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Blume RY, Rabokon AM, Pydiura M, Yemets AI, Pirko YV, Blume YB. Genome-wide identification and evolution of the tubulin gene family in Camelina sativa. BMC Genomics 2024; 25:599. [PMID: 38877397 PMCID: PMC11177405 DOI: 10.1186/s12864-024-10503-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 06/06/2024] [Indexed: 06/16/2024] Open
Abstract
BACKGROUND Tubulins play crucial roles in numerous fundamental processes of plant development. In flowering plants, tubulins are grouped into α-, β- and γ-subfamilies, while α- and β-tubulins possess a large isotype diversity and gene number variations among different species. This circumstance leads to insufficient recognition of orthologous isotypes and significantly complicates extrapolation of obtained experimental results, and brings difficulties for the identification of particular tubulin isotype function. The aim of this research is to identify and characterize tubulins of an emerging biofuel crop Camelina sativa. RESULTS We report comprehensive identification and characterization of tubulin gene family in C. sativa, including analyses of exon-intron organization, duplicated genes comparison, proper isotype designation, phylogenetic analysis, and expression patterns in different tissues. 17 α-, 34 β- and 6 γ-tubulin genes were identified and assigned to a particular isotype. Recognition of orthologous tubulin isotypes was cross-referred, involving data of phylogeny, synteny analyses and genes allocation on reconstructed genomic blocks of Ancestral Crucifer Karyotype. An investigation of expression patterns of tubulin homeologs revealed the predominant role of N6 (A) and N7 (B) subgenomes in tubulin expression at various developmental stages, contrarily to general the dominance of transcripts of H7 (C) subgenome. CONCLUSIONS For the first time a complete set of tubulin gene family members was identified and characterized for allohexaploid C. sativa species. The study demonstrates the comprehensive approach of precise inferring gene orthology. The applied technique allowed not only identifying C. sativa tubulin orthologs in model Arabidopsis species and tracking tubulin gene evolution, but also uncovered that A. thaliana is missing orthologs for several particular isotypes of α- and β-tubulins.
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Affiliation(s)
- Rostyslav Y Blume
- Institute of Food Biotechnology and Genomics of National Academy of Sciences of Ukraine, Kyiv, 02000, Ukraine.
| | - Anastasiia M Rabokon
- Institute of Food Biotechnology and Genomics of National Academy of Sciences of Ukraine, Kyiv, 02000, Ukraine
| | - Mykola Pydiura
- Institute of Food Biotechnology and Genomics of National Academy of Sciences of Ukraine, Kyiv, 02000, Ukraine
- JSC "Farmak", Kyiv, 04080, Ukraine
| | - Alla I Yemets
- Institute of Food Biotechnology and Genomics of National Academy of Sciences of Ukraine, Kyiv, 02000, Ukraine
| | - Yaroslav V Pirko
- Institute of Food Biotechnology and Genomics of National Academy of Sciences of Ukraine, Kyiv, 02000, Ukraine
| | - Yaroslav B Blume
- Institute of Food Biotechnology and Genomics of National Academy of Sciences of Ukraine, Kyiv, 02000, Ukraine
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Yemets A, Shadrina R, Blume R, Plokhovska S, Blume Y. Autophagy formation, microtubule disorientation, and alteration of ATG8 and tubulin gene expression under simulated microgravity in Arabidopsis thaliana. NPJ Microgravity 2024; 10:31. [PMID: 38499552 PMCID: PMC10948825 DOI: 10.1038/s41526-024-00381-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 03/08/2024] [Indexed: 03/20/2024] Open
Abstract
Autophagy plays an important role in plant growth and development, pathogen invasion and modulates plant response and adaptation to various abiotic stress stimuli. The biogenesis and trafficking of autophagosomes involve microtubules (MTs) as important actors in the autophagic process. However, initiation of autophagy in plants under microgravity has not been previously studied. Here we demonstrate how simulated microgravity induces autophagy development involving microtubular reorganization during period of autophagosome formation. It was shown that induction of autophagy with maximal autophagosome formation in root cells of Arabidopsis thaliana is observed after 6 days of clinostating, along with MT disorganization, which leads to visible changes in root morphology. Gradual decrease of autophagosome number was indicated on 9th and 12th days of the experiment as well as no significant re-orientation of MTs were identified. Respectively, analysis of α- and β-tubulins and ATG8 gene expression was carried out. In particular, the most pronounced increase of expression on both 6th and 9th days in response to simulated microgravity was detected for non-paralogous AtATG8b, AtATG8f, AtATG8i, and AtTUA2, AtTUA3 genes, as well as for the pair of β-tubulin duplicates, namely AtTUB2 and AtTUB3. Overall, the main autophagic response was observed after 6 and 9 days of exposure to simulated microgravity, followed by adaptive response after 12 days. These findings provide a key basis for further studies of cellular mechanisms of autophagy and involvement of cytoskeletal structures in autophagy biogenesis under microgravity, which would enable development of new approaches, aimed on enhancing plant adaptation to microgravity.
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Affiliation(s)
- Alla Yemets
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Baidy-Vyshnevetskoho St., 2a, Kyiv, 04123, Ukraine.
| | - Ruslana Shadrina
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Baidy-Vyshnevetskoho St., 2a, Kyiv, 04123, Ukraine
| | - Rostyslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Baidy-Vyshnevetskoho St., 2a, Kyiv, 04123, Ukraine.
| | - Svitlana Plokhovska
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Baidy-Vyshnevetskoho St., 2a, Kyiv, 04123, Ukraine
| | - Yaroslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Baidy-Vyshnevetskoho St., 2a, Kyiv, 04123, Ukraine.
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Yuan G, Gao H, Yang T. Exploring the Role of the Plant Actin Cytoskeleton: From Signaling to Cellular Functions. Int J Mol Sci 2023; 24:15480. [PMID: 37895158 PMCID: PMC10607326 DOI: 10.3390/ijms242015480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/06/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023] Open
Abstract
The plant actin cytoskeleton is characterized by the basic properties of dynamic array, which plays a central role in numerous conserved processes that are required for diverse cellular functions. Here, we focus on how actins and actin-related proteins (ARPs), which represent two classical branches of a greatly diverse superfamily of ATPases, are involved in fundamental functions underlying signal regulation of plant growth and development. Moreover, we review the structure, assembly dynamics, and biological functions of filamentous actin (F-actin) from a molecular perspective. The various accessory proteins known as actin-binding proteins (ABPs) partner with F-actin to finely tune actin dynamics, often in response to various cell signaling pathways. Our understanding of the significance of the actin cytoskeleton in vital cellular activities has been furthered by comparison of conserved functions of actin filaments across different species combined with advanced microscopic techniques and experimental methods. We discuss the current model of the plant actin cytoskeleton, followed by examples of the signaling mechanisms under the supervision of F-actin related to cell morphogenesis, polar growth, and cytoplasmic streaming. Determination of the theoretical basis of how the cytoskeleton works is important in itself and is beneficial to future applications aimed at improving crop biomass and production efficiency.
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Affiliation(s)
| | | | - Tao Yang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; (G.Y.); (H.G.)
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Wei G, Wang C, Lei X, Gao X, Li J, Zhang S, Guo J. IodoTMT-labeled redox proteomics reveals the involvement of oxidative post-translational modification in response to para-hydroxybenzoic acid and hydrogen peroxide stresses in poplar. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 259:115033. [PMID: 37224778 DOI: 10.1016/j.ecoenv.2023.115033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 05/01/2023] [Accepted: 05/16/2023] [Indexed: 05/26/2023]
Abstract
Poplar is widely planted as an economic and ecological tree species. However, accumulation of the phenolic acid allelochemical para-hydroxybenzoic acid (pHBA) in soil is a severe threat to the growth and productivity of poplar. pHBA stress leads to excessive production of reactive oxygen species (ROS). However, it is unclear which redox-sensitive proteins are involved in the pHBA-induced cellular homeostasis regulatory mechanism. We here identified reversible redox-modified proteins and modified cysteine (Cys) sites in exogenous pHBA- and hydrogen peroxide (H2O2)-treated poplar seedling leaves by using the iodoacetyl tandem mass tag-labeled redox proteomics method. In total, 4786 redox modification sites were identified in 3176 proteins, with 104 and 91 proteins being differentially modified at 118 and 101 Cys sites in response to pHBA and H2O2 stresses, respectively. The differentially modified proteins (DMPs) were predicted to be mainly localized in the chloroplast and cytoplasm, with most proteins being enzymes with catalytic activities. The KEGG enrichment analysis of these DMPs revealed that proteins related to the MAPK signaling pathway, soluble sugar metabolism, amino acid metabolism, photosynthesis, and phagosome pathways were extensively regulated by redox modifications. Moreover, combined with our previous quantitative proteomics data, 8 proteins were upregulated and oxidized under both pHBA and H2O2 stresses. Reversible oxidation of Cys sites in these proteins might be actively responsible for the regulation of tolerance to pHBA-induced oxidative stress. Based on the aforementioned results, a redox regulatory model activated by pHBA- and H2O2-induced oxidative stress was proposed. This study conducts the first redox proteomics analysis of poplar in response to pHBA stress and provides a new insight into the mechanistic framework of reversible oxidative post-translational modifications to gain a better understanding of pHBA-induced chemosensory effects on poplar.
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Affiliation(s)
- Guoqing Wei
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an, 271018, China
| | - Changxi Wang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiaoyan Lei
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an, 271018, China
| | - Xue Gao
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an, 271018, China
| | - Junru Li
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an, 271018, China
| | - Shuyong Zhang
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an, 271018, China.
| | - Jing Guo
- State Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an, 271018, China.
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Lykholat YV, Rabokon AM, Blume RY, Khromykh NO, Didur OO, Sakharova VH, Kabar AM, Pirko YV, Blume YB. Characterization of β-Tubulin Genes in Prunus persica and Prunus dulcis for Fingerprinting of their Interspecific Hybrids. CYTOL GENET+ 2022. [DOI: 10.3103/s009545272206007x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Identification of the Major Effector StSROs in Potato: A Potential StWRKY- SRO6 Regulatory Pathway Enhances Plant Tolerance to Cadmium Stress. Int J Mol Sci 2022; 23:ijms232214318. [PMID: 36430795 PMCID: PMC9698690 DOI: 10.3390/ijms232214318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/07/2022] [Accepted: 11/14/2022] [Indexed: 11/22/2022] Open
Abstract
SIMILAR TO RCD-ONE (SRO) family members and transcription factors (TFs) often improve plant antioxidant capacity through interaction and co-regulation and participate in plant resistance to drought and high-salt stress. However, whether SROs are involved in the response to heavy metal stress, especially SRO genes with a specific response and tolerance characteristics to cadmium (Cd) stress, remains unclear. We first identified six SRO genes in the potato genome by PARP and RST domains. Special and conserved StSROs were found, and the spatio temporal tissue-specific expression patterns and co-expression network diagrams of StSROs under the stress of 5 heavy metals were constructed. Second, we identified StSRO6 as a major effector gene (StSRO6-MEG) and StSRO5 as a secondary effector gene (StSRO5-SEG) through a comprehensive analysis. Interestingly, they may hold true for various physiological or stress responses in plants. In addition, using systematic genomics and comparative omics techniques, the key gene StSRO6 that affects the difference in Cd accumulation was discovered, cloned in the low-Cd accumulation "Yunshu 505", and transformed into the yeast mutant ycf1 for overexpression. The results proved that StSRO6 could confer Cd tolerance. Finally, through transient expression and in vitro culture tests, we hypothesized that StSROs 5/6 are regulated by the transcription factor StWRKY6 and mediates the reactive oxygen species (ROS) system to confer Cd tolerance. These findings offer a new perspective for understanding the mechanisms underlying Cd tolerance in plants, and simultaneously provide clues for the development of biological agents for preventing and controlling Cd migration and transformation.
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Duan Y, Chen Q, Chen Q, Zheng K, Cai Y, Long Y, Zhao J, Guo Y, Sun F, Qu Y. Analysis of transcriptome data and quantitative trait loci enables the identification of candidate genes responsible for fiber strength in Gossypium barbadense. G3 GENES|GENOMES|GENETICS 2022; 12:6650278. [PMID: 35881688 PMCID: PMC9434320 DOI: 10.1093/g3journal/jkac167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022]
Abstract
Gossypium barbadense possesses a superior fiber quality because of its fiber length and strength. An in-depth analysis of the underlying genetic mechanism could aid in filling the gap in research regarding fiber strength and could provide helpful information for Gossypium barbadense breeding. Three quantitative trait loci related to fiber strength were identified from a Gossypium barbadense recombinant inbred line (PimaS-7 × 5917) for further analysis. RNA sequencing was performed in the fiber tissues of PimaS-7 × 5917 0–35 days postanthesis. Four specific modules closely related to the secondary wall-thickening stage were obtained using the weighted gene coexpression network analysis. In total, 55 genes were identified as differentially expressed from 4 specific modules. Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes were used for enrichment analysis, and Gbar_D11G032910, Gbar_D08G020540, Gbar_D08G013370, Gbar_D11G033670, and Gbar_D11G029020 were found to regulate fiber strength by playing a role in the composition of structural constituents of cytoskeleton and microtubules during fiber development. Quantitative real-time PCR results confirmed the accuracy of the transcriptome data. This study provides a quick strategy for exploring candidate genes and provides new insights for improving fiber strength in cotton.
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Affiliation(s)
- Yajie Duan
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Qin Chen
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Quanjia Chen
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Kai Zheng
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Yongsheng Cai
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Yilei Long
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Jieyin Zhao
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Yaping Guo
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Fenglei Sun
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
| | - Yanying Qu
- College of Agronomy, Xinjiang Agricultural University , Urumqi, Xinjiang 830052, China
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Ereful NC, Lalusin AG, Laurena AC. RNA-Seq Reveals Differentially Expressed Genes Associated with High Fiber Quality in Abaca (Musa textilis Nee). Genes (Basel) 2022; 13:genes13030519. [PMID: 35328071 PMCID: PMC8953247 DOI: 10.3390/genes13030519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/07/2022] [Accepted: 03/10/2022] [Indexed: 02/01/2023] Open
Abstract
Despite the importance of and current demand for abaca (Musa textilis Nee) fiber, there has been limited study that capitalizes on RNA-seq to identify candidate genes associated with high fiber quality and bunchy top virus (AbBTV) resistance. Three varieties (Abuab, Inosa, and Tangongon), one wild banana variety (Musa balbisiana Colla) Pacol, and two developed backcrosses (Abuab × Pacol BC2 and BC3) were grown at the Institute of Plant Breeding (IPB), Laguna, Philippines. The pseudostems of 3-month-old suckers of each genotype were sampled for RNA-seq. Datasets were analyzed for differential expression (DE) implementing various model frameworks, including pairwise, genotypic and non-DE models. Results indicate that Abuab and BC3 induce the highest proportion (70%) of abaca-specific genes. Gene ontology (GO) enrichment analysis showed several genes associated with cellulose synthase activity, callose synthase, ß-glucosidase activity, glucan biosynthetic process, etc. KEGG pathway analysis showed several genes encoding for enzymes involved in the lignin biosynthetic pathway. Analysis using genotypic DE (GDE) between abaca bunchy top virus (AbBTV)-resistant and -susceptible groups revealed genes such as pathogenesis-related protein and NBS-LRR. As the genotypes were not infected with the pathogen, these genes are yet to be confirmed for their roles in disease resistance and are an interesting subject for further investigation.
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Affiliation(s)
- Nelzo C. Ereful
- Philippine Genome Center for Agriculture, University of the Philippines Los Baños, Laguna 4031, Philippines;
- Plant Physiology Laboratory, Institute of Plant Breeding (IPB), College of Agriculture and Food Science, University of the Philippines Los Baños, Laguna 4031, Philippines
- Correspondence:
| | - Antonio G. Lalusin
- Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, Laguna 4031, Philippines;
| | - Antonio C. Laurena
- Philippine Genome Center for Agriculture, University of the Philippines Los Baños, Laguna 4031, Philippines;
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Povkhova LV, Melnikova NV, Rozhmina TA, Novakovskiy RO, Pushkova EN, Dvorianinova EM, Zhuchenko AA, Kamionskaya AM, Krasnov GS, Dmitriev AA. Genes Associated with the Flax Plant Type (Oil or Fiber) Identified Based on Genome and Transcriptome Sequencing Data. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122616. [PMID: 34961087 PMCID: PMC8707629 DOI: 10.3390/plants10122616] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 06/14/2023]
Abstract
As a result of the breeding process, there are two main types of flax (Linum usitatissimum L.) plants. Linseed is used for obtaining seeds, while fiber flax is used for fiber production. We aimed to identify the genes associated with the flax plant type, which could be important for the formation of agronomically valuable traits. A search for polymorphisms was performed in genes involved in the biosynthesis of cell wall components, lignans, fatty acids, and ion transport based on genome sequencing data for 191 flax varieties. For 143 of the 424 studied genes (4CL, C3'H, C4H, CAD, CCR, CCoAOMT, COMT, F5H, HCT, PAL, CTL, BGAL, ABC, HMA, DIR, PLR, UGT, TUB, CESA, RGL, FAD, SAD, and ACT families), one or more polymorphisms had a strong correlation with the flax type. Based on the transcriptome sequencing data, we evaluated the expression levels for each flax type-associated gene in a wide range of tissues and suggested genes that are important for the formation of linseed or fiber flax traits. Such genes were probably subjected to the selection press and can determine not only the traits of seeds and stems but also the characteristics of the root system or resistance to stresses at a particular stage of development, which indirectly affects the ability of flax plants to produce seeds or fiber.
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Affiliation(s)
- Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
| | - Tatiana A. Rozhmina
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia; (T.A.R.); (A.A.Z.)
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
| | - Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - Alexander A. Zhuchenko
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia; (T.A.R.); (A.A.Z.)
- All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery, 115598 Moscow, Russia
| | - Anastasia M. Kamionskaya
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (L.V.P.); (N.V.M.); (R.O.N.); (E.N.P.); (E.M.D.); (G.S.K.)
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Genome-Wide Analysis of Tubulin Gene Family in Cassava and Expression of Family Member FtsZ2-1 during Various Stress. PLANTS 2021; 10:plants10040668. [PMID: 33807152 PMCID: PMC8065747 DOI: 10.3390/plants10040668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/25/2021] [Accepted: 03/28/2021] [Indexed: 12/02/2022]
Abstract
Filamentous temperature-sensitive protein Z (Tubulin/FtsZ) family is a group of conserved GTP-binding (guanine nucleotide-binding) proteins, which are closely related to plant tissue development and organ formation as the major component of the cytoskeleton. According to the published genome sequence information of cassava (Manihot esculenta Crantz), 23 tubulin genes (MeTubulins) were identified, which were divided into four main groups based on their type and phylogenetic characteristics. The same grouping generally has the same or similar motif composition and exon–intron structure. Collinear analysis showed that fragment repetition event is the main factor in amplification of cassava tubulin superfamily gene. The expression profiles of MeTubulin genes in various tissue were analyzed, and it was found that MeTubulins were mainly expressed in leaf, petiole, and stem, while FtsZ2-1 was highly expressed in storage root. The qRT-PCR results of the FtsZ2-1 gene under hormone and abiotic stresses showed that indole-3-acetic acid (IAA) and gibberellin A3 (GA3) stresses could significantly increase the expression of the FtsZ2-1 gene, thereby revealing the potential role of FtsZ2-1 in IAA and GA3 stress-induced responses.
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Blume YB. A journey through a plant cytoskeleton: Hot spots in signaling and functioning. Cell Biol Int 2019; 44:1262-1266. [PMID: 31486567 DOI: 10.1002/cbin.11224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 08/03/2019] [Indexed: 01/20/2023]
Abstract
This survey paper contains a brief analysis of publications included in the special issue of the scientific journal Cell Biology International titled "Plant Cytoskeleton Structure, Dynamics and Functions". The manuscripts in this special issue reflect some new aspects of plant cytoskeleton organization, signaling and functioning, and results from different Ukrainian research groups, and focuses on bringing together scientists working across different instrumental scales.
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Affiliation(s)
- Yaroslav B Blume
- Department of Genomics and Molecular Biotechnology, Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskoho Str., 2a, Kyiv, 04123, Ukraine
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Blume YB. A JOURNEY THROUGH PLANT CYTOSKELETON: HOT SPOTS IN SIGNALING AND FUNCTIONING. Cell Biol Int 2019; 43:978-982. [PMID: 31415134 DOI: 10.1002/cbin.11210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yaroslav B Blume
- Department of Genomics and Molecular Biotechnology, Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskoho Str., 2a, Kyiv, 04123, Ukraine
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Morello L, Pydiura N, Galinousky D, Blume Y, Breviario D. Flax tubulin and CesA superfamilies represent attractive and challenging targets for a variety of genome- and base-editing applications. Funct Integr Genomics 2019; 20:163-176. [PMID: 30826923 DOI: 10.1007/s10142-019-00667-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 02/07/2019] [Indexed: 02/07/2023]
Abstract
Flax is both a valuable resource and an interesting model crop. Despite a long history of flax genetic transformation only one transgenic linseed cultivar has been so far registered in Canada. Implementation and use of the genome-editing technologies that allow site-directed modification of endogenous genes without the introduction of foreign genes might improve this situation. Besides its potential for boosting crop yields, genome editing is now one of the best tools for carrying out reverse genetics and it is emerging as an especially versatile tool for studying basic biology. A complex interplay between the flax tubulin family (6 α-, 14 β-, and 2 γ-tubulin genes), the building block of microtubules, and the CesA (15-16 genes), the subunit of the multimeric cellulose-synthesizing complex devoted to the oriented deposition of the cellulose microfibrils is fundamental for the biosynthesis of the cell wall. The role of the different members of each family in providing specificities to the assembled complexes in terms of structure, dynamics, activity, and interaction remains substantially obscure. Genome-editing strategies, recently shown to be successful in flax, can therefore be useful to unravel the issue of functional redundancy and provide evidence for specific interactions between different members of the tubulin and CesA gene families, in relation to different phase and mode of cell wall biosynthesis.
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Affiliation(s)
- Laura Morello
- Istituto di Biologia e Biotecnologia Agraria IBBA-CNR, Via Alfonso Corti 12, 20133, Milan, Italy
| | - Nikolay Pydiura
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskoho St. 2a, Kyiv, 04123, Ukraine
| | - Dmitry Galinousky
- Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Akademicheskaya St. 27, 220072, Minsk, Belarus
| | - Yaroslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskoho St. 2a, Kyiv, 04123, Ukraine.
| | - Diego Breviario
- Istituto di Biologia e Biotecnologia Agraria IBBA-CNR, Via Alfonso Corti 12, 20133, Milan, Italy.
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14
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Pirko Y, Postovoitova A, Rabokon A, Kalafat L, Privаlikhin S, Bilonozhko Y, Pirko N, Blume Y. Study of intron length polymorphism of the α-tubulin genes as a method of analysis the genetic differentiation in plants. UKRAINIAN BOTANICAL JOURNAL 2019. [DOI: 10.15407/ukrbotj75.06.576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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15
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Postovoitova AS, Yotka OY, Pirko YV, Blume YB. Molecular Genetic Evaluation of Ukrainian Flax Cultivar Homogeneity Based on Intron Length Polymorphism of Actin Genes and Microsatellite Loci. CYTOL GENET+ 2018. [DOI: 10.3103/s0095452718060099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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