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Penning BW, Shiga TM, Klimek JF, SanMiguel PJ, Shreve J, Thimmapuram J, Sykes RW, Davis MF, McCann MC, Carpita NC. Expression profiles of cell-wall related genes vary broadly between two common maize inbreds during stem development. BMC Genomics 2019; 20:785. [PMID: 31664907 PMCID: PMC6819468 DOI: 10.1186/s12864-019-6117-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/20/2019] [Indexed: 11/23/2022] Open
Abstract
Background The cellular machinery for cell wall synthesis and metabolism is encoded by members of large multi-gene families. Maize is both a genetic model for grass species and a potential source of lignocellulosic biomass from crop residues. Genetic improvement of maize for its utility as a bioenergy feedstock depends on identification of the specific gene family members expressed during secondary wall development in stems. Results High-throughput sequencing of transcripts expressed in developing rind tissues of stem internodes provided a comprehensive inventory of cell wall-related genes in maize (Zea mays, cultivar B73). Of 1239 of these genes, 854 were expressed among the internodes at ≥95 reads per 20 M, and 693 of them at ≥500 reads per 20 M. Grasses have cell wall compositions distinct from non-commelinid species; only one-quarter of maize cell wall-related genes expressed in stems were putatively orthologous with those of the eudicot Arabidopsis. Using a slope-metric algorithm, five distinct patterns for sub-sets of co-expressed genes were defined across a time course of stem development. For the subset of genes associated with secondary wall formation, fifteen sequence motifs were found in promoter regions. The same members of gene families were often expressed in two maize inbreds, B73 and Mo17, but levels of gene expression between them varied, with 30% of all genes exhibiting at least a 5-fold difference at any stage. Although presence-absence and copy-number variation might account for much of these differences, fold-changes of expression of a CADa and a FLA11 gene were attributed to polymorphisms in promoter response elements. Conclusions Large genetic variation in maize as a species precludes the extrapolation of cell wall-related gene expression networks even from one common inbred line to another. Elucidation of genotype-specific expression patterns and their regulatory controls will be needed for association panels of inbreds and landraces to fully exploit genetic variation in maize and other bioenergy grass species.
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Affiliation(s)
- Bryan W Penning
- Department of Botany & Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA.,Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA.,, Present Address: USDA-ARS, Wheat Quality Research Unit, 1680 Madison Avenue, Wooster, OH, 44691, USA
| | - Tânia M Shiga
- Department of Botany & Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA.,Present Address: Departamento de Alimentos e Nutrição Experimental, FCF-USP F, 3091-3647 / 3091-3007, Av. Prof. Lineu Prestes, 580 - BL-14 CEP 05508-000, Butantã, Sâo Paulo, SP, Brazil
| | - John F Klimek
- Department of Botany & Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
| | - Philip J SanMiguel
- Genomics Core Facility, Purdue University, 170 South University Street, Purdue University, West Lafayette, IN, 47907, USA
| | - Jacob Shreve
- Bioinformatics Core Facility, Purdue University, 155 South Grant Street, West Lafayette, IN, 47907, USA.,, Present Address: Department of Internal Medicine, Cleveland Clinic, 9500 Euclid Ave, Cleveland, OH, 44195, USA
| | - Jyothi Thimmapuram
- Present Address: Departamento de Alimentos e Nutrição Experimental, FCF-USP F, 3091-3647 / 3091-3007, Av. Prof. Lineu Prestes, 580 - BL-14 CEP 05508-000, Butantã, Sâo Paulo, SP, Brazil.,Bioinformatics Core Facility, Purdue University, 155 South Grant Street, West Lafayette, IN, 47907, USA
| | - Robert W Sykes
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,, Present Address: Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, NM, Los Alamos, NM, 87545, USA
| | - Mark F Davis
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Maureen C McCann
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA.,Purdue Center for Plant Biology, West Lafayette, USA
| | - Nicholas C Carpita
- Department of Botany & Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA. .,Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA. .,Purdue Center for Plant Biology, West Lafayette, USA.
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Maksimov IV, Cherepanova EA, Burkhanova GF, Sorokan' AV, Kuzmina OI. Structural-functional features of plant isoperoxidases. BIOCHEMISTRY (MOSCOW) 2011; 76:609-21. [PMID: 21639841 DOI: 10.1134/s0006297911060010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Current data on structural--functional features of plant peroxidases and their involvement in functioning of the pro-/antioxidant system responding to stress factors, especially those of biotic origin, are analyzed. The collection of specific features of individual isoforms allows a plant to withstand an aggressive influence of the environment. Expression of some genes encoding different isoperoxidases is regulated by pathogens (and their metabolites), elicitors, and hormone-like compounds; specific features of this regulation are considered in detail. It is suggested that isoperoxidases interacting with polysaccharides are responsible for a directed deposition of lignin on the cell walls, and this lignin in turn is concurrently an efficient strengthening material and protects the plants against pathogens.
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Affiliation(s)
- I V Maksimov
- Institute of Biochemistry and Genetics, Ufa Scientific Center, Russian Academy of Sciences, Ufa, 450054, Russia.
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Sasaki K, Ito H, Mitsuhara I, Hiraga S, Seo S, Matsui H, Ohashi Y. A novel wound-responsive cis-element, VWRE, of the vascular system-specific expression of a tobacco peroxidase gene, tpoxN1. PLANT MOLECULAR BIOLOGY 2006; 62:753-68. [PMID: 16941212 DOI: 10.1007/s11103-006-9055-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2005] [Accepted: 07/11/2006] [Indexed: 05/11/2023]
Abstract
The wound-induced expression of tpoxN1, encoding a tobacco peroxidase, is unique because of its vascular system-specific expression and insensitivity to known wound-signal compounds such as jasmonic acid, ethylene, and plant hormones [Sasaki et al. (2002) Plant Cell Physiol 43:108-117]. To study the mechanism of expression, the 2-kbp tpoxN1 promoter region and successive 5'-deletion of the promoter were introduced as GUS fusion genes into tobacco plants. Analysis of GUS activity in transgenic plants indicated that a vascular system-specific and wound-responsive cis-element (VWRE) is present at the -239/-200 region of the promoter. Gel mobility shift assays suggested that a nuclear factor(s) prepared from wounded tobacco stems binds a 14-bp sequence (-229/-215) in the -239/-200 region in a sequence-specific manner. A mutation in this 14-bp region of the -239 promoter fragment resulted in a considerable decrease in wound-responsive GUS activity in transgenic plants. An 11-bp sequence, which completely overlaps with the 14-bp sequence, was found in the 5' distal region (-420/-410) and is thought to contribute to the wound-induced expression together with the 14-bp. The -114-bp core promoter of the tpoxN1 gene was indispensable for wound-induced expression, indicating that the 14-bp region is a novel wound-responsive cis-element VWRE, which may work cooperatively with other factors in the promoter.
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Affiliation(s)
- Katsutomo Sasaki
- Division of Plant Sciences, Organization of National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
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Kawaoka A, Matsunaga E, Endo S, Kondo S, Yoshida K, Shinmyo A, Ebinuma H. Ectopic expression of a horseradish peroxidase enhances growth rate and increases oxidative stress resistance in hybrid aspen. PLANT PHYSIOLOGY 2003; 132:1177-85. [PMID: 12857800 PMCID: PMC167058 DOI: 10.1104/pp.102.019794] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2002] [Revised: 01/24/2003] [Accepted: 04/04/2003] [Indexed: 05/18/2023]
Abstract
We previously demonstrated that overexpression of the horseradish (Armoracia rusticana) peroxidase prxC1a gene stimulated the growth rate of tobacco (Nicotiana tabacum) plants. Here, the cauliflower mosaic virus 35S::prxC1a construct was introduced into hybrid aspen (Populus sieboldii x Populus grandidentata). The growth rate of these transformed hybrid aspen plants was substantially increased under greenhouse conditions. The average stem length of transformed plants was 25% greater than that of control plants. There was no other obvious phenotypic difference between the transformed and control plants. Fast-growing transformed hybrid aspen showed high levels of expression of prxC1a and had elevated peroxidase activities toward guaiacol and ascorbate. However, there was no increase of the endogenous class I ascorbate peroxidase activities in the transformed plants by separate assay and activity staining of native polyacrylamide gel electrophoresis. Furthermore, calli derived from the transformed hybrid aspen grew faster than those from control plants and were resistant to the oxidative stress imposed by hydrogen peroxide. Therefore, enhanced peroxidase activity affects plant growth rate and oxidative stress resistance.
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Affiliation(s)
- Akiyoshi Kawaoka
- Pulp and Paper Research Laboratory, Nippon Paper Industries Co. Ltd., 5-21-1 Oji, Kita-ku, Tokyo 114-0002, Japan.
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Kawaoka A, Ebinuma H. Transcriptional control of lignin biosynthesis by tobacco LIM protein. PHYTOCHEMISTRY 2001; 57:1149-57. [PMID: 11430987 DOI: 10.1016/s0031-9422(01)00054-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Lignin is a complex phenolic plant polymer that is essential for mechanical support, defense, and water transport in higher plants. The AC-rich motif, Pal-box is an important cis-acting element for gene expression in phenylpropanoid biosynthesis. We isolated a cDNA clone (Ntlim1) encoding a Pal-box binding protein by Southwestern screening. The deduced amino acid sequence of Ntlim1 is highly similar to members of the LIM protein family that contain a zinc finger motif. Moreover, Ntlim1 had a specific DNA-binding ability and transiently activated transcription of a beta-glucuronidase reporter gene driven by the Pal-box sequence. The results of transient expression assays with tobacco cultured cells showed that fusion proteins between GFP and Ntlim1 can enter nuclei. Transgenic tobacco plants with antisense Ntlim1 showed low levels of transcripts from some key phenylpropanoid pathway genes such as phenylalanine ammonia-lyase, hydroxycinnamate CoA ligase and cinnamyl alcohol dehydrogenase. Furthermore, a greater than 20% reduction in lignin content was observed in transgenic tobacco with antisense Ntlim1.
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Affiliation(s)
- A Kawaoka
- Nippon Paper Industries Co., Ltd, Pulp and Paper Research Laboratory, 5-21-1, Oji, Kita-ku, Tokyo 114-0002, Japan.
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Hiraga S, Sasaki K, Ito H, Ohashi Y, Matsui H. A large family of class III plant peroxidases. PLANT & CELL PHYSIOLOGY 2001; 42:462-8. [PMID: 11382811 DOI: 10.1093/pcp/pce061] [Citation(s) in RCA: 447] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Class III plant peroxidase (POX), a plant-specific oxidoreductase, is one of the many types of peroxidases that are widely distributed in animals, plants and microorganisms. POXs exist as isoenzymes in individual plant species, and each isoenzyme has variable amino acid sequences and shows diverse expression profiles, suggesting their involvement in various physiological processes. Indeed, studies have provided evidence that POXs participate in lignification, suberization, auxin catabolism, wound healing and defense against pathogen infection. Little, however, is known about the signal transduction for inducing expression of the pox genes. Recent studies have provided information on the regulatory mechanisms of wound- and pathogen-induced expression of some pox genes. These studies suggest that pox genes are induced via different signal transduction pathways from those of other known defense-related genes.
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Affiliation(s)
- S Hiraga
- Department of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
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