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Karnatam KS, Chhabra G, Saini DK, Singh R, Kaur G, Praba UP, Kumar P, Goyal S, Sharma P, Ranjan R, Sandhu SK, Kumar R, Vikal Y. Genome-Wide Meta-Analysis of QTLs Associated with Root Traits and Implications for Maize Breeding. Int J Mol Sci 2023; 24:ijms24076135. [PMID: 37047112 PMCID: PMC10093813 DOI: 10.3390/ijms24076135] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 04/14/2023] Open
Abstract
Root system architecture (RSA), also known as root morphology, is critical in plant acquisition of soil resources, plant growth, and yield formation. Many QTLs associated with RSA or root traits in maize have been identified using several bi-parental populations, particularly in response to various environmental factors. In the present study, a meta-analysis of QTLs associated with root traits was performed in maize using 917 QTLs retrieved from 43 mapping studies published from 1998 to 2020. A total of 631 QTLs were projected onto a consensus map involving 19,714 markers, which led to the prediction of 68 meta-QTLs (MQTLs). Among these 68 MQTLs, 36 MQTLs were validated with the marker-trait associations available from previous genome-wide association studies for root traits. The use of comparative genomics approaches revealed several gene models conserved among the maize, sorghum, and rice genomes. Among the conserved genomic regions, the ortho-MQTL analysis uncovered 20 maize MQTLs syntenic to 27 rice MQTLs for root traits. Functional analysis of some high-confidence MQTL regions revealed 442 gene models, which were then subjected to in silico expression analysis, yielding 235 gene models with significant expression in various tissues. Furthermore, 16 known genes viz., DXS2, PHT, RTP1, TUA4, YUC3, YUC6, RTCS1, NSA1, EIN2, NHX1, CPPS4, BIGE1, RCP1, SKUS13, YUC5, and AW330564 associated with various root traits were present within or near the MQTL regions. These results could aid in QTL cloning and pyramiding in developing new maize varieties with specific root architecture for proper plant growth and development under optimum and abiotic stress conditions.
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Affiliation(s)
- Krishna Sai Karnatam
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141001, India
| | - Gautam Chhabra
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141001, India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana 141001, India
| | - Rajveer Singh
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141001, India
| | - Gurwinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141001, India
| | - Umesh Preethi Praba
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141001, India
| | - Pankaj Kumar
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141001, India
| | - Simran Goyal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141001, India
| | - Priti Sharma
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141001, India
| | - Rumesh Ranjan
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana 141001, India
| | - Surinder K Sandhu
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana 141001, India
| | - Ramesh Kumar
- Indian Institute of Maize Research, Ludhiana 141001, India
| | - Yogesh Vikal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141001, India
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Nunes RDO, Domiciano Abrahão G, de Sousa Alves W, Aparecida de Oliveira J, César Sousa Nogueira F, Pasqualoto Canellas L, Lopes Olivares F, Benedeta Zingali R, Soares MR. Quantitative proteomic analysis reveals altered enzyme expression profile in Zea mays roots during the early stages of colonization by Herbaspirillum seropedicae. Proteomics 2021; 21:e2000129. [PMID: 33570822 DOI: 10.1002/pmic.202000129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 11/09/2022]
Abstract
The use of plant growth-promoting bacteria as agricultural inoculants of plants should be encouraged because of their prominent role in biological nitrogen fixation, the increase of nutrient uptake by roots, abiotic stress mitigation, and disease control. The complex mechanisms underlying the association between plant and beneficial bacteria have been increasingly studied, and proteomic tools can expand our perception regarding the fundamental molecular processes modulated by the interaction. In this study, we investigated the changes in protein expression in maize roots in response to treatment with the endophytic diazotrophic Herbaspirillum seropedicae and the activities of enzymes related to nitrogen metabolism. To identify maize proteins whose expression levels were altered in the presence of bacteria, a label-free quantitative proteomic approach was employed. Using this approach, we identified 123 differentially expressed proteins, of which 34 were upregulated enzymes, in maize roots cultivated with H. seropedicae. The maize root colonization of H. seropedicae modulated the differential expression of enzymes involved in the stress response, such as peroxidases, phenylalanine ammonia-lyase, and glutathione transferase. The differential protein profile obtained in the inoculated roots reflects the effect of colonization on plant growth and development compared with control plants.
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Affiliation(s)
- Rosane de Oliveira Nunes
- Departamento de Bioquímica/Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Giselli Domiciano Abrahão
- Departamento de Bioquímica/Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Wilber de Sousa Alves
- Departamento de Ensino Médio e Técnico, Centro Federal de Educação Tecnológica Celso Suckow da Fonseca, Rio de Janeiro, Brazil
| | - Jaqueline Aparecida de Oliveira
- Núcleo de Desenvolvimento de Insumos Biológicos para Agricultura, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Fábio César Sousa Nogueira
- Laboratório de Proteômica/LADETEC, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Unidade de Proteômica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luciano Pasqualoto Canellas
- Núcleo de Desenvolvimento de Insumos Biológicos para Agricultura, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Fábio Lopes Olivares
- Núcleo de Desenvolvimento de Insumos Biológicos para Agricultura, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Russolina Benedeta Zingali
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Márcia Regina Soares
- Departamento de Bioquímica/Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Sun X, Basnet RK, Yan Z, Bucher J, Cai C, Zhao J, Bonnema G. Genome-wide transcriptome analysis reveals molecular pathways involved in leafy head formation of Chinese cabbage ( Brassica rapa). HORTICULTURE RESEARCH 2019; 6:130. [PMID: 31814983 PMCID: PMC6885048 DOI: 10.1038/s41438-019-0212-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/21/2019] [Accepted: 10/19/2019] [Indexed: 05/10/2023]
Abstract
Chinese cabbage plants go through seedling and rosette stages before forming their leafy head. Chinese cabbage plants resemble pak-choi plants at their seedling stage, but in their rosette stage the leaves of Chinese cabbage differentiate, as they increase in size with shorter petioles. In order to understand the molecular pathways that play a role in leafy head formation, transcript abundance of young emerging leaves was profiled during development of two Chinese cabbage genotypes and a single pak-choi genotype. The two Chinese cabbages differed in many aspects, among others earliness, leaf size and shape, leaf numbers, and leafy head shape. Genome-wide transcriptome analysis clearly separated the seedling stages of all three genotypes together with the later stages from pak-choi, from the later developmental stages of both Chinese cabbages (rosette, folding, and heading). Weighted correlation network analysis and hierarchical clustering using Euclidean distances resulted in gene clusters with transcript abundance patterns distinguishing the two Chinese cabbages from pak-choi. Three clusters included genes with transcript abundance affected by both genotype and developmental stage, whereas two clusters showed only genotype effects. This included a genotype by developmental stage cluster highly enriched with the MapMan category photosynthesis, with high expression during rosette and folding in Chinese cabbages and low expression in the heading inner leaves that are not exposed to light. The other clusters contained many genes in the MapMan categories Cell, showing again differences between pak-choi and both Chinese cabbages. We discuss how this relates to the differences in leaf blade growth between Chinese cabbage and pak-choi, especially at the rosette stage. Overall, comparison of the transcriptome between leaves of two very different Chinese cabbages with pak-choi during plant development allowed the identification of specific gene categories associated with leafy head formation.
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Affiliation(s)
- XiaoXue Sun
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Department of Horticulture, Hebei Agricultural University, Baoding, 071001 China
- Plant Breeding, Wageningen University and Research, Wageningen, 6708PB The Netherlands
| | - Ram Kumar Basnet
- Quantitative genetics department, Rijk Zwaan Breeding B.V., Eerste Kruisweg 9, Fijnaart, 4793 RS The Netherlands
| | - Zhichun Yan
- Plant Breeding, Wageningen University and Research, Wageningen, 6708PB The Netherlands
| | - Johan Bucher
- Plant Breeding, Wageningen University and Research, Wageningen, 6708PB The Netherlands
| | - Chengcheng Cai
- Plant Breeding, Wageningen University and Research, Wageningen, 6708PB The Netherlands
| | - Jianjun Zhao
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Department of Horticulture, Hebei Agricultural University, Baoding, 071001 China
| | - Guusje Bonnema
- Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Department of Horticulture, Hebei Agricultural University, Baoding, 071001 China
- Plant Breeding, Wageningen University and Research, Wageningen, 6708PB The Netherlands
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Sheoran IS, Koonjul P, Attieh J, Saini HS. Water-stress-induced inhibition of α-tubulin gene expression during growth, and its implications for reproductive success in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 80:291-299. [PMID: 24814750 DOI: 10.1016/j.plaphy.2014.04.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 04/13/2014] [Indexed: 06/03/2023]
Abstract
A drought-suppressed cDNA (RiP-3), encoding a putative α-tubulin protein was isolated from rice panicle at pollen-mother-cell meiosis stage. Analysis of its deduced amino acid sequence showed all the typical structural motifs for plant α-tubulins. The expression of α-tubulin transcripts was observed in all the reproductive organs of rice panicle, and in 5- or 15-day old seedlings, but not in mature leaves. Expression levels were positively correlated with the regions and periods of high growth, and the transcript level declined in parallel with drought-induced reduction in growth rates in all tissues examined. Immunoblot analysis of proteins separated by SDS-PAGE with anti-α-tubulin monoclonal antibody showed that the level of protein paralleled the changes in the transcript abundance in these organs. In situ immunolocalization of the α-tubulin protein in sections of the basal part of 5-day old seedlings showed that the highest levels of the protein were associated with the fastest growing leaf whorls, and the protein level declined upon a brief episode of water stress. Given the known critical role of tubulin in cell division and elongation, the results indicate that the expression of α-tubulin gene may be part of the events that suppress panicle elongation during water deficit, which is in turn a suspected cause of male reproductive failure and yield reduction in rice.
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Affiliation(s)
- Inder S Sheoran
- Institut de recherche en biologie végétale, Université de Montréal, Montreal, QC H1X 2B2, Canada.
| | - Priyum Koonjul
- Institut de recherche en biologie végétale, Université de Montréal, Montreal, QC H1X 2B2, Canada.
| | - Jihad Attieh
- Institut de recherche en biologie végétale, Université de Montréal, Montreal, QC H1X 2B2, Canada.
| | - Hargurdeep S Saini
- Institut de recherche en biologie végétale, Université de Montréal, Montreal, QC H1X 2B2, Canada.
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Breviario D, Gianì S, Morello L. Multiple tubulins: evolutionary aspects and biological implications. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:202-18. [PMID: 23662651 DOI: 10.1111/tpj.12243] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 05/03/2013] [Accepted: 05/09/2013] [Indexed: 05/05/2023]
Abstract
Plant tubulin is a dimeric protein that contributes to formation of microtubules, major intracellular structures that are involved in the control of fundamental processes such as cell division, polarity of growth, cell-wall deposition, intracellular trafficking and communications. Because it is a structural protein whose function is confined to the role of microtubule formation, tubulin may be perceived as an uninteresting gene product, but such a perception is incorrect. In fact, tubulin represents a key molecule for studying fundamental biological issues such as (i) microtubule evolution (also with reference to prokaryotic precursors and the formation of cytomotive filaments), (ii) protein structure with reference to the various biochemical features of members of the FstZ/tubulin superfamily, (iii) isoform variations contributed by the existence of multi-gene families and various kinds of post-translational modifications, (iv) anti-mitotic drug interactions and mode of action, (v) plant and cell symmetry, as determined using a series of tubulin mutants, (vi) multiple and sophisticated mechanisms of gene regulation, and (vii) intron molecular evolution. In this review, we present and discuss many of these issues, and offer an updated interpretation of the multi-tubulin hypothesis.
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Affiliation(s)
- Diego Breviario
- Istituto Biologia e Biotecnologia Agraria, Via Bassini 15, 20133 Milano, Italy.
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Zhang J, Zhang C, Cheng Y, Qi L, Wang S, Hou X. Microtubule and male sterility in a gene-cytoplasmic male sterile line of non-heading Chinese cabbage. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2012; 92:3046-3054. [PMID: 22581783 DOI: 10.1002/jsfa.5722] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 12/17/2011] [Accepted: 04/04/2012] [Indexed: 05/31/2023]
Abstract
BACKGROUND Microtubules are the basic components of the cytoskeleton in eukaryotic cells and are made up of 13 parallel protofilaments, each composed of α- and β-tubulin unit molecules aligned along the longitudinal axis of the microtubule. RESULTS α-Tubulin gene TUBA2 from non-heading Chinese cabbage (Brassica campestris ssp. chinensis Makino) was expressed at the highest level in stamens and at lower levels in other organs. In addition, it was expressed at a much lower level in the cytoplasmic male sterile (CMS) line than in the maintainer line. Furthermore, at the microsporocyte stage of development in the CMS line the microtubule bundles were knitted together in random organisation, which differed significantly from the radiate microtubule bundles running circumferentially around the nucleus in the maintainer line. Also, large vacuoles appeared within the cytoplasm in the CMS line with no dyed microtubules. CONCLUSION TUBA2 was very important to pollen development, which might be closely related to male sterility. Large vacuoles might replace the nuclei close to the cell walls and lead to a lack of microtubules when the cells abort. Abnormalities and defects in the organisation and composition of microtubules in the male sterile line highlighted the complex interaction between microtubules and cytoplasmic male sterility.
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Affiliation(s)
- Jingyi Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
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Fang WP, Jiang CJ, Yu M, Ye AH, Wan ZX. Differentially expression of Tua1, a tubulin-encoding gene, during flowering of tea plant Camellia sinensis (L.) O. Kuntze using cDNA amplified fragment length polymorphism technique. Acta Biochim Biophys Sin (Shanghai) 2006; 38:653-62. [PMID: 16953305 DOI: 10.1111/j.1745-7270.2006.00202.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The complementary DNA (cDNA) amplified fragment length polymorphism technique was used to isolate transcript-derived fragments corresponding to genes involved in the flowering of tea plant. Comparative sequence analysis of an approximately 300 bp differential fragment amplified by primer combination E11M11 revealed 80%-84% similarity to the corresponding part of an a-tubulin gene of other species. The complete cDNA sequence of this a-tubulin was cloned by the rapid amplification of cDNA ends technique; its full length is 1537 bp and contains an open reading frame of 450 amino acid residues with two N-glycosylation sites and four protein kinase C phosphorylation sites. The deduced amino acid sequences did show significant homology to the a-tubulin from other plants that has been reported to be a pollen-specific protein and could be correlated with plant cytoplasm-nucleus-interacted male sterility. We named this complete cDNA Tua1. The nucleotide and amino acid sequence data of Tua1 have been recorded in the GenBank sequence database. This Tua1 gene was cloned into the pET-32a expression system and expressed in Escherichia coli BL21trxB(DE3). The molecular weight of expressed protein was deduced to be approximately 49 kDa. Western blot analysis was used to identify the temporal expression of Tua1 in tea plant. Further studies of the effect of Tua1 protein on pollen tube growth indicated the Tua1 solution obviously promoted the growth of tea pollen tube.
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Affiliation(s)
- Wan-Ping Fang
- Key Laboratory of Tea Biochemistry and Biotechnology, Ministry of Agriculture, Anhui Agricultural University, Hefei 230036, China
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Warren JM, Covert SF. Differential expression of pine and Cronartium quercuum f. sp. fusiforme genes in fusiform rust galls. Appl Environ Microbiol 2004; 70:441-51. [PMID: 14711673 PMCID: PMC321230 DOI: 10.1128/aem.70.1.441-451.2004] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2003] [Accepted: 10/07/2003] [Indexed: 11/20/2022] Open
Abstract
Cronartium quercuum f. sp. fusiforme is the causative agent of fusiform rust disease of southern pines in the United States. This disease is characterized by the formation of woody branch and stem galls. Differential display was used to identify pine genes whose expression is altered by C. quercuum f. sp. fusiforme infection and to identify C. quercuum f. sp. fusiforme genes that are expressed in fusiform rust galls. Six pine cDNAs that appeared to be differentially expressed in galled and healthy stems and 13 C. quercuum f. sp. fusiforme cDNAs expressed in galled tissues were identified. A probe that hybridizes specifically to C. quercuum f. sp. fusiforme 18S rRNA was used to estimate that 14% of the total RNA in fusiform rust galls was from C. quercuum f. sp. fusiforme. This finding was used to calibrate gene expression levels in galls when comparing them to expression levels in uninfected pines or in isolated C. quercuum f. sp. fusiforme cultures. According to Northern analysis and reverse transcriptase PCR analysis, all six of the pine clones were expressed at lower levels in galls than in healthy tissues. Seven of the nine C. quercuum f. sp. fusiforme clones that were assayed were expressed at higher levels in galls than in axenic culture. A number of the cDNAs encode proteins that are similar to those that play roles in plant development, plant defense, or fungal stress responses.
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Affiliation(s)
- Jaimie M Warren
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
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Wasteneys GO, Galway ME. Remodeling the cytoskeleton for growth and form: an overview with some new views. ANNUAL REVIEW OF PLANT BIOLOGY 2003; 54:691-722. [PMID: 14503008 DOI: 10.1146/annurev.arplant.54.031902.134818] [Citation(s) in RCA: 184] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The cytoskeleton coordinates all aspects of growth in plant cells, including exocytosis of membrane and wall components during cell expansion. This review seeks to integrate current information about cytoskeletal components in plants and the role they play in generating cell form. Advances in genome analysis have fundamentally changed the nature of research strategies and generated an explosion of new information on the cytoskeleton-associated proteins, their regulation, and their role in signaling to the cytoskeleton. Some of these proteins appear novel to plants, but many have close homologues in other eukaryotic systems. It is becoming clear that the mechanisms behind cell growth are essentially similar across the growth continuum, which ranges from tip growth to diffuse expansion. Remodeling of the actin cytoskeleton at sites of exocytosis is an especially critical feature of polarized and may also contribute to axial growth. We evaluate the most recent work on the signaling mechanisms that continually remodel the actin cytoskeleton via the activation of actin-binding proteins (ABPs) and consider the role the microtubule cytoskeleton plays in this process.
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Affiliation(s)
- Geoffrey O Wasteneys
- Plant Cell Biology Group, Research School of Biological Sciences, Australian National University, Canberra ACT 2601, Australia.
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Li XB, Cai L, Cheng NH, Liu JW. Molecular characterization of the cotton GhTUB1 gene that is preferentially expressed in fiber. PLANT PHYSIOLOGY 2002; 130:666-74. [PMID: 12376634 PMCID: PMC166596 DOI: 10.1104/pp.005538] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2002] [Revised: 04/25/2002] [Accepted: 06/11/2002] [Indexed: 05/17/2023]
Abstract
Each fiber of cotton (Gossypium hirsutum) is a single epidermal cell that rapidly elongates to 2.5 to 3.0 cm from the ovule surface within about 16 d after anthesis. A large number of genes are required for fiber differentiation and development, but so far, little is known about how these genes control and regulate the process of fiber development. To investigate gene expression patterns in fiber, a cDNA, GhTUB1, encoding beta-tubulin was isolated from a cotton fiber cDNA library. The analyses of RNA northern-blot hybridization and reverse transcriptase-polymerase chain reaction demonstrated that GhTUB1 transcripts preferentially accumulated at high levels in fiber, at low levels in ovules at the early stage of cotton boll development, and at very low levels in other tissues of cotton. The corresponding GhTUB1 gene including the promoter region was isolated by screening a cotton genomic DNA library. To demonstrate the specificity of the GhTUB1 promoter, the 5'-flanking region including the promoter and 5'-untranslated region was fused with the beta-glucuronidase reporter gene. The expression of the reporter chimera was examined in a large number of transgenic cotton plants. Histochemical assays demonstrated that GhTUB1::beta-glucuronidase fusion genes were expressed preferentially at high levels in fiber and primary root tip of 1- to 3-d-old seedlings and at low levels in other tissues such as ovule, pollen, seedling cotyledon, and root basal portion. The results suggested that the GhTUB1 gene may play a distinct and required role in fiber development. In addition, the GhTUB1 promoter may have great potential for cotton improvement by genetic engineering.
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Affiliation(s)
- Xue-Bao Li
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604.
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11
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Cho Y, Fernandes J, Kim SH, Walbot V. Gene-expression profile comparisons distinguish seven organs of maize. Genome Biol 2002; 3:research0045. [PMID: 12225584 PMCID: PMC126870 DOI: 10.1186/gb-2002-3-9-research0045] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2002] [Revised: 07/03/2002] [Accepted: 07/05/2002] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND A maize array was fabricated with 5,376 unique expressed sequence tag (EST) clones sequenced from 4-day-old roots, immature ears and adult organ cDNA libraries. To elucidate organ relationships, relative mRNA levels were quantified by hybridization with embryos, three maize vegetative organs (leaf blades, leaf sheaths and roots) from multiple developmental stages, husk leaves and two types of floral organs (immature ears and silks). RESULTS Clustering analyses of the hybridization data suggest that maize utilizes both the PEPCK and NADP-ME C(4) photosynthetic routes as genes in these pathways are co-regulated. Husk RNA has a gene-expression profile more similar to floral organs than to vegetative leaves. Only 7% of the genes were highly organ specific, showing over a fourfold difference in at least one of 12 comparisons and 37% showed a two- to fourfold difference. The majority of genes were expressed in diverse organs with little difference in transcript levels. Cross-hybridization among closely related genes within multigene families could obscure tissue specificity. As a first step in elucidating individual gene-expression patterns, we show that 45-nucleotide oligo probes produce signal intensities and signal ratios comparable to PCR probes on the same matrix. CONCLUSIONS Gene-expression profile studies with cDNA microarrays provide a new molecular tool for defining plant organs and their relationships and for discovering new biological processes in silico. cDNA microarrays are insufficient for differentiating recently duplicated genes. Gene-specific oligo probes printed along with cDNA probes can query individual gene-expression profiles and gene families simultaneously.
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Affiliation(s)
- Yangrae Cho
- Department of Biological Sciences, Stanford University, Stanford, CA 94305-5020, USA.
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Morello L, Bardini M, Sala F, Breviario D. A long leader intron of the Ostub16 rice beta-tubulin gene is required for high-level gene expression and can autonomously promote transcription both in vivo and in vitro. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2002; 29:33-44. [PMID: 12060225 DOI: 10.1046/j.0960-7412.2001.01192.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A 2 kb DNA fragment, upstream of the rice beta-tubulin isotype 16 (Ostub16) coding sequence, was isolated using inverse PCR and screening of a tubulin-enriched lambda library. An intron (863 bp) present in the 5' untranslated region (5' UTR) is spliced out to produce the most abundant mRNA species which corresponds to the previously cloned Ostub16 cDNA. Transient expression assays performed on rice embryogenic calluses with chimeric Ostub16::GUS constructs demonstrated that the entire 2 kb upstream sequence has a strong promoter activity, and that the 863 bp intron is required for high-level GUS expression. In addition, the intron sequence is capable per se of sustaining a weak but consistent GUS expression. Two rare Ostub16 transcripts, with a start site mapping within this intron sequence, were detected in rice coleoptile cells. The transcription start site mapped at position -290 with respect to the ATG codon, and the shorter molecule originated from splicing of the same precursor mRNA. Therefore transcriptional expression of rice beta-tubulin isotype 16 results in the synthesis of two premRNA molecules (I and II) encoding for three different mRNA species. We discuss these findings in terms of function and molecular evolution of the mechanisms that control plant beta-tubulin gene expression.
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Affiliation(s)
- Laura Morello
- Istituto Biosintesi Vegetali, CNR, Via Bassini 15, 20133 Milano, Italy
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Abstract
Molecular motors that hydrolyze ATP and use the derived energy to generate force are involved in a variety of diverse cellular functions. Genetic, biochemical, and cellular localization data have implicated motors in a variety of functions such as vesicle and organelle transport, cytoskeleton dynamics, morphogenesis, polarized growth, cell movements, spindle formation, chromosome movement, nuclear fusion, and signal transduction. In non-plant systems three families of molecular motors (kinesins, dyneins, and myosins) have been well characterized. These motors use microtubules (in the case of kinesines and dyneins) or actin filaments (in the case of myosins) as tracks to transport cargo materials intracellularly. During the last decade tremendous progress has been made in understanding the structure and function of various motors in animals. These studies are yielding interesting insights into the functions of molecular motors and the origin of different families of motors. Furthermore, the paradigm that motors bind cargo and move along cytoskeletal tracks does not explain the functions of some of the motors. Relatively little is known about the molecular motors and their roles in plants. In recent years, by using biochemical, cell biological, molecular, and genetic approaches a few molecular motors have been isolated and characterized from plants. These studies indicate that some of the motors in plants have novel features and regulatory mechanisms. The role of molecular motors in plant cell division, cell expansion, cytoplasmic streaming, cell-to-cell communication, membrane trafficking, and morphogenesis is beginning to be understood. Analyses of the Arabidopsis genome sequence database (51% of genome) with conserved motor domains of kinesin and myosin families indicates the presence of a large number (about 40) of molecular motors and the functions of many of these motors remain to be discovered. It is likely that many more motors with novel regulatory mechanisms that perform plant-specific functions are yet to be discovered. Although the identification of motors in plants, especially in Arabidopsis, is progressing at a rapid pace because of the ongoing plant genome sequencing projects, only a few plant motors have been characterized in any detail. Elucidation of function and regulation of this multitude of motors in a given species is going to be a challenging and exciting area of research in plant cell biology. Structural features of some plant motors suggest calcium, through calmodulin, is likely to play a key role in regulating the function of both microtubule- and actin-based motors in plants.
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Affiliation(s)
- A S Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins 80523, USA
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Breviario D, Nick P. Plant tubulins: a melting pot for basic questions and promising applications. Transgenic Res 2000; 9:383-93. [PMID: 11206967 DOI: 10.1023/a:1026598710430] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- D Breviario
- Istituto Biosintesi Vegetali CNR, Milano, Italy.
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Jeon JS, Lee S, Jung KH, Jun SH, Kim C, An G. Tissue-preferential expression of a rice alpha-tubulin gene, OsTubA1, mediated by the first intron. PLANT PHYSIOLOGY 2000; 123:1005-14. [PMID: 10889249 PMCID: PMC59063 DOI: 10.1104/pp.123.3.1005] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/1999] [Accepted: 03/13/2000] [Indexed: 05/18/2023]
Abstract
The genomic clone encoding an alpha-tubulin, OsTubA1, has been isolated from rice (Oryza sativa L.). The gene consists of four exons and three introns. RNA-blot analysis showed that the gene is strongly expressed in actively dividing tissues, including root tips, young leaves, and young flowers. Analysis of chimeric fusions between OsTubA1 and beta-glucuronidase (GUS) revealed that the intron 1 was required for high-level GUS expression in actively dividing tissues, corresponding with normal expression pattern of OsTubA1. Fusion constructs lacking the intron 1 showed more GUS staining in mature tissues rather than young tissues. When the intron 1 was placed at the distal region from 5'-upstream region or at the 3'-untranslated region, no enhancement of GUS expression was observed. Sequential deletions of the OsTubA1 intron 1 brought about a gradual reduction of GUS activity in calli. These results suggest that tissue-preferential expression of the OsTubA1 gene is mediated by the intron 1 and that it may be involved in a mechanism for an efficient RNA splicing that is position dependent.
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Affiliation(s)
- J S Jeon
- Department of Life Science and National Research Laboratory of Plant Functional Genomics, Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
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Abstract
Growth and development of all plant cells and organs relies on a fully functional cytoskeleton comprised principally of microtubules and microfilaments. These two polymeric macromolecules, because of their location within the cell, confer structure upon, and convey information to, the peripheral regions of the cytoplasm where much of cellular growth is controlled and the formation of cellular identity takes place. Other ancillary molecules, such as motor proteins, are also important in assisting the cytoskeleton to participate in this front-line work of cellular development. Roots provide not only a ready source of cells for fundamental analyses of the cytoskeleton, but the formative zone at their apices also provides a locale whereby experimental studies can be made of how the cytoskeleton permits cells to communicate between themselves and to cooperate with growth-regulating information supplied from the apoplasm.
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Affiliation(s)
- Peter W. Barlow
- IACR-Long Ashton Research Station, Department of Agricultural Sciences, University of Bristol, Long Ashton, Bristol BS41 9AF, United Kingdom; e-mail: , Botanisches Institut, Rheinische Friedrich-Wilhelms-Universitat Bonn, Kirschallee 1, D-53115 Bonn, Germany; e-mail:
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Whittaker DJ, Triplett BA. Gene-specific changes in alpha-tubulin transcript accumulation in developing cotton fibers. PLANT PHYSIOLOGY 1999; 121:181-8. [PMID: 10482673 PMCID: PMC59366 DOI: 10.1104/pp.121.1.181] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The fibers of cotton (Gossypium hirsutum) are single-cell trichomes that undergo rapid and synchronous elongation. Cortical microtubules provide spatial information necessary for the alignment of cellulose microfibrils that confine and regulate cell elongation. We used gene-specific probes to investigate alpha-tubulin transcript levels in elongating cotton fibers. Two discrete patterns of transcript accumulation were observed. Whereas transcripts of alpha-tubulin genes GhTua2/3 and GhTua4 increased in abundance from 10 to 20 d post anthesis (DPA), GhTua1 and GhTua5 transcripts were abundant only through to 14 DPA, and dropped significantly at 16 DPA with the onset of secondary wall synthesis. This is the first report, to our knowledge, of gene-specific changes in tubulin transcript levels during the development of a terminally differentiated plant cell. The decrease in abundance of GhTua1 and GhTua5 transcripts was correlated with pronounced changes in cell wall structure, suggesting that alpha-tubulin isoforms may be functionally distinct in elongating fiber cells. Although total alpha-tubulin transcript levels were much higher in fiber than several other tissues, including the hypocotyl and pollen, none of the alpha-tubulins was specific to fiber cells.
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Affiliation(s)
- D J Whittaker
- Cotton Fiber Bioscience, United States Department of Agriculture-Agricultural Research Service, Southern Regional Research Center, 1100 Robert E. Lee Boulevard, New Orleans, Louisiana 70124, USA
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Okamura S, Okahara K, Iida T, Ozaki M, Asano S, Morita M, Imanaka T. Isotype-specific changes in the amount of beta-tubulin RNA in synchronized tobacco BY2 cells. Cell Struct Funct 1999; 24:117-22. [PMID: 10462173 DOI: 10.1247/csf.24.117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The 3'-ends of the beta-tubulin cDNA were amplified from tobacco BY2 polyA+ RNA. According to the differences in the predicted amino acid sequence at the extreme C-terminal, they were grouped into three different isotypes, NTB1 in which "EEGDYYEEDEEDLNEA", NTB2 in which "EEEYYEDEEEA QED" and NTB3 in which "DECEYEEEEEYDHEGN" follows the conservative "YQQYQDATAD" sequence. Using unique 3'-untranslated regions as probes, changes in the RNA levels of each beta-tubulin isotype were determined by dot-blot hybridization. The levels exhibited characteristic rhythms in the cell cycle. NTB1 RNA was highest in S phase in comparison to NTB2 RNA level which was highest in late G2. On the other hand, NTB3 RNA level was highest in early G2.
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Affiliation(s)
- S Okamura
- Faculty of Pharmaceutical Sciences, Toyama Medical and Pharmaceutical University, Japan.
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Lu Q, Moore GD, Walss C, Ludueña RF. Structural and functional properties of tubulin isotypes. ADVANCES IN STRUCTURAL BIOLOGY 1999. [DOI: 10.1016/s1064-6000(98)80012-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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