201
|
Bhattacharjee A, Ghangal R, Garg R, Jain M. Genome-wide analysis of homeobox gene family in legumes: identification, gene duplication and expression profiling. PLoS One 2015; 10:e0119198. [PMID: 25745864 PMCID: PMC4352023 DOI: 10.1371/journal.pone.0119198] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 01/11/2015] [Indexed: 02/03/2023] Open
Abstract
Homeobox genes encode transcription factors that are known to play a major role in different aspects of plant growth and development. In the present study, we identified homeobox genes belonging to 14 different classes in five legume species, including chickpea, soybean, Medicago, Lotus and pigeonpea. The characteristic differences within homeodomain sequences among various classes of homeobox gene family were quite evident. Genome-wide expression analysis using publicly available datasets (RNA-seq and microarray) indicated that homeobox genes are differentially expressed in various tissues/developmental stages and under stress conditions in different legumes. We validated the differential expression of selected chickpea homeobox genes via quantitative reverse transcription polymerase chain reaction. Genome duplication analysis in soybean indicated that segmental duplication has significantly contributed in the expansion of homeobox gene family. The Ka/Ks ratio of duplicated homeobox genes in soybean showed that several members of this family have undergone purifying selection. Moreover, expression profiling indicated that duplicated genes might have been retained due to sub-functionalization. The genome-wide identification and comprehensive gene expression profiling of homeobox gene family members in legumes will provide opportunities for functional analysis to unravel their exact role in plant growth and development.
Collapse
Affiliation(s)
- Annapurna Bhattacharjee
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Rajesh Ghangal
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Rohini Garg
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Mukesh Jain
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| |
Collapse
|
202
|
Bajaj D, Saxena MS, Kujur A, Das S, Badoni S, Tripathi S, Upadhyaya HD, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK. Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1271-90. [PMID: 25504138 PMCID: PMC4339591 DOI: 10.1093/jxb/eru478] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Phylogenetic footprinting identified 666 genome-wide paralogous and orthologous CNMS (conserved non-coding microsatellite) markers from 5'-untranslated and regulatory regions (URRs) of 603 protein-coding chickpea genes. The (CT)n and (GA)n CNMS carrying CTRMCAMV35S and GAGA8BKN3 regulatory elements, respectively, are abundant in the chickpea genome. The mapped genic CNMS markers with robust amplification efficiencies (94.7%) detected higher intraspecific polymorphic potential (37.6%) among genotypes, implying their immense utility in chickpea breeding and genetic analyses. Seventeen differentially expressed CNMS marker-associated genes showing strong preferential and seed tissue/developmental stage-specific expression in contrasting genotypes were selected to narrow down the gene targets underlying seed weight quantitative trait loci (QTLs)/eQTLs (expression QTLs) through integrative genetical genomics. The integration of transcript profiling with seed weight QTL/eQTL mapping, molecular haplotyping, and association analyses identified potential molecular tags (GAGA8BKN3 and RAV1AAT regulatory elements and alleles/haplotypes) in the LOB-domain-containing protein- and KANADI protein-encoding transcription factor genes controlling the cis-regulated expression for seed weight in the chickpea. This emphasizes the potential of CNMS marker-based integrative genetical genomics for the quantitative genetic dissection of complex seed weight in chickpea.
Collapse
Affiliation(s)
- Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Maneesha S Saxena
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Alice Kujur
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shouvik Das
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Saurabh Badoni
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi 110012, India
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - C L L Gowda
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Shivali Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Sube Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| |
Collapse
|
203
|
Furumizu C, Alvarez JP, Sakakibara K, Bowman JL. Antagonistic roles for KNOX1 and KNOX2 genes in patterning the land plant body plan following an ancient gene duplication. PLoS Genet 2015; 11:e1004980. [PMID: 25671434 PMCID: PMC4335488 DOI: 10.1371/journal.pgen.1004980] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 01/04/2015] [Indexed: 12/23/2022] Open
Abstract
Neofunctionalization following gene duplication is thought to be one of the key drivers in generating evolutionary novelty. A gene duplication in a common ancestor of land plants produced two classes of KNOTTED-like TALE homeobox genes, class I (KNOX1) and class II (KNOX2). KNOX1 genes are linked to tissue proliferation and maintenance of meristematic potentials of flowering plant and moss sporophytes, and modulation of KNOX1 activity is implicated in contributing to leaf shape diversity of flowering plants. While KNOX2 function has been shown to repress the gametophytic (haploid) developmental program during moss sporophyte (diploid) development, little is known about KNOX2 function in flowering plants, hindering syntheses regarding the relationship between two classes of KNOX genes in the context of land plant evolution. Arabidopsis plants harboring loss-of-function KNOX2 alleles exhibit impaired differentiation of all aerial organs and have highly complex leaves, phenocopying gain-of-function KNOX1 alleles. Conversely, gain-of-function KNOX2 alleles in conjunction with a presumptive heterodimeric BELL TALE homeobox partner suppressed SAM activity in Arabidopsis and reduced leaf complexity in the Arabidopsis relative Cardamine hirsuta, reminiscent of loss-of-function KNOX1 alleles. Little evidence was found indicative of epistasis or mutual repression between KNOX1 and KNOX2 genes. KNOX proteins heterodimerize with BELL TALE homeobox proteins to form functional complexes, and contrary to earlier reports based on in vitro and heterologous expression, we find high selectivity between KNOX and BELL partners in vivo. Thus, KNOX2 genes confer opposing activities rather than redundant roles with KNOX1 genes, and together they act to direct the development of all above-ground organs of the Arabidopsis sporophyte. We infer that following the KNOX1/KNOX2 gene duplication in an ancestor of land plants, neofunctionalization led to evolution of antagonistic biochemical activity thereby facilitating the evolution of more complex sporophyte transcriptional networks, providing plasticity for the morphological evolution of land plant body plans.
Collapse
Affiliation(s)
- Chihiro Furumizu
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - John Paul Alvarez
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Keiko Sakakibara
- School of Biological Sciences, Monash University, Melbourne, Australia
- Graduate School of Science, University of Tokyo, Hongo, Tokyo, Japan
| | - John L. Bowman
- School of Biological Sciences, Monash University, Melbourne, Australia
- Department of Plant Biology, University of California Davis, Davis, California, United States of America
| |
Collapse
|
204
|
ten Hove CA, Lu KJ, Weijers D. Building a plant: cell fate specification in the early Arabidopsis embryo. Development 2015; 142:420-30. [DOI: 10.1242/dev.111500] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Embryogenesis is the beginning of plant development, yet the cell fate decisions and patterning steps that occur during this time are reiterated during development to build the post-embryonic architecture. In Arabidopsis, embryogenesis follows a simple and predictable pattern, making it an ideal model with which to understand how cellular and tissue developmental processes are controlled. Here, we review the early stages of Arabidopsis embryogenesis, focusing on the globular stage, during which time stem cells are first specified and all major tissues obtain their identities. We discuss four different aspects of development: the formation of outer versus inner layers; the specification of vascular and ground tissues; the determination of shoot and root domains; and the establishment of the first stem cells.
Collapse
Affiliation(s)
- Colette A. ten Hove
- Wageningen University, Laboratory of Biochemistry, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Kuan-Ju Lu
- Wageningen University, Laboratory of Biochemistry, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Dolf Weijers
- Wageningen University, Laboratory of Biochemistry, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| |
Collapse
|
205
|
Abstract
Plants use 24-nucleotide small interfering RNAs (24-nt siRNAs) and long non-coding RNAs (lncRNAs) to direct de novo DNA methylation and transcriptional gene silencing. This process is called RNA-directed DNA methylation (RdDM). An important question in the RdDM model is what explains the target specificity of RNA polymerase IV (Pol IV), the enzyme that initiates siRNA production. Two recent papers addressed this question by characterizing the DTF1/SHH1 protein, which contains a homeodomain in the N-terminus and a novel histone-binding domain SAWADEE in the C terminus. Here we review the main results of the two studies and discuss several possible mechanisms that could contribute to Pol IV and Pol V recruitment.
Collapse
Affiliation(s)
- Heng Zhang
- Shanghai Center for Plant Stress Biology; Shanghai Institute of Biological Sciences; Chinese Academy of Sciences; Shanghai, P.R. China
| | - Xinjian He
- National Institute of Biological Sciences; Beijing, P.R. China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology; Shanghai Institute of Biological Sciences; Chinese Academy of Sciences; Shanghai, P.R. China; Department of Horticulture and Landscape Architecture; Purdue University; West Lafayette, IN USA
| |
Collapse
|
206
|
Vogt JHM, Schippers JHM. Setting the PAS, the role of circadian PAS domain proteins during environmental adaptation in plants. FRONTIERS IN PLANT SCIENCE 2015; 6:513. [PMID: 26217364 PMCID: PMC4496561 DOI: 10.3389/fpls.2015.00513] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The per-ARNT-sim (PAS) domain represents an ancient protein module that can be found across all kingdoms of life. The domain functions as a sensing unit for a diverse array of signals, including molecular oxygen, small metabolites, and light. In plants, several PAS domain-containing proteins form an integral part of the circadian clock and regulate responses to environmental change. Moreover, these proteins function in pathways that control development and plant stress adaptation responses. Here, we discuss the role of PAS domain-containing proteins in anticipation, and adaptation to environmental changes in plants.
Collapse
Affiliation(s)
- Julia H. M. Vogt
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jos H. M. Schippers
- Institute for Biology I, RWTH Aachen University, Aachen, Germany
- *Correspondence: Jos H. M. Schippers, Institute for Biology I, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany,
| |
Collapse
|
207
|
Belamkar V, Weeks NT, Bharti AK, Farmer AD, Graham MA, Cannon SB. Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress. BMC Genomics 2014; 15:950. [PMID: 25362847 PMCID: PMC4226900 DOI: 10.1186/1471-2164-15-950] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 10/16/2014] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The homeodomain leucine zipper (HD-Zip) transcription factor family is one of the largest plant specific superfamilies, and includes genes with roles in modulation of plant growth and response to environmental stresses. Many HD-Zip genes are characterized in Arabidopsis (Arabidopsis thaliana), and members of the family are being investigated for abiotic stress responses in rice (Oryza sativa), maize (Zea mays), poplar (Populus trichocarpa) and cucumber (Cucmis sativus). Findings in these species suggest HD-Zip genes as high priority candidates for crop improvement. RESULTS In this study we have identified members of the HD-Zip gene family in soybean cv. 'Williams 82', and characterized their expression under dehydration and salt stress. Homology searches with BLASTP and Hidden Markov Model guided sequence alignments identified 101 HD-Zip genes in the soybean genome. Phylogeny reconstruction coupled with domain and gene structure analyses using soybean, Arabidopsis, rice, grape (Vitis vinifera), and Medicago truncatula homologues enabled placement of these sequences into four previously described subfamilies. Of the 101 HD-Zip genes identified in soybean, 88 exist as whole-genome duplication-derived gene pairs, indicating high retention of these genes following polyploidy in Glycine ~13 Mya. The HD-Zip genes exhibit ubiquitous expression patterns across 24 conditions that include 17 tissues of soybean. An RNA-Seq experiment performed to study differential gene expression at 0, 1, 6 and 12 hr soybean roots under dehydration and salt stress identified 20 differentially expressed (DE) genes. Several of these DE genes are orthologs of genes previously reported to play a role under abiotic stress, implying conservation of HD-Zip gene functions across species. Screening of HD-Zip promoters identified transcription factor binding sites that are overrepresented in the DE genes under both dehydration and salt stress, providing further support for the role of HD-Zip genes in abiotic stress responses. CONCLUSIONS We provide a thorough description of soybean HD-Zip genes, and identify potential candidates with probable roles in dehydration and salt stress. Expression profiles generated for all soybean genes, under dehydration and salt stress, at four time points, will serve as an important resource for the soybean research community, and will aid in understanding plant responses to abiotic stress.
Collapse
Affiliation(s)
- Vikas Belamkar
- />Interdepartmental Genetics, Iowa State University, Ames, IA 50011 USA
- />Department of Agronomy, Iowa State University, Ames, IA 50011 USA
| | - Nathan T Weeks
- />United States Department of Agriculture - Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011 USA
| | - Arvind K Bharti
- />National Center for Genome Resources, Santa Fe, NM 87505 USA
| | - Andrew D Farmer
- />National Center for Genome Resources, Santa Fe, NM 87505 USA
| | - Michelle A Graham
- />Department of Agronomy, Iowa State University, Ames, IA 50011 USA
- />United States Department of Agriculture - Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011 USA
| | - Steven B Cannon
- />Department of Agronomy, Iowa State University, Ames, IA 50011 USA
- />United States Department of Agriculture - Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011 USA
| |
Collapse
|
208
|
Costanzo E, Trehin C, Vandenbussche M. The role of WOX genes in flower development. ANNALS OF BOTANY 2014; 114:1545-53. [PMID: 24973416 PMCID: PMC4204783 DOI: 10.1093/aob/mcu123] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 04/29/2014] [Indexed: 05/21/2023]
Abstract
BACKGROUND WOX (Wuschel-like homeobOX) genes form a family of plant-specific HOMEODOMAIN transcription factors, the members of which play important developmental roles in a diverse range of processes. WOX genes were first identified as determining cell fate during embryo development, as well as playing important roles in maintaining stem cell niches in the plant. In recent years, new roles have been identified in plant architecture and organ development, particularly at the flower level. SCOPE In this review, the role of WOX genes in flower development and flower architecture is highlighted, as evidenced from data obtained in the last few years. The roles played by WOX genes in different species and different flower organs are compared, and differential functional recruitment of WOX genes during flower evolution is considered. CONCLUSIONS This review compares available data concerning the role of WOX genes in flower and organ architecture among different species of angiosperms, including representatives of monocots and eudicots (rosids and asterids). These comparative data highlight the usefulness of the WOX gene family for evo-devo studies of floral development.
Collapse
Affiliation(s)
- Enrico Costanzo
- Laboratory of Reproduction and Development of Plants, UMR5667 (ENS de Lyon, CNRS, INRA, UCBL), Ecole Normale Supérieure de Lyon, Lyon, France Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Christophe Trehin
- Laboratory of Reproduction and Development of Plants, UMR5667 (ENS de Lyon, CNRS, INRA, UCBL), Ecole Normale Supérieure de Lyon, Lyon, France
| | - Michiel Vandenbussche
- Laboratory of Reproduction and Development of Plants, UMR5667 (ENS de Lyon, CNRS, INRA, UCBL), Ecole Normale Supérieure de Lyon, Lyon, France
| |
Collapse
|
209
|
Dunker AK, Bondos SE, Huang F, Oldfield CJ. Intrinsically disordered proteins and multicellular organisms. Semin Cell Dev Biol 2014; 37:44-55. [PMID: 25307499 DOI: 10.1016/j.semcdb.2014.09.025] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 09/15/2014] [Accepted: 09/30/2014] [Indexed: 12/12/2022]
Abstract
Intrinsically disordered proteins (IDPs) and IDP regions lack stable tertiary structure yet carry out numerous biological functions, especially those associated with signaling, transcription regulation, DNA condensation, cell division, and cellular differentiation. Both post-translational modifications (PTMs) and alternative splicing (AS) expand the functional repertoire of IDPs. Here we propose that an "IDP-based developmental toolkit," which is comprised of IDP regions, PTMs, especially multiple PTMs, within these IDP regions, and AS events within segments of pre-mRNA that code for these same IDP regions, allows functional diversification and environmental responsiveness for molecules that direct the development of complex metazoans.
Collapse
Affiliation(s)
- A Keith Dunker
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University Schools of Medicine and Informatics, Indianapolis, IN 46202, United States.
| | - Sarah E Bondos
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843, United States.
| | - Fei Huang
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University Schools of Medicine and Informatics, Indianapolis, IN 46202, United States.
| | - Christopher J Oldfield
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University Schools of Medicine and Informatics, Indianapolis, IN 46202, United States.
| |
Collapse
|
210
|
Dwivedi KK, Roche DJ, Clemente TE, Ge Z, Carman JG. The OCL3 promoter from Sorghum bicolor directs gene expression to abscission and nutrient-transfer zones at the bases of floral organs. ANNALS OF BOTANY 2014; 114:489-98. [PMID: 25081518 PMCID: PMC4204675 DOI: 10.1093/aob/mcu148] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 06/11/2014] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS During seed fill in cereals, nutrients are symplasmically unloaded to vascular parenchyma in ovules, but thereafter nutrient transport is less certain. In Zea mays, two mechanisms of nutrient passage through the chalaza and nucellus have been hypothesized, apoplasmic and symplasmic. In a recent study, nutrients first passed non-selectively to the chalazal apoplasm and were then selectively absorbed by the nucellus before being released to the endosperm apoplasm. This study reports that the promoter of OUTER CELL LAYER3 (PSbOCL3) from Sorghum bicolor (sorghum) directs gene expression to chalazal cells where the apoplasmic barrier is thought to form. The aims were to elucidate PSbOCL3 expression patterns in sorghum and relate them to processes of nutrient pathway development in kernels and to recognized functions of the homeodomain-leucine zipper (HD-Zip) IV transcription factor family to which the promoter belongs. METHODS PSbOCL3 was cloned and transformed into sorghum as a promoter-GUS (β-glucuronidase) construct. Plant tissues from control and transformed plants were then stained for GUS, and kernels were cleared and characterized using differential interference contrast microscopy. KEY RESULTS A symplasmic disconnect between the chalaza and nucellus during seed fill is inferred by the combination of two phenomena: differentiation of a distinct nucellar epidermis adjacent to the chalaza, and lysis of GUS-stained chalazal cells immediately proximal to the nucellar epidermis. Compression of the GUS-stained chalazal cells during kernel maturation produced the kernel abscission zone (closing layer). CONCLUSIONS The results suggest that the HD-Zip IV transcription factor SbOCL3 regulates kernel nutrition and abscission. The latter is consistent with evidence that members of this transcription factor group regulate silique abscission and dehiscence in Arabidopsis thaliana. Collectively, the findings suggest that processes of floral organ abscission are conserved among angiosperms and may in some respects differ from processes of leaf abscission.
Collapse
Affiliation(s)
- Krishna K Dwivedi
- Caisson Laboratories, Inc., 1740 Research Park Way, North Logan, UT 84341, USA Crop Improvement Division, Indian Grassland and Fodder Research Institute, Jhansi (UP) 284003, India Plants, Soils and Climate Department, Utah State University, Logan, UT 84322-4820, USA
| | - Dominique J Roche
- Caisson Laboratories, Inc., 1740 Research Park Way, North Logan, UT 84341, USA PhytoGen Seed Co. LLC, Western Research Station, 850 Plymouth Avenue, Corcoran, CA 93212, USA
| | - Tom E Clemente
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - Zhengxiang Ge
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
| | - John G Carman
- Caisson Laboratories, Inc., 1740 Research Park Way, North Logan, UT 84341, USA Plants, Soils and Climate Department, Utah State University, Logan, UT 84322-4820, USA
| |
Collapse
|
211
|
Zhang Z, Chen X, Guan X, Liu Y, Chen H, Wang T, Mouekouba LDO, Li J, Wang A. A genome-wide survey of homeodomain-leucine zipper genes and analysis of cold-responsive HD-Zip I members’ expression in tomato. Biosci Biotechnol Biochem 2014; 78:1337-49. [DOI: 10.1080/09168451.2014.923292] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Abstract
Homeodomain-leucine zipper (HD-Zip) proteins are a kind of transcriptional factors that play a vital role in plant growth and development. However, no detailed information of HD-Zip family in tomato has been reported till now. In this study, 51 HD-Zip genes (SlHZ01-51) in this family were identified and categorized into 4 classes by exon–intron and protein structure in tomato (Solanum lycopersicum) genome. The synthetical phylogenetic tree of tomato, Arabidopsis and rice HD-Zip genes were established for an insight into their evolutionary relationships and putative functions. The results showed that the contribution of segmental duplication was larger than that of tandem duplication for expansion and evolution of genes in this family of tomato. The expression profile results under abiotic stress suggested that all SlHZ I genes were responsive to cold stress. This study will provide a clue for the further investigation of functional identification and the role of tomato HD-Zip I subfamily in plant cold stress responses and developmental events.
Collapse
Affiliation(s)
- Zhenzhu Zhang
- College of Life Science, Northeast Agricultural University, Harbin, P.R. China
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, P.R. China
| | - Xiuling Chen
- College of Horticulture, Northeast Agricultural University, Harbin, P.R. China
| | - Xin Guan
- College of Horticulture, Northeast Agricultural University, Harbin, P.R. China
| | - Yang Liu
- College of Life Science, Northeast Agricultural University, Harbin, P.R. China
| | - Hongyu Chen
- College of Life Science, Northeast Agricultural University, Harbin, P.R. China
| | - Tingting Wang
- College of Horticulture, Northeast Agricultural University, Harbin, P.R. China
| | | | - Jingfu Li
- College of Horticulture, Northeast Agricultural University, Harbin, P.R. China
| | - Aoxue Wang
- College of Life Science, Northeast Agricultural University, Harbin, P.R. China
- College of Horticulture, Northeast Agricultural University, Harbin, P.R. China
| |
Collapse
|
212
|
Gong SY, Huang GQ, Sun X, Qin LX, Li Y, Zhou L, Li XB. Cotton KNL1, encoding a class II KNOX transcription factor, is involved in regulation of fibre development. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:4133-47. [PMID: 24831118 PMCID: PMC4112624 DOI: 10.1093/jxb/eru182] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In this study, the GhKNL1 (KNOTTED1-LIKE) gene, encoding a classical class II KNOX protein was identified in cotton (Gossypium hirsutum). GhKNL1 was preferentially expressed in developing fibres at the stage of secondary cell wall (SCW) biosynthesis. GhKNL1 was localized in the cell nucleus, and could interact with GhOFP4, as well as AtOFP1, AtOFP4, and AtMYB75. However, GhKNL1 lacked transcriptional activation activity. Dominant repression of GhKNL1 affected fibre development of cotton. The expression levels of genes related to fibre elongation and SCW biosynthesis were altered in transgenic fibres of cotton. As a result, transgenic cotton plants produced aberrant, shrunken, and collapsed fibre cells. Length and cell-wall thickness of fibres of transgenic cotton plants were significantly reduced compared with the wild type. Furthermore, overexpression and dominant repression of GhKNL1 in Arabidopsis resulted in a reduction in interfascicular fibre cell-wall thickening of basal stems of transgenic plants. Complementation revealed that GhKNL1 rescued the defective phenotype of Arabidopsis knat7 mutant in some extent. These data suggest that GhKNL1, as a transcription factor, participates in regulating fibre development of cotton.
Collapse
Affiliation(s)
- Si-Ying Gong
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Geng-Qing Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Xiang Sun
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Li-Xia Qin
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Yang Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Li Zhou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Xue-Bao Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Sciences, Central China Normal University, Wuhan 430079, China
| |
Collapse
|
213
|
OsSLI1, a homeodomain containing transcription activator, involves abscisic acid related stress response in rice (Oryza sativa L.). ScientificWorldJournal 2014; 2014:809353. [PMID: 25089296 PMCID: PMC4095735 DOI: 10.1155/2014/809353] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 05/27/2014] [Indexed: 12/18/2022] Open
Abstract
Homeodomain-leucine zipper type I (HD-Zip I) proteins are involved in the regulation of plant development and response to environmental stresses. In this study, OsSLI1 (Oryza sativa stress largely induced 1), encoding a member of the HD-Zip I subfamily, was isolated from rice. The expression of OsSLI1 was dramatically induced by multiple abiotic stresses and exogenous abscisic acid (ABA). In silico sequence analysis discovered several cis-acting elements including multiple ABREs (ABA-responsive element binding factors) in the upstream promoter region of OsSLI1. The OsSLI1-GFP fusion protein was localized in the nucleus of rice protoplast cells and the transcriptional activity of OsSLI1 was confirmed by the yeast hybrid system. Further, it was found that OsSLI1 expression was enhanced in an ABI5-Like1 (ABL1) deficiency rice mutant abl1 under stress conditions, suggesting that ABL1 probably negatively regulates OsSLI1 gene expression. Moreover, it was found that OsSLI1 was regulated in panicle development. Taken together, OsSLI1 may be a transcriptional activator regulating stress-responsive gene expression and panicle development in rice.
Collapse
|
214
|
Brandt R, Cabedo M, Xie Y, Wenkel S. Homeodomain leucine-zipper proteins and their role in synchronizing growth and development with the environment. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:518-26. [PMID: 24528801 DOI: 10.1111/jipb.12185] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 01/25/2014] [Indexed: 05/21/2023]
Abstract
The Arabidopsis (Arabidopsis thaliana L.) genome encodes for four distinct classes of homeodomain leucine-zipper (HD-ZIP) transcription factors (HD-ZIPI to HD-ZIPIV), which are all organized in multi-gene families. HD-ZIP transcription factors act as sequence-specific DNA-binding proteins that are able to control the expression level of target genes. While HD-ZIPI and HD-ZIPII proteins are mainly associated with environmental responses, HD-ZIPIII and HD-ZIPIV are primarily known to act as patterning factors. Recent studies have challenged this view. It appears that several of the different HD-ZIP families interact genetically to align both morphogenesis and environmental responses, most likely by modulating phytohormone-signaling networks.
Collapse
Affiliation(s)
- Ronny Brandt
- Center for Plant Molecular Biology, University of Tübingen, Germany; Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | | | | | | |
Collapse
|
215
|
Li J, Zhu L, Lu G, Zhan XB, Lin CC, Zheng ZY. Curdlan β-1,3-glucooligosaccharides induce the defense responses against Phytophthora infestans infection of potato (Solanum tuberosum L. cv. McCain G1) leaf cells. PLoS One 2014; 9:e97197. [PMID: 24816730 PMCID: PMC4016274 DOI: 10.1371/journal.pone.0097197] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 04/15/2014] [Indexed: 01/06/2023] Open
Abstract
Activation of the innate immune system before the invasion of pathogens is a promising way to improve the resistance of plant against infection while reducing the use of agricultural chemicals. Although several elicitors were used to induce the resistance of potato plant to microbial pathogen infection, the role of curdlan oligosaccharide (CurdO) has not been established. In the current study, the defense responses were investigated at biochemical and proteomic levels to elucidate the elicitation effect of CurdOs in foliar tissues of potato (Solanum tuberosum L. cv. McCain G1). The results indicate that the CurdOs exhibit activation effect on the early- and late-defense responses in potato leaves. In addition, glucopentaose was proved to be the shortest active curdlan molecule based on the accumulation of H₂O₂ and salicylic acid and the activities of phenylalanine amino-lyase, β-1,3-glucanase and chitinase. The 2D-PAGE analysis reveals that CurdOs activate the integrated response reactions in potato cells, as a number of proteins with various functions are up-regulated including disease/defense, metabolism, transcription, and cell structure. The pathogenesis assay shows that the ratio of lesion area of potato leaf decreased from 15.82%±5.44% to 7.79%±3.03% when the plants were treated with CurdOs 1 day before the infection of Phytophthora infestans. Furthermore, the results on potato yield and induction reactions indicate that the defense responses induced by CurdOs lasted for short period of time but disappeared gradually.
Collapse
Affiliation(s)
- Jing Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Li Zhu
- Jiangsu Rayguang Biotech Company, Ltd., Wuxi, Jiangsu, China
| | - Guangxing Lu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiao-Bei Zhan
- Key Laboratory of Carbohydrate Chemistry and Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Rayguang Biotech Company, Ltd., Wuxi, Jiangsu, China
| | - Chi-Chung Lin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Zhi-Yong Zheng
- Key Laboratory of Carbohydrate Chemistry and Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| |
Collapse
|
216
|
Rice EA, Khandelwal A, Creelman RA, Griffith C, Ahrens JE, Taylor JP, Murphy LR, Manjunath S, Thompson RL, Lingard MJ, Back SL, Larue H, Brayton BR, Burek AJ, Tiwari S, Adam L, Morrell JA, Caldo RA, Huai Q, Kouadio JLK, Kuehn R, Sant AM, Wingbermuehle WJ, Sala R, Foster M, Kinser JD, Mohanty R, Jiang D, Ziegler TE, Huang MG, Kuriakose SV, Skottke K, Repetti PP, Reuber TL, Ruff TG, Petracek ME, Loida PJ. Expression of a truncated ATHB17 protein in maize increases ear weight at silking. PLoS One 2014; 9:e94238. [PMID: 24736658 PMCID: PMC3988052 DOI: 10.1371/journal.pone.0094238] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 03/12/2014] [Indexed: 12/11/2022] Open
Abstract
ATHB17 (AT2G01430) is an Arabidopsis gene encoding a member of the α-subclass of the homeodomain leucine zipper class II (HD-Zip II) family of transcription factors. The ATHB17 monomer contains four domains common to all class II HD-Zip proteins: a putative repression domain adjacent to a homeodomain, leucine zipper, and carboxy terminal domain. However, it also possesses a unique N-terminus not present in other members of the family. In this study we demonstrate that the unique 73 amino acid N-terminus is involved in regulation of cellular localization of ATHB17. The ATHB17 protein is shown to function as a transcriptional repressor and an EAR-like motif is identified within the putative repression domain of ATHB17. Transformation of maize with an ATHB17 expression construct leads to the expression of ATHB17Δ113, a truncated protein lacking the first 113 amino acids which encodes a significant portion of the repression domain. Because ATHB17Δ113 lacks the repression domain, the protein cannot directly affect the transcription of its target genes. ATHB17Δ113 can homodimerize, form heterodimers with maize endogenous HD-Zip II proteins, and bind to target DNA sequences; thus, ATHB17Δ113 may interfere with HD-Zip II mediated transcriptional activity via a dominant negative mechanism. We provide evidence that maize HD-Zip II proteins function as transcriptional repressors and that ATHB17Δ113 relieves this HD-Zip II mediated transcriptional repression activity. Expression of ATHB17Δ113 in maize leads to increased ear size at silking and, therefore, may enhance sink potential. We hypothesize that this phenotype could be a result of modulation of endogenous HD-Zip II pathways in maize.
Collapse
Affiliation(s)
- Elena A. Rice
- Monsanto Company, St. Louis, Missouri, United States of America
| | - Abha Khandelwal
- Monsanto Company, St. Louis, Missouri, United States of America
| | - Robert A. Creelman
- Mendel Biotechnology Inc., Hayward, California, United States of America
| | - Cara Griffith
- Monsanto Company, St. Louis, Missouri, United States of America
| | | | | | | | - Siva Manjunath
- Monsanto Company, St. Louis, Missouri, United States of America
| | | | | | | | - Huachun Larue
- Monsanto Company, St. Louis, Missouri, United States of America
| | - Bonnie R. Brayton
- Dupont-Pioneer Hi-Bred International, Waipahu, Hawaii, United States of America
| | - Amanda J. Burek
- Mendel Biotechnology Inc., Hayward, California, United States of America
| | - Shiv Tiwari
- Dupont-Pioneer Hi-Bred International, Hayward, California, United States of America
| | - Luc Adam
- ABCAM, Burlingame, California, United States of America
| | | | - Rico A. Caldo
- Monsanto Company, St. Louis, Missouri, United States of America
| | - Qing Huai
- Monsanto Company, Cambridge, Massachusetts, United States of America
| | | | - Rosemarie Kuehn
- Monsanto Company, St. Louis, Missouri, United States of America
| | - Anagha M. Sant
- Monsanto Company, St. Louis, Missouri, United States of America
| | | | - Rodrigo Sala
- Monsanto Company, St. Louis, Missouri, United States of America
| | - Matt Foster
- Monsanto Company, St. Louis, Missouri, United States of America
| | - Josh D. Kinser
- Monsanto Company, St. Louis, Missouri, United States of America
| | - Radha Mohanty
- Monsanto Company, St. Louis, Missouri, United States of America
| | - Dongming Jiang
- Monsanto Company, St. Louis, Missouri, United States of America
| | - Todd E. Ziegler
- Monsanto Company, St. Louis, Missouri, United States of America
| | - Mingya G. Huang
- Monsanto Company, St. Louis, Missouri, United States of America
| | | | - Kyle Skottke
- Monsanto Company, St. Louis, Missouri, United States of America
| | - Peter P. Repetti
- Mendel Biotechnology Inc., Hayward, California, United States of America
| | - T. Lynne Reuber
- Mendel Biotechnology Inc., Hayward, California, United States of America
| | - Thomas G. Ruff
- Monsanto Company, St. Louis, Missouri, United States of America
| | | | - Paul J. Loida
- Monsanto Company, St. Louis, Missouri, United States of America
- * E-mail:
| |
Collapse
|
217
|
Xu Y, Wang Y, Long Q, Huang J, Wang Y, Zhou K, Zheng M, Sun J, Chen H, Chen S, Jiang L, Wang C, Wan J. Overexpression of OsZHD1, a zinc finger homeodomain class homeobox transcription factor, induces abaxially curled and drooping leaf in rice. PLANTA 2014; 239:803-16. [PMID: 24385091 DOI: 10.1007/s00425-013-2009-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 12/08/2013] [Indexed: 05/05/2023]
Abstract
Leaf rolling is receiving considerable attention as an important agronomic trait in rice (Oryza sativa L.). However, little has been known on the molecular mechanism of rice leaf rolling, especially the abaxial rolling. We identified a novel abaxially curled and drooping leaf-dominant mutant from a T₁ transgenic rice line. The abaxially curled leaf phenotypes, co-segregating with the inserted transferred DNA, were caused by overexpression of a zinc finger homeodomain class homeobox transcription factor (OsZHD1). OsZHD1 exhibited a constitutive expression pattern in wild-type plants and accumulated in the developing leaves and panicles. Artificial overexpression of OsZHD1 or its closest homolog OsZHD2 induced the abaxial leaf curling. Histological analysis indicated that both the increased number and the abnormal arrangement of bulliform cells in leaf were responsible for the abaxially curled leaves. We herein reported OsZHD1 with key roles in rice morphogenesis, especially in the modulating of leaf rolling, which provided a novel insight into the molecular mechanism of leaf development in rice.
Collapse
Affiliation(s)
- Yang Xu
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
218
|
Chen X, Chen Z, Zhao H, Zhao Y, Cheng B, Xiang Y. Genome-wide analysis of soybean HD-Zip gene family and expression profiling under salinity and drought treatments. PLoS One 2014; 9:e87156. [PMID: 24498296 PMCID: PMC3911943 DOI: 10.1371/journal.pone.0087156] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 12/18/2013] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Homeodomain-leucine zipper (HD-Zip) proteins, a group of homeobox transcription factors, participate in various aspects of normal plant growth and developmental processes as well as environmental responses. To date, no overall analysis or expression profiling of the HD-Zip gene family in soybean (Glycine max) has been reported. METHODS AND FINDINGS An investigation of the soybean genome revealed 88 putative HD-Zip genes. These genes were classified into four subfamilies, I to IV, based on phylogenetic analysis. In each subfamily, the constituent parts of gene structure and motif were relatively conserved. A total of 87 out of 88 genes were distributed unequally on 20 chromosomes with 36 segmental duplication events, indicating that segmental duplication is important for the expansion of the HD-Zip family. Analysis of the Ka/Ks ratios showed that the duplicated genes of the HD-Zip family basically underwent purifying selection with restrictive functional divergence after the duplication events. Analysis of expression profiles showed that 80 genes differentially expressed across 14 tissues, and 59 HD-Zip genes are differentially expressed under salinity and drought stress, with 20 paralogous pairs showing nearly identical expression patterns and three paralogous pairs diversifying significantly under drought stress. Quantitative real-time RT-PCR (qRT-PCR) analysis of six paralogous pairs of 12 selected soybean HD-Zip genes under both drought and salinity stress confirmed their stress-inducible expression patterns. CONCLUSIONS This study presents a thorough overview of the soybean HD-Zip gene family and provides a new perspective on the evolution of this gene family. The results indicate that HD-Zip family genes may be involved in many plant responses to stress conditions. Additionally, this study provides a solid foundation for uncovering the biological roles of HD-Zip genes in soybean growth and development.
Collapse
Affiliation(s)
- Xue Chen
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Zhu Chen
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Hualin Zhao
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Yang Zhao
- Key Laboratory of Crop Biology of Anhui Agriculture University, Hefei, China
| | - Beijiu Cheng
- Key Laboratory of Crop Biology of Anhui Agriculture University, Hefei, China
| | - Yan Xiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| |
Collapse
|
219
|
Kurdyukov S, Song Y, Sheahan MB, Rose RJ. Transcriptional regulation of early embryo development in the model legume Medicago truncatula. PLANT CELL REPORTS 2014; 33:349-62. [PMID: 24258241 PMCID: PMC3909251 DOI: 10.1007/s00299-013-1535-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/23/2013] [Accepted: 11/02/2013] [Indexed: 05/18/2023]
Abstract
Cultivated legumes account for more than a quarter of primary crop production worldwide. The protein- and oil-rich seed of cultivated legumes provides around one-third of the protein in the average human diet, with soybeans (Glycine max (L.) Merr) being the single largest source of vegetable oil. Despite their critical importance to human and animal nutrition, we lack an understanding of how early seed development in legumes is orchestrated at the transcriptional level. We developed a method to isolate ovules from the model legume, Medicago truncatula Gaertn, at specific stages of embryogenesis, on the basis of flower and pod morphology. Using these isolated ovules we profiled the expression of candidate homeobox, AP2 domain and B3 domain-containing transcription factors. These genes were identified by available information and sequence homology, and five distinctive patterns of transcription were found that correlated with specific stages of early seed growth and development. Co-expression of some genes could be related to common regulatory sequences in the promoter or 3'-UTR regions. These expression patterns were also related to the expression of B3-domain transcription factors important in seed filling (MtFUS3-like and MtABI3-like). Localisation of gene expression by promoter-GUS fusions or in situ hybridisation aided understanding of the role of the transcription factors. This study provides a framework to enhance the understanding of the integrated transcriptional regulation of legume embryo growth and development and seed filling.
Collapse
Affiliation(s)
- Sergey Kurdyukov
- Australian Research Council Centre of Excellence for Integrative Legume Research, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308 Australia
- Present Address: Kolling Institute of Medical Research, Kolling Building, Royal North Shore Hospital, St Leonards, NSW 2065 Australia
| | - Youhong Song
- Australian Research Council Centre of Excellence for Integrative Legume Research, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308 Australia
| | - Michael B. Sheahan
- Australian Research Council Centre of Excellence for Integrative Legume Research, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308 Australia
| | - Ray J. Rose
- Australian Research Council Centre of Excellence for Integrative Legume Research, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308 Australia
| |
Collapse
|
220
|
Origins and evolution of WUSCHEL-related homeobox protein family in plant kingdom. ScientificWorldJournal 2014; 2014:534140. [PMID: 24511289 PMCID: PMC3913392 DOI: 10.1155/2014/534140] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 09/19/2013] [Indexed: 12/24/2022] Open
Abstract
WUSCHEL-related homeobox (WOX) is a large group of transcription factors specifically found in plants. WOX members contain the conserved homeodomain essential for plant development by regulating cell division and differentiation. However, the evolutionary relationship of WOX members in plant kingdom remains to be elucidated. In this study, we searched 350 WOX members from 50 species in plant kingdom. Linkage analysis of WOX protein sequences demonstrated that amino acid residues 141-145 and 153-160 located in the homeodomain are possibly associated with the function of WOXs during the evolution. These 350 members were grouped into 3 clades: the first clade represents the conservative WOXs from the lower plant algae to higher plants; the second clade has the members from vascular plant species; the third clade has the members only from spermatophyte species. Furthermore, among the members of Arabidopsis thaliana and Oryza sativa, we observed ubiquitous expression of genes in the first clade and the diversified expression pattern of WOX genes in distinct organs in the second clade and the third clade. This work provides insight into the origin and evolutionary process of WOXs, facilitating their functional investigations in the future.
Collapse
|
221
|
Arnaud N, Pautot V. Ring the BELL and tie the KNOX: roles for TALEs in gynoecium development. FRONTIERS IN PLANT SCIENCE 2014; 5:93. [PMID: 24688486 PMCID: PMC3960571 DOI: 10.3389/fpls.2014.00093] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 02/25/2014] [Indexed: 05/17/2023]
Abstract
Carpels are leaf-like structures that bear ovules, and thus play a crucial role in the plant life cycle. In angiosperms, carpels are the last organs produced by the floral meristem and they differentiate a specialized meristematic tissue from which ovules develop. Members of the three-amino-acid-loop-extension (TALE) class of homeoproteins constitute major regulators of meristematic activity. This family contains KNOTTED-like (KNOX) and BEL1-like (BLH or BELL) homeodomain proteins, which function as heterodimers. KNOX proteins can have different BELL partners, leading to multiple combinations with distinct activities, and thus regulate many aspects of plant morphogenesis, including gynoecium development. TALE proteins act primarily through direct regulation of hormonal pathways and key transcriptional regulators. This review focuses on the contribution of TALE proteins to gynoecium development and connects TALE transcription factors to carpel gene regulatory networks.
Collapse
Affiliation(s)
- Nicolas Arnaud
- UMR 1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Institut Jean-Pierre Bourgin Versailles, France
| | - Véronique Pautot
- UMR 1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Institut Jean-Pierre Bourgin Versailles, France
| |
Collapse
|
222
|
Chen X, Chen Z, Zhao H, Zhao Y, Cheng B, Xiang Y. Genome-wide analysis of soybean HD-Zip gene family and expression profiling under salinity and drought treatments. PLoS One 2014. [PMID: 24498296 DOI: 10.3390/ijms1303317610.1371/journal.pone.0087156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Homeodomain-leucine zipper (HD-Zip) proteins, a group of homeobox transcription factors, participate in various aspects of normal plant growth and developmental processes as well as environmental responses. To date, no overall analysis or expression profiling of the HD-Zip gene family in soybean (Glycine max) has been reported. METHODS AND FINDINGS An investigation of the soybean genome revealed 88 putative HD-Zip genes. These genes were classified into four subfamilies, I to IV, based on phylogenetic analysis. In each subfamily, the constituent parts of gene structure and motif were relatively conserved. A total of 87 out of 88 genes were distributed unequally on 20 chromosomes with 36 segmental duplication events, indicating that segmental duplication is important for the expansion of the HD-Zip family. Analysis of the Ka/Ks ratios showed that the duplicated genes of the HD-Zip family basically underwent purifying selection with restrictive functional divergence after the duplication events. Analysis of expression profiles showed that 80 genes differentially expressed across 14 tissues, and 59 HD-Zip genes are differentially expressed under salinity and drought stress, with 20 paralogous pairs showing nearly identical expression patterns and three paralogous pairs diversifying significantly under drought stress. Quantitative real-time RT-PCR (qRT-PCR) analysis of six paralogous pairs of 12 selected soybean HD-Zip genes under both drought and salinity stress confirmed their stress-inducible expression patterns. CONCLUSIONS This study presents a thorough overview of the soybean HD-Zip gene family and provides a new perspective on the evolution of this gene family. The results indicate that HD-Zip family genes may be involved in many plant responses to stress conditions. Additionally, this study provides a solid foundation for uncovering the biological roles of HD-Zip genes in soybean growth and development.
Collapse
Affiliation(s)
- Xue Chen
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Zhu Chen
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Hualin Zhao
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Yang Zhao
- Key Laboratory of Crop Biology of Anhui Agriculture University, Hefei, China
| | - Beijiu Cheng
- Key Laboratory of Crop Biology of Anhui Agriculture University, Hefei, China
| | - Yan Xiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China
| |
Collapse
|
223
|
Zhang L, Wang L, Yang Y, Cui J, Chang F, Wang Y, Ma H. Analysis of Arabidopsis floral transcriptome: detection of new florally expressed genes and expansion of Brassicaceae-specific gene families. FRONTIERS IN PLANT SCIENCE 2014; 5:802. [PMID: 25653662 PMCID: PMC4299442 DOI: 10.3389/fpls.2014.00802] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/22/2014] [Indexed: 05/20/2023]
Abstract
The flower is essential for sexual reproduction of flowering plants and has been extensively studied. However, it is still not clear how many genes are expressed in the flower. Here, we performed RNA-seq analysis as a highly sensitive approach to investigate the Arabidopsis floral transcriptome at three developmental stages. We provide evidence that at least 23, 961 genes are active in the Arabidopsis flower, including 8512 genes that have not been reported as florally expressed previously. We compared gene expression at different stages and found that many genes encoding transcription factors are preferentially expressed in early flower development. Other genes with expression at distinct developmental stages included DUF577 in meiotic cells and DUF220, DUF1216, and Oleosin in stage 12 flowers. DUF1216 and DUF577 are Brassicaceae specific, and together with other families experienced expansion within the Brassicaceae lineage, suggesting novel/greater roles in Brassicaceae floral development than other plants. The large dataset from this study can serve as a resource for expression analysis of genes involved in flower development in Arabidopsis and for comparison with other species. Together, this work provides clues regarding molecular networks underlying flower development.
Collapse
Affiliation(s)
- Liangsheng Zhang
- Department of Pharmacy, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji UniversityShanghai, China
- Advanced Institute of Translational Medicine, Tongji UniversityShanghai, China
| | - Lei Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plants Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan UniversityShanghai, China
- Institutes of Biomedical Sciences, Fudan UniversityShanghai, China
| | - Yulin Yang
- Department of Pharmacy, Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji UniversityShanghai, China
| | - Jie Cui
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plants Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan UniversityShanghai, China
| | - Fang Chang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plants Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan UniversityShanghai, China
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plants Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan UniversityShanghai, China
- *Correspondence: Yingxiang Wang and Hong Ma, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China e-mail: ;
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering and Institute of Biodiversity Sciences, Institute of Plants Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan UniversityShanghai, China
- Institutes of Biomedical Sciences, Fudan UniversityShanghai, China
- *Correspondence: Yingxiang Wang and Hong Ma, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China e-mail: ;
| |
Collapse
|
224
|
Pabón-Mora N, Wong GKS, Ambrose BA. Evolution of fruit development genes in flowering plants. FRONTIERS IN PLANT SCIENCE 2014; 5:300. [PMID: 25018763 PMCID: PMC4071287 DOI: 10.3389/fpls.2014.00300] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 06/07/2014] [Indexed: 05/18/2023]
Abstract
The genetic mechanisms regulating dry fruit development and opercular dehiscence have been identified in Arabidopsis thaliana. In the bicarpellate silique, valve elongation and differentiation is controlled by FRUITFULL (FUL) that antagonizes SHATTERPROOF1-2 (SHP1/SHP2) and INDEHISCENT (IND) at the dehiscence zone where they control normal lignification. SHP1/2 are also repressed by REPLUMLESS (RPL), responsible for replum formation. Similarly, FUL indirectly controls two other factors ALCATRAZ (ALC) and SPATULA (SPT) that function in the proper formation of the separation layer. FUL and SHP1/2 belong to the MADS-box family, IND and ALC belong to the bHLH family and RPL belongs to the homeodomain family, all of which are large transcription factor families. These families have undergone numerous duplications and losses in plants, likely accompanied by functional changes. Functional analyses of homologous genes suggest that this network is fairly conserved in Brassicaceae and less conserved in other core eudicots. Only the MADS box genes have been functionally characterized in basal eudicots and suggest partial conservation of the functions recorded for Brassicaceae. Here we do a comprehensive search of SHP, IND, ALC, SPT, and RPL homologs across core-eudicots, basal eudicots, monocots and basal angiosperms. Based on gene-tree analyses we hypothesize what parts of the network for fruit development in Brassicaceae, in particular regarding direct and indirect targets of FUL, might be conserved across angiosperms.
Collapse
Affiliation(s)
- Natalia Pabón-Mora
- Instituto de Biología, Universidad de AntioquiaMedellín, Colombia
- The New York Botanical GardenBronx, NY, USA
- *Correspondence: Natalia Pabón-Mora, Instituto de Biología, Universidad de Antioquia, Calle 70 No 52-21, AA 1226 Medellín, Colombia e-mail:
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of AlbertaEdmonton, AB, Canada
- Department of Medicine, University of AlbertaEdmonton, AB, Canada
- BGI-Shenzhen, Beishan Industrial ZoneShenzhen, China
| | | |
Collapse
|
225
|
Liu W, Fu R, Li Q, Li J, Wang L, Ren Z. Genome-wide identification and expression profile of homeodomain-leucine zipper Class I gene family in Cucumis sativus. Gene 2013; 531:279-87. [DOI: 10.1016/j.gene.2013.08.089] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 08/17/2013] [Accepted: 08/28/2013] [Indexed: 12/28/2022]
|
226
|
Dong J, Gao Z, Liu S, Li G, Yang Z, Huang H, Xu L. SLIDE, the protein interacting domain of Imitation Switch remodelers, binds DDT-domain proteins of different subfamilies in chromatin remodeling complexes. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2013; 55:928-937. [PMID: 23691993 DOI: 10.1111/jipb.12069] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 05/13/2013] [Indexed: 06/02/2023]
Abstract
The Imitation Switch (ISWI) type adenosine triphosphate (ATP)-dependent chromatin remodeling factors are conserved proteins in eukaryotes, and some of them are known to form stable remodeling complexes with members from a family of proteins, termed DDT-domain proteins. Although it is well documented that ISWIs play important roles in different biological processes in many eukaryotic species, the molecular basis for protein interactions in ISWI complexes has not been fully addressed. Here, we report the identification of interaction domains for both ISWI and DDT-domain proteins. By analyzing CHROMATIN REMODELING11 (CHR11) and RINGLET1 (RLT1), an Arabidopsis thaliana ISWI (AtISWI) and AtDDT-domain protein, respectively, we show that the SLIDE domain of CHR11 and the DDT domain together with an adjacent sequence of RLT1 are responsible for their binding. The Arabidopsis genome contains at least 12 genes that encode DDT-domain proteins, which could be grouped into five subfamilies based on the sequence similarity. The SLIDE domain of AtISWI is able to bind members from different AtDDT subfamilies. Moreover, a human ISWI protein SNF2H is capable of binding AtDDT-domain proteins through its SLIDE domain, suggesting that binding to DDT-domain proteins is a conserved biochemical function for the SLIDE domain of ISWIs in eukaryotes.
Collapse
Affiliation(s)
- Jiaqiang Dong
- National Laboratory of Plant Molecular Genetics, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, Shanghai, 200032, China
| | | | | | | | | | | | | |
Collapse
|
227
|
Zalewski CS, Floyd SK, Furumizu C, Sakakibara K, Stevenson DW, Bowman JL. Evolution of the class IV HD-zip gene family in streptophytes. Mol Biol Evol 2013; 30:2347-65. [PMID: 23894141 PMCID: PMC3773374 DOI: 10.1093/molbev/mst132] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Class IV homeodomain leucine zipper (C4HDZ) genes are plant-specific transcription factors that, based on phenotypes in Arabidopsis thaliana, play an important role in epidermal development. In this study, we sampled all major extant lineages and their closest algal relatives for C4HDZ homologs and phylogenetic analyses result in a gene tree that mirrors land plant evolution with evidence for gene duplications in many lineages, but minimal evidence for gene losses. Our analysis suggests an ancestral C4HDZ gene originated in an algal ancestor of land plants and a single ancestral gene was present in the last common ancestor of land plants. Independent gene duplications are evident within several lineages including mosses, lycophytes, euphyllophytes, seed plants, and, most notably, angiosperms. In recently evolved angiosperm paralogs, we find evidence of pseudogenization via mutations in both coding and regulatory sequences. The increasing complexity of the C4HDZ gene family through the diversification of land plants correlates to increasing complexity in epidermal characters.
Collapse
Affiliation(s)
| | - Sandra K. Floyd
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Chihiro Furumizu
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Keiko Sakakibara
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
- Graduate School of Science, University of Tokyo, Hongo, Tokyo, Japan
| | | | - John L. Bowman
- Section of Plant Biology, University of California, Davis
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| |
Collapse
|
228
|
Reinhart BJ, Liu T, Newell NR, Magnani E, Huang T, Kerstetter R, Michaels S, Barton MK. Establishing a framework for the Ad/abaxial regulatory network of Arabidopsis: ascertaining targets of class III homeodomain leucine zipper and KANADI regulation. THE PLANT CELL 2013; 25:3228-49. [PMID: 24076978 PMCID: PMC3809529 DOI: 10.1105/tpc.113.111518] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 08/08/2013] [Accepted: 08/27/2013] [Indexed: 05/18/2023]
Abstract
The broadly conserved Class III homeodomain leucine zipper (HD-ZIPIII) and KANADI transcription factors have opposing and transformational effects on polarity and growth in all tissues and stages of the plant's life. To obtain a comprehensive understanding of how these factors work, we have identified transcripts that change in response to induced HD-ZIPIII or KANADI function. Additional criteria used to identify high-confidence targets among this set were presence of an adjacent HD-ZIPIII binding site, expression enriched within a subdomain of the shoot apical meristem, mutant phenotype showing defect in polar leaf and/or meristem development, physical interaction between target gene product and HD-ZIPIII protein, opposite regulation by HD-ZIPIII and KANADI, and evolutionary conservation of the regulator-target relationship. We find that HD-ZIPIII and KANADI regulate tissue-specific transcription factors involved in subsidiary developmental decisions, nearly all major hormone pathways, and new actors (such as indeterminate domain4) in the ad/abaxial regulatory network. Multiple feedback loops regulating HD-ZIPIII and KANADI are identified, as are mechanisms through which HD-ZIPIII and KANADI oppose each other. This work lays the foundation needed to understand the components, structure, and workings of the ad/abaxial regulatory network directing basic plant growth and development.
Collapse
Affiliation(s)
- Brenda J. Reinhart
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Tie Liu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Nicole R. Newell
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Enrico Magnani
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Tengbo Huang
- Rutgers University of New Jersey, New Brunswick, New Jersey 08901
| | | | | | - M. Kathryn Barton
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
- Address correspondence to
| |
Collapse
|
229
|
Zimmer AD, Lang D, Buchta K, Rombauts S, Nishiyama T, Hasebe M, Van de Peer Y, Rensing SA, Reski R. Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions. BMC Genomics 2013; 14:498. [PMID: 23879659 PMCID: PMC3729371 DOI: 10.1186/1471-2164-14-498] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 07/19/2013] [Indexed: 11/24/2022] Open
Abstract
Background The moss Physcomitrella patens as a model species provides an important reference for early-diverging lineages of plants and the release of the genome in 2008 opened the doors to genome-wide studies. The usability of a reference genome greatly depends on the quality of the annotation and the availability of centralized community resources. Therefore, in the light of accumulating evidence for missing genes, fragmentary gene structures, false annotations and a low rate of functional annotations on the original release, we decided to improve the moss genome annotation. Results Here, we report the complete moss genome re-annotation (designated V1.6) incorporating the increased transcript availability from a multitude of developmental stages and tissue types. We demonstrate the utility of the improved P. patens genome annotation for comparative genomics and new extensions to the cosmoss.org resource as a central repository for this plant “flagship” genome. The structural annotation of 32,275 protein-coding genes results in 8387 additional loci including 1456 loci with known protein domains or homologs in Plantae. This is the first release to include information on transcript isoforms, suggesting alternative splicing events for at least 10.8% of the loci. Furthermore, this release now also provides information on non-protein-coding loci. Functional annotations were improved regarding quality and coverage, resulting in 58% annotated loci (previously: 41%) that comprise also 7200 additional loci with GO annotations. Access and manual curation of the functional and structural genome annotation is provided via the http://www.cosmoss.org model organism database. Conclusions Comparative analysis of gene structure evolution along the green plant lineage provides novel insights, such as a comparatively high number of loci with 5’-UTR introns in the moss. Comparative analysis of functional annotations reveals expansions of moss house-keeping and metabolic genes and further possibly adaptive, lineage-specific expansions and gains including at least 13% orphan genes.
Collapse
Affiliation(s)
- Andreas D Zimmer
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
230
|
Zimmer EA, Wen J. Reprint of: using nuclear gene data for plant phylogenetics: progress and prospects. Mol Phylogenet Evol 2013; 66:539-50. [PMID: 23375140 DOI: 10.1016/j.ympev.2013.01.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 06/14/2012] [Accepted: 07/16/2012] [Indexed: 12/25/2022]
Abstract
The paper reviews the current state of low and single copy nuclear markers that have been applied successfully in plant phylogenetics to date, and discusses case studies highlighting the potential of massively parallel high throughput or next-generation sequencing (NGS) approaches for molecular phylogenetic and evolutionary investigations. The current state, prospects and challenges of specific single- or low-copy plant nuclear markers as well as phylogenomic case studies are presented and evaluated.
Collapse
Affiliation(s)
- Elizabeth A Zimmer
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA.
| | | |
Collapse
|
231
|
Di Giacomo E, Iannelli MA, Frugis G. TALE and Shape: How to Make a Leaf Different. PLANTS (BASEL, SWITZERLAND) 2013. [PMID: 27137378 DOI: 10.3390/plantas2020317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The Three Amino acid Loop Extension (TALE) proteins constitute an ancestral superclass of homeodomain transcription factors conserved in animals, plants and fungi. In plants they comprise two classes, KNOTTED1-LIKE homeobox (KNOX) and BEL1-like homeobox (BLH or BELL, hereafter referred to as BLH), which are involved in shoot apical meristem (SAM) function, as well as in the determination and morphological development of leaves, stems and inflorescences. Selective protein-protein interactions between KNOXs and BLHs affect heterodimer subcellular localization and target affinity. KNOXs exert their roles by maintaining a proper balance between undifferentiated and differentiated cell state through the modulation of multiple hormonal pathways. A pivotal function of KNOX in evolutionary diversification of leaf morphology has been assessed. In the SAM of both simple- and compound-leafed seed species, downregulation of most class 1 KNOX (KNOX1) genes marks the sites of leaf primordia initiation. However, KNOX1 expression is re-established during leaf primordia development of compound-leafed species to maintain transient indeterminacy and morphogenetic activity at the leaf margins. Despite the increasing knowledge available about KNOX1 protein function in plant development, a comprehensive view on their downstream effectors remains elusive. This review highlights the role of TALE proteins in leaf initiation and morphological plasticity with a focus on recent advances in the identification of downstream target genes and pathways.
Collapse
Affiliation(s)
- Elisabetta Di Giacomo
- Istituto di Biologia e Biotecnologia Agraria, UOS Roma, Consiglio Nazionale delle Ricerche, Via Salaria Km. 29,300, Monterotondo Scalo, 00015 Roma, Italy.
| | - Maria Adelaide Iannelli
- Istituto di Biologia e Biotecnologia Agraria, UOS Roma, Consiglio Nazionale delle Ricerche, Via Salaria Km. 29,300, Monterotondo Scalo, 00015 Roma, Italy.
| | - Giovanna Frugis
- Istituto di Biologia e Biotecnologia Agraria, UOS Roma, Consiglio Nazionale delle Ricerche, Via Salaria Km. 29,300, Monterotondo Scalo, 00015 Roma, Italy.
| |
Collapse
|
232
|
Di Giacomo E, Iannelli MA, Frugis G. TALE and Shape: How to Make a Leaf Different. PLANTS 2013; 2:317-42. [PMID: 27137378 PMCID: PMC4844364 DOI: 10.3390/plants2020317] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 04/10/2013] [Accepted: 04/19/2013] [Indexed: 11/25/2022]
Abstract
The Three Amino acid Loop Extension (TALE) proteins constitute an ancestral superclass of homeodomain transcription factors conserved in animals, plants and fungi. In plants they comprise two classes, KNOTTED1-LIKE homeobox (KNOX) and BEL1-like homeobox (BLH or BELL, hereafter referred to as BLH), which are involved in shoot apical meristem (SAM) function, as well as in the determination and morphological development of leaves, stems and inflorescences. Selective protein-protein interactions between KNOXs and BLHs affect heterodimer subcellular localization and target affinity. KNOXs exert their roles by maintaining a proper balance between undifferentiated and differentiated cell state through the modulation of multiple hormonal pathways. A pivotal function of KNOX in evolutionary diversification of leaf morphology has been assessed. In the SAM of both simple- and compound-leafed seed species, downregulation of most class 1 KNOX (KNOX1) genes marks the sites of leaf primordia initiation. However, KNOX1 expression is re-established during leaf primordia development of compound-leafed species to maintain transient indeterminacy and morphogenetic activity at the leaf margins. Despite the increasing knowledge available about KNOX1 protein function in plant development, a comprehensive view on their downstream effectors remains elusive. This review highlights the role of TALE proteins in leaf initiation and morphological plasticity with a focus on recent advances in the identification of downstream target genes and pathways.
Collapse
Affiliation(s)
- Elisabetta Di Giacomo
- Istituto di Biologia e Biotecnologia Agraria, UOS Roma, Consiglio Nazionale delle Ricerche, Via Salaria Km. 29,300, Monterotondo Scalo, 00015 Roma, Italy.
| | - Maria Adelaide Iannelli
- Istituto di Biologia e Biotecnologia Agraria, UOS Roma, Consiglio Nazionale delle Ricerche, Via Salaria Km. 29,300, Monterotondo Scalo, 00015 Roma, Italy.
| | - Giovanna Frugis
- Istituto di Biologia e Biotecnologia Agraria, UOS Roma, Consiglio Nazionale delle Ricerche, Via Salaria Km. 29,300, Monterotondo Scalo, 00015 Roma, Italy.
| |
Collapse
|
233
|
Sun Q, Csorba T, Skourti-Stathaki K, Proudfoot NJ, Dean C. R-loop stabilization represses antisense transcription at the Arabidopsis FLC locus. Science 2013; 340:619-21. [PMID: 23641115 PMCID: PMC5144995 DOI: 10.1126/science.1234848] [Citation(s) in RCA: 276] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Roles for long noncoding RNAs (lncRNAs) in gene expression are emerging, but regulation of the lncRNA itself is poorly understood. We have identified a homeodomain protein, AtNDX, that regulates COOLAIR, a set of antisense transcripts originating from the 3' end of Arabidopsis FLOWERING LOCUS C (FLC). AtNDX associates with single-stranded DNA rather than double-stranded DNA non-sequence-specifically in vitro, and localizes to a heterochromatic region in the COOLAIR promoter in vivo. Single-stranded DNA was detected in vivo as part of an RNA-DNA hybrid, or R-loop, that covers the COOLAIR promoter. R-loop stabilization mediated by AtNDX inhibits COOLAIR transcription, which in turn modifies FLC expression. Differential stabilization of R-loops could be a general mechanism influencing gene expression in many organisms.
Collapse
MESH Headings
- Amino Acid Sequence
- Arabidopsis/genetics
- Arabidopsis/metabolism
- Arabidopsis Proteins/chemistry
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- Chromatin/metabolism
- DNA, Plant/chemistry
- DNA, Plant/metabolism
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/metabolism
- Gene Expression Regulation, Plant
- Homeodomain Proteins/chemistry
- Homeodomain Proteins/metabolism
- MADS Domain Proteins/genetics
- MADS Domain Proteins/metabolism
- Molecular Sequence Data
- Nucleic Acid Conformation
- Promoter Regions, Genetic
- Protein Binding
- RNA, Antisense/chemistry
- RNA, Antisense/genetics
- RNA, Antisense/metabolism
- RNA, Long Noncoding/chemistry
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Plant/chemistry
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Transcription Termination, Genetic
- Transcription, Genetic
Collapse
Affiliation(s)
- Qianwen Sun
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Tibor Csorba
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | | | | | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| |
Collapse
|
234
|
Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1. Nature 2013; 498:385-9. [PMID: 23636332 DOI: 10.1038/nature12178] [Citation(s) in RCA: 250] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Accepted: 04/12/2013] [Indexed: 12/31/2022]
Abstract
DNA methylation is an epigenetic modification that has critical roles in gene silencing, development and genome integrity. In Arabidopsis, DNA methylation is established by DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) and targeted by 24-nucleotide small interfering RNAs (siRNAs) through a pathway termed RNA-directed DNA methylation (RdDM). This pathway requires two plant-specific RNA polymerases: Pol-IV, which functions to initiate siRNA biogenesis, and Pol-V, which functions to generate scaffold transcripts that recruit downstream RdDM factors. To understand the mechanisms controlling Pol-IV targeting we investigated the function of SAWADEE HOMEODOMAIN HOMOLOG 1 (SHH1), a Pol-IV-interacting protein. Here we show that SHH1 acts upstream in the RdDM pathway to enable siRNA production from a large subset of the most active RdDM targets, and that SHH1 is required for Pol-IV occupancy at these same loci. We also show that the SHH1 SAWADEE domain is a novel chromatin-binding module that adopts a unique tandem Tudor-like fold and functions as a dual lysine reader, probing for both unmethylated K4 and methylated K9 modifications on the histone 3 (H3) tail. Finally, we show that key residues within both lysine-binding pockets of SHH1 are required in vivo to maintain siRNA and DNA methylation levels as well as Pol-IV occupancy at RdDM targets, demonstrating a central role for methylated H3K9 binding in SHH1 function and providing the first insights into the mechanism of Pol-IV targeting. Given the parallels between methylation systems in plants and mammals, a further understanding of this early targeting step may aid our ability to control the expression of endogenous and newly introduced genes, which has broad implications for agriculture and gene therapy.
Collapse
|
235
|
Stammler A, Meyer SS, Plant AR, Townsley BT, Becker A, Gleissberg S. Duplicated STM-like KNOX I genes act in floral meristem activity in Eschscholzia californica (Papaveraceae). Dev Genes Evol 2013; 223:289-301. [DOI: 10.1007/s00427-013-0446-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 04/01/2013] [Indexed: 01/06/2023]
|
236
|
DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV. Proc Natl Acad Sci U S A 2013; 110:8290-5. [PMID: 23637343 DOI: 10.1073/pnas.1300585110] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
DNA methylation is an important epigenetic mark in many eukaryotic organisms. De novo DNA methylation in plants can be achieved by the RNA-directed DNA methylation (RdDM) pathway, where the plant-specific DNA-dependent RNA polymerase IV (Pol IV) transcribes target sequences to initiate 24-nt siRNA production and action. The putative DNA binding protein DTF1/SHH1 of Arabidopsis has been shown to associate with Pol IV and is required for 24-nt siRNA accumulation and transcriptional silencing at several RdDM target loci. However, the extent and mechanism of DTF1 function in RdDM is unclear. We show here that DTF1 is necessary for the accumulation of the majority of Pol IV-dependent 24-nt siRNAs. It is also required for a large proportion of Pol IV-dependent de novo DNA methylation. Interestingly, there is a group of RdDM target loci where 24-nt siRNA accumulation but not DNA methylation is dependent on DTF1. DTF1 interacts directly with the chromatin remodeling protein CLASSY 1 (CLSY1), and both DTF1 and CLSY1 are associated in vivo with Pol IV but not Pol V, which functions downstream in the RdDM effector complex. DTF1 and DTF2 (a DTF1-like protein) contain a SAWADEE domain, which was found to bind specifically to histone H3 containing H3K9 methylation. Taken together, our results show that DTF1 is a core component of the RdDM pathway, and suggest that DTF1 interacts with CLSY1 to assist in the recruitment of Pol IV to RdDM target loci where H3K9 methylation may be an important feature. Our results also suggest the involvement of DTF1 in an important negative feedback mechanism for DNA methylation at some RdDM target loci.
Collapse
|
237
|
Chew W, Hrmova M, Lopato S. Role of Homeodomain leucine zipper (HD-Zip) IV transcription factors in plant development and plant protection from deleterious environmental factors. Int J Mol Sci 2013; 14:8122-47. [PMID: 23584027 PMCID: PMC3645734 DOI: 10.3390/ijms14048122] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 03/26/2013] [Accepted: 04/03/2013] [Indexed: 01/11/2023] Open
Abstract
Homeobox genes comprise an important group of genes that are responsible for regulation of developmental processes. These genes determine cell differentiation and cell fate in all eukaryotic organisms, starting from the early stages of embryo development. Homeodomain leucine zipper (HD-Zip) transcription factors are unique to the plant kingdom. Members of the HD-Zip IV subfamily have a complex domain topology and can bind several cis-elements with overlapping sequences. Many of the reported HD-Zip IV genes were shown to be specifically or preferentially expressed in plant epidermal or sub-epidermal cells. HD-Zip IV TFs were found to be associated with differentiation and maintenance of outer cell layers, and regulation of lipid biosynthesis and transport. Insights about the role of these proteins in plant cuticle formation, and hence their possible involvement in plant protection from pathogens and abiotic stresses has just started to emerge. These roles make HD-Zip IV proteins an attractive tool for genetic engineering of crop plants. To this end, there is a need for in-depth studies to further clarify the function of each HD-Zip IV subfamily member in commercially important plant species.
Collapse
Affiliation(s)
- William Chew
- Australian Centre for Plant Functional Genomics, University of Adelaide, Waite Campus, Glen Osmond, South Australia 5064, Australia.
| | | | | |
Collapse
|
238
|
Peterson KM, Shyu C, Burr CA, Horst RJ, Kanaoka MM, Omae M, Sato Y, Torii KU. Arabidopsis homeodomain-leucine zipper IV proteins promote stomatal development and ectopically induce stomata beyond the epidermis. Development 2013; 140:1924-35. [PMID: 23515473 DOI: 10.1242/dev.090209] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The shoot epidermis of land plants serves as a crucial interface between plants and the atmosphere: pavement cells protect plants from desiccation and other environmental stresses, while stomata facilitate gas exchange and transpiration. Advances have been made in our understanding of stomatal patterning and differentiation, and a set of 'master regulatory' transcription factors of stomatal development have been identified. However, they are limited to specifying stomatal differentiation within the epidermis. Here, we report the identification of an Arabidopsis homeodomain-leucine zipper IV (HD-ZIP IV) protein, HOMEODOMAIN GLABROUS2 (HDG2), as a key epidermal component promoting stomatal differentiation. HDG2 is highly enriched in meristemoids, which are transient-amplifying populations of stomatal-cell lineages. Ectopic expression of HDG2 confers differentiation of stomata in internal mesophyll tissues and occasional multiple epidermal layers. Conversely, a loss-of-function hdg2 mutation delays stomatal differentiation and, rarely but consistently, results in aberrant stomata. A closely related HD-ZIP IV gene, Arabidopsis thaliana MERISTEM LAYER1 (AtML1), shares overlapping function with HDG2: AtML1 overexpression also triggers ectopic stomatal differentiation in the mesophyll layer and atml1 mutation enhances the stomatal differentiation defects of hdg2. Consistently, HDG2 and AtML1 bind the same DNA elements, and activate transcription in yeast. Furthermore, HDG2 transactivates expression of genes that regulate stomatal development in planta. Our study highlights the similarities and uniqueness of these two HD-ZIP IV genes in the specification of protodermal identity and stomatal differentiation beyond predetermined tissue layers.
Collapse
Affiliation(s)
- Kylee M Peterson
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | | | | | | | | | | | | | | |
Collapse
|
239
|
Tammimies K, Vitezic M, Matsson H, Le Guyader S, Bürglin TR, Ohman T, Strömblad S, Daub CO, Nyman TA, Kere J, Tapia-Páez I. Molecular networks of DYX1C1 gene show connection to neuronal migration genes and cytoskeletal proteins. Biol Psychiatry 2013; 73:583-90. [PMID: 23036959 DOI: 10.1016/j.biopsych.2012.08.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2012] [Revised: 08/07/2012] [Accepted: 08/08/2012] [Indexed: 11/28/2022]
Abstract
BACKGROUND The dyslexia susceptibility 1 candidate 1 (DYX1C1) gene has recently been associated with dyslexia and reading scores in several population samples. The DYX1C1 has also been shown to affect neuronal migration and modulate estrogen receptor signaling. METHODS We have analyzed the molecular networks of DYX1C1 by gene expression and protein interaction profiling in a human neuroblastoma cell line. RESULTS We find that DYX1C1 can modulate the expression of nervous system development and neuronal migration genes such as RELN and associate with a number of cytoskeletal proteins. We also show by live cell imaging that DYX1C1 regulates cell migration of the human neuroblastoma cell line dependent on its tetratricopeptide repeat and DYX1 protein domains. The DYX1 domain is a novel highly conserved domain identified in this study by multiple sequence alignment of DYX1C1 proteins recovered from a wide range of eukaryotic species. CONCLUSIONS Our results contribute to the hypothesis that dyslexia has a developmental neurobiological basis by linking DYX1C1 with many genes involved in neuronal migration disorders.
Collapse
Affiliation(s)
- Kristiina Tammimies
- Center for Biosciences, Department of Biosciences and Nutrition, Novum, Karolinska Institutet, Huddinge, Sweden
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
240
|
Sakakibara K, Ando S, Yip HK, Tamada Y, Hiwatashi Y, Murata T, Deguchi H, Hasebe M, Bowman JL. KNOX2 genes regulate the haploid-to-diploid morphological transition in land plants. Science 2013; 339:1067-70. [PMID: 23449590 DOI: 10.1126/science.1230082] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Unlike animals, land plants undergo an alternation of generations, producing multicellular bodies in both haploid (1n: gametophyte) and diploid (2n: sporophyte) generations. Plant body plans in each generation are regulated by distinct developmental programs initiated at either meiosis or fertilization, respectively. In mosses, the haploid gametophyte generation is dominant, whereas in vascular plants-including ferns, gymnosperms, and angiosperms-the diploid sporophyte generation is dominant. Deletion of the class 2 KNOTTED1-LIKE HOMEOBOX (KNOX2) transcription factors in the moss Physcomitrella patens results in the development of gametophyte bodies from diploid embryos without meiosis. Thus, KNOX2 acts to prevent the haploid-specific body plan from developing in the diploid plant body, indicating a critical role for the evolution of KNOX2 in establishing an alternation of generations in land plants.
Collapse
Affiliation(s)
- Keiko Sakakibara
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Japan.
| | | | | | | | | | | | | | | | | |
Collapse
|
241
|
Affiliation(s)
- William E. Friedman
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Arnold Arboretum of Harvard University, Boston, MA 02131, USA
| |
Collapse
|
242
|
Park MY, Kim SA, Lee SJ, Kim SY. ATHB17 is a positive regulator of abscisic acid response during early seedling growth. Mol Cells 2013; 35:125-33. [PMID: 23456334 PMCID: PMC3887901 DOI: 10.1007/s10059-013-2245-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 12/19/2012] [Accepted: 12/21/2012] [Indexed: 01/02/2023] Open
Abstract
We performed activation tagging screen to isolate abscisic acid (ABA) response mutants. One of the mutants, designated ahs10 (ABA-hypersensitive 10), exhibited ABA-hypersensitive phenotypes. TAIL-PCR analysis of the mutant revealed that T-DNA was inserted in the promoter region of the Arabidopsis gene, At2g01430, which encodes a homeodomain-leucine zipper protein ATHB17. Subsequent expression analysis indicated that ATHB17 was activated in ahs10. To recapitulate the mutant phenotypes, we prepared ATHB17 OX lines and investigated their phenotypes. The results showed that ATHB17 confers ABA-hypersensitivity and drought tolerance. On the contrary, ATHB17 knockout lines were ABA-insensitive and drought-sensitive, further demonstrating that ATHB17 is involved in ABA and water-stress responses. Interestingly, the ATHB17 effect on seedling growth in the presence of ABA was observed only during the postgermination seedling establishment stage, suggesting that it functions during a narrow developmental window of early seedling growth.
Collapse
Affiliation(s)
- Min Young Park
- Department of Molecular Biotechnology and Kumho Life Science Laboratory, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757,
Korea
| | - Sung-ah Kim
- Department of Molecular Biotechnology and Kumho Life Science Laboratory, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757,
Korea
| | - Sun-ji Lee
- Department of Molecular Biotechnology and Kumho Life Science Laboratory, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757,
Korea
| | - Soo Young Kim
- Department of Molecular Biotechnology and Kumho Life Science Laboratory, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 500-757,
Korea
| |
Collapse
|
243
|
Lin H, Niu L, McHale NA, Ohme-Takagi M, Mysore KS, Tadege M. Evolutionarily conserved repressive activity of WOX proteins mediates leaf blade outgrowth and floral organ development in plants. Proc Natl Acad Sci U S A 2013; 110:366-71. [PMID: 23248305 PMCID: PMC3538250 DOI: 10.1073/pnas.1215376110] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The WUSCHEL related homeobox (WOX) genes play key roles in stem cell maintenance, embryonic patterning, and lateral organ development. WOX genes have been categorized into three clades--ancient, intermediate, and modern/WUS--based on phylogenetic analysis, but a functional basis for this classification has not been established. Using the classical bladeless lam1 mutant of Nicotiana sylvestris as a genetic tool, we examined the function of the Medicago truncatula WOX gene, STENOFOLIA (STF), in controlling leaf blade outgrowth. STF and LAM1 are functional orthologs. We found that the introduction of mutations into the WUS-box of STF (STFm1) reduces its ability to complement the lam1 mutant. Fusion of an exogenous repressor domain to STFm1 restores complementation, whereas fusion of an exogenous activator domain to STFm1 enhances the narrow leaf phenotype. These results indicate that transcriptional repressor activity mediated by the WUS-box of STF acts to promote blade outgrowth. With the exception of WOX7, the WUS-box is conserved in the modern clade WOX genes, but is not found in members of the intermediate or ancient clades. Consistent with this, all members of the modern clade except WOX7 can complement the lam1 mutant when expressed using the STF promoter, but members of the intermediate and ancient clades cannot. Furthermore, we found that fusion of either the WUS-box or an exogenous repressor domain to WOX7 or to members of intermediate and ancient WOX clades results in a gain-of-function ability to complement lam1 blade outgrowth. These results suggest that modern clade WOX genes have evolved for repressor activity through acquisition of the WUS-box.
Collapse
Affiliation(s)
- Hao Lin
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK 73401
| | - Lifang Niu
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK 73401
| | - Neil A. McHale
- Department of Biochemistry and Genetics, Connecticut Agricultural Experiment Station, New Haven, CT 06504
| | - Masaru Ohme-Takagi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8562, Japan; and
| | | | - Million Tadege
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK 73401
| |
Collapse
|
244
|
Zhang S, Haider I, Kohlen W, Jiang L, Bouwmeester H, Meijer AH, Schluepmann H, Liu CM, Ouwerkerk PBF. Function of the HD-Zip I gene Oshox22 in ABA-mediated drought and salt tolerances in rice. PLANT MOLECULAR BIOLOGY 2012; 80:571-85. [PMID: 23109182 DOI: 10.1007/s11103-012-9967-1] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 09/04/2012] [Indexed: 05/02/2023]
Abstract
Oshox22 belongs to the homeodomain-leucine zipper (HD-Zip) family I of transcription factors, most of which have unknown functions. Here we show that the expression of Oshox22 is strongly induced by salt stress, abscisic acid (ABA), and polyethylene glycol treatment (PEG), and weakly by cold stress. Trans-activation assays in yeast and transient expression analyses in rice protoplasts demonstrated that Oshox22 is able to bind the CAAT(G/C)ATTG element and acts as a transcriptional activator that requires both the HD and Zip domains. Rice plants homozygous for a T-DNA insertion in the promoter region of Oshox22 showed reduced Oshox22 expression and ABA content, decreased sensitivity to ABA, and enhanced tolerance to drought and salt stresses at the seedling stage. In contrast, transgenic rice over-expressing Oshox22 showed increased sensitivity to ABA, increased ABA content, and decreased drought and salt tolerances. Based on these results, we conclude that Oshox22 affects ABA biosynthesis and regulates drought and salt responses through ABA-mediated signal transduction pathways.
Collapse
Affiliation(s)
- Shuxin Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | | | | | | | | | | | | | | | | |
Collapse
|
245
|
Zimmer EA, Wen J. Using nuclear gene data for plant phylogenetics: Progress and prospects. Mol Phylogenet Evol 2012; 65:774-85. [DOI: 10.1016/j.ympev.2012.07.015] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 06/14/2012] [Accepted: 07/16/2012] [Indexed: 10/28/2022]
|
246
|
Li G, Zhang J, Li J, Yang Z, Huang H, Xu L. Imitation Switch chromatin remodeling factors and their interacting RINGLET proteins act together in controlling the plant vegetative phase in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 72:261-70. [PMID: 22694359 DOI: 10.1111/j.1365-313x.2012.05074.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
During their life cycle, flowering plants must experience a transition from vegetative to reproductive growth. Here, we report that double mutations in the Arabidopsis thaliana IMITATION SWITCH (AtISWI) genes, CHROMATIN REMODELING11 (CHR11) and CHR17, and the plant-specific DDT-domain containing genes, RINGLET1 (RLT1) and RLT2, resulted in plants with similar developmental defects, including the dramatically accelerated vegetative-to-reproductive transition. We demonstrated that AtISWI physically interacts with RLTs in preventing plants from activating the vegetative-to-reproductive transition early by regulating several key genes that contribute to flower timing. In particular, AtISWI and RLTs repress FT, SEP1, SEP3, FUL, and SOC1, but promote FLC in the leaf. Furthermore, AtISWI and RLTs may directly repress FT and SEP3 through associating with the FT and SEP3 loci. Our study reveals that AtISWI and RLTs represent a previously unrecognized genetic pathway that is required for the maintenance of the plant vegetative phase.
Collapse
Affiliation(s)
- Guang Li
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | | | | | | | | | | |
Collapse
|
247
|
Holland PWH. Evolution of homeobox genes. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2012; 2:31-45. [DOI: 10.1002/wdev.78] [Citation(s) in RCA: 179] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
248
|
Testone G, Condello E, Verde I, Nicolodi C, Caboni E, Dettori MT, Vendramin E, Bruno L, Bitonti MB, Mele G, Giannino D. The peach (Prunus persica L. Batsch) genome harbours 10 KNOX genes, which are differentially expressed in stem development, and the class 1 KNOPE1 regulates elongation and lignification during primary growth. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:5417-35. [PMID: 22888130 PMCID: PMC3444263 DOI: 10.1093/jxb/ers194] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The KNOTTED-like (KNOX) genes encode homeodomain transcription factors and regulate several processes of plant organ development. The peach (Prunus persica L. Batsch) genome was found to contain 10 KNOX members (KNOPE genes); six of them were experimentally located on the Prunus reference map and the class 1 KNOPE1 was found to link to a quantitative trait locus (QTL) for the internode length in the peach×Ferganensis population. All the KNOPE genes were differentially transcribed in the internodes of growing shoots; the KNOPE1 mRNA abundance decreased progressively from primary (elongation) to secondary growth (radial expansion). During primary growth, the KNOPE1 mRNA was localized in the cortex and in the procambium/metaphloem zones, whereas it was undetected in incipient phloem and xylem fibres. KNOPE1 overexpression in the Arabidopsis bp4 loss-of-function background (35S:KNOPE1/bp genotype) restored the rachis length, suggesting, together with the QTL association, a role for KNOPE1 in peach shoot elongation. Several lignin biosynthesis genes were up-regulated in the bp4 internodes but repressed in the 35S:KNOPE1/bp lines similarly to the wild type. Moreover, the lignin deposition pattern of the 35S:KNOPE1/bp and the wild-type internodes were the same. The KNOPE1 protein was found to recognize in vitro one of the typical KNOX DNA-binding sites that recurred in peach and Arabidopsis lignin genes. KNOPE1 expression was inversely correlated with that of lignin genes and lignin deposition along the peach shoot stems and was down-regulated in lignifying vascular tissues. These data strongly support that KNOPE1 prevents cell lignification by repressing lignin genes during peach stem primary growth.
Collapse
Affiliation(s)
- Giulio Testone
- Institute of Agricultural Biology and Biotechnology, National Research Council of Italy (CNR), via Salaria km 29,300, 00015, Monterotondo Scalo, Rome, Italy
- These authors contributed equally to this work
| | - Emiliano Condello
- Fruit Tree Research Centre, Agriculture Research Council (CRA), Via di Fioranello 52, 00134 Rome, Italy
- These authors contributed equally to this work
| | - Ignazio Verde
- Fruit Tree Research Centre, Agriculture Research Council (CRA), Via di Fioranello 52, 00134 Rome, Italy
| | - Chiara Nicolodi
- Institute of Agricultural Biology and Biotechnology, National Research Council of Italy (CNR), via Salaria km 29,300, 00015, Monterotondo Scalo, Rome, Italy
| | - Emilia Caboni
- Fruit Tree Research Centre, Agriculture Research Council (CRA), Via di Fioranello 52, 00134 Rome, Italy
| | - Maria Teresa Dettori
- Fruit Tree Research Centre, Agriculture Research Council (CRA), Via di Fioranello 52, 00134 Rome, Italy
| | - Elisa Vendramin
- Fruit Tree Research Centre, Agriculture Research Council (CRA), Via di Fioranello 52, 00134 Rome, Italy
| | - Leonardo Bruno
- Department of Ecology, University of Calabria, Ponte Bucci, 87030 Arcavacata di Rende, Cosenza, Italy
| | - Maria Beatrice Bitonti
- Department of Ecology, University of Calabria, Ponte Bucci, 87030 Arcavacata di Rende, Cosenza, Italy
| | - Giovanni Mele
- Institute of Agricultural Biology and Biotechnology, National Research Council of Italy (CNR), via Salaria km 29,300, 00015, Monterotondo Scalo, Rome, Italy
| | | |
Collapse
|
249
|
Noguchi C, Rapp JB, Skorobogatko YV, Bailey LD, Noguchi E. Swi1 associates with chromatin through the DDT domain and recruits Swi3 to preserve genomic integrity. PLoS One 2012; 7:e43988. [PMID: 22952839 PMCID: PMC3431386 DOI: 10.1371/journal.pone.0043988] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 07/27/2012] [Indexed: 11/19/2022] Open
Abstract
Swi1 and Swi3 form the replication fork protection complex and play critical roles in proper activation of the replication checkpoint and stabilization of replication forks in the fission yeast Schizosaccharomyces pombe. However, the mechanisms by which the Swi1-Swi3 complex regulates these processes are not well understood. Here, we report functional analyses of the Swi1-Swi3 complex in fission yeast. Swi1 possesses the DDT domain, a putative DNA binding domain found in a variety of chromatin remodeling factors. Consistently, the DDT domain-containing region of Swi1 interacts with DNA in vitro, and mutations in the DDT domain eliminate the association of Swi1 with chromatin in S. pombe cells. DDT domain mutations also render cells highly sensitive to S-phase stressing agents and induce strong accumulation of Rad22-DNA repair foci, indicating that the DDT domain is involved in the activity of the Swi1-Swi3 complex. Interestingly, DDT domain mutations also abolish Swi1's ability to interact with Swi3 in cells. Furthermore, we show that Swi1 is required for efficient chromatin association of Swi3 and that the Swi1 C-terminal domain directly interacts with Swi3. These results indicate that Swi1 associates with chromatin through its DDT domain and recruits Swi3 to function together as the replication fork protection complex.
Collapse
Affiliation(s)
- Chiaki Noguchi
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jordan B. Rapp
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Yuliya V. Skorobogatko
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Lauren D. Bailey
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Eishi Noguchi
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
250
|
Takacs EM, Li J, Du C, Ponnala L, Janick-Buckner D, Yu J, Muehlbauer GJ, Schnable PS, Timmermans MC, Sun Q, Nettleton D, Scanlon MJ. Ontogeny of the maize shoot apical meristem. THE PLANT CELL 2012; 24:3219-34. [PMID: 22911570 PMCID: PMC3462627 DOI: 10.1105/tpc.112.099614] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The maize (Zea mays) shoot apical meristem (SAM) arises early in embryogenesis and functions during stem cell maintenance and organogenesis to generate all the aboveground organs of the plant. Despite its integral role in maize shoot development, little is known about the molecular mechanisms of SAM initiation. Laser microdissection of apical domains from developing maize embryos and seedlings was combined with RNA sequencing for transcriptomic analyses of SAM ontogeny. Molecular markers of key events during maize embryogenesis are described, and comprehensive transcriptional data from six stages in maize shoot development are generated. Transcriptomic profiling before and after SAM initiation indicates that organogenesis precedes stem cell maintenance in maize; analyses of the first three lateral organs elaborated from maize embryos provides insight into their homology and to the identity of the single maize cotyledon. Compared with the newly initiated SAM, the mature SAM is enriched for transcripts that function in transcriptional regulation, hormonal signaling, and transport. Comparisons of shoot meristems initiating juvenile leaves, adult leaves, and husk leaves illustrate differences in phase-specific (juvenile versus adult) and meristem-specific (SAM versus lateral meristem) transcript accumulation during maize shoot development. This study provides insight into the molecular genetics of SAM initiation and function in maize.
Collapse
Affiliation(s)
| | - Jie Li
- Department of Statistics and Statistical Laboratory, Iowa State University, Ames, Iowa 50011
| | - Chuanlong Du
- Department of Statistics and Statistical Laboratory, Iowa State University, Ames, Iowa 50011
| | - Lalit Ponnala
- Computational Biology Service Unit, Cornell University, Ithaca, New York 14853
| | | | - Jianming Yu
- Department of Agronomy, Kansas State University, Manhattan, Kansas 66506
| | - Gary J. Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | | | | | - Qi Sun
- Computational Biology Service Unit, Cornell University, Ithaca, New York 14853
| | - Dan Nettleton
- Department of Statistics and Statistical Laboratory, Iowa State University, Ames, Iowa 50011
| | - Michael J. Scanlon
- Department of Plant Biology, Cornell University, Ithaca, New York 14583
- Address correspondence to
| |
Collapse
|