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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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Zou X, Zhen Z, Ge Q, Fan S, Liu A, Gong W, Li J, Gong J, Shi Y, Wang Y, Liu R, Duan L, Lei K, Zhang Q, Jiang X, Zhang S, Jia T, Zhang L, Shang H, Yuan Y. Genome-wide identification and analysis of the evolution and expression patterns of the cellulose synthase gene superfamily in Gossypium species. Gene 2017; 646:28-38. [PMID: 29278771 DOI: 10.1016/j.gene.2017.12.043] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 12/03/2017] [Accepted: 12/20/2017] [Indexed: 12/30/2022]
Abstract
The cellulose synthase gene superfamily, which includes the cellulose synthase (Ces) and cellulose synthase-like (Csl) families, is involved in the synthesis of cellulose and hemicellulose. This superfamily is critical for cotton fiber development in Gossypium species. Applying a series of bioinformatic methods, we identified 228 Ces/Csl genes from four Gossypium species (G. hirsutum, G. barbadense, G. arboreum, and G. raimondii). These genes were then grouped into 11 subfamilies based on phylogenetic relationships. A subsequent analysis of gene evolution revealed sites in CSLG and CSLJ genes that were under long-term positive selection pressure, with a posterior probability >0.95. Moreover, the dN:dS value for the CSLJ clade was 1.305, suggesting this subfamily was under positive selection pressure. Our data indicated that the dN:dS value ranged from 0.0084 to 0.9693 among the homologous Ces/Csl genes, implying they were under purifying selection pressure. Our transcriptome and qRT-PCR analyses revealed that CesA genes were more highly expressed in tetraploids than in diploids. However, the Csl expression levels exhibited the opposite trend. Furthermore, changes to promoter sequences may have influenced the expression of homologous Ces/Csl genes. Our findings may provide novel insights into the evolutionary relationships and expression patterns of the Ces/Csl genes in Gossypium species.
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Affiliation(s)
- Xianyan Zou
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Zhang Zhen
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Senmiao Fan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Aiying Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Junwen Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Juwu Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Yuzhen Shi
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Yanling Wang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Ruixian Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Li Duan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Kang Lei
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Qi Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Xiao Jiang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Shuya Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Tingting Jia
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Lipeng Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
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Gavazzi F, Pigna G, Braglia L, Gianì S, Breviario D, Morello L. Evolutionary characterization and transcript profiling of β-tubulin genes in flax (Linum usitatissimum L.) during plant development. BMC PLANT BIOLOGY 2017; 17:237. [PMID: 29221437 PMCID: PMC5721616 DOI: 10.1186/s12870-017-1186-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 11/29/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND Microtubules, polymerized from alpha and beta-tubulin monomers, play a fundamental role in plant morphogenesis, determining the cell division plane, the direction of cell expansion and the deposition of cell wall material. During polarized pollen tube elongation, microtubules serve as tracks for vesicular transport and deposition of proteins/lipids at the tip membrane. Such functions are controlled by cortical microtubule arrays. Aim of this study was to first characterize the flax β-tubulin family by sequence and phylogenetic analysis and to investigate differential expression of β-tubulin genes possibly related to fibre elongation and to flower development. RESULTS We report the cloning and characterization of the complete flax β-tubulin gene family: exon-intron organization, duplicated gene comparison, phylogenetic analysis and expression pattern during stem and hypocotyl elongation and during flower development. Sequence analysis of the fourteen expressed β-tubulin genes revealed that the recent whole genome duplication of the flax genome was followed by massive retention of duplicated tubulin genes. Expression analysis showed that β-tubulin mRNA profiles gradually changed along with phloem fibre development in both the stem and hypocotyl. In flowers, changes in relative tubulin transcript levels took place at anthesis in anthers, but not in carpels. CONCLUSIONS Phylogenetic analysis supports the origin of extant plant β-tubulin genes from four ancestral genes pre-dating angiosperm separation. Expression analysis suggests that particular tubulin subpopulations are more suitable to sustain different microtubule functions such as cell elongation, cell wall thickening or pollen tube growth. Tubulin genes possibly related to different microtubule functions were identified as candidate for more detailed studies.
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Affiliation(s)
- Floriana Gavazzi
- Istituto Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Via A. Corti, 12, Milan, 20133 Italy
| | - Gaia Pigna
- Istituto Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Via A. Corti, 12, Milan, 20133 Italy
| | - Luca Braglia
- Istituto Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Via A. Corti, 12, Milan, 20133 Italy
| | - Silvia Gianì
- Istituto Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Via A. Corti, 12, Milan, 20133 Italy
| | - Diego Breviario
- Istituto Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Via A. Corti, 12, Milan, 20133 Italy
| | - Laura Morello
- Istituto Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Via A. Corti, 12, Milan, 20133 Italy
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Galinousky D, Padvitski T, Bayer G, Pirko Y, Pydiura N, Anisimova N, Nikitinskaya T, Khotyleva L, Yemets A, Kilchevsky A, Blume Y. Expression analysis of cellulose synthase and main cytoskeletal protein genes in flax (
Linum usitatissimum
L.). Cell Biol Int 2017; 43:1065-1071. [DOI: 10.1002/cbin.10837] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/07/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Dmitry Galinousky
- Institute of Genetics and CytologyThe National Academy of Sciences of BelarusAkademicheskaya st., 27220072 Minsk Belarus
| | - Tsimafei Padvitski
- Institute of Genetics and CytologyThe National Academy of Sciences of BelarusAkademicheskaya st., 27220072 Minsk Belarus
| | - Galina Bayer
- Institute of Food Biotechnology and GenomicsThe National Academy of Sciences of UkraineОsipovskogo str., 2A04123 Kyiv Ukraine
| | - Yaroslav Pirko
- Institute of Food Biotechnology and GenomicsThe National Academy of Sciences of UkraineОsipovskogo str., 2A04123 Kyiv Ukraine
| | - Nikolay Pydiura
- Institute of Food Biotechnology and GenomicsThe National Academy of Sciences of UkraineОsipovskogo str., 2A04123 Kyiv Ukraine
| | - Natallia Anisimova
- Institute of Genetics and CytologyThe National Academy of Sciences of BelarusAkademicheskaya st., 27220072 Minsk Belarus
| | - Tatyana Nikitinskaya
- Institute of Genetics and CytologyThe National Academy of Sciences of BelarusAkademicheskaya st., 27220072 Minsk Belarus
| | - Liubov Khotyleva
- Institute of Genetics and CytologyThe National Academy of Sciences of BelarusAkademicheskaya st., 27220072 Minsk Belarus
| | - Alla Yemets
- Institute of Food Biotechnology and GenomicsThe National Academy of Sciences of UkraineОsipovskogo str., 2A04123 Kyiv Ukraine
| | - Aleksandr Kilchevsky
- Institute of Genetics and CytologyThe National Academy of Sciences of BelarusAkademicheskaya st., 27220072 Minsk Belarus
| | - Yaroslav Blume
- Institute of Food Biotechnology and GenomicsThe National Academy of Sciences of UkraineОsipovskogo str., 2A04123 Kyiv Ukraine
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Abstract
Abstract
In this work, we attempted to elucidate mechanisms of flax fiber biogenesis by measuring, using qPCR, expression of the cellwall related genes (cellulose synthase, cellulose synthase-like and chitinase-like genes) in stems of two contrasting fiber quality subspecies of flax (Linum usitatissimum L.). We studied elongatum Vav. et Ell. (cultivar Blakit, Belarus) and crepitans Boenn. (dehiscent flax) subspecies, which are differed in the height of plants, width of stems etc. Amongst all measured genes chitinase- like Ctl19 and Ctl21 genes showed drastic difference in expression between stems of the two flax varieties, showing higher expression level in the fiber flax versus the dehiscent flax. In contrast, cellulose synthase-like CslG4 gene had lower expression levels in the stem of fiber flax than in dehiscent flax. We suggest that hemicellulose composition and cellulose - non-cellulose glycan organisation can vary between stalk cells of different flax subspecies.
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Affiliation(s)
- Dmitry Galinousky
- Laboratory of Ecological Genetics and Biotechnology, Institute of Genetics & Cytology, Novosibirsk , Belarus
| | - Tsimafei Padvitski
- Laboratory of Ecological Genetics and Biotechnology, Institute of Genetics & Cytology, Novosibirsk , Belarus
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