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Hu Y, Ma M, Zhao W, Niu P, Li R, Luo J. Identification of hub genes involved in gibberellin-regulated elongation of coleoptiles of rice seeds germinating under submerged conditions. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3862-3876. [PMID: 38571323 DOI: 10.1093/jxb/erae144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 04/03/2024] [Indexed: 04/05/2024]
Abstract
Rapid elongation of coleoptiles from rice seeds to reach the water surface enables plants to survive submergence stress and therefore plays a crucial role in allowing direct seeding in rice cultivation. Gibberellin (GA) positively influences growth in rice, but the molecular mechanisms underlying its regulation of coleoptile elongation under submerged conditions remain unclear. In this study, we performed a weighted gene co-expression network analysis to conduct a preliminarily examination of the mechanisms. Four key modules were identified with high correlations to the GA regulation of submergence tolerance. The genes within these modules were mainly involved in the Golgi apparatus and carbohydrate metabolic pathways, suggesting their involvement in enhancing submergence tolerance. Further analysis of natural variation revealed that the specific hub genes Os03g0337900, Os03g0355600, and Os07g0638400 exhibited strong correlations with subspecies divergence of the coleoptile elongation phenotype. Consistent with this analysis, mutation of Os07g0638400 resulted in a lower germination potential and a stronger inhibition of coleoptile elongation under submerged conditions. The hub genes identified in this study provide new insights into the molecular mechanisms underlying GA-dependent tolerance to submergence stress in rice, and a potential basis for future modification of rice germplasm to allow for direct seeding.
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Affiliation(s)
- Yunfei Hu
- College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, China
| | - Mingqing Ma
- College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, China
| | - Wenlong Zhao
- College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, China
| | - Pengwei Niu
- College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, China
| | - Rongbai Li
- College of Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, China
| | - Jijing Luo
- College of Life Science and Technology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, China
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Li H, Zou T, Chen S, Zhong M. Genome-wide identification, characterization and expression analysis of the DUF668 gene family in tomato. PeerJ 2024; 12:e17537. [PMID: 38912042 PMCID: PMC11192028 DOI: 10.7717/peerj.17537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 05/19/2024] [Indexed: 06/25/2024] Open
Abstract
The domain of unknown function 668 (DUF668) is a gene family that may play a key role in plant growth and development as well as in responding to adversity coercion stresses. However, the DUF668 gene family has not yet been well identified and characterized in tomato. In this study, a total of nine putative SlDUF668 genes were identified in tomato, distributed on six chromosomes. Phylogenetic analyses revealed that SlDUF668 proteins were classified into two major groups. Members within the same group largely displayed analogous gene structure and conserved motif compositions. Several cis-elements were exhibited in the upstream sequences of the SlDUF668 genes, including elements implicated in plant growth and development processes, abiotic stress and hormone responses. Further, the study assessed the expression patterns of the SlDUF668 gene family in various tomato tissues, five plant hormones treatments, three abiotic stresses using qRT-PCR. The SlDUF668 genes expressed ubiquitously in various tissues, and five genes (SlDUF668-04, SlDUF668-06, SlDUF668-07, SlDUF668-08 and SlDUF668-09) showed tissue specificity. And SlDUF668 genes responded to abiotic stresses such as salt, drought and cold to varying degrees. Overall, our study provided a base for the tomato DUF668 gene family and laid a foundation for further understanding the functional characteristics of DUF668 genes in tomato plants.
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Affiliation(s)
- Hui Li
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agriculture University, Shenyang, China
| | - Tingrui Zou
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agriculture University, Shenyang, China
| | - Shuisen Chen
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agriculture University, Shenyang, China
| | - Ming Zhong
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agriculture University, Shenyang, China
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Delmer D, Dixon RA, Keegstra K, Mohnen D. The plant cell wall-dynamic, strong, and adaptable-is a natural shapeshifter. THE PLANT CELL 2024; 36:1257-1311. [PMID: 38301734 PMCID: PMC11062476 DOI: 10.1093/plcell/koad325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/19/2023] [Indexed: 02/03/2024]
Abstract
Mythology is replete with good and evil shapeshifters, who, by definition, display great adaptability and assume many different forms-with several even turning themselves into trees. Cell walls certainly fit this definition as they can undergo subtle or dramatic changes in structure, assume many shapes, and perform many functions. In this review, we cover the evolution of knowledge of the structures, biosynthesis, and functions of the 5 major cell wall polymer types that range from deceptively simple to fiendishly complex. Along the way, we recognize some of the colorful historical figures who shaped cell wall research over the past 100 years. The shapeshifter analogy emerges more clearly as we examine the evolving proposals for how cell walls are constructed to allow growth while remaining strong, the complex signaling involved in maintaining cell wall integrity and defense against disease, and the ways cell walls adapt as they progress from birth, through growth to maturation, and in the end, often function long after cell death. We predict the next century of progress will include deciphering cell type-specific wall polymers; regulation at all levels of polymer production, crosslinks, and architecture; and how walls respond to developmental and environmental signals to drive plant success in diverse environments.
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Affiliation(s)
- Deborah Delmer
- Section of Plant Biology, University of California Davis, Davis, CA 95616, USA
| | - Richard A Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
| | - Kenneth Keegstra
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48823, USA
| | - Debra Mohnen
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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Li S, Chang L, Sun R, Dong J, Zhong C, Gao Y, Zhang H, Wei L, Wei Y, Zhang Y, Wang G, Sun J. Combined transcriptomic and metabolomic analysis reveals a role for adenosine triphosphate-binding cassette transporters and cell wall remodeling in response to salt stress in strawberry. FRONTIERS IN PLANT SCIENCE 2022; 13:996765. [PMID: 36147238 PMCID: PMC9486094 DOI: 10.3389/fpls.2022.996765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 07/28/2022] [Indexed: 05/25/2023]
Abstract
Strawberry (Fragaria × ananassa Duch) are sensitive to salt stress, and breeding salt-tolerant strawberry cultivars is the primary method to develop resistance to increased soil salinization. However, the underlying molecular mechanisms mediating the response of strawberry to salinity stress remain largely unknown. This study evaluated the salinity tolerance of 24 strawberry varieties, and transcriptomic and metabolomic analysis were performed of 'Sweet Charlie' (salt-tolerant) and 'Benihoppe' (salt-sensitive) to explore salt tolerance mechanisms in strawberry. Compared with the control, we identified 3412 differentially expressed genes (DEGs) and 209 differentially accumulated metabolites (DAMs) in 'Benihoppe,' and 5102 DEGs and 230 DAMs in 'Sweet Charlie.' DEGs Gene Ontology (GO) enrichment analyses indicated that the DEGs in 'Benihoppe' were enriched for ion homeostasis related terms, while in 'Sweet Charlie,' terms related to cell wall remodeling were over-represented. DEGs related to ion homeostasis and cell wall remodeling exhibited differential expression patterns in 'Benihoppe' and 'Sweet Charlie.' In 'Benihoppe,' 21 ion homeostasis-related DEGs and 32 cell wall remodeling-related DEGs were upregulated, while 23 ion homeostasis-related DEGs and 138 cell wall remodeling-related DEGs were downregulated. In 'Sweet Charlie,' 72 ion homeostasis-related DEGs and 275 cell wall remodeling-related DEGs were upregulated, while 11 ion homeostasis-related DEGs and 20 cell wall remodeling-related DEGs were downregulated. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed only four KEGG enriched pathways were shared between 'Benihoppe' and 'Sweet Charlie,' including flavonoid biosynthesis, phenylalanine metabolism, phenylpropanoid biosynthesis and ubiquinone, and other terpenoid-quinone biosynthesis. Integrating the results of transcriptomic and metabolomics analyses showed that adenosine triphosphate-binding cassette (ABC) transporters and flavonoid pathway genes might play important roles in the salt stress response in strawberry, and DAMs and DEGs related to ABC transporter and flavonoid pathways were differentially expressed or accumulated. The results of this study reveal that cell wall remodeling and ABC transporters contribute to the response to salt stress in strawberry, and that related genes showed differential expression patterns in varieties with different salt tolerances. These findings provide new insights into the underlying molecular mechanism of strawberry response to salt stress and suggest potential targets for the breeding of salt-tolerant strawberry varieties.
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Affiliation(s)
- Shuangtao Li
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Linlin Chang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Rui Sun
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Jing Dong
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Chuanfei Zhong
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Yongshun Gao
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Hongli Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Lingzhi Wei
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Yongqing Wei
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Yuntao Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Guixia Wang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Jian Sun
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Engineering Research Center for Strawberry, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
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Liu Z, Gao S, Zhang H, Xu Z, Qian W. Genome-Wide Association Study Reveals That PvGUX1_1 Is Associated with Pod Stringlessness in Snap Bean (Phaseolus vulgaris L.). BIOLOGY 2022; 11:biology11040611. [PMID: 35453811 PMCID: PMC9024788 DOI: 10.3390/biology11040611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 04/10/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Using 138 snap bean accessions as plant materials, we investigated their suture strings across two years. With the goal of identifying the gene(s) responsible for the formation of suture strings, we conducted a genome-wide association study. A strong association signal was found in a 266.19 kb region on Chr02. Within the region, 23 candidate genes were identified. Importantly, the sequence and gene expression of PvGUX1_1 differed significantly between sutured pods and non-sutured pods. In addition, PvGUX1_1 was also a domesticated locus that diverged from PvGUX1_2 during an early stage. The results obtained in this study can provide important information for the improvement of pod quality in snap beans. Abstract Suture strings are a particularly important pod trait that determine the quality and texture of snap beans (Phaseolus vulgaris L.). The St locus on chromosome 2 has been described as a major locus associated with suture strings. However, the gene and genetic basis underlying this locus remain unknown. Here, we investigated the suture strings of 138 snap bean accessions across two years. A total of 3.66 million single-nucleotide polymorphisms (SNPs) were obtained by deep resequencing. Based on these SNPs, we identified a strong association signal on Chr02 and a promising candidate gene, PvGUX1_1. Further analysis revealed that the 2 bp deletion in the exon of PvGUX1_1 was significantly associated with stringlessness. Comparative mapping indicated that PvGUX1_1 was a domesticated locus and diverged from PvGUX1_2 during an early stage. Our study provides important insights into the genetic mechanism of suture string formation and useful information for snap bean improvement.
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Tian X, Niu X, Chang Z, Zhang X, Wang R, Yang Q, Li G. DUF1005 Family Identification, Evolution Analysis in Plants, and Primary Root Elongation Regulation of CiDUF1005 From Caragana intermedia. Front Genet 2022; 13:807293. [PMID: 35422842 PMCID: PMC9001952 DOI: 10.3389/fgene.2022.807293] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 02/08/2022] [Indexed: 11/13/2022] Open
Abstract
Proteins with a domain of unknown function (DUF) represent a number of gene families that encode functionally uncharacterized proteins in eukaryotes. In particular, members of the DUF1005 family in plants have a 411-amino-acid conserved domain, and this family has not been described previously. In this study, a total of 302 high-confidence DUF1005 family members were identified from 58 plant species, and none were found in the four algae that were selected. Thus, this result showed that DUF1005s might belong to a kind of plant-specific gene family, and this family has not been evolutionarily expanded. Phylogenetic analysis showed that the DUF1005 family genes could be classified into four subgroups in 58 plant species. The earliest group to emerge was Group I, including a total of 100 gene sequences, and this group was present in almost all selected species spanning from mosses to seed plants. Group II and Group III, with 69 and 74 members, respectively, belong to angiosperms. Finally, with 59 members, Group IV was the last batch of genes to emerge, and this group is unique to dicotyledons. Expression pattern analysis of the CiDUF1005, a member of the DUF1005 family from Caragana intermedia, showed that CiDUF1005 genes were differentially regulated under various treatments. Compared to the wild type, transgenic lines with heterologous CiDUF1005 expression in Arabidopsis thaliana had longer primary roots and more lateral roots. These results expanded our knowledge of the evolution of the DUF1005 family in plants and will contribute to elucidating biological functions of the DUF1005 family in the future.
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Affiliation(s)
- Xiaona Tian
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaocui Niu
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Ziru Chang
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiujuan Zhang
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Ruigang Wang
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Qi Yang
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China
| | - Guojing Li
- Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot, China.,Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, China.,Key Laboratory of Grassland Resources, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
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Gregorio Jorge J, Villalobos-López MA, Chavarría-Alvarado KL, Ríos-Meléndez S, López-Meyer M, Arroyo-Becerra A. Genome-wide transcriptional changes triggered by water deficit on a drought-tolerant common bean cultivar. BMC PLANT BIOLOGY 2020; 20:525. [PMID: 33203368 PMCID: PMC7672829 DOI: 10.1186/s12870-020-02664-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 09/23/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUND Common bean (Phaseolus vulgaris L.) is a relevant crop cultivated over the world, largely in water insufficiency vulnerable areas. Since drought is the main environmental factor restraining worldwide crop production, efforts have been invested to amend drought tolerance in commercial common bean varieties. However, scarce molecular data are available for those cultivars of P. vulgaris with drought tolerance attributes. RESULTS As a first approach, Pinto Saltillo (PS), Azufrado Higuera (AH), and Negro Jamapa Plus (NP) were assessed phenotypically and physiologically to determine the outcome in response to drought on these common bean cultivars. Based on this, a Next-generation sequencing approach was applied to PS, which was the most drought-tolerant cultivar to determine the molecular changes at the transcriptional level. The RNA-Seq analysis revealed that numerous PS genes are dynamically modulated by drought. In brief, 1005 differentially expressed genes (DEGs) were identified, from which 645 genes were up-regulated by drought stress, whereas 360 genes were down-regulated. Further analysis showed that the enriched categories of the up-regulated genes in response to drought fit to processes related to carbohydrate metabolism (polysaccharide metabolic processes), particularly genes encoding proteins located within the cell periphery (cell wall dynamics). In the case of down-regulated genes, heat shock-responsive genes, mainly associated with protein folding, chloroplast, and oxidation-reduction processes were identified. CONCLUSIONS Our findings suggest that secondary cell wall (SCW) properties contribute to P. vulgaris L. drought tolerance through alleviation or mitigation of drought-induced osmotic disturbances, making cultivars more adaptable to such stress. Altogether, the knowledge derived from this study is significant for a forthcoming understanding of the molecular mechanisms involved in drought tolerance on common bean, especially for drought-tolerant cultivars such as PS.
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Affiliation(s)
- Josefat Gregorio Jorge
- Consejo Nacional de Ciencia y Tecnología - Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional (CIBA-IPN), Ex-Hacienda San Juan Molino, Carretera Estatal Tecuexcomac- Tepetitla de Lardizábal Km 1.5, 90700 Tlaxcala, Mexico
| | - Miguel Angel Villalobos-López
- Laboratorio de Genómica Funcional y Biotecnología de Plantas, Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional (CIBA-IPN), Ex-Hacienda San Juan Molino, Carretera Estatal Tecuexcomac- Tepetitla de Lardizábal Km 1.5, 90700 Tlaxcala, Mexico
| | - Karen Lizeth Chavarría-Alvarado
- Laboratorio de Genómica Funcional y Biotecnología de Plantas, Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional (CIBA-IPN), Ex-Hacienda San Juan Molino, Carretera Estatal Tecuexcomac- Tepetitla de Lardizábal Km 1.5, 90700 Tlaxcala, Mexico
| | - Selma Ríos-Meléndez
- Laboratorio de Genómica Funcional y Biotecnología de Plantas, Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional (CIBA-IPN), Ex-Hacienda San Juan Molino, Carretera Estatal Tecuexcomac- Tepetitla de Lardizábal Km 1.5, 90700 Tlaxcala, Mexico
| | - Melina López-Meyer
- Departamento de Biotecnología Agrícola, Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional, Instituto Politécnico Nacional (CIIDIR-IPN Unidad Sinaloa), Boulevard Juan de Dios Bátiz Paredes 250, Colonia San Joachin, 81101 Guasave, Sinaloa Mexico
| | - Analilia Arroyo-Becerra
- Laboratorio de Genómica Funcional y Biotecnología de Plantas, Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional (CIBA-IPN), Ex-Hacienda San Juan Molino, Carretera Estatal Tecuexcomac- Tepetitla de Lardizábal Km 1.5, 90700 Tlaxcala, Mexico
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Gao D, Sun W, Wang D, Dong H, Zhang R, Yu S. A xylan glucuronosyltransferase gene exhibits pleiotropic effects on cellular composition and leaf development in rice. Sci Rep 2020; 10:3726. [PMID: 32111928 PMCID: PMC7048734 DOI: 10.1038/s41598-020-60593-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 02/10/2020] [Indexed: 11/09/2022] Open
Abstract
Leaf chlorophyll content is an important physiological indicator of plant growth, metabolism and nutritional status, and it is highly correlated with leaf nitrogen content and photosynthesis. In this study, we report the cloning and identification of a xylan glucuronosyltransferase gene (OsGUX1) that affects relative chlorophyll content in rice leaf. Using a set of chromosomal segment substitution lines derived from a cross of wild rice accession ACC10 and indica variety Zhenshan 97 (ZS97), we identified numerous quantitative trait loci for relative chlorophyll content. One major locus of them for relative chlorophyll content was mapped to a 10.3-kb region that contains OsGUX1. The allele OsGUX1AC from ACC10 significantly decreases nitrogen content and chlorophyll content of leaf compared with OsGUX1ZS from ZS97. The overexpression of OsGUX1 reduced chlorophyll content, and the suppression of this gene increased chlorophyll content of rice leaf. OsGUX1 is located in Golgi apparatus, and highly expressed in seedling leaf and the tissues in which primary cell wall synthesis occurring. Our experimental data indicate that OsGUX1 is responsible for addition of glucuronic acid residues onto xylan and participates in accumulation of cellulose and hemicellulose in the cell wall deposition, thus thickening the primary cell wall of mesophyll cells, which might lead to reduced chlorophyll content in rice leaf. These findings provide insights into the association of cell wall components with leaf nitrogen content in rice.
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Affiliation(s)
- Dawei Gao
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenqiang Sun
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dianwen Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hualin Dong
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ran Zhang
- Biomass & Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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Wang JG, Zhao TT, Wang WZ, Feng CL, Feng XY, Xiong GR, Shen LB, Zhang SZ, Wang WQ, Zhang ZX. Culm transcriptome sequencing of Badila (Saccharum officinarum L.) and analysis of major genes involved in sucrose accumulation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 144:455-465. [PMID: 31655344 DOI: 10.1016/j.plaphy.2019.10.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 10/10/2019] [Accepted: 10/14/2019] [Indexed: 06/10/2023]
Abstract
Sugarcane is an important sugar and energy crop worldwide. It utilises highly efficient C4 photosynthesis and accumulates sucrose in its culms. The sucrose content in sugarcane culms is a quantitative trait controlled by multiple genes. The regulatory mechanism underlying the maximum sucrose level in sugarcane culms remains unclear. We used transcriptome sequences to identify the potential regulatory genes involved in sucrose accumulation in Saccarum officinarum L. cv. Badila. The sucrose accumulating internodes at the elongation and mature growth stage and the immature internodes with low sucrose content at the mature stage were used for RNA sequencing. The obtained differentially expressed genes (DEGs) related to sucrose accumulation were analysed. Results showed that the transcripts encoding invertase (beta-fructofuranosidase, EC: 3.2.1.26) which catalyses sucrose hydrolysis and 6-phosphofructokinase (PFK, EC: 2.7.1.11), a key glycolysis regulatory enzyme, were downregulated in the high sucrose accumulation internodes. The transcripts encoding key enzymes for ABA, gibberellin and ethylene synthesis were also downregulated during sucrose accumulation. Furthermore, regulated protein kinase, transcription factor and sugar transporter genes were also obtained. This research can clarify the molecular regulation network of sucrose accumulation in sugarcane.
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Affiliation(s)
- Jun-Gang Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China; Institute of Tropical Bioscience and Biotechnology of Chinese Academy of Tropical Agricultural Sciences, Sugarcane Research Center of Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, Hainan, 571101, China
| | - Ting-Ting Zhao
- Institute of Tropical Bioscience and Biotechnology of Chinese Academy of Tropical Agricultural Sciences, Sugarcane Research Center of Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, Hainan, 571101, China
| | - Wen-Zhi Wang
- Institute of Tropical Bioscience and Biotechnology of Chinese Academy of Tropical Agricultural Sciences, Sugarcane Research Center of Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, Hainan, 571101, China
| | - Cui-Lian Feng
- Institute of Tropical Bioscience and Biotechnology of Chinese Academy of Tropical Agricultural Sciences, Sugarcane Research Center of Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, Hainan, 571101, China
| | - Xiao-Yan Feng
- Institute of Tropical Bioscience and Biotechnology of Chinese Academy of Tropical Agricultural Sciences, Sugarcane Research Center of Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, Hainan, 571101, China
| | - Guo-Ru Xiong
- Institute of Tropical Bioscience and Biotechnology of Chinese Academy of Tropical Agricultural Sciences, Sugarcane Research Center of Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, Hainan, 571101, China
| | - Lin-Bo Shen
- Institute of Tropical Bioscience and Biotechnology of Chinese Academy of Tropical Agricultural Sciences, Sugarcane Research Center of Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, Hainan, 571101, China
| | - Shu-Zhen Zhang
- Institute of Tropical Bioscience and Biotechnology of Chinese Academy of Tropical Agricultural Sciences, Sugarcane Research Center of Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, Hainan, 571101, China.
| | - Wen-Quan Wang
- Institute of Tropical Bioscience and Biotechnology of Chinese Academy of Tropical Agricultural Sciences, Sugarcane Research Center of Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, Hainan, 571101, China.
| | - Zu-Xing Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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Tan QW, Mutwil M. Inferring biosynthetic and gene regulatory networks from Artemisia annua RNA sequencing data on a credit card-sized ARM computer. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1863:194429. [PMID: 31634636 DOI: 10.1016/j.bbagrm.2019.194429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/06/2019] [Accepted: 09/06/2019] [Indexed: 02/05/2023]
Abstract
Prediction of gene function and gene regulatory networks is one of the most active topics in bioinformatics. The accumulation of publicly available gene expression data for hundreds of plant species, together with advances in bioinformatical methods and affordable computing, sets ingenuity as one of the major bottlenecks in understanding gene function and regulation. Here, we show how a credit card-sized computer retailing for <50 USD can be used to rapidly predict gene function and infer regulatory networks from RNA sequencing data. To achieve this, we constructed a bioinformatical pipeline that downloads and allows quality-control of RNA sequencing data; and generates a gene co-expression network that can reveal enzymes and transcription factors participating and controlling a given biosynthetic pathway. We exemplify this by first identifying genes and transcription factors involved in the biosynthesis of secondary cell wall in the plant Artemisia annua, the main natural source of the anti-malarial drug artemisinin. Networks were then used to dissect the artemisinin biosynthesis pathway, which suggest potential transcription factors regulating artemisinin biosynthesis. We provide the source code of our pipeline (https://github.com/mutwil/LSTrAP-Lite) and envision that the ubiquity of affordable computing, availability of biological data and increased bioinformatical training of biologists will transform the field of bioinformatics. This article is part of a Special Issue entitled: Transcriptional Profiles and Regulatory Gene Networks edited by Dr. Dr. Federico Manuel Giorgi and Dr. Shaun Mahony.
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Affiliation(s)
- Qiao Wen Tan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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11
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Wierzbicki MP, Christie N, Pinard D, Mansfield SD, Mizrachi E, Myburg AA. A systems genetics analysis in Eucalyptus reveals coordination of metabolic pathways associated with xylan modification in wood-forming tissues. THE NEW PHYTOLOGIST 2019; 223:1952-1972. [PMID: 31144333 DOI: 10.1111/nph.15972] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 05/01/2019] [Indexed: 06/09/2023]
Abstract
Acetyl- and methylglucuronic acid decorations of xylan, the dominant hemicellulose in secondary cell walls (SCWs) of woody dicots, affect its interaction with cellulose and lignin to determine SCW structure and extractability. Genes and pathways involved in these modifications may be targets for genetic engineering; however, little is known about the regulation of xylan modifications in woody plants. To address this, we assessed genetic and gene expression variation associated with xylan modification in developing xylem of Eucalyptus grandis × Eucalyptus urophylla interspecific hybrids. Expression quantitative trait locus (eQTL) mapping identified potential regulatory polymorphisms affecting gene expression modules associated with xylan modification. We identified 14 putative xylan modification genes that are members of five expression modules sharing seven trans-eQTL hotspots. The xylan modification genes are prevalent in two expression modules. The first comprises nucleotide sugar interconversion pathways supplying the essential precursors for cellulose and xylan biosynthesis. The second contains genes responsible for phenylalanine biosynthesis and S-adenosylmethionine biosynthesis required for glucuronic acid and monolignol methylation. Co-expression and co-regulation analyses also identified four metabolic sources of acetyl coenxyme A that appear to be transcriptionally coordinated with xylan modification. Our systems genetics analysis may provide new avenues for metabolic engineering to alter wood SCW biology for enhanced biomass processability.
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Affiliation(s)
- Martin P Wierzbicki
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Nanette Christie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Desré Pinard
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Shawn D Mansfield
- Department of Wood Science, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Eshchar Mizrachi
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Alexander A Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
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Menon RR, Kumari S, Kumar P, Verma A, Krishnamurthi S, Rameshkumar N. Sphingomonas pokkalii sp. nov., a novel plant associated rhizobacterium isolated from a saline tolerant pokkali rice and its draft genome analysis. Syst Appl Microbiol 2019; 42:334-342. [PMID: 30808585 DOI: 10.1016/j.syapm.2019.02.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/29/2019] [Accepted: 02/08/2019] [Indexed: 02/03/2023]
Abstract
Three strains L3B27T, 3CNBAF, L1A4 isolated from a brackish cultivated pokkali rice rhizosphere were characterised using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA and recA gene sequences revealed that these strains were highly similar among each other and formed a separate monophyletic cluster within the genus Sphingomonas with Sphingomonas pituitosa DSM 13101T, Sphingomonas azotifigens DSM 18530T and Sphingomonas trueperi DSM 7225T as their closest relatives sharing 97.9-98.3% 16S rRNA similarity and 91.3-94.0% recA similarity values, respectively. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridisation (dDDH) values between L3B27T (representative of the novel strains) and its phylogenetically closest Sphingomonas species were well below the established cut-off <94% (ANI/AAI) and <70% (dDDH) for species delineation. Further, the novel strains can be distinguished from its closest relatives based on several phenotypic traits. Thus, based on the polyphasic approach, we describe a novel Sphingomonas species for which the name Sphingomonas pokkalii sp. nov (type strain L3B27T=KCTC 42098T=MCC 3001T) is proposed. In addition, the novel strains were characterised for their plant associated properties and found to possess several phenotypic traits which probably explain its plant associated lifestyle. This was further confirmed by the presence of several plant associated gene features in the genome of L3B27T. Also, we could identify gene features which may likely involve in brackish water adaptation. Thus, this study provides first insights into the plant associated lifestyle, genome and taxonomy of a novel brackish adapted plant associated Sphingomonas.
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13
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Wierzbicki MP, Maloney V, Mizrachi E, Myburg AA. Xylan in the Middle: Understanding Xylan Biosynthesis and Its Metabolic Dependencies Toward Improving Wood Fiber for Industrial Processing. FRONTIERS IN PLANT SCIENCE 2019; 10:176. [PMID: 30858858 PMCID: PMC6397879 DOI: 10.3389/fpls.2019.00176] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 02/04/2019] [Indexed: 05/14/2023]
Abstract
Lignocellulosic biomass, encompassing cellulose, lignin and hemicellulose in plant secondary cell walls (SCWs), is the most abundant source of renewable materials on earth. Currently, fast-growing woody dicots such as Eucalyptus and Populus trees are major lignocellulosic (wood fiber) feedstocks for bioproducts such as pulp, paper, cellulose, textiles, bioplastics and other biomaterials. Processing wood for these products entails separating the biomass into its three main components as efficiently as possible without compromising yield. Glucuronoxylan (xylan), the main hemicellulose present in the SCWs of hardwood trees carries chemical modifications that are associated with SCW composition and ultrastructure, and affect the recalcitrance of woody biomass to industrial processing. In this review we highlight the importance of xylan properties for industrial wood fiber processing and how gaining a greater understanding of xylan biosynthesis, specifically xylan modification, could yield novel biotechnology approaches to reduce recalcitrance or introduce novel processing traits. Altering xylan modification patterns has recently become a focus of plant SCW studies due to early findings that altered modification patterns can yield beneficial biomass processing traits. Additionally, it has been noted that plants with altered xylan composition display metabolic differences linked to changes in precursor usage. We explore the possibility of using systems biology and systems genetics approaches to gain insight into the coordination of SCW formation with other interdependent biological processes. Acetyl-CoA, s-adenosylmethionine and nucleotide sugars are precursors needed for xylan modification, however, the pathways which produce metabolic pools during different stages of fiber cell wall formation still have to be identified and their co-regulation during SCW formation elucidated. The crucial dependence on precursor metabolism provides an opportunity to alter xylan modification patterns through metabolic engineering of one or more of these interdependent pathways. The complexity of xylan biosynthesis and modification is currently a stumbling point, but it may provide new avenues for woody biomass engineering that are not possible for other biopolymers.
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Affiliation(s)
| | | | | | - Alexander A. Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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14
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Ajengui A, Bertolini E, Ligorio A, Chebil S, Ippolito A, Sanzani SM. Comparative transcriptome analysis of two citrus germplasms with contrasting susceptibility to Phytophthora nicotianae provides new insights into tolerance mechanisms. PLANT CELL REPORTS 2018; 37:483-499. [PMID: 29290008 DOI: 10.1007/s00299-017-2244-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 12/26/2017] [Indexed: 06/07/2023]
Abstract
Host perception of Phytophthora nicotianae switching to necrotrophy is fundamental for disease tolerance of citrus. It involves an HR-like response, strengthening of the cell wall structure and hormonal signaling. Stem rot caused by P. nicotianae is a worldwide disease of several important crops, including citrus. Given the growing awareness of chemical fungicides drawbacks, genetic improvement of citrus rootstocks remains the best alternative. However, the molecular basis underlying the successful response of resistant and/or tolerant genotypes remains poorly understood. Therefore, we performed a transcriptomic analysis to examine the differential defense response to P. nicotianae of two germplasms-tolerant sour orange (SO, Citrus aurantium) and susceptible Madam Vinous (MV, C. sinensis)-in both the biotrophic and necrotrophic phases of host-pathogen interaction. Our results revealed the necrotrophic phase as a decisive turning point, since it included stronger modulation of a number of genes implicated in pathogen perception, signal transduction, HR-like response, transcriptional reprogramming, hormone signaling, and cell wall modifications. In particular, the pathogen perception category reflected the ability of SO to perceive the pathogen even after its switch to necrotrophy, and thus to cope successfully with the infection, while MV failed. The concomitant changes in genes involved in the remaining functional categories seemed to prevent pathogen spread. This investigation provided further understanding of the successful defense mechanisms of C. aurantium against P. nicotianae, which might be exploited in post-genomic strategies to develop resistant Citrus genotypes.
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Affiliation(s)
- Arwa Ajengui
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj-Cédria, 2050, Hammam-Lif, Tunisia
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari "Aldo Moro", Via Amendola 165/A, 70126, Bari, Italy
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar, 2092, Tunis, Tunisia
| | - Edoardo Bertolini
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy
| | - Angela Ligorio
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari "Aldo Moro", Via Amendola 165/A, 70126, Bari, Italy
| | - Samir Chebil
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj-Cédria, 2050, Hammam-Lif, Tunisia
| | - Antonio Ippolito
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari "Aldo Moro", Via Amendola 165/A, 70126, Bari, Italy
| | - Simona Marianna Sanzani
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari "Aldo Moro", Via Amendola 165/A, 70126, Bari, Italy.
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15
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Rains MK, Gardiyehewa de Silva ND, Molina I. Reconstructing the suberin pathway in poplar by chemical and transcriptomic analysis of bark tissues. TREE PHYSIOLOGY 2018; 38:340-361. [PMID: 28575526 DOI: 10.1093/treephys/tpx060] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 05/18/2017] [Indexed: 05/09/2023]
Abstract
The tree bark periderm confers the first line of protection against pathogen invasion and abiotic stresses. The phellogen (cork cambium) externally produces cork (phellem) cells that are dead at maturity; while metabolically active, these tissues synthesize cell walls, as well as cell wall modifications, namely suberin and waxes. Suberin is a heteropolymer with aliphatic and aromatic domains, composed of acylglycerols, cross-linked polyphenolics and solvent-extractable waxes. Although suberin is essentially ubiquitous in vascular plants, the biochemical functions of many enzymes and the genetic regulation of its synthesis are poorly understood. We have studied suberin and wax composition in four developmental stages of hybrid poplar (Populus tremula x Populus alba) stem periderm. The amounts of extracellular ester-linked acyl lipids per unit area increased with tissue age, a trend not observed with waxes. We used RNA-Seq deep-sequencing technology to investigate the cork transcriptome at two developmental stages. The transcript analysis yielded 455 candidates for the biosynthesis and regulation of poplar suberin, including genes with proven functions in suberin metabolism, genes highlighted as candidates in other plant species and novel candidates. Among these, a gene encoding a putative lipase/acyltransferase of the GDSL-motif family emerged as a suberin polyester synthase candidate, and specific isoforms of peroxidase and laccase genes were preferentially expressed in cork, suggesting that their corresponding proteins may be involved in cross-linking aromatics to form lignin-like polyphenolics. Many transcriptional regulators with possible roles in meristem identity, cork differentiation and acyl-lipid metabolism were also identified. Our work provides the first large-scale transcriptomic dataset on the suberin-synthesizing tissue of poplar bark, contributing to our understanding of tree bark development at the molecular level. Based on these data, we have proposed a number of hypotheses that can be used in future research leading to novel biological insights into suberin biosynthesis and its physiological function.
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Affiliation(s)
- Meghan K Rains
- Department of Biology, Biosciences Complex, Queen's University, 116 Barrie St., Kingston, ON, Canada K7L 3N6
- Department of Biology, Essar Convergence Centre, Algoma University, 1520 Queen Street East, Sault Ste Marie, ON, Canada P6A 2G4
| | - Nayana Dilini Gardiyehewa de Silva
- Department of Biology and Institute of Biochemistry, Nesbitt Biology Building, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1S 5B6
| | - Isabel Molina
- Department of Biology, Biosciences Complex, Queen's University, 116 Barrie St., Kingston, ON, Canada K7L 3N6
- Department of Biology, Essar Convergence Centre, Algoma University, 1520 Queen Street East, Sault Ste Marie, ON, Canada P6A 2G4
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16
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Zhao X, Liu N, Shang N, Zeng W, Ebert B, Rautengarten C, Zeng QY, Li H, Chen X, Beahan C, Bacic A, Heazlewood JL, Wu AM. Three UDP-xylose transporters participate in xylan biosynthesis by conveying cytosolic UDP-xylose into the Golgi lumen in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1125-1134. [PMID: 29300997 PMCID: PMC6018967 DOI: 10.1093/jxb/erx448] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 11/26/2017] [Indexed: 05/20/2023]
Abstract
UDP-xylose (UDP-Xyl) is synthesized by UDP-glucuronic acid decarboxylases, also termed UDP-Xyl synthases (UXSs). The Arabidopsis genome encodes six UXSs, which fall into two groups based upon their subcellular location: the Golgi lumen and the cytosol. The latter group appears to play an important role in xylan biosynthesis. Cytosolic UDP-Xyl is transported into the Golgi lumen by three UDP-Xyl transporters (UXT1, 2, and 3). However, while single mutants affected in the UDP-Xyl transporter 1 (UXT1) showed a substantial reduction in cell wall xylose content, a double mutant affected in UXT2 and UXT3 had no obvious effect on cell wall xylose deposition. This prompted us to further investigate redundancy among the members of the UXT family. Multiple uxt mutants were generated, including a triple mutant, which exhibited collapsed vessels and reduced cell wall thickness in interfascicular fiber cells. Monosaccharide composition, molecular weight, nuclear magnetic resonance, and immunolabeling studies demonstrated that both xylan biosynthesis (content) and fine structure were significantly affected in the uxt triple mutant, leading to phenotypes resembling those of the irx mutants. Pollination was also impaired in the uxt triple mutant, likely due to reduced filament growth and anther dehiscence caused by alterations in the composition of the cell walls. Moreover, analysis of the nucleotide sugar composition of the uxt mutants indicated that nucleotide sugar interconversion is influenced by the cytosolic UDP-Xyl pool within the cell. Taken together, our results underpin the physiological roles of the UXT family in xylan biosynthesis and provide novel insights into the nucleotide sugar metabolism and trafficking in plants.
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Affiliation(s)
- Xianhai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Nian Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Na Shang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Wei Zeng
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Berit Ebert
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | | | - Qing-Yin Zeng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Huiling Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Xiaoyang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Cherie Beahan
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Antony Bacic
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Joshua L Heazlewood
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
- Correspondence: ;
| | - Ai-Min Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Correspondence: ;
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17
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Rao X, Shen H, Pattathil S, Hahn MG, Gelineo-Albersheim I, Mohnen D, Pu Y, Ragauskas AJ, Chen X, Chen F, Dixon RA. Dynamic changes in transcriptome and cell wall composition underlying brassinosteroid-mediated lignification of switchgrass suspension cells. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:266. [PMID: 29213317 PMCID: PMC5707915 DOI: 10.1186/s13068-017-0954-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/02/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Plant cell walls contribute the majority of plant biomass that can be used to produce transportation fuels. However, the complexity and variability in composition and structure of cell walls, particularly the presence of lignin, negatively impacts their deconstruction for bioenergy. Metabolic and genetic changes associated with secondary wall development in the biofuel crop switchgrass (Panicum virgatum) have yet to be reported. RESULTS Our previous studies have established a cell suspension system for switchgrass, in which cell wall lignification can be induced by application of brassinolide (BL). We have now collected cell wall composition and microarray-based transcriptome profiles for BL-induced and non-induced suspension cultures to provide an overview of the dynamic changes in transcriptional reprogramming during BL-induced cell wall modification. From this analysis, we have identified changes in candidate genes involved in cell wall precursor synthesis, cellulose, hemicellulose, and pectin formation and ester-linkage generation. We have also identified a large number of transcription factors with expression correlated with lignin biosynthesis genes, among which are candidates for control of syringyl (S) lignin accumulation. CONCLUSION Together, this work provides an overview of the dynamic compositional changes during brassinosteroid-induced cell wall remodeling, and identifies candidate genes for future plant genetic engineering to overcome cell wall recalcitrance.
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Affiliation(s)
- Xiaolan Rao
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN USA
| | - Hui Shen
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX USA
- Present Address: Marker-assisted Breeding and Traits, Chromatin Inc, Lubbock, TX 79404 USA
| | - Sivakumar Pattathil
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN USA
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, GA 30602 USA
- Present Address: Mascoma LLC (Lallemand Company), 67 Etna Road, Lebanon, NH 03766 USA
| | - Michael G. Hahn
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN USA
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, GA 30602 USA
| | - Ivana Gelineo-Albersheim
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN USA
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, GA 30602 USA
| | - Debra Mohnen
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN USA
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Rd, Athens, GA 30602 USA
| | - Yunqiao Pu
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN USA
| | - Arthur J. Ragauskas
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN USA
| | - Xin Chen
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN USA
- Present Address: Center for Applied Mathematics, Tianjin University, Tianjin, 300072 China
| | - Fang Chen
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN USA
| | - Richard A. Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory (ORNL), Oak Ridge, TN USA
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18
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Grantham NJ, Wurman-Rodrich J, Terrett OM, Lyczakowski JJ, Stott K, Iuga D, Simmons TJ, Durand-Tardif M, Brown SP, Dupree R, Busse-Wicher M, Dupree P. An even pattern of xylan substitution is critical for interaction with cellulose in plant cell walls. NATURE PLANTS 2017; 3:859-865. [PMID: 28993612 DOI: 10.1038/s41477-017-0030-8] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/13/2017] [Indexed: 05/18/2023]
Abstract
Xylan and cellulose are abundant polysaccharides in vascular plants and essential for secondary cell wall strength. Acetate or glucuronic acid decorations are exclusively found on even-numbered residues in most of the glucuronoxylan polymer. It has been proposed that this even-specific positioning of the decorations might permit docking of xylan onto the hydrophilic face of a cellulose microfibril 1-3 . Consequently, xylan adopts a flattened ribbon-like twofold screw conformation when bound to cellulose in the cell wall 4 . Here we show that ESKIMO1/XOAT1/TBL29, a xylan-specific O-acetyltransferase, is necessary for generation of the even pattern of acetyl esters on xylan in Arabidopsis. The reduced acetylation in the esk1 mutant deregulates the position-specific activity of the xylan glucuronosyltransferase GUX1, and so the even pattern of glucuronic acid on the xylan is lost. Solid-state NMR of intact cell walls shows that, without the even-patterned xylan decorations, xylan does not interact normally with cellulose fibrils. We conclude that the even pattern of xylan substitutions seen across vascular plants enables the interaction of xylan with hydrophilic faces of cellulose fibrils, and is essential for development of normal plant secondary cell walls.
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Affiliation(s)
- Nicholas J Grantham
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Joel Wurman-Rodrich
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Oliver M Terrett
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Jan J Lyczakowski
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Katherine Stott
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Dinu Iuga
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
| | - Thomas J Simmons
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Mylene Durand-Tardif
- Institut Jean-Pierre Bourgin, UMR 1318, INRA AgroParisTech CNRS, Université Paris-Saclay, 78026, Versailles Cedex, France
| | - Steven P Brown
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
| | - Ray Dupree
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
| | - Marta Busse-Wicher
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK.
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Gorshkov O, Mokshina N, Gorshkov V, Chemikosova S, Gogolev Y, Gorshkova T. Transcriptome portrait of cellulose-enriched flax fibres at advanced stage of specialization. PLANT MOLECULAR BIOLOGY 2017; 93:431-449. [PMID: 27981388 DOI: 10.1007/s11103-016-0571-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 12/02/2016] [Indexed: 05/13/2023]
Abstract
Functional specialization of cells is among the most fundamental processes of higher organism ontogenesis. The major obstacle to studying this phenomenon in plants is the difficulty of isolating certain types of cells at defined stages of in planta development for in-depth analysis. A rare opportunity is given by the developed model system of flax (Linum usitatissimum L.) phloem fibres that can be purified from the surrounding tissues at the stage of the tertiary cell wall deposition. The performed comparison of the whole transcriptome profile in isolated fibres and other portions of the flax stem, together with fibre metabolism characterization, helped to elucidate the general picture of the advanced stage of plant cell specialization and to reveal novel participants potentially involved in fibre metabolism regulation and cell wall formation. Down-regulation of all genes encoding proteins involved in xylan and lignin synthesis and up-regulation of genes for the specific set of transcription factors transcribed during tertiary cell wall formation were revealed. The increased abundance of transcripts for several glycosyltransferases indicated the enzymes that may be involved in synthesis of fibre-specific version of rhamnogalacturonan I.
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Affiliation(s)
- Oleg Gorshkov
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Science, Lobachevsky str., 2/31, Kazan, 420111, Russia
| | - Natalia Mokshina
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Science, Lobachevsky str., 2/31, Kazan, 420111, Russia
| | - Vladimir Gorshkov
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Science, Lobachevsky str., 2/31, Kazan, 420111, Russia
| | - Svetlana Chemikosova
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Science, Lobachevsky str., 2/31, Kazan, 420111, Russia
| | - Yuri Gogolev
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Science, Lobachevsky str., 2/31, Kazan, 420111, Russia
| | - Tatyana Gorshkova
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Science, Lobachevsky str., 2/31, Kazan, 420111, Russia.
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20
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Ihsan MZ, Ahmad SJN, Shah ZH, Rehman HM, Aslam Z, Ahuja I, Bones AM, Ahmad JN. Gene Mining for Proline Based Signaling Proteins in Cell Wall of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2017; 8:233. [PMID: 28289422 PMCID: PMC5326801 DOI: 10.3389/fpls.2017.00233] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 02/07/2017] [Indexed: 05/29/2023]
Abstract
The cell wall (CW) as a first line of defense against biotic and abiotic stresses is of primary importance in plant biology. The proteins associated with cell walls play a significant role in determining a plant's sustainability to adverse environmental conditions. In this work, the genes encoding cell wall proteins (CWPs) in Arabidopsis were identified and functionally classified using geneMANIA and GENEVESTIGATOR with published microarrays data. This yielded 1605 genes, out of which 58 genes encoded proline-rich proteins (PRPs) and glycine-rich proteins (GRPs). Here, we have focused on the cellular compartmentalization, biological processes, and molecular functioning of proline-rich CWPs along with their expression at different plant developmental stages. The mined genes were categorized into five classes on the basis of the type of PRPs encoded in the cell wall of Arabidopsis thaliana. We review the domain structure and function of each class of protein, many with respect to the developmental stages of the plant. We have then used networks, hierarchical clustering and correlations to analyze co-expression, co-localization, genetic, and physical interactions and shared protein domains of these PRPs. This has given us further insight into these functionally important CWPs and identified a number of potentially new cell-wall related proteins in A. thaliana.
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Affiliation(s)
- Muhammad Z. Ihsan
- Cholistan Institute of Desert Studies, The Islamia University BahawalpurBahawalpur, Pakistan
| | - Samina J. N. Ahmad
- Plant Stress Physiology and Molecular Biology Lab, Department of Botany, University of Agriculture FaisalabadFaisalabad, Pakistan
- Integrated Genomics Cellular Developmental and Biotechnology Lab, Department of Entomology, University of Agriculture FaisalabadFaisalabad, Pakistan
| | - Zahid Hussain Shah
- Department of Arid Land Agriculture, Faculty of Meteorology, King Abdulaziz UniversityJeddah, Saudi Arabia
| | - Hafiz M. Rehman
- Department of Electronic and Biomedical Engineering, Chonnam National UniversityGwangju, South Korea
| | - Zubair Aslam
- Department of Agronomy, University of Agriculture FaisalabadFaisalabad, Pakistan
| | - Ishita Ahuja
- Department of Biology, Norwegian University of Science and TechnologyTrondheim, Norway
| | - Atle M. Bones
- Department of Biology, Norwegian University of Science and TechnologyTrondheim, Norway
| | - Jam N. Ahmad
- Plant Stress Physiology and Molecular Biology Lab, Department of Botany, University of Agriculture FaisalabadFaisalabad, Pakistan
- Integrated Genomics Cellular Developmental and Biotechnology Lab, Department of Entomology, University of Agriculture FaisalabadFaisalabad, Pakistan
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21
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Walker JA, Pattathil S, Bergeman LF, Beebe ET, Deng K, Mirzai M, Northen TR, Hahn MG, Fox BG. Determination of glycoside hydrolase specificities during hydrolysis of plant cell walls using glycome profiling. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:31. [PMID: 28184246 PMCID: PMC5288845 DOI: 10.1186/s13068-017-0703-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/06/2017] [Indexed: 05/29/2023]
Abstract
BACKGROUND Glycoside hydrolases (GHs) are enzymes that hydrolyze polysaccharides into simple sugars. To better understand the specificity of enzyme hydrolysis within the complex matrix of polysaccharides found in the plant cell wall, we studied the reactions of individual enzymes using glycome profiling, where a comprehensive collection of cell wall glycan-directed monoclonal antibodies are used to detect polysaccharide epitopes remaining in the walls after enzyme treatment and quantitative nanostructure initiator mass spectrometry (oxime-NIMS) to determine soluble sugar products of their reactions. RESULTS Single, purified enzymes from the GH5_4, GH10, and GH11 families of glycoside hydrolases hydrolyzed hemicelluloses as evidenced by the loss of specific epitopes from the glycome profiles in enzyme-treated plant biomass. The glycome profiling data were further substantiated by oxime-NIMS, which identified hexose products from hydrolysis of cellulose, and pentose-only and mixed hexose-pentose products from the hydrolysis of hemicelluloses. The GH10 enzyme proved to be reactive with the broadest diversity of xylose-backbone polysaccharide epitopes, but was incapable of reacting with glucose-backbone polysaccharides. In contrast, the GH5 and GH11 enzymes studied here showed the ability to react with both glucose- and xylose-backbone polysaccharides. CONCLUSIONS The identification of enzyme specificity for a wide diversity of polysaccharide structures provided by glycome profiling, and the correlated identification of soluble oligosaccharide hydrolysis products provided by oxime-NIMS, offers a unique combination to understand the hydrolytic capabilities and constraints of individual enzymes as they interact with plant biomass.
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Affiliation(s)
- Johnnie A. Walker
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Sivakumar Pattathil
- US Department of Energy Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Lai F. Bergeman
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Emily T. Beebe
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Kai Deng
- US Department of Energy Joint Bioenergy Institute, Emeryville, CA 94608 USA
- Sandia National Laboratories, Livermore, CA 94551 USA
| | - Maryam Mirzai
- US Department of Energy Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Trent R. Northen
- US Department of Energy Joint Bioenergy Institute, Emeryville, CA 94608 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Michael G. Hahn
- US Department of Energy Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Brian G. Fox
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
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22
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Peralta AG, Venkatachalam S, Stone SC, Pattathil S. Xylan epitope profiling: an enhanced approach to study organ development-dependent changes in xylan structure, biosynthesis, and deposition in plant cell walls. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:245. [PMID: 29213310 PMCID: PMC5707906 DOI: 10.1186/s13068-017-0935-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/19/2017] [Indexed: 05/02/2023]
Abstract
BACKGROUND Xylan is a major hemicellulosic component in the cell walls of higher plants especially in the secondary walls of vascular cells which are playing important roles in physiological processes and overall mechanical strength. Being the second most abundant cell wall polymer after cellulose, xylan is an abundant non-cellulosic carbohydrate constituent of plant biomass. Xylan structures have been demonstrated to contribute to plant biomass recalcitrance during bioenergy applications. A critical understanding of xylan composition, structure, and biosynthesis in developing plant stems will allow an increased understanding of how cell walls are put together in this organ in a basic research, and, in applied research, will improve strategies in xylan engineering to reduce biomass recalcitrance for economically feasible biofuel production. METHODS We describe an approach to enable the monitoring of xylan epitope structures in cell walls during the stem maturation process in Arabidopsis. The technique integrates glycome profiling, an in vitro immunoanalytical platform, and in situ immunolocalisation to provide comprehensive details on the presence, relative abundances, and dynamics with which diverse xylan epitope structures are integrated to the cell walls throughout the stem maturation process. RESULTS Our experimental results and the supporting in silico analysis demonstrated that xylan deposition in stems occurs early on in stem development; however, xylan epitope types (representing substituted and unsubstituted regions on xylan backbone made of β-(1,4)-linked xylose residues) and the strength of their integration into the final wall structure vary during stem maturation. CONCLUSIONS Our novel approach thus provides a method to comprehensively survey the differences in xylan epitope patterning and deposition occurring in stem development and thereby providing a robust tool for characterising altered xylan integration patterns in cell walls during the stem maturation process in diverse plant cell wall biosynthetic mutants. Our findings also suggest that this approach could rapidly and reliably delineate xylan deposition patterns in the cell walls of plants belonging to diverse phylogenetic classes providing novel insights into the functional roles of xylans in overall growth and development.
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Affiliation(s)
- Angelo G. Peralta
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30605 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Sivasankari Venkatachalam
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30605 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Sydney C. Stone
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30605 USA
| | - Sivakumar Pattathil
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30605 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Present Address: Mascoma LLC (Lallemand Inc.), 67 Etna Road, Lebanon, NH 03766 USA
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23
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Lin F, Manisseri C, Fagerström A, Peck ML, Vega-Sánchez ME, Williams B, Chiniquy DM, Saha P, Pattathil S, Conlin B, Zhu L, Hahn MG, Willats WGT, Scheller HV, Ronald PC, Bartley LE. Cell Wall Composition and Candidate Biosynthesis Gene Expression During Rice Development. PLANT & CELL PHYSIOLOGY 2016; 57:2058-2075. [PMID: 27481893 DOI: 10.1093/pcp/pcw125] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 07/09/2016] [Indexed: 05/02/2023]
Abstract
Cell walls of grasses, including cereal crops and biofuel grasses, comprise the majority of plant biomass and intimately influence plant growth, development and physiology. However, the functions of many cell wall synthesis genes, and the relationships among and the functions of cell wall components remain obscure. To better understand the patterns of cell wall accumulation and identify genes that act in grass cell wall biosynthesis, we characterized 30 samples from aerial organs of rice (Oryza sativa cv. Kitaake) at 10 developmental time points, 3-100 d post-germination. Within these samples, we measured 15 cell wall chemical components, enzymatic digestibility and 18 cell wall polysaccharide epitopes/ligands. We also used quantitative reverse transcription-PCR to measure expression of 50 glycosyltransferases, 15 acyltransferases and eight phenylpropanoid genes, many of which had previously been identified as being highly expressed in rice. Most cell wall components vary significantly during development, and correlations among them support current understanding of cell walls. We identified 92 significant correlations between cell wall components and gene expression and establish nine strong hypotheses for genes that synthesize xylans, mixed linkage glucan and pectin components. This work provides an extensive analysis of cell wall composition throughout rice development, identifies genes likely to synthesize grass cell walls, and provides a framework for development of genetically improved grasses for use in lignocellulosic biofuel production and agriculture.
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Affiliation(s)
- Fan Lin
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Chithra Manisseri
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Alexandra Fagerström
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark
| | - Matthew L Peck
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Miguel E Vega-Sánchez
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616, USA
- Monsanto Company, Chesterfield Village Campus, Chesterfield, MO 63017, USA
| | - Brian Williams
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616, USA
| | - Dawn M Chiniquy
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616, USA
| | - Prasenjit Saha
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Sivakumar Pattathil
- Bioenergy Science Center, Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Brian Conlin
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616, USA
| | - Lan Zhu
- Department of Statistics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Michael G Hahn
- Bioenergy Science Center, Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - William G T Willats
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark
| | - Henrik V Scheller
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Pamela C Ronald
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark
| | - Laura E Bartley
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Denmark
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24
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Mal C, Deb A, Aftabuddin M, Kundu S. A network analysis of miRNA mediated gene regulation of rice: crosstalk among biological processes. MOLECULAR BIOSYSTEMS 2016; 11:2273-80. [PMID: 26066638 DOI: 10.1039/c5mb00222b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To understand the network architecture of miRNA mediated regulations at the genomic and functional levels of rice, we have made an unambiguous annotation of the experimentally verified miRNAs, predicted their targets and the possible biological functions they can affect. Some functions, namely translational and protein modifications and photosynthesis are targeted by higher percentage of miRNA. Using transformation procedures, we constructed a genome scale miRNA-miRNA functional synergistic network (MFSN). The analysis of MFSN modules help to identify miRNAs co-regulating target genes having several interrelated biological processes. Some of these target genes are also co-expressed under particular conditions. For example, the genes co-expressed under drought conditions as well as those targeted by miRNAs present in a MFSN module have interdependent biological processes namely, photosynthesis, cell-wall biogenesis, root development and xylan synthesis. The stress-induced miRNAs and their distributions, and the presence of transcription factors in the target set of MFSN modules were also analyzed.
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Affiliation(s)
- Chittabrata Mal
- Department of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India.
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25
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Kim RJ, Kim HJ, Shim D, Suh MC. Molecular and biochemical characterizations of the monoacylglycerol lipase gene family of Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:758-71. [PMID: 26932457 DOI: 10.1111/tpj.13146] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 02/09/2016] [Accepted: 02/15/2016] [Indexed: 05/23/2023]
Abstract
Monoacylglycerol lipase (MAGL) catalyzes the last step of triacylglycerol breakdown, which is the hydrolysis of monoacylglycerol (MAG) to fatty acid and glycerol. Arabidopsis harbors over 270 genes annotated as 'lipase', the largest class of acyl lipid metabolism genes that have not been characterized experimentally. In this study, computational modeling suggested that 16 Arabidopsis putative MAGLs (AtMAGLs) have a three-dimensional structure that is similar to a human MAGL. Heterologous expression and enzyme assays indicated that 11 of the 16 encoded proteins indeed possess MAG lipase activity. Additionally, AtMAGL4 displayed hydrolase activity with lysophosphatidylcholine and lysophosphatidylethanolamine (LPE) substrates and AtMAGL1 and 2 utilized LPE as a substrate. All recombinant AtMAGLs preferred MAG substrates with unsaturated fatty acids over saturated fatty acids and AtMAGL8 exhibited the highest hydrolase activities with MAG containing 20:1 fatty acids. Except for AtMAGL4, -14 and -16, all AtMAGLs showed similar activity with both sn-1 and sn-2 MAG isomers. Spatial, temporal and stress-induced expression of the 16 AtMAGL genes was analyzed by transcriptome analyses. AtMAGL:eYFP fusion proteins provided initial evidence that AtMAGL1, -3, -6, -7, -8, -11, -13, -14 and -16 are targeted to the endoplasmic reticulum and/or Golgi network, AtMAGL10, -12 and -15 to the cytosol and AtMAGL2, -4 and -5 to the chloroplasts. Furthermore, AtMAGL8 was associated with the surface of oil bodies in germinating seeds and leaves accumulating oil bodies. This study provides the broad characterization of one of the least well-understood groups of Arabidopsis lipid-related enzymes and will be useful for better understanding their roles in planta.
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Affiliation(s)
- Ryeo Jin Kim
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 500-757, Korea
| | - Hae Jin Kim
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 500-757, Korea
| | - Donghwan Shim
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 500-757, Korea
| | - Mi Chung Suh
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 500-757, Korea
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26
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Pattathil S, Avci U, Zhang T, Cardenas CL, Hahn MG. Immunological Approaches to Biomass Characterization and Utilization. Front Bioeng Biotechnol 2015; 3:173. [PMID: 26579515 PMCID: PMC4623462 DOI: 10.3389/fbioe.2015.00173] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/12/2015] [Indexed: 11/13/2022] Open
Abstract
Plant biomass is the major renewable feedstock resource for sustainable generation of alternative transportation fuels to replace fossil carbon-derived fuels. Lignocellulosic cell walls are the principal component of plant biomass. Hence, a detailed understanding of plant cell wall structure and biosynthesis is an important aspect of bioenergy research. Cell walls are dynamic in their composition and structure, varying considerably among different organs, cells, and developmental stages of plants. Hence, tools are needed that are highly efficient and broadly applicable at various levels of plant biomass-based bioenergy research. The use of plant cell wall glycan-directed probes has seen increasing use over the past decade as an excellent approach for the detailed characterization of cell walls. Large collections of such probes directed against most major cell wall glycans are currently available worldwide. The largest and most diverse set of such probes consists of cell wall glycan-directed monoclonal antibodies (McAbs). These McAbs can be used as immunological probes to comprehensively monitor the overall presence, extractability, and distribution patterns among cell types of most major cell wall glycan epitopes using two mutually complementary immunological approaches, glycome profiling (an in vitro platform) and immunolocalization (an in situ platform). Significant progress has been made recently in the overall understanding of plant biomass structure, composition, and modifications with the application of these immunological approaches. This review focuses on such advances made in plant biomass analyses across diverse areas of bioenergy research.
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Affiliation(s)
- Sivakumar Pattathil
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- Oak Ridge National Laboratory, BioEnergy Science Center (BESC), Oak Ridge, TN, USA
| | - Utku Avci
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- Oak Ridge National Laboratory, BioEnergy Science Center (BESC), Oak Ridge, TN, USA
| | - Tiantian Zhang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Claudia L. Cardenas
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Michael G. Hahn
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- Oak Ridge National Laboratory, BioEnergy Science Center (BESC), Oak Ridge, TN, USA
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27
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Bi Z, Merl-Pham J, Uehlein N, Zimmer I, Mühlhans S, Aichler M, Walch AK, Kaldenhoff R, Palme K, Schnitzler JP, Block K. RNAi-mediated downregulation of poplar plasma membrane intrinsic proteins (PIPs) changes plasma membrane proteome composition and affects leaf physiology. J Proteomics 2015; 128:321-32. [PMID: 26248320 DOI: 10.1016/j.jprot.2015.07.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/16/2015] [Accepted: 07/23/2015] [Indexed: 11/19/2022]
Abstract
Plasma membrane intrinsic proteins (PIPs) are one subfamily of aquaporins that mediate the transmembrane transport of water. To reveal their function in poplar, we generated transgenic poplar plants in which the translation of PIP genes was downregulated by RNA interference investigated these plants with a comprehensive leaf plasma membrane proteome and physiome analysis. First, inhibition of PIP synthesis strongly altered the leaf plasma membrane protein composition. Strikingly, several signaling components and transporters involved in the regulation of stomatal movement were differentially regulated in transgenic poplars. Furthermore, hormonal crosstalk related to abscisic acid, auxin and brassinosteroids was altered, in addition to cell wall biosynthesis/cutinization, the organization of cellular structures and membrane trafficking. A physiological analysis confirmed the proteomic results. The leaves had wider opened stomata and higher net CO2 assimilation and transpiration rates as well as greater mesophyll conductance for CO2 (gm) and leaf hydraulic conductance (Kleaf). Based on these results, we conclude that PIP proteins not only play essential roles in whole leaf water and CO2 flux but have important roles in the regulation of stomatal movement.
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Affiliation(s)
- Zhen Bi
- Research Unit Environmental Simulation, Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Ingolstädter Landstr.1, 85764 Neuherberg, Germany
| | - Juliane Merl-Pham
- Research Unit Protein Science-Core Facility Proteomics, Helmholtz Zentrum München, Ingolstädter Landstr.1, 85764 Neuherberg, Germany
| | - Norbert Uehlein
- Institute of Applied Plant Science, University of Technology Darmstadt, Schnittspahndtr.10, 64287 Darmstadt, Germany
| | - Ina Zimmer
- Research Unit Environmental Simulation, Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Ingolstädter Landstr.1, 85764 Neuherberg, Germany
| | - Stefanie Mühlhans
- Research Unit Environmental Simulation, Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Ingolstädter Landstr.1, 85764 Neuherberg, Germany
| | - Michaela Aichler
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Ingolstädter Landstr.1, 85764 Neuherberg, Germany
| | - Axel Karl Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Ingolstädter Landstr.1, 85764 Neuherberg, Germany
| | - Ralf Kaldenhoff
- Institute of Applied Plant Science, University of Technology Darmstadt, Schnittspahndtr.10, 64287 Darmstadt, Germany
| | - Klaus Palme
- BIOSS Centre for Biological Signalling Studies, ZBSA Centre for Biosystems Studies, Faculty of Biology, Schänzlestr. 1, University of Freiburg, 79104 Freiburg, Germany
| | - Jörg-Peter Schnitzler
- Research Unit Environmental Simulation, Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Ingolstädter Landstr.1, 85764 Neuherberg, Germany
| | - Katja Block
- Research Unit Environmental Simulation, Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Ingolstädter Landstr.1, 85764 Neuherberg, Germany.
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28
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Song L, Zeng W, Wu A, Picard K, Lampugnani ER, Cheetamun R, Beahan C, Cassin A, Lonsdale A, Doblin MS, Bacic A. Asparagus Spears as a Model to Study Heteroxylan Biosynthesis during Secondary Wall Development. PLoS One 2015; 10:e0123878. [PMID: 25894575 PMCID: PMC4404143 DOI: 10.1371/journal.pone.0123878] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 02/23/2015] [Indexed: 11/18/2022] Open
Abstract
Garden asparagus (Asparagus officinalis L.) is a commercially important crop species utilized for its excellent source of vitamins, minerals and dietary fiber. However, after harvest the tissue hardens and its quality rapidly deteriorates because spear cell walls become rigidified due to lignification and substantial increases in heteroxylan content. This latter observation prompted us to investigate the in vitro xylan xylosyltransferase (XylT) activity in asparagus. The current model system for studying heteroxylan biosynthesis, Arabidopsis, whilst a powerful genetic system, displays relatively low xylan XylT activity in in vitro microsomal preparations compared with garden asparagus therefore hampering our ability to study the molecular mechanism(s) of heteroxylan assembly. Here, we analyzed physiological and biochemical changes of garden asparagus spears stored at 4 °C after harvest and detected a high level of xylan XylT activity that accounts for this increased heteroxylan. The xylan XylT catalytic activity is at least thirteen-fold higher than that reported for previously published species, including Arabidopsis and grasses. A biochemical assay was optimized and up to seven successive Xyl residues were incorporated to extend the xylotetraose (Xyl4) acceptor backbone. To further elucidate the xylan biosynthesis mechanism, we used RNA-seq to generate an Asparagus reference transcriptome and identified five putative xylan biosynthetic genes (AoIRX9, AoIRX9-L, AoIRX10, AoIRX14_A, AoIRX14_B) with AoIRX9 having an expression profile that is distinct from the other genes. We propose that Asparagus provides an ideal biochemical system to investigate the biochemical aspects of heteroxylan biosynthesis and also offers the additional benefit of being able to study the lignification process during plant stem maturation.
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Affiliation(s)
- Lili Song
- Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, Hangzhou, 311300, P. R. China
- ARC Centre of Excellence in Plant Cell Walls, School of Botany, the University of Melbourne, Parkville, VIC 3010, Australia
| | - Wei Zeng
- ARC Centre of Excellence in Plant Cell Walls, School of Botany, the University of Melbourne, Parkville, VIC 3010, Australia
| | - Aimin Wu
- College of Forestry, South China Agricultural University, Guangzhou, 510642, China
| | - Kelsey Picard
- ARC Centre of Excellence in Plant Cell Walls, School of Botany, the University of Melbourne, Parkville, VIC 3010, Australia
| | - Edwin R. Lampugnani
- ARC Centre of Excellence in Plant Cell Walls, School of Botany, the University of Melbourne, Parkville, VIC 3010, Australia
| | - Roshan Cheetamun
- ARC Centre of Excellence in Plant Cell Walls, School of Botany, the University of Melbourne, Parkville, VIC 3010, Australia
| | - Cherie Beahan
- ARC Centre of Excellence in Plant Cell Walls, School of Botany, the University of Melbourne, Parkville, VIC 3010, Australia
| | - Andrew Cassin
- ARC Centre of Excellence in Plant Cell Walls, School of Botany, the University of Melbourne, Parkville, VIC 3010, Australia
| | - Andrew Lonsdale
- ARC Centre of Excellence in Plant Cell Walls, School of Botany, the University of Melbourne, Parkville, VIC 3010, Australia
| | - Monika S. Doblin
- ARC Centre of Excellence in Plant Cell Walls, School of Botany, the University of Melbourne, Parkville, VIC 3010, Australia
| | - Antony Bacic
- ARC Centre of Excellence in Plant Cell Walls, School of Botany, the University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, the University of Melbourne, Parkville, VIC 3010, Australia
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Ebert B, Rautengarten C, Guo X, Xiong G, Stonebloom S, Smith-Moritz AM, Herter T, Chan LJG, Adams PD, Petzold CJ, Pauly M, Willats WGT, Heazlewood JL, Scheller HV. Identification and Characterization of a Golgi-Localized UDP-Xylose Transporter Family from Arabidopsis. THE PLANT CELL 2015; 27:1218-27. [PMID: 25804536 PMCID: PMC4558686 DOI: 10.1105/tpc.114.133827] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 03/05/2015] [Indexed: 05/02/2023]
Abstract
Most glycosylation reactions require activated glycosyl donors in the form of nucleotide sugars to drive processes such as posttranslational modifications and polysaccharide biosynthesis. Most plant cell wall polysaccharides are biosynthesized in the Golgi apparatus from cytosolic-derived nucleotide sugars, which are actively transferred into the Golgi lumen by nucleotide sugar transporters (NSTs). An exception is UDP-xylose, which is biosynthesized in both the cytosol and the Golgi lumen by a family of UDP-xylose synthases. The NST-based transport of UDP-xylose into the Golgi lumen would appear to be redundant. However, employing a recently developed approach, we identified three UDP-xylose transporters in the Arabidopsis thaliana NST family and designated them UDP-XYLOSE TRANSPORTER1 (UXT1) to UXT3. All three transporters localize to the Golgi apparatus, and UXT1 also localizes to the endoplasmic reticulum. Mutants in UXT1 exhibit ∼30% reduction in xylose in stem cell walls. These findings support the importance of the cytosolic UDP-xylose pool and UDP-xylose transporters in cell wall biosynthesis.
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Affiliation(s)
- Berit Ebert
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, C 1871 Copenhagen, Denmark ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Carsten Rautengarten
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Xiaoyuan Guo
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, C 1871 Copenhagen, Denmark
| | - Guangyan Xiong
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Solomon Stonebloom
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Andreia M Smith-Moritz
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Thomas Herter
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Leanne Jade G Chan
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Paul D Adams
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 Department of Bioengineering, University of California, Berkeley, California 94720
| | - Christopher J Petzold
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Markus Pauly
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - William G T Willats
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, C 1871 Copenhagen, Denmark
| | - Joshua L Heazlewood
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Henrik Vibe Scheller
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
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Mikkelsen MD, Harholt J, Ulvskov P, Johansen IE, Fangel JU, Doblin MS, Bacic A, Willats WGT. Evidence for land plant cell wall biosynthetic mechanisms in charophyte green algae. ANNALS OF BOTANY 2014; 114:1217-36. [PMID: 25204387 PMCID: PMC4195564 DOI: 10.1093/aob/mcu171] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 07/08/2014] [Indexed: 05/26/2023]
Abstract
BACKGROUND AND AIMS The charophyte green algae (CGA) are thought to be the closest living relatives to the land plants, and ancestral CGA were unique in giving rise to the land plant lineage. The cell wall has been suggested to be a defining structure that enabled the green algal ancestor to colonize land. These cell walls provide support and protection, are a source of signalling molecules, and provide developmental cues for cell differentiation and elongation. The cell wall of land plants is a highly complex fibre composite, characterized by cellulose cross-linked by non-cellulosic polysaccharides, such as xyloglucan, embedded in a matrix of pectic polysaccharides. How the land plant cell wall evolved is currently unknown: early-divergent chlorophyte and prasinophyte algae genomes contain a low number of glycosyl transferases (GTs), while land plants contain hundreds. The number of GTs in CGA is currently unknown, as no genomes are available, so this study sought to give insight into the evolution of the biosynthetic machinery of CGA through an analysis of available transcriptomes. METHODS Available CGA transcriptomes were mined for cell wall biosynthesis GTs and compared with GTs characterized in land plants. In addition, gene cloning was employed in two cases to answer important evolutionary questions. KEY RESULTS Genetic evidence was obtained indicating that many of the most important core cell wall polysaccharides have their evolutionary origins in the CGA, including cellulose, mannan, xyloglucan, xylan and pectin, as well as arabino-galactan protein. Moreover, two putative cellulose synthase-like D family genes (CSLDs) from the CGA species Coleochaete orbicularis and a fragment of a putative CSLA/K-like sequence from a CGA Spirogyra species were cloned, providing the first evidence that all the cellulose synthase/-like genes present in early-divergent land plants were already present in CGA. CONCLUSIONS The results provide new insights into the evolution of cell walls and support the notion that the CGA were pre-adapted to life on land by virtue of the their cell wall biosynthetic capacity. These findings are highly significant for understanding plant cell wall evolution as they imply that some features of land plant cell walls evolved prior to the transition to land, rather than having evolved as a result of selection pressures inherent in this transition.
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Affiliation(s)
- Maria D Mikkelsen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Jesper Harholt
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Peter Ulvskov
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Ida E Johansen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Jonatan U Fangel
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Monika S Doblin
- ARC Centre of Excellence in Plant Cell Walls, School of Botany, University of Melbourne, Victoria 3010, Australia
| | - Antony Bacic
- ARC Centre of Excellence in Plant Cell Walls, School of Botany, University of Melbourne, Victoria 3010, Australia
| | - William G T Willats
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
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Rennie EA, Ebert B, Miles GP, Cahoon RE, Christiansen KM, Stonebloom S, Khatab H, Twell D, Petzold CJ, Adams PD, Dupree P, Heazlewood JL, Cahoon EB, Scheller HV. Identification of a sphingolipid α-glucuronosyltransferase that is essential for pollen function in Arabidopsis. THE PLANT CELL 2014; 26:3314-25. [PMID: 25122154 PMCID: PMC4371831 DOI: 10.1105/tpc.114.129171] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 06/20/2014] [Accepted: 07/22/2014] [Indexed: 05/20/2023]
Abstract
Glycosyl inositol phosphorylceramide (GIPC) sphingolipids are a major class of lipids in fungi, protozoans, and plants. GIPCs are abundant in the plasma membrane in plants, comprising around a quarter of the total lipids in these membranes. Plant GIPCs contain unique glycan decorations that include a conserved glucuronic acid (GlcA) residue and various additional sugars; however, no proteins responsible for glycosylating GIPCs have been identified to date. Here, we show that the Arabidopsis thaliana protein INOSITOL PHOSPHORYLCERAMIDE GLUCURONOSYLTRANSFERASE1 (IPUT1) transfers GlcA from UDP-GlcA to GIPCs. To demonstrate IPUT1 activity, we introduced the IPUT1 gene together with genes for a UDP-glucose dehydrogenase from Arabidopsis and a human UDP-GlcA transporter into a yeast mutant deficient in the endogenous inositol phosphorylceramide (IPC) mannosyltransferase. In this engineered yeast strain, IPUT1 transferred GlcA to IPC. Overexpression or silencing of IPUT1 in Nicotiana benthamiana resulted in an increase or a decrease, respectively, in IPC glucuronosyltransferase activity in vitro. Plants in which IPUT1 was silenced accumulated IPC, the immediate precursor, as well as ceramides and glucosylceramides. Plants overexpressing IPUT1 showed an increased content of GIPCs. Mutations in IPUT1 are not transmitted through pollen, indicating that these sphingolipids are essential in plants.
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Affiliation(s)
- Emilie A Rennie
- Joint BioEnergy Institute, Emeryville, California 94608 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Berit Ebert
- Joint BioEnergy Institute, Emeryville, California 94608 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Godfrey P Miles
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Rebecca E Cahoon
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588
| | - Katy M Christiansen
- Joint BioEnergy Institute, Emeryville, California 94608 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Solomon Stonebloom
- Joint BioEnergy Institute, Emeryville, California 94608 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Hoda Khatab
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588
| | - David Twell
- Department of Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Christopher J Petzold
- Joint BioEnergy Institute, Emeryville, California 94608 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Paul D Adams
- Joint BioEnergy Institute, Emeryville, California 94608 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 Department of Bioengineering, University of California, Berkeley, California 94720
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Joshua L Heazlewood
- Joint BioEnergy Institute, Emeryville, California 94608 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Edgar B Cahoon
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588
| | - Henrik Vibe Scheller
- Joint BioEnergy Institute, Emeryville, California 94608 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
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Mewalal R, Mizrachi E, Mansfield SD, Myburg AA. Cell wall-related proteins of unknown function: missing links in plant cell wall development. PLANT & CELL PHYSIOLOGY 2014; 55:1031-43. [PMID: 24683037 DOI: 10.1093/pcp/pcu050] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Lignocellulosic biomass is an important feedstock for the pulp and paper industry as well as emerging biofuel and biomaterial industries. However, the recalcitrance of the secondary cell wall to chemical or enzymatic degradation remains a major hurdle for efficient extraction of economically important biopolymers such as cellulose. It has been estimated that approximately 10-15% of about 27,000 protein-coding genes in the Arabidopsis genome are dedicated to cell wall development; however, only about 130 Arabidopsis genes thus far have experimental evidence validating cell wall function. While many genes have been implicated through co-expression analysis with known genes, a large number are broadly classified as proteins of unknown function (PUFs). Recently the functionality of some of these unknown proteins in cell wall development has been revealed using reverse genetic approaches. Given the large number of cell wall-related PUFs, how do we approach and subsequently prioritize the investigation of such unknown genes that may be essential to or influence plant cell wall development and structure? Here, we address the aforementioned question in two parts; we first identify the different kinds of PUFs based on known and predicted features such as protein domains. Knowledge of inherent features of PUFs may allow for functional inference and a concomitant link to biological context. Secondly, we discuss omics-based technologies and approaches that are helping identify and prioritize cell wall-related PUFs by functional association. In this way, hypothesis-driven experiments can be designed for functional elucidation of many proteins that remain missing links in our understanding of plant cell wall biosynthesis.
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Affiliation(s)
- Ritesh Mewalal
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Eshchar Mizrachi
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Shawn D Mansfield
- Department of Wood Science, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Alexander A Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Hatfield, Pretoria, 0028, South Africa
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Grienenberger E, Douglas CJ. Arabidopsis VASCULAR-RELATED UNKNOWN PROTEIN1 regulates xylem development and growth by a conserved mechanism that modulates hormone signaling. PLANT PHYSIOLOGY 2014; 164:1991-2010. [PMID: 24567189 PMCID: PMC3982757 DOI: 10.1104/pp.114.236406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 02/22/2014] [Indexed: 05/17/2023]
Abstract
Despite a strict conservation of the vascular tissues in vascular plants (tracheophytes), our understanding of the genetic basis underlying the differentiation of secondary cell wall-containing cells in the xylem of tracheophytes is still far from complete. Using coexpression analysis and phylogenetic conservation across sequenced tracheophyte genomes, we identified a number of Arabidopsis (Arabidopsis thaliana) genes of unknown function whose expression is correlated with secondary cell wall deposition. Among these, the Arabidopsis VASCULAR-RELATED UNKNOWN PROTEIN1 (VUP1) gene encodes a predicted protein of 24 kD with no annotated functional domains but containing domains that are highly conserved in tracheophytes. Here, we show that the VUP1 expression pattern, determined by promoter-β-glucuronidase reporter gene expression, is associated with vascular tissues, while vup1 loss-of-function mutants exhibit collapsed morphology of xylem vessel cells. Constitutive overexpression of VUP1 caused dramatic and pleiotropic developmental defects, including severe dwarfism, dark green leaves, reduced apical dominance, and altered photomorphogenesis, resembling brassinosteroid-deficient mutants. Constitutive overexpression of VUP homologs from multiple tracheophyte species induced similar defects. Whole-genome transcriptome analysis revealed that overexpression of VUP1 represses the expression of many brassinosteroid- and auxin-responsive genes. Additionally, deletion constructs and site-directed mutagenesis were used to identify critical domains and amino acids required for VUP1 function. Altogether, our data suggest a conserved role for VUP1 in regulating secondary wall formation during vascular development by tissue- or cell-specific modulation of hormone signaling pathways.
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Zhang Q, Cheetamun R, Dhugga KS, Rafalski JA, Tingey SV, Shirley NJ, Taylor J, Hayes K, Beatty M, Bacic A, Burton RA, Fincher GB. Spatial gradients in cell wall composition and transcriptional profiles along elongating maize internodes. BMC PLANT BIOLOGY 2014; 14:27. [PMID: 24423166 PMCID: PMC3927872 DOI: 10.1186/1471-2229-14-27] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 12/27/2013] [Indexed: 05/11/2023]
Abstract
BACKGROUND The elongating maize internode represents a useful system for following development of cell walls in vegetative cells in the Poaceae family. Elongating internodes can be divided into four developmental zones, namely the basal intercalary meristem, above which are found the elongation, transition and maturation zones. Cells in the basal meristem and elongation zones contain mainly primary walls, while secondary cell wall deposition accelerates in the transition zone and predominates in the maturation zone. RESULTS The major wall components cellulose, lignin and glucuronoarabinoxylan (GAX) increased without any abrupt changes across the elongation, transition and maturation zones, although GAX appeared to increase more between the elongation and transition zones. Microarray analyses show that transcript abundance of key glycosyl transferase genes known to be involved in wall synthesis or re-modelling did not match the increases in cellulose, GAX and lignin. Rather, transcript levels of many of these genes were low in the meristematic and elongation zones, quickly increased to maximal levels in the transition zone and lower sections of the maturation zone, and generally decreased in the upper maturation zone sections. Genes with transcript profiles showing this pattern included secondary cell wall CesA genes, GT43 genes, some β-expansins, UDP-Xylose synthase and UDP-Glucose pyrophosphorylase, some xyloglucan endotransglycosylases/hydrolases, genes involved in monolignol biosynthesis, and NAM and MYB transcription factor genes. CONCLUSIONS The data indicated that the enzymic products of genes involved in cell wall synthesis and modification remain active right along the maturation zone of elongating maize internodes, despite the fact that corresponding transcript levels peak earlier, near or in the transition zone.
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Affiliation(s)
- Qisen Zhang
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, 5064 Adelaide, South Australia, Australia
| | - Roshan Cheetamun
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Botany, University of Melbourne, 3010 Parkville, Victoria, Australia
| | - Kanwarpal S Dhugga
- Genetic Discovery Group, Crop Genetics Research and Development, Pioneer Hi-Bred International Inc. 7300 NW 62nd Avenue, 50131-1004 Johnston, IA, USA
| | - J Antoni Rafalski
- Genetic Discovery Group, DuPont Crop Genetics Research, DuPont Experimental Station, Building E353, 198803 Wilmington, DE, USA
| | - Scott V Tingey
- Genetic Discovery Group, DuPont Crop Genetics Research, DuPont Experimental Station, Building E353, 198803 Wilmington, DE, USA
| | - Neil J Shirley
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, 5064 Adelaide, South Australia, Australia
| | - Jillian Taylor
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, 5064 Adelaide, South Australia, Australia
| | - Kevin Hayes
- Genetic Discovery Group, Crop Genetics Research and Development, Pioneer Hi-Bred International Inc. 7300 NW 62nd Avenue, 50131-1004 Johnston, IA, USA
| | - Mary Beatty
- Genetic Discovery Group, Crop Genetics Research and Development, Pioneer Hi-Bred International Inc. 7300 NW 62nd Avenue, 50131-1004 Johnston, IA, USA
| | - Antony Bacic
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Botany, University of Melbourne, 3010 Parkville, Victoria, Australia
| | - Rachel A Burton
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, 5064 Adelaide, South Australia, Australia
| | - Geoffrey B Fincher
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, 5064 Adelaide, South Australia, Australia
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Burton RA, Fincher GB. Evolution and development of cell walls in cereal grains. FRONTIERS IN PLANT SCIENCE 2014; 5:456. [PMID: 25309555 PMCID: PMC4161051 DOI: 10.3389/fpls.2014.00456] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 08/23/2014] [Indexed: 05/20/2023]
Abstract
The composition of cell walls in cereal grains and other grass species differs markedly from walls in seeds of other plants. In the maternal tissues that surround the embryo and endosperm of the grain, walls contain higher levels of cellulose and in many cases are heavily lignified. This may be contrasted with walls of the endosperm, where the amount of cellulose is relatively low, and the walls are generally not lignified. The low cellulose and lignin contents are possible because the walls of the endosperm perform no load-bearing function in the mature grain and indeed the low levels of these relatively intractable wall components are necessary because they allow rapid degradation of the walls following germination of the grain. The major non-cellulosic components of endosperm walls are usually heteroxylans and (1,3;1,4)-β-glucans, with lower levels of xyloglucans, glucomannans, and pectic polysaccharides. Pectic polysaccharides and xyloglucans are the major non-cellulosic wall constituents in most dicot species, in which (1,3;1,4)-β-glucans are usually absent and heteroxylans are found at relatively low levels. Thus, the "core" non-cellulosic wall polysaccharides in grain of the cereals and other grasses are the heteroxylans and, more specifically, arabinoxylans. The (1,3;1,4)-β-glucans appear in the endosperm of some grass species but are essentially absent from others; they may constitute from zero to more than 45% of the cell walls of the endosperm, depending on the species. It is clear that in some cases these (1,3;1,4)-β-glucans function as a major store of metabolizable glucose in the grain. Cereal grains and their constituent cell wall polysaccharides are centrally important as a source of dietary fiber in human societies and breeders have started to select for high levels of non-cellulosic wall polysaccharides in grain. To meet end-user requirements, it is important that we understand cell wall biology in the grain both during development and following germination.
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Affiliation(s)
| | - Geoffrey B. Fincher
- *Correspondence: Geoffrey B. Fincher, Australian Research Council Centre of Excellence in Plant Cell Walls – School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia e-mail:
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Plant Cell Wall Polysaccharides: Structure and Biosynthesis. POLYSACCHARIDES 2014. [DOI: 10.1007/978-3-319-03751-6_73-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Lee C, Teng Q, Zhong R, Yuan Y, Ye ZH. Functional roles of rice glycosyltransferase family GT43 in xylan biosynthesis. PLANT SIGNALING & BEHAVIOR 2014; 9:e27809. [PMID: 24525904 PMCID: PMC4091335 DOI: 10.4161/psb.27809] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Xylan is the major hemicellulose present in both primary and secondary cell walls of rice vegetative tissues. Since xylan is one of the factors contributing to biomass recalcitrance, understanding how xylan is synthesized in rice will potentially provide tools to modify grass biomass composition better suited for biofuel production. Studies of xylan biosynthesis in Arabidopsis have revealed that family GT43 glycosyltransferases, which form 2 functionally nonredundant groups, IRX9/IRX9 homolog and IRX14/IRX14 homolog, are required for xylan backbone elongation. The rice genome harbors 10 genes encoding family GT43 members and it is currently unknown whether they are all involved in xylan biosynthesis. In this report, we performed biochemical analysis of xylan xylosyltransferase activity in rice stem microsomes and investigated the roles of 4 representative rice GT43 members, OsGT43A (LOC_Os05 g03174), OsGT43E (LOC_Os05 g48600), OsGT43H (LOC_Os04 g01280), and OsGT43J (LOC_Os06 g47340), in xylan biosynthesis. OsGT43 proteins were shown to be localized in the Golgi, where xylan biosynthesis occurs. Complementation analysis by expression of OsGT43s in Arabidopsis irx9 and irx14 mutants demonstrated that OsGT43A and OsGT43E but not OsGT43H and OsGT43J were able to rescue the mutant phenotypes conferred by the irx9 mutation, including defective stem mechanical strength, vessel morphology, xylan content, GlcA side chains, xylan chain length, and xylosyltransferase activity. On the other hand, OsGT43J but not OsGT43A, OsGT43E, and OsGT43H restored the defective xylan phenotype in the irx14 mutant. These results indicate that the rice GT43 family evolved to retain the involvement of 2 functionally nonredundant groups, OsGT43A and OsGT43E (IRX9 homologs) vs. OsGT43J (an IRX14 homolog), in xylan backbone biosynthesis.
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Affiliation(s)
- Chanhui Lee
- Department of Plant Biology; University of Georgia; Athens, GA USA
- Department of Plant and Environmental New Resources; Kyung Hee University; Yongin, South Korea
| | - Quincy Teng
- Department of Pharmaceutical and Biomedical Sciences; University of Georgia; Athens, GA USA
| | - Ruiqin Zhong
- Department of Plant Biology; University of Georgia; Athens, GA USA
| | - Youxi Yuan
- Department of Plant Biology; University of Georgia; Athens, GA USA
| | - Zheng-Hua Ye
- Department of Plant Biology; University of Georgia; Athens, GA USA
- Correspondence to: Zheng-Hua Ye,
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Doblin MS, Johnson KL, Humphries J, Newbigin EJ, Bacic A. Are designer plant cell walls a realistic aspiration or will the plasticity of the plant's metabolism win out? Curr Opin Biotechnol 2013; 26:108-14. [PMID: 24679266 DOI: 10.1016/j.copbio.2013.11.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 10/15/2013] [Accepted: 11/28/2013] [Indexed: 01/28/2023]
Abstract
Plants have been redesigned by humans since the advent of modern agriculture some 10000 years ago, to provide ever increasing benefits to society. The phenomenal success of the green revolution in converting biomass from vegetative tissues into grain yield has sustained a growing population. At the dawn of the 21st century the need to further optimise plant biomass (largely plant walls) for a sustainable future is increasingly evident as our supply of fossil fuels is finite and the quality of our crop-based foods (functional foods; also determined by the composition of walls) are critical to maintaining a healthy lifestyle. Our capacity to engineer 'designer walls' suited to particular purposes is challenging plant breeders and biotechnologists in unprecedented ways. In this review we provide an overview of the critical steps in the assembly and remodelling of walls, the success (or otherwise) of such approaches and highlight another complex network, the cell surface, as a cell wall integrity (CWI) sensor that exerts control over wall composition and will need to be considered in any future modification of walls for agro-industrial purposes.
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Affiliation(s)
- Monika S Doblin
- The Australian Research Council Centre of Excellence in Plant Cell Walls, School of Botany, University of Melbourne, Parkville, Vic. 3010, Australia
| | - Kim L Johnson
- The Australian Research Council Centre of Excellence in Plant Cell Walls, School of Botany, University of Melbourne, Parkville, Vic. 3010, Australia
| | - John Humphries
- The Australian Research Council Centre of Excellence in Plant Cell Walls, School of Botany, University of Melbourne, Parkville, Vic. 3010, Australia
| | - Ed J Newbigin
- School of Botany, University of Melbourne, Parkville, Vic. 3010, Australia
| | - Antony Bacic
- The Australian Research Council Centre of Excellence in Plant Cell Walls, School of Botany, University of Melbourne, Parkville, Vic. 3010, Australia.
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Rennie EA, Scheller HV. Xylan biosynthesis. Curr Opin Biotechnol 2013; 26:100-7. [PMID: 24679265 DOI: 10.1016/j.copbio.2013.11.013] [Citation(s) in RCA: 171] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 09/05/2013] [Accepted: 11/28/2013] [Indexed: 12/24/2022]
Abstract
Plant cells are surrounded by a rigid wall made up of cellulose microfibrils, pectins, hemicelluloses, and lignin. This cell wall provides structure and protection for plant cells. In grasses and in dicot secondary cell walls, the major hemicellulose is a polymer of β-(1,4)-linked xylose units called xylan. Unlike cellulose--which is synthesized by large complexes at the plasma membrane--xylan is synthesized by enzymes in the Golgi apparatus. Xylan synthesis thus requires the coordinated action and regulation of these synthetic enzymes as well as others that synthesize and transport substrates into the Golgi. Recent research has identified several genes involved in xylan synthesis, some of which have already been used in engineering efforts to create plants that are better suited for biofuel production.
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Affiliation(s)
- Emilie A Rennie
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Henrik Vibe Scheller
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA.
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Ulvskov P, Paiva DS, Domozych D, Harholt J. Classification, naming and evolutionary history of glycosyltransferases from sequenced green and red algal genomes. PLoS One 2013; 8:e76511. [PMID: 24146880 PMCID: PMC3797821 DOI: 10.1371/journal.pone.0076511] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 08/28/2013] [Indexed: 02/06/2023] Open
Abstract
The Archaeplastida consists of three lineages, Rhodophyta, Virideplantae and Glaucophyta. The extracellular matrix of most members of the Rhodophyta and Viridiplantae consists of carbohydrate-based or a highly glycosylated protein-based cell wall while the Glaucophyte covering is poorly resolved. In order to elucidate possible evolutionary links between the three advanced lineages in Archaeplastida, a genomic analysis was initiated. Fully sequenced genomes from the Rhodophyta and Virideplantae and the well-defined CAZy database on glycosyltransferases were included in the analysis. The number of glycosyltransferases found in the Rhodophyta and Chlorophyta are generally much lower then in land plants (Embryophyta). Three specific features exhibited by land plants increase the number of glycosyltransferases in their genomes: (1) cell wall biosynthesis, the more complex land plant cell walls require a larger number of glycosyltransferases for biosynthesis, (2) a richer set of protein glycosylation, and (3) glycosylation of secondary metabolites, demonstrated by a large proportion of family GT1 being involved in secondary metabolite biosynthesis. In a comparative analysis of polysaccharide biosynthesis amongst the taxa of this study, clear distinctions or similarities were observed in (1) N-linked protein glycosylation, i.e., Chlorophyta has different mannosylation and glucosylation patterns, (2) GPI anchor biosynthesis, which is apparently missing in the Rhodophyta and truncated in the Chlorophyta, (3) cell wall biosynthesis, where the land plants have unique cell wall related polymers not found in green and red algae, and (4) O-linked glycosylation where comprehensive orthology was observed in glycosylation between the Chlorophyta and land plants but not between the target proteins.
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Affiliation(s)
- Peter Ulvskov
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Dionisio Soares Paiva
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - David Domozych
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York, United States of America
| | - Jesper Harholt
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
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Hirano K, Aya K, Morinaka Y, Nagamatsu S, Sato Y, Antonio BA, Namiki N, Nagamura Y, Matsuoka M. Survey of Genes Involved in Rice Secondary Cell Wall Formation Through a Co-Expression Network. ACTA ACUST UNITED AC 2013; 54:1803-21. [DOI: 10.1093/pcp/pct121] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Bromley JR, Busse-Wicher M, Tryfona T, Mortimer JC, Zhang Z, Brown DM, Dupree P. GUX1 and GUX2 glucuronyltransferases decorate distinct domains of glucuronoxylan with different substitution patterns. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 74:423-34. [PMID: 23373848 DOI: 10.1111/tpj.12135] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 01/22/2013] [Accepted: 01/27/2013] [Indexed: 05/17/2023]
Abstract
Xylan comprises up to one-third of plant cell walls, and it influences the properties and processing of biomass. Glucuronoxylan in Arabidopsis is characterized by a linear β-(1,4)-linked backbone of xylosyl residues substituted by glucuronic acid and 4-O-methylglucuronic acid (collectively termed [Me]GlcA). The role of these substitutions remains unclear. GUX1 (glucuronic acid substitution of xylan 1) and GUX2, recently identified as glucuronyltransferases, are both required for substitution of the xylan backbone with [Me]GlcA. Here, we demonstrate clear differences in the pattern of [Me]GlcA substitution generated by each of these glucuronyltransferases. GUX1 decorates xylan with a preference for addition of [Me]GlcA at evenly spaced xylosyl residues. Intervals of eight or 10 residues dominate, but larger intervals are observed. GUX2, in contrast, produces more tightly clustered decorations with most frequent spacing of five, six or seven xylosyl residues, with no preference for odd or even spacing. Moreover, each of these GUX transferases substitutes a distinct domain of secondary cell wall xylan, which we call the major and minor domains. These major and minor xylan domains were not separable from each other by size or charge, a finding that suggests that they are tightly associated. The presence of both differently [Me]GlcA decorated domains may produce a xylan molecule that is heterogeneous in its properties. We speculate that the major and minor domains of xylan may be specialised, such as for interaction with cellulose or lignin. These findings have substantial implications for our understanding of xylan synthesis and structure, and for models of the molecular architecture of the lignocellulosic matrix of plant cell walls.
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Affiliation(s)
- Jennifer R Bromley
- Department of Biochemistry, University Of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
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Chiniquy D, Varanasi P, Oh T, Harholt J, Katnelson J, Singh S, Auer M, Simmons B, Adams PD, Scheller HV, Ronald PC. Three Novel Rice Genes Closely Related to the Arabidopsis IRX9, IRX9L, and IRX14 Genes and Their Roles in Xylan Biosynthesis. FRONTIERS IN PLANT SCIENCE 2013; 4:83. [PMID: 23596448 PMCID: PMC3622038 DOI: 10.3389/fpls.2013.00083] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 03/21/2013] [Indexed: 05/02/2023]
Abstract
Xylan is the second most abundant polysaccharide on Earth, and represents a major component of both dicot wood and the cell walls of grasses. Much knowledge has been gained from studies of xylan biosynthesis in the model plant, Arabidopsis. In particular, the irregular xylem (irx) mutants, named for their collapsed xylem cells, have been essential in gaining a greater understanding of the genes involved in xylan biosynthesis. In contrast, xylan biosynthesis in grass cell walls is poorly understood. We identified three rice genes Os07g49370 (OsIRX9), Os01g48440 (OsIRX9L), and Os06g47340 (OsIRX14), from glycosyltransferase family 43 as putative orthologs to the putative β-1,4-xylan backbone elongating Arabidopsis IRX9, IRX9L, and IRX14 genes, respectively. We demonstrate that the over-expression of the closely related rice genes, in full or partly complement the two well-characterized Arabidopsis irregular xylem (irx) mutants: irx9 and irx14. Complementation was assessed by measuring dwarfed phenotypes, irregular xylem cells in stem cross sections, xylose content of stems, xylosyltransferase (XylT) activity of stems, and stem strength. The expression of OsIRX9 in the irx9 mutant resulted in XylT activity of stems that was over double that of wild type plants, and the stem strength of this line increased to 124% above that of wild type. Taken together, our results suggest that OsIRX9/OsIRX9L, and OsIRX14, have similar functions to the Arabidopsis IRX9 and IRX14 genes, respectively. Furthermore, our expression data indicate that OsIRX9 and OsIRX9L may function in building the xylan backbone in the secondary and primary cell walls, respectively. Our results provide insight into xylan biosynthesis in rice and how expression of a xylan synthesis gene may be modified to increase stem strength.
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Affiliation(s)
- Dawn Chiniquy
- Department of Plant Pathology, The Genome Center, University of CaliforniaDavis, CA, USA
- Joint BioEnergy InstituteEmeryville, CA, USA
| | - Patanjali Varanasi
- Joint BioEnergy InstituteEmeryville, CA, USA
- Sandia National LabsLivermore, CA, USA
- Physical Biosciences Division, Lawrence Berkeley National LaboratoryBerkeley, CA, USA
| | - Taeyun Oh
- Department of Plant Pathology, The Genome Center, University of CaliforniaDavis, CA, USA
| | - Jesper Harholt
- Section for Plant Glycobiology, Department of Plant and Environmental Sciences, VKR Research Centre Pro-Active Plants, University of CopenhagenFrederiksberg C, Denmark
| | | | - Seema Singh
- Joint BioEnergy InstituteEmeryville, CA, USA
- Sandia National LabsLivermore, CA, USA
- Physical Biosciences Division, Lawrence Berkeley National LaboratoryBerkeley, CA, USA
| | - Manfred Auer
- Joint BioEnergy InstituteEmeryville, CA, USA
- Life Sciences Division, Lawrence Berkeley National LaboratoryBerkeley, CA, USA
| | - Blake Simmons
- Joint BioEnergy InstituteEmeryville, CA, USA
- Sandia National LabsLivermore, CA, USA
- Physical Biosciences Division, Lawrence Berkeley National LaboratoryBerkeley, CA, USA
| | | | - Henrik V. Scheller
- Joint BioEnergy InstituteEmeryville, CA, USA
- Physical Biosciences Division, Lawrence Berkeley National LaboratoryBerkeley, CA, USA
- Department of Plant and Microbial Biology, University of CaliforniaBerkeley, CA, USA
| | - Pamela C. Ronald
- Department of Plant Pathology, The Genome Center, University of CaliforniaDavis, CA, USA
- Joint BioEnergy InstituteEmeryville, CA, USA
- Department of Plant Molecular Systems Biotechnology and Crop Biotech Institute, Kyung Hee UniversityYongin, Korea
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Xu P, Kong Y, Li X, Li L. Identification of molecular processes needed for vascular formation through transcriptome analysis of different vascular systems. BMC Genomics 2013; 14:217. [PMID: 23548001 PMCID: PMC3620544 DOI: 10.1186/1471-2164-14-217] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 03/22/2013] [Indexed: 11/24/2022] Open
Abstract
Background Vascular system formation has been studied through molecular and genetic approaches in Arabidopsis, a herbaceous dicot that is used as a model system. Different vascular systems have developed in other plants such as crops and trees. Uncovering shared mechanisms underlying vascular development by transcriptome analysis of different vascular systems may help to transfer knowledge acquired from Arabidopsis to other economically important species. Results Conserved vascular genes and biological processes fundamental to vascular development were explored across various plants. Through comparative transcriptome analysis, 226 genes from Arabidopsis, 217 genes from poplar and 281 genes from rice were identified as constituting 107 conserved vascular gene groups. These gene groups are expressed mainly in vascular tissues and form a complex coexpression network with multiple functional connections. To date, only half of the groups have been experimentally investigated. The conserved vascular gene groups were classified into 9 essential processes for vascular development. 18 groups (17%) lack of annotations were classified as having unknown functions. Conclusion The study provides a map of fundamental biological processes conserved across different vascular systems. It identifies gaps in the experimental investigation of pathways active in vascular formation, which if explored, could lead to a more complete understanding of vascular development.
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Affiliation(s)
- Peng Xu
- National Key Laboratory of Plant Molecular Genetics and Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai 200032, China
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Comparative genomics approaches to understanding and manipulating plant metabolism. Curr Opin Biotechnol 2013; 24:278-84. [DOI: 10.1016/j.copbio.2012.07.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 07/29/2012] [Accepted: 07/30/2012] [Indexed: 12/11/2022]
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Jensen JK, Johnson N, Wilkerson CG. Discovery of diversity in xylan biosynthetic genes by transcriptional profiling of a heteroxylan containing mucilaginous tissue. FRONTIERS IN PLANT SCIENCE 2013; 4:183. [PMID: 23761806 PMCID: PMC3675317 DOI: 10.3389/fpls.2013.00183] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 05/20/2013] [Indexed: 05/07/2023]
Abstract
The exact biochemical steps of xylan backbone synthesis remain elusive. In Arabidopsis, three non-redundant genes from two glycosyltransferase (GT) families, IRX9 and IRX14 from GT43 and IRX10 from GT47, are candidates for forming the xylan backbone. In other plants, evidence exists that different tissues express these three genes at widely different levels, which suggests that diversity in the makeup of the xylan synthase complex exists. Recently we have profiled the transcripts present in the developing mucilaginous tissue of psyllium (Plantago ovata Forsk). This tissue was found to have high expression levels of an IRX10 homolog, but very low levels of the two GT43 family members. This contrasts with recent wheat endosperm tissue profiling that found a relatively high abundance of the GT43 family members. We have performed an in-depth analysis of all GTs genes expressed in four developmental stages of the psyllium mucilagenous layer and in a single stage of the psyllium stem using RNA-Seq. This analysis revealed several IRX10 homologs, an expansion in GT61 (homologs of At3g18170/At3g18180), and several GTs from other GT families that are highly abundant and specifically expressed in the mucilaginous tissue. Our current hypothesis is that the four IRX10 genes present in the mucilagenous tissues have evolved to function without the GT43 genes. These four genes represent some of the most divergent IRX10 genes identified to date. Conversely, those present in the psyllium stem are very similar to those in other eudicots. This suggests these genes are under selective pressure, likely due to the synthesis of the various xylan structures present in mucilage that has a different biochemical role than that present in secondary walls. The numerous GT61 family members also show a wide sequence diversity and may be responsible for the larger number of side chain structures present in the psyllium mucilage.
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Affiliation(s)
- Jacob K. Jensen
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, USA
- DOE Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, USA
| | - Nathan Johnson
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, USA
- DOE Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, USA
| | - Curtis G. Wilkerson
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, USA
- DOE Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, USA
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast Lansing, MI, USA
- *Correspondence: Curtis G. Wilkerson, Department of Plant Biology, Michigan State University, 612 Wilson Rd., Room 122, East Lansing, MI 48824-1312 USA e-mail:
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Oikawa A, Lund CH, Sakuragi Y, Scheller HV. Golgi-localized enzyme complexes for plant cell wall biosynthesis. TRENDS IN PLANT SCIENCE 2013; 18:49-58. [PMID: 22925628 DOI: 10.1016/j.tplants.2012.07.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 07/13/2012] [Accepted: 07/18/2012] [Indexed: 05/18/2023]
Abstract
The plant cell wall mostly comprises complex glycans, which are synthesized by numerous enzymes located in the Golgi apparatus and plasma membrane. Protein-protein interactions have been shown to constitute an important organizing principle for glycan biosynthetic enzymes in mammals and yeast. Recent genetic and biochemical data also indicate that such interactions could be common in plant cell wall biosynthesis. In this review, we examine the new findings in protein-protein interactions among plant cell wall biosynthetic enzymes and discuss the possibilities for enzyme complexes in the Golgi apparatus. These new insights in the field may contribute to novel strategies for molecular engineering of the cell wall.
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Affiliation(s)
- Ai Oikawa
- Joint BioEnergy Institute, Feedstocks Division, Emeryville, CA 94608, USA
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Wang Y, Mortimer JC, Davis J, Dupree P, Keegstra K. Identification of an additional protein involved in mannan biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 73:105-17. [PMID: 22966747 PMCID: PMC3558879 DOI: 10.1111/tpj.12019] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 08/24/2012] [Accepted: 09/07/2012] [Indexed: 05/18/2023]
Abstract
Galactomannans comprise a β-1,4-mannan backbone substituted with α-1,6-galactosyl residues. Genes encoding the enzymes that are primarily responsible for backbone synthesis and side-chain addition of galactomannans were previously identified and characterized. To identify additional genes involved in galactomannan biosynthesis, we previously performed deep EST profiling of fenugreek (Trigonella foenum-graecum L.) seed endosperm, which accumulates large quantities of galactomannans as a reserve carbohydrate during seed development. One of the candidate genes encodes a protein that is likely to be a glycosyltransferase. Because this protein is involved in mannan biosynthesis, we named it 'mannan synthesis-related' (MSR). Here, we report the characterization of a fenugreek MSR gene (TfMSR) and its two Arabidopsis homologs, AtMSR1 and AtMSR2. TfMSR was highly and specifically expressed in the endosperm. TfMSR, AtMSR1 and AtMSR2 proteins were all determined to be localized to the Golgi by fluorescence confocal microscopy. The level of mannosyl residues in stem glucomannans decreased by approximately 40% for Arabidopsis msr1 single T-DNA insertion mutants and by more than 50% for msr1 msr2 double mutants, but remained unchanged for msr2 single mutants. In addition, in vitro mannan synthase activity from the stems of msr1 single and msr1 msr2 double mutants also decreased. Expression of AtMSR1 or AtMSR2 in the msr1 msr2 double mutant completely or partially restored mannosyl levels. From these results, we conclude that the MSR protein is important for mannan biosynthesis, and offer some ideas about its role.
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Affiliation(s)
- Yan Wang
- Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Energy Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, 48824, USA
| | | | - Jonathan Davis
- Department of Energy Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
| | - Paul Dupree
- Department of Biochemistry, University of CambridgeCambridge, CB2 1QW, UK
| | - Kenneth Keegstra
- Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Energy Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
- *For correspondence (e-mail )
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Voxeur A, André A, Breton C, Lerouge P. Identification of putative rhamnogalacturonan-II specific glycosyltransferases in Arabidopsis using a combination of bioinformatics approaches. PLoS One 2012; 7:e51129. [PMID: 23272088 PMCID: PMC3522684 DOI: 10.1371/journal.pone.0051129] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 10/31/2012] [Indexed: 01/24/2023] Open
Abstract
Rhamnogalacturonan-II (RG-II) is a complex plant cell wall polysaccharide that is composed of an α(1,4)-linked homogalacturonan backbone substituted with four side chains. It exists in the cell wall in the form of a dimer that is cross-linked by a borate di-ester. Despite its highly complex structure, RG-II is evolutionarily conserved in the plant kingdom suggesting that this polymer has fundamental functions in the primary wall organisation. In this study, we have set up a bioinformatics strategy aimed at identifying putative glycosyltransferases (GTs) involved in RG-II biosynthesis. This strategy is based on the selection of candidate genes encoding type II membrane proteins that are tightly coexpressed in both rice and Arabidopsis with previously characterised genes encoding enzymes involved in the synthesis of RG-II and exhibiting an up-regulation upon isoxaben treatment. This study results in the final selection of 26 putative Arabidopsis GTs, including 10 sequences already classified in the CAZy database. Among these CAZy sequences, the screening protocol allowed the selection of α-galacturonosyltransferases involved in the synthesis of α4-GalA oligogalacturonides present in both homogalacturonans and RG-II, and two sialyltransferase-like sequences previously proposed to be involved in the transfer of Kdo and/or Dha on the pectic backbone of RG-II. In addition, 16 non-CAZy GT sequences were retrieved in the present study. Four of them exhibited a GT-A fold. The remaining sequences harbored a GT-B like fold and a fucosyltransferase signature. Based on homologies with glycosyltransferases of known functions, putative roles in the RG-II biosynthesis are proposed for some GT candidates.
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Affiliation(s)
- Aline Voxeur
- Laboratoire Glyco-MEV, EA 4358, Institut de Recherche et d'Innovation Biotechnologique, University of Rouen, Mont-Saint-Aignan, France
| | - Aurélie André
- Laboratoire Glyco-MEV, EA 4358, Institut de Recherche et d'Innovation Biotechnologique, University of Rouen, Mont-Saint-Aignan, France
| | | | - Patrice Lerouge
- Laboratoire Glyco-MEV, EA 4358, Institut de Recherche et d'Innovation Biotechnologique, University of Rouen, Mont-Saint-Aignan, France
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