revealed tissue-/organ- and development stage-specific expression patterns of SlGRAS genes. Moreover, their expression patterns in response to different hormone and abiotic stress treatments were also investigated. CONCLUSIONS This study provides the first comprehensive analysis of GRAS gene family in the tomato genome. The data will undoubtedly be useful for better understanding the potential functions of GRAS genes, and their possible roles in mediating hormone cross-talk and abiotic stress in tomato as well as in some other relative species.
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Affiliation(s)
- Wei Huang
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China.
| | - Zhiqiang Xian
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China.
| | - Xia Kang
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China.
| | - Ning Tang
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China.
| | - Zhengguo Li
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 400044, People's Republic China.
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63
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Long Y, Scheres B, Blilou I. The logic of communication: roles for mobile transcription factors in plants. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1133-44. [PMID: 25635110 DOI: 10.1093/jxb/eru548] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Mobile transcription factors play many roles in plant development. Here, we compare the use of mobile transcription factors as signals with some canonical signal transduction processes in prokaryotes and eukaryotes. After an initial survey, we focus on the SHORT-ROOT pathway in Arabidopsis roots to show that, despite the simplicity of the concept of mobile transcription factor signalling, many lines of evidence reveal a surprising complexity in control mechanisms linked to this process. We argue that these controls bestow precision, robustness, and versatility on mobile transcription factor signalling.
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Affiliation(s)
- Yuchen Long
- Plant Developmental Biology, Plant Sciences, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| | - Ben Scheres
- Plant Developmental Biology, Plant Sciences, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| | - Ikram Blilou
- Plant Developmental Biology, Plant Sciences, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands.
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Wu N, Zhu Y, Song W, Li Y, Yan Y, Hu Y. Unusual tandem expansion and positive selection in subgroups of the plant GRAS transcription factor superfamily. BMC PLANT BIOLOGY 2014; 14:373. [PMID: 25524588 PMCID: PMC4279901 DOI: 10.1186/s12870-014-0373-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Accepted: 12/08/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND GRAS proteins belong to a plant transcription factor family that is involved with multifarious roles in plants. Although previous studies of this protein family have been reported for Arabidopsis, rice, Chinese cabbage and other species, investigation of expansion patterns and evolutionary rate on the basis of comparative genomics in different species remains inadequate. RESULTS A total of 289 GRAS genes were identified in Arabidopsis, B. distachyon, rice, soybean, S. moellendorffii, and P. patens and were grouped into seven subfamilies, supported by the similarity of their exon-intron patterns and structural motifs. All of tandem duplicated genes were found in group II except one cluster of rice, indicating that tandem duplication greatly promoted the expansion of group II. Furthermore, segment duplications were mainly found in the soybean genome, whereas no single expansion pattern dominated in other plant species indicating that GRAS genes from these five species might be subject to a more complex evolutionary mechanism. Interestingly, branch-site model analyses of positive selection showed that a number of sites were positively selected under foreground branches I and V. These results strongly indicated that these groups were experiencing higher positive selection pressure. Meanwhile, the site-specific model revealed that the GRAS genes were under strong positive selection in P. patens. DIVERGE v2.0 was used to detect critical amino acid sites, and the results showed that the shifted evolutionary rate was mainly attributed to the functional divergence between the GRAS genes in the two groups. In addition, the results also demonstrated the expression divergence of the GRAS duplicated genes in the evolution. In short, the results above provide a solid foundation for further functional dissection of the GRAS gene superfamily. CONCLUSIONS In this work, differential expression, evolutionary rate, and expansion patterns of the GRAS gene family in the six species were predicted. Especially, tandem duplication events played an important role in expansion of group II. Together, these results contribute to further functional analysis and the molecular evolution of the GRAS gene superfamily.
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Affiliation(s)
- Ningning Wu
- College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Yan Zhu
- College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Wanlu Song
- College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Yaxuan Li
- College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Yueming Yan
- College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Yingkao Hu
- College of Life Sciences, Capital Normal University, Beijing, 100048 China
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Song XM, Liu TK, Duan WK, Ma QH, Ren J, Wang Z, Li Y, Hou XL. Genome-wide analysis of the GRAS gene family in Chinese cabbage (Brassica rapa ssp. pekinensis). Genomics 2013; 103:135-46. [PMID: 24365788 DOI: 10.1016/j.ygeno.2013.12.004] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 11/08/2013] [Accepted: 12/16/2013] [Indexed: 12/23/2022]
Abstract
The GRAS gene family is one of the most important families of transcriptional regulators. In this study, 48 GRAS genes are identified from Chinese cabbage, and they are classified into eight groups according to the classification of Arabidopsis. The characterization, classification, gene structure and phylogenetic construction of GRAS proteins are performed. Distribution mapping shows that GRAS proteins are nonrandomly localized in 10 chromosomes. Fifty-five orthologous gene pairs are shared by Chinese cabbage and Arabidopsis, and interaction networks of these orthologous genes are constructed. The expansion of GRAS genes in Chinese cabbage results from genome triplication. Among the 17 species examined, 14 higher plants carry the GRAS genes, whereas two lower plants and one fungi species do not. Furthermore, the expression patterns of GRAS genes exhibit differences in three tissues based on RNA-seq data. Taken together, this comprehensive analysis will provide rich resources for studying GRAS protein functions in Chinese cabbage.
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Affiliation(s)
- Xiao-Ming Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Tong-Kun Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei-Ke Duan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Qing-Hua Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun Ren
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhen Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xi-Lin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
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Wang Y, Deng D. Molecular basis and evolutionary pattern of GA-GID1-DELLA regulatory module. Mol Genet Genomics 2013; 289:1-9. [PMID: 24322346 DOI: 10.1007/s00438-013-0797-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 12/03/2013] [Indexed: 11/26/2022]
Abstract
The tetracyclic diterpenoid carboxylic acids, gibberellins (GAs), orchestrate a broad spectrum of biological programs. In nature, GAs or GA-like substance is produced in bacteria, fungi, and plants. The function of GAs in microorganisms remains largely unknown. Phytohormones GAs mediate diverse growth and developmental processes through the life cycle of plants. The GA biosynthetic and metabolic pathways in bacteria, fungi, and plants are remarkably divergent. In vascular plants, phytohormone GA, receptor GID1, and repressor DELLA shape the GA-GID1-DELLA module in GA signaling cascade. Sequence reshuffling, functional divergence, and adaptive selection are main driving forces during the evolution of GA pathway components. The GA-GID1-DELLA complex interacts with second messengers and other plant hormones to integrate environmental and endogenous cues, which is beneficial to phytohormones homeostasis and other biological events. In this review, we first briefly describe GA metabolism pathway, signaling perception, and its second messengers. Then, we examine the evolution of GA pathway genes. Finally, we focus on reviewing the crosstalk between GA-GID1-DELLA module and phytohormones. Deciphering mechanisms underlying plant hormonal interactions are not only beneficial to addressing basic biological questions, but also have practical implications for developing crops with ideotypes to meet the future demand.
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Affiliation(s)
- Yijun Wang
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou, 225009, China,
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