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Mihók E, Polgári D, Lenykó-Thegze A, Makai D, Fábián A, Ali M, Kis A, Sepsi A, Sági L. Plasticity of parental CENH3 incorporation into the centromeres in wheat × barley F1 hybrids. FRONTIERS IN PLANT SCIENCE 2024; 15:1324817. [PMID: 38313805 PMCID: PMC10834757 DOI: 10.3389/fpls.2024.1324817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/04/2024] [Indexed: 02/06/2024]
Abstract
Incorporating the centromere-specific histone H3 protein CENH3 into the centromeric nucleosomes is indispensable for accurate centromere function and balanced chromosome segregation in most eukaryotes, including higher plants. In the cell nuclei of interspecific hybrids, divergent centromeric DNAs cohabit and lead the corresponding parental chromosomes through the mitotic and meiotic cell divisions. Depending on the transmission of the parental chromosomes carrying the CENH3-encoding genes, CENH3 proteins from one or both parents may be present in these hybrids. The incorporation of parental CENH3 proteins into the divergent centromeres and their role in the chromosome elimination process in interspecific hybrids is still poorly understood. Here, we produced wheat × barley F1 hybrids that carried different combinations of barley chromosomes with genes encoding for either one (αCENH3) or both barley CENH3 protein variants (α- and βCENH3). We generated specific antibodies distinguishing between the wheat CENH3 proteins and barley αCENH3 and applied them together with FISH probes to detect the precise pattern of parental CENH3 deposition into the wheat and barley centromeric nucleosomes. Analysis of somatic and meiotic nuclei of the wheat × barley hybrids revealed the plasticity of the maternal (wheat) CENH3 proteins to become incorporated into the paternal (barley) centromeric nucleosomes. However, no evidence for paternal CENH3 plasticity was detected in this study. The significance of the unilateral centromere plasticity and possible patterns of CENH3 incorporation into centromeres in interspecific hybrids are discussed.
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Affiliation(s)
- Edit Mihók
- Centre for Agricultural Research, Hungarian Research Network, Martonvásár, Hungary
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Dávid Polgári
- Centre for Agricultural Research, Hungarian Research Network, Martonvásár, Hungary
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Centre for Agricultural Research, Martonvásár, Hungary
| | - Andrea Lenykó-Thegze
- Centre for Agricultural Research, Hungarian Research Network, Martonvásár, Hungary
| | - Diána Makai
- Centre for Agricultural Research, Hungarian Research Network, Martonvásár, Hungary
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Attila Fábián
- Centre for Agricultural Research, Hungarian Research Network, Martonvásár, Hungary
| | - Mohammad Ali
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - András Kis
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Adél Sepsi
- Centre for Agricultural Research, Hungarian Research Network, Martonvásár, Hungary
| | - László Sági
- Centre for Agricultural Research, Hungarian Research Network, Martonvásár, Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Centre for Agricultural Research, Martonvásár, Hungary
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Raipuria RK, Watts A, Sharma BB, Watts A, Bhattacharya R. Decoding allelic diversity, transcript variants and transcriptional complexity of CENH3 gene in Brassica oleracea var. botrytis. PROTOPLASMA 2023; 260:1149-1162. [PMID: 36705736 DOI: 10.1007/s00709-023-01837-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 01/07/2023] [Indexed: 06/07/2023]
Abstract
Histone proteins play a critical role in the primary organization of nucleosomes, which is the fundamental unit of chromatin. Among the five types of the histones, histone H3 has multiple variants, and the number differs among the species. Amongst histone H3 variants, centromeric histone H3 (CENH3) is crucial for centromere identification and proper chromosomal segregation during cell division. In the present study, we have identified 17 putative histone H3 genes of Brassica oleracea. Furthermore, we have done a detailed characterization of the CENH3 gene of B. oleracea. We showed that a single CENH3 gene exhibits allelic diversity with at least two alleles and alternative splicing pattern. Also, we have identified a CENH3 gene-specific co-dominant cleaved amplified polymorphic sequence marker SNP34(A/C) to distinguish CENH3 alleles and follow their expression in leaf and flower tissues. The gene structure analysis of the CENH3 gene revealed the conserved 5'-CAGCAG-3' sequence at the intron 3-exon 4 junction in B. oleracea, which serves as an alternative splicing site with one-codon (alanine) addition/deletion. However, this one-codon alternative splicing feature is not conserved in the CENH3 genes of wild allied Brassica species. Our finding suggests that transcriptional complexity and alternative splicing might play a key role in the transcriptional regulation and function of the CENH3 gene in B. oleracea. Altogether, data generated from the present study can serve as a primary information resource and can be used to engineer CENH3 gene towards developing haploid inducer lines in B. oleracea.
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Affiliation(s)
- Ritesh Kumar Raipuria
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Anshul Watts
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India.
| | - Brij Bihari Sharma
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
| | - Archana Watts
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India
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Vershinin AV, Elisafenko EA, Evtushenko EV. Genetic Redundancy in Rye Shows in a Variety of Ways. PLANTS (BASEL, SWITZERLAND) 2023; 12:282. [PMID: 36678994 PMCID: PMC9862056 DOI: 10.3390/plants12020282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Fifty years ago Susumu Ohno formulated the famous C-value paradox, which states that there is no correlation between the physical sizes of the genome, i.e., the amount of DNA, and the complexity of the organism, and highlighted the problem of genome redundancy. DNA that does not have a positive effect on the fitness of organisms has been characterized as "junk or selfish DNA". The controversial concept of junk DNA remains viable. Rye is a convenient subject for yet another test of the correctness and scientific significance of this concept. The genome of cultivated rye, Secale cereale L., is considered one of the largest among species of the tribe Triticeae and thus it tops the average angiosperm genome and the genomes of its closest evolutionary neighbors, such as species of barley, Hordeum (by approximately 30-35%), and diploid wheat species, Triticum (approximately 25%). The review provides an analysis of the structural organization of various regions of rye chromosomes with a description of the molecular mechanisms contributing to their size increase during evolution and the classes of DNA sequences involved in these processes. The history of the development of the concept of eukaryotic genome redundancy is traced and the current state of this problem is discussed.
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Affiliation(s)
- Alexander V. Vershinin
- Institute of Molecular and Cellular Biology, SB RAS, Acad. Lavrentiev Ave. 8/2, 630090 Novosibirsk, Russia
| | - Evgeny A. Elisafenko
- Institute of Molecular and Cellular Biology, SB RAS, Acad. Lavrentiev Ave. 8/2, 630090 Novosibirsk, Russia
- Institute of Cytology and Genetics, SB RAS, Acad. Lavrentiev Ave. 10, 630090 Novosibirsk, Russia
| | - Elena V. Evtushenko
- Institute of Molecular and Cellular Biology, SB RAS, Acad. Lavrentiev Ave. 8/2, 630090 Novosibirsk, Russia
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Caro L, Raman P, Steiner FA, Ailion M, Malik HS. Recurrent but Short-Lived Duplications of Centromeric Proteins in Holocentric Caenorhabditis Species. Mol Biol Evol 2022; 39:6731087. [PMID: 36173809 PMCID: PMC9577544 DOI: 10.1093/molbev/msac206] [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] [Indexed: 12/15/2022] Open
Abstract
Centromeric histones (CenH3s) are essential for chromosome inheritance during cell division in most eukaryotes. CenH3 genes have rapidly evolved and undergone repeated gene duplications and diversification in many plant and animal species. In Caenorhabditis species, two independent duplications of CenH3 (named hcp-3 for HoloCentric chromosome-binding Protein 3) were previously identified in C. elegans and C. remanei. Using phylogenomic analyses in 32 Caenorhabditis species, we find strict retention of the ancestral hcp-3 gene and 10 independent duplications. Most hcp-3L (hcp-3-like) paralogs are only found in 1-2 species, are expressed in both males and females/hermaphrodites, and encode histone fold domains with 69-100% identity to ancestral hcp-3. We identified novel N-terminal protein motifs, including putative kinetochore protein-interacting motifs and a potential separase cleavage site, which are well conserved across Caenorhabditis HCP-3 proteins. Other N-terminal motifs vary in their retention across paralogs or species, revealing potential subfunctionalization or functional loss following duplication. An N-terminal extension in the hcp-3L gene of C. afra revealed an unprecedented protein fusion, where hcp-3L fused to duplicated segments from hcp-4 (nematode CENP-C). By extending our analyses beyond CenH3, we found gene duplications of six inner and outer kinetochore genes in Caenorhabditis, which appear to have been retained independent of hcp-3 duplications. Our findings suggest that centromeric protein duplications occur frequently in Caenorhabditis nematodes, are selectively retained for short evolutionary periods, then degenerate or are lost entirely. We hypothesize that unique challenges associated with holocentricity in Caenorhabditis may lead to this rapid "revolving door" of kinetochore protein paralogs.
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Affiliation(s)
- Lews Caro
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA.,Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Pravrutha Raman
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Florian A Steiner
- Department of Molecular Biology and Cellular Biology, Section of Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - Michael Ailion
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA.,Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.,Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
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Karimi-Ashtiyani R, Schubert V, Houben A. Only the Rye Derived Part of the 1BL/1RS Hybrid Centromere Incorporates CENH3 of Wheat. FRONTIERS IN PLANT SCIENCE 2021; 12:802222. [PMID: 34966406 PMCID: PMC8710534 DOI: 10.3389/fpls.2021.802222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 11/22/2021] [Indexed: 05/04/2023]
Abstract
The precise assembly of the kinetochore complex at the centromere is epigenetically determined by substituting histone H3 with the centromere-specific histone H3 variant CENH3 in centromeric nucleosomes. The wheat-rye 1BL/1RS translocation chromosome in the background of wheat resulted from a centric misdivision followed by the fusion of the broken arms of chromosomes 1B and 1R from wheat and rye, respectively. The resulting hybrid (dicentric)centromere is composed of both wheat and rye centromeric repeats. As CENH3 is a marker for centromere activity, we applied Immuno-FISH followed by ultrastructural super-resolution microscopy to address whether both or only parts of the hybrid centromere are active. Our study demonstrates that only the rye-derived centromere part incorporates CENH3 of wheat in the 1BL/1RS hybrid centromere. This finding supports the notion that one centromere part of a translocated chromosome undergoes inactivation, creating functional monocentric chromosomes to maintain chromosome stability.
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Affiliation(s)
- Raheleh Karimi-Ashtiyani
- Department of Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- *Correspondence: Raheleh Karimi-Ashtiyani,
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Andreas Houben,
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