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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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Aggarwal B, Karlowski WM, Nuc P, Jarmolowski A, Szweykowska-Kulinska Z, Pietrykowska H. MiRNAs differentially expressed in vegetative and reproductive organs of Marchantia polymorpha - insights into their expression pattern, gene structures and function. RNA Biol 2024; 21:1-12. [PMID: 38303117 PMCID: PMC10841014 DOI: 10.1080/15476286.2024.2303555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2024] [Indexed: 02/03/2024] Open
Abstract
MicroRNAs regulate gene expression affecting a variety of plant developmental processes. The evolutionary position of Marchantia polymorpha makes it a significant model to understand miRNA-mediated gene regulatory pathways in plants. Previous studies focused on conserved miRNA-target mRNA modules showed their critical role in Marchantia development. Here, we demonstrate that the differential expression of conserved miRNAs among land plants and their targets in selected organs of Marchantia additionally underlines their role in regulating fundamental developmental processes. The main aim of this study was to characterize selected liverwort-specific miRNAs, as there is a limited knowledge on their biogenesis, accumulation, targets, and function in Marchantia. We demonstrate their differential accumulation in vegetative and generative organs. We reveal that all liverwort-specific miRNAs examined are encoded by independent transcriptional units. MpmiR11737a, MpmiR11887 and MpmiR11796, annotated as being encoded within protein-encoding genes, have their own independent transcription start sites. The analysis of selected liverwort-specific miRNAs and their pri-miRNAs often reveal correlation in their levels, suggesting transcriptional regulation. However, MpmiR11796 shows a reverse correlation to its pri-miRNA level, suggesting post-transcriptional regulation. Moreover, we identify novel targets for selected liverwort-specific miRNAs and demonstrate an inverse correlation between their expression and miRNA accumulation. In the case of one miRNA precursor, we provide evidence that it encodes two functional miRNAs with two independent targets. Overall, our research sheds light on liverwort-specific miRNA gene structure, provides new data on their biogenesis and expression regulation. Furthermore, identifying their targets, we hypothesize the potential role of these miRNAs in early land plant development and functioning.
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Affiliation(s)
- Bharti Aggarwal
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Wojciech Maciej Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Przemyslaw Nuc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Halina Pietrykowska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
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Wang S, Wen B, Yang Y, Long S, Liu J, Li M. Genome-Wide Identification and Expression Analysis of the RADIALIS-like Gene Family in Camellia sinensis. PLANTS (BASEL, SWITZERLAND) 2023; 12:3039. [PMID: 37687288 PMCID: PMC10490161 DOI: 10.3390/plants12173039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/09/2023] [Accepted: 08/15/2023] [Indexed: 09/10/2023]
Abstract
The RADIALIS-like (RL) proteins are v-myb avian myeloblastosis viral oncogene homolog (MYB)-related transcription factors (TFs), and are involved in many biological processes, including metabolism, development, and response to biotic and abiotic stresses. However, the studies on the RL genes of Camellia sinensis are not comprehensive enough. Therefore, we undertook this study and identified eight CsaRLs based on the typical conserved domain SANT Associated domain (SANT) of RL. These genes have low molecular weights and theoretical pI values ranging from 5.67 to 9.76. Gene structure analysis revealed that six CsaRL genes comprise two exons and one intron, while the other two contain a single exon encompassing motifs 1 and 2, and part of motif 3. The phylogenetic analysis divided one hundred and fifty-eight RL proteins into five primary classes, in which CsaRLs clustered in Group V and were homologous with CssRLs of the Shuchazao variety. In addition, we selected different tissue parts to analyze the expression profile of CsaRLs, and the results show that almost all genes displayed variable expression levels across tissues, with CsaRL1a relatively abundant in all tissues. qRT-PCR (real-time fluorescence quantitative PCR) was used to detect the relative expression levels of the CsaRL genes under various abiotic stimuli, and it was found that CsaRL1a expression levels were substantially higher than other genes, with abscisic acid (ABA) causing the highest expression. The self-activation assay with yeast two-hybrid system showed that CsaRL1a has no transcriptional activity. According to protein functional interaction networks, CsaRL1a was well connected with WIN1-like, lysine histidine transporter-1-like, β-amylase 3 chloroplastic-like, carbonic anhydrase-2-like (CA2), and carbonic anhydrase dnaJC76 (DJC76). This study adds to our understanding of the RL family and lays the groundwork for further research into the function and regulatory mechanisms of the CsaRLs gene family in Camellia sinensis.
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Affiliation(s)
| | | | | | | | - Jianjun Liu
- College of Tea Sciences, Guizhou University, Guiyang 550025, China; (S.W.); (B.W.); (Y.Y.); (S.L.)
| | - Meifeng Li
- College of Tea Sciences, Guizhou University, Guiyang 550025, China; (S.W.); (B.W.); (Y.Y.); (S.L.)
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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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Wang C, Liu B, Chen M, Ning J, Lu X, Wang C. Mutations in Growth-Related Genes Induced by EMS Treatment in Scallops. Front Genet 2022; 13:879844. [PMID: 35559043 PMCID: PMC9086186 DOI: 10.3389/fgene.2022.879844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The goal of genetic breeding is to select variants with mutations that are related to expected traits, such as fast growth. Artificial induction has been widely used to obtain strains with more mutations for further selection. Ethylmethylsulfone (EMS) is one of the most commonly used chemical mutagens in plant and microorganism breeding. However, the application of EMS mutagenesis in shellfish has not been reported. The aim of this study is to evaluate the potential use of EMS as a mutagen in scallop breeding, especially in characterization of mutations in growth-related genes. Results: Our results indicated that hatching of about 50% of fertilized eggs was blocked by treatment with 20 mM EMS for 3 h and the resulted larvae developed normally into adult stages. We then evaluated the mutagenic effects of EMS by sequencing the genomes of 4 adult scallops from the control group and 12 from the treatment group at 8 months after fertilization. On average, after removing shared types of mutations, there were 1,151,380 ± 258,188 SNPs (Single Nucleotide Polymorphisms) and 229,256 ± 51,714 InDels (insertion-deletion) in each animal in the EMS treatment group, while there were only134841 ± 10,115 SNPs and 42,605 ± 5,136 InDels in the control group. The average mutation rate in the genome of the EMS treatment group (0.0137 ± 0.0013%) was about 9 times that of the control group (0.0015 ± 0.0002%). GO (Gene Ontology) annotation and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analyses revealed that mutations induced by EMS occurred evenly in most biological processes, cellular components and functions, as well in most pathways. However, significant lower percentage of mutations were found in the exonic region, in non-synonymous or Stopgain/Stoploss SNPs and in coding domains, suggesting apparent DNA repair or selection during grow-out stage. Analyses of the growth-related genes with mutations indicated that mutations in MFS (Major Facilitator Superfamily) and Tubulin were only found in the large-sized group (Five largest scallops: Treated-1, Treated-2, Treated-3, Treated-4, and Treated-5) and Homeobox and Socs (Suppressor of cytokine signaling) only in the small group (Two smallest scallops: Treated-11 and Treated-12). These results suggested that these genes may be involved in the regulation of growth in these animals, although further verification is certainly warranted. Conclusion: Treatment of fertilized eggs with 20 mM EMS for 3 h induced 9 times more mutations in scallop genomes. We found that mutations in MFS and Tubulin may be related to fast growth in the large-sized group and those mutations in Homeobox and SOCs may be involved in the slow growth in the small-sized scallops. EMS can be used to accelerate selection of economically important traits in molluscs.
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Affiliation(s)
- Caihui Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Bo Liu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Min Chen
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Junhao Ning
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Xia Lu
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Chunde Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
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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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Wollenweber TE, van Deenen N, Roelfs KU, Prüfer D, Gronover CS. Microscopic and Transcriptomic Analysis of Pollination Processes in Self-Incompatible Taraxacum koksaghyz. PLANTS 2021; 10:plants10030555. [PMID: 33809548 PMCID: PMC7998978 DOI: 10.3390/plants10030555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 11/23/2022]
Abstract
The transition of the Russian dandelion Taraxacum koksaghyz (Asteraceae) to a profitable, alternative crop producing natural rubber and inulin requires the optimization of several agronomic traits, cultivation conditions and harvesting procedures to improve the yield. However, efficient breeding is hindered by the obligatory sexual outcrossing of this species. Several other asters have been investigated to determine the mechanism of self-incompatibility, but the underlying molecular basis remains unclear. We therefore investigated the self-pollination and cross-pollination of two compatible T. koksaghyz varieties (TkMS2 and TkMS3) by microscopy and transcriptomic analysis to shed light on the pollination process. Self-pollination showed typical sporophytic self-incompatibility characteristics, with the rare pollen swelling at the pollen tube apex. In contrast, cross-pollination was characterized by pollen germination and penetration of the stigma by the growing pollen tubes. RNA-Seq was used to profile gene expression in the floret tissue during self-pollination and cross-pollination, and the differentially expressed genes were identified. This revealed three candidates for the early regulation of pollination in T. koksaghyz, which can be used to examine self-incompatibility mechanisms in more detail and to facilitate breeding programs.
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Affiliation(s)
- Tassilo Erik Wollenweber
- Institute of Plant Biology and Biotechnology, University of Muenster, Schlossplatz 8, 48143 Muenster, Germany; (T.E.W.); (N.v.D.); (D.P.)
| | - Nicole van Deenen
- Institute of Plant Biology and Biotechnology, University of Muenster, Schlossplatz 8, 48143 Muenster, Germany; (T.E.W.); (N.v.D.); (D.P.)
| | - Kai-Uwe Roelfs
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, 48143 Muenster, Germany;
| | - Dirk Prüfer
- Institute of Plant Biology and Biotechnology, University of Muenster, Schlossplatz 8, 48143 Muenster, Germany; (T.E.W.); (N.v.D.); (D.P.)
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, 48143 Muenster, Germany;
| | - Christian Schulze Gronover
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, 48143 Muenster, Germany;
- Correspondence: ; Tel.: +49(0)251-83-24998
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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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Gong B, Yan Y, Zhang L, Cheng F, Liu Z, Shi Q. Unravelling GSNOR-Mediated S-Nitrosylation and Multiple Developmental Programs in Tomato Plants. PLANT & CELL PHYSIOLOGY 2019; 60:2523-2537. [PMID: 31350547 DOI: 10.1093/pcp/pcz143] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 07/15/2019] [Indexed: 05/03/2023]
Abstract
Nitric oxide (NO) impacts multiple developmental events and stress responses in plants. S-nitrosylation, regulated by S-nitrosoglutathione reductase (GSNOR), is considered as an important route for NO bioactivity. However, genetic evidence for GSNOR-mediated plant development and S-nitrosylation remains elusive in crop species. Genetic and site-specific nitrosoproteomic approach was used to obtain GSNOR-mediated phenotype and S-nitrosylated network. Knockdown of GSNOR increased the endogenous NO level and S-nitrosylation, resulting in higher germination rate, inhibition of root and hypocotyl growth, decreased photosynthesis, reduced plant growth, altered plant architecture, dysplastic pollen grains, and low fructification rate and fruit yield. For nitrosoproteomic analysis, 395 endogenously S-nitrosylated proteins with 554 S-nitrosylation sites were identified within a wide range of biological processes, especially for energy metabolism. Physiological and exogenous energy-support testing were consistent with the omic result, suggesting that GSNOR-mediated S-nitrosylation of energy metabolism plays key roles in impacting plant growth and development. Taken together, GSNOR is actively involved in the regulation of multiple developmental processes related to agronomically important traits. In addition, our results provide valuable resources and new clues for the study of S-nitrosylation-regulated metabolism in plants.
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Affiliation(s)
- Biao Gong
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, P.R. China
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huanghuai Region, Ministry of Agriculture and Rural Affairs, P.R. China
| | - Yanyan Yan
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, P.R. China
| | - Lili Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, P.R. China
| | - Fei Cheng
- Qingdao Agricultural University, Qingdao, P.R. China
| | - Zhen Liu
- Jingjie PTM Biolab Co. Ltd, Hangzhou, P.R. China
| | - Qinghua Shi
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, P.R. China
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huanghuai Region, Ministry of Agriculture and Rural Affairs, P.R. China
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Mokshina N, Makshakova O, Nazipova A, Gorshkov O, Gorshkova T. Flax rhamnogalacturonan lyases: phylogeny, differential expression and modeling of protein structure. PHYSIOLOGIA PLANTARUM 2019; 167:173-187. [PMID: 30474196 DOI: 10.1111/ppl.12880] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/09/2018] [Accepted: 11/13/2018] [Indexed: 06/09/2023]
Abstract
Rhamnogalacturonan lyases (RGLs; EC 4.2.2.23) degrade the rhamnogalacturonan I (RG-I) backbone of pectins present in the plant cell wall. These enzymes belong to polysaccharide lyase family 4, members of which are mainly from plants and plant pathogens. RGLs are investigated, as a rule, as pathogen 'weapons' for plant cell wall degradation and subsequent infection. Despite the presence of genes annotated as RGLs in plant genomes and the presence of substrates for enzyme activity in plant cells, evidence supporting the involvement of this enzyme in certain processes is limited. The differential expression of some RGL genes in flax (Linum usitatissimum L.) tissues, revealed in our previous work, prompted us to carry out a total revision (phylogenetic analysis, analysis of expression and protein structure modeling) of all the sequences of flax predicted as coding for RGLs. Comparison of the expressions of LusRGL in various tissues of flax stem revealed that LusRGLs belong to distinct phylogenetic clades, which correspond to two co-expression groups. One of these groups comprised LusRGL6-A and LusRGL6-B genes and was specifically upregulated in flax fibers during deposition of the tertiary cell wall, which has complex RG-I as a key noncellulosic component. The results of homology modeling and docking demonstrated that the topology of the LusRGL6-A catalytic site allowed binding to the RG-I ligand. These findings lead us to suggest the presence of RGL activity in planta and the involvement of special isoforms of RGLs in the modification of RG-I of the tertiary cell wall in plant fibers.
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Affiliation(s)
- Natalia Mokshina
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center 'Kazan Scientific Center of RAS', Kazan, 420111, Russian Federation
| | - Olga Makshakova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center 'Kazan Scientific Center of RAS', Kazan, 420111, Russian Federation
| | - Alsu Nazipova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center 'Kazan Scientific Center of RAS', Kazan, 420111, Russian Federation
| | - Oleg Gorshkov
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center 'Kazan Scientific Center of RAS', Kazan, 420111, Russian Federation
| | - Tatyana Gorshkova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center 'Kazan Scientific Center of RAS', Kazan, 420111, Russian Federation
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12
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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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13
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Morello L, Braglia L, Gavazzi F, Gianì S, Breviario D. Tubulin-Based DNA Barcode: Principle and Applications to Complex Food Matrices. Genes (Basel) 2019; 10:genes10030229. [PMID: 30889932 PMCID: PMC6471244 DOI: 10.3390/genes10030229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/14/2019] [Accepted: 03/14/2019] [Indexed: 12/13/2022] Open
Abstract
The DNA polymorphism diffusely present in the introns of the members of the Eukaryotic beta-tubulin gene families, can be conveniently used to establish a DNA barcoding method, named tubulin-based polymorphism (TBP), that can reliably assign specific genomic fingerprintings to any plant or/and animal species. Similarly, many plant varieties can also be barcoded by TBP. The method is based on a simple cell biology concept that finds a conveniently exploitable molecular basis. It does not depend on DNA sequencing as the most classically established DNA barcode strategies. Successful applications, diversified for the different target sequences or experimental purposes, have been reported in many different plant species and, of late, a new a version applicable to animal species, including fishes, has been developed. Also, the TBP method is currently used for the genetic authentication of plant material and derived food products. Due to the use of a couple of universal primer pairs, specific for plant and animal organisms, respectively, it is effective in metabarcoding a complex matrix allowing an easy and rapid recognition of the different species present in a mixture. A simple, dedicated database made up by the genomic profile of reference materials is also part of the analytical procedure. Here we will provide some example of the TBP application and will discuss its features and uses in comparison with the DNA sequencing-based methods.
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Key Words
- The DNA polymorphism diffusely present in the introns of the members of the Eukaryotic beta-tubulin gene families, can be conveniently used to establish a DNA barcoding method, named tubulin-based polymorphism (TBP), that can reliably assign specific genomic fingerprintings to any plant or/and animal species. Similarly, many plant varieties can also be barcoded by TBP. The method is based on a simple cell biology concept that finds a conveniently exploitable molecular basis. It does not depend on DNA sequencing as the most classically established DNA barcode strategies. Successful applications, diversified for the different target sequences or experimental purposes, have been reported in many different plant species and, of late, a new a version applicable to animal species, including fishes, has been developed. Also, the TBP method is currently used for the genetic authentication of plant material and derived food products. Due to the use of a couple of universal primer pairs, specific for plant and animal organisms, respectively, it is effective in metabarcoding a complex matrix allowing an easy and rapid recognition of the different species present in a mixture. A simple, dedicated database made up by the genomic profile of reference materials is also part of the analytical procedure. Here we will provide some example of the TBP application and will discuss its features and uses in comparison with the DNA sequencing-based methods.
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Affiliation(s)
- Laura Morello
- Istituto Biologia e Biotecnologia Agraria, Via Adolfo Corti 12, 20131 Milano, Italy.
| | - Luca Braglia
- Istituto Biologia e Biotecnologia Agraria, Via Adolfo Corti 12, 20131 Milano, Italy.
| | - Floriana Gavazzi
- Istituto Biologia e Biotecnologia Agraria, Via Adolfo Corti 12, 20131 Milano, Italy.
| | - Silvia Gianì
- Istituto Biologia e Biotecnologia Agraria, Via Adolfo Corti 12, 20131 Milano, Italy.
| | - Diego Breviario
- Istituto Biologia e Biotecnologia Agraria, Via Adolfo Corti 12, 20131 Milano, Italy.
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14
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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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15
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Pydiura N, Pirko Y, Galinousky D, Postovoitova A, Yemets A, Kilchevsky A, Blume Y. Genome‐wide identification, phylogenetic classification, and exon–intron structure characterization of the tubulin and actin genes in flax (Linum usitatissimum). Cell Biol Int 2018; 43:1010-1019. [DOI: 10.1002/cbin.11001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 05/31/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Nikolay Pydiura
- Institute of Food Biotechnology and GenomicsNational Academy of Sciences of UkraineKyiv Osipovskogo St. 2a04123 Ukraine
| | - Yaroslav Pirko
- Institute of Food Biotechnology and GenomicsNational Academy of Sciences of UkraineKyiv Osipovskogo St. 2a04123 Ukraine
| | - Dmitry Galinousky
- Institute of Genetics and CytologyNational Academy of Sciences of BelarusMinsk Akademicheskaya st., 27220072 Belarus
| | - Anastasiia Postovoitova
- Institute of Food Biotechnology and GenomicsNational Academy of Sciences of UkraineKyiv Osipovskogo St. 2a04123 Ukraine
| | - Alla Yemets
- Institute of Food Biotechnology and GenomicsNational Academy of Sciences of UkraineKyiv Osipovskogo St. 2a04123 Ukraine
| | - Aleksandr Kilchevsky
- Institute of Genetics and CytologyNational Academy of Sciences of BelarusMinsk Akademicheskaya st., 27220072 Belarus
| | - Yaroslav Blume
- Institute of Food Biotechnology and GenomicsNational Academy of Sciences of UkraineKyiv Osipovskogo St. 2a04123 Ukraine
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