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Peng Z, Yu S, Meng J, Jia KH, Zhang J, Li X, Gao W, Wan S. Alternative polyadenylation regulates acetyl-CoA carboxylase function in peanut. BMC Genomics 2023; 24:637. [PMID: 37875812 PMCID: PMC10594767 DOI: 10.1186/s12864-023-09696-5] [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: 05/29/2023] [Accepted: 09/21/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Polyadenylation is a crucial process that terminates mRNA molecules at their 3'-ends. It has been observed that alternative polyadenylation (APA) can generate multiple transcripts from a single gene locus, each with different polyadenylation sites (PASs). This leads to the formation of several 3' untranslated regions (UTRs) that vary in length and composition. APA has a significant impact on approximately 60-70% of eukaryotic genes and has far-reaching implications for cell proliferation, differentiation, and tumorigenesis. RESULTS In this study, we conducted long-read, single-molecule sequencing of mRNA from peanut seeds. Our findings revealed that over half of all peanut genes possess over two PASs, with older developing seeds containing more PASs. This suggesting that the PAS exhibits high tissue specificity and plays a crucial role in peanut seed maturation. For the peanut acetyl-CoA carboxylase A1 (AhACCA1) gene, we discovered four 3' UTRs referred to UTR1-4. RT-PCR analysis showed that UTR1-containing transcripts are predominantly expressed in roots, leaves, and early developing seeds. Transcripts containing UTR2/3 accumulated mainly in roots, flowers, and seeds, while those carrying UTR4 were constitutively expressed. In Nicotiana benthamiana leaves, we transiently expressed all four UTRs, revealing that each UTR impacted protein abundance but not subcellular location. For functional validation, we introduced each UTR into yeast cells and found UTR2 enhanced AhACCA1 expression compared to a yeast transcription terminator, whereas UTR3 did not. Furthermore, we determined ACC gene structures in seven plant species and identified 51 PASs for 15 ACC genes across four plant species, confirming that APA of the ACC gene family is universal phenomenon in plants. CONCLUSION Our data demonstrate that APA is widespread in peanut seeds and plays vital roles in peanut seed maturation. We have identified four 3' UTRs for AhACCA1 gene, each showing distinct tissue-specific expression patterns. Through subcellular location experiment and yeast transformation test, we have determined that UTR2 has a stronger impact on gene expression regulation compared to the other three UTRs.
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Affiliation(s)
- Zhenying Peng
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Science, Jinan, 250100, China.
| | - Shuang Yu
- College of Agricultural, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Jingjing Meng
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Science, Jinan, 250100, China
| | - Kai-Hua Jia
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Science, Jinan, 250100, China
| | - Jialei Zhang
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Science, Jinan, 250100, China
| | - Xinguo Li
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Science, Jinan, 250100, China
| | - Wenwei Gao
- College of Agricultural, Xinjiang Agricultural University, Urumqi, 830052, China.
| | - Shubo Wan
- Shandong Academy of Agricultural Science, Jinan, 250100, China.
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Rychel-Bielska S, Plewiński P, Kozak B, Galek R, Ksia̧żkiewicz M. Photoperiod and Vernalization Control of Flowering-Related Genes: A Case Study of the Narrow-Leafed Lupin ( Lupinus angustifolius L.). FRONTIERS IN PLANT SCIENCE 2020; 11:572135. [PMID: 33193508 PMCID: PMC7663182 DOI: 10.3389/fpls.2020.572135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/24/2020] [Indexed: 06/11/2023]
Abstract
Narrow-leafed lupin (Lupinus angustifolius L.) is a moderate-yielding legume crop known for its high grain protein content and contribution to soil improvement. It is cultivated under photoperiods ranging from 9 to 17 h, as a spring-sown (in colder locations) or as an autumn-sown crop (in warmer regions). Wild populations require a prolonged cold period, called vernalization, to induce flowering. The key achievement of L. angustifolius domestication was the discovery of two natural mutations (named Ku and Jul) conferring vernalization independence. These mutations are overlapping deletion variants in the promoter of LanFTc1, a homolog of the Arabidopsis thaliana FLOWERING LOCUS T (FT) gene. The third deletion, named here as Pal, was recently found in primitive germplasm. In this study, we genotyped L. angustifolius germplasm that differs in domestication status and geographical origin for LanFTc1 alleles, which we then phenotyped to establish flowering time and vernalization responsiveness. The Ku and Jul lines were vernalization-independent and early flowering, wild (ku) lines were vernalization-dependent and late flowering, whereas the Pal line conferred intermediate phenotype. Three lines representing ku, Pal, and Ku alleles were subjected to gene expression surveys under 8- and 16-h photoperiods. FT homologs (LanFTa1, LanFTa2, LanFTc1, and LanFTc2) and some genes selected by recent expression quantitative trait loci mapping were analyzed. Expression profiles of LanFTc1 and LanAGL8 (AGAMOUS-like 8) matched observed differences in flowering time between genotypes, highlighted by high induction after vernalization in the ku line. Moreover, these genes revealed altered circadian clock control in Pal line under short days. LanFD (FD) and LanCRLK1 (CALCIUM/CALMODULIN-REGULATED RECEPTOR-LIKE KINASE 1) were negatively responsive to vernalization in Ku and Pal lines but positively responsive or variable in ku, whereas LanUGT85A2 (UDP-GLUCOSYL TRANSFERASE 85A2) was significantly suppressed by vernalization in all lines. Such a pattern suggests the opposite regulation of these gene pairs in the vernalization pathway. LanCRLK1 and LanUGT85A2 are homologs of A. thaliana genes involved in the FLOWERING LOCUS C (FLC) vernalization pathway. Lupins, like many other legumes, do not have any FLC homologs. Therefore, candidate genes surveyed in this study, namely LanFTc1, LanAGL8, LanCRLK1, and LanUGT85A2, may constitute anchors for further elucidation of molecular components contributing to vernalization response in legumes.
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Affiliation(s)
- Sandra Rychel-Bielska
- Department of Genetics, Plant Breeding and Seed Production, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Piotr Plewiński
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Bartosz Kozak
- Department of Genetics, Plant Breeding and Seed Production, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Renata Galek
- Department of Genetics, Plant Breeding and Seed Production, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Michał Ksia̧żkiewicz
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
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Arendsee Z, Li J, Singh U, Seetharam A, Dorman K, Wurtele ES. phylostratr: a framework for phylostratigraphy. Bioinformatics 2020; 35:3617-3627. [PMID: 30873536 DOI: 10.1093/bioinformatics/btz171] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/27/2019] [Accepted: 03/13/2019] [Indexed: 12/20/2022] Open
Abstract
MOTIVATION The goal of phylostratigraphy is to infer the evolutionary origin of each gene in an organism. This is done by searching for homologs within increasingly broad clades. The deepest clade that contains a homolog of the protein(s) encoded by a gene is that gene's phylostratum. RESULTS We have created a general R-based framework, phylostratr, to estimate the phylostratum of every gene in a species. The program fully automates analysis: selecting species for balanced representation, retrieving sequences, building databases, inferring phylostrata and returning diagnostics. Key diagnostics include: detection of genes with inferred homologs in old clades, but not intermediate ones; proteome quality assessments; false-positive diagnostics, and checks for missing organellar genomes. phylostratr allows extensive customization and systematic comparisons of the influence of analysis parameters or genomes on phylostrata inference. A user may: modify the automatically generated clade tree or use their own tree; provide custom sequences in place of those automatically retrieved from UniProt; replace BLAST with an alternative algorithm; or tailor the method and sensitivity of the homology inference classifier. We show the utility of phylostratr through case studies in Arabidopsis thaliana and Saccharomyces cerevisiae. AVAILABILITY AND IMPLEMENTATION Source code available at https://github.com/arendsee/phylostratr. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zebulun Arendsee
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.,Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA, USA
| | - Jing Li
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.,Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
| | - Urminder Singh
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.,Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
| | - Arun Seetharam
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Genome Informatics Facility, Iowa State University, Ames, IA, USA
| | - Karin Dorman
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.,Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Department of Statistics, Iowa State University, Ames, IA, USA
| | - Eve Syrkin Wurtele
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.,Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA, USA
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A Tale of Two Families: Whole Genome and Segmental Duplications Underlie Glutamine Synthetase and Phosphoenolpyruvate Carboxylase Diversity in Narrow-Leafed Lupin ( Lupinus angustifolius L.). Int J Mol Sci 2020; 21:ijms21072580. [PMID: 32276381 PMCID: PMC7177731 DOI: 10.3390/ijms21072580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/04/2020] [Accepted: 04/06/2020] [Indexed: 01/04/2023] Open
Abstract
Narrow-leafed lupin (Lupinus angustifolius L.) has recently been supplied with advanced genomic resources and, as such, has become a well-known model for molecular evolutionary studies within the legume family—a group of plants able to fix nitrogen from the atmosphere. The phylogenetic position of lupins in Papilionoideae and their evolutionary distance to other higher plants facilitates the use of this model species to improve our knowledge on genes involved in nitrogen assimilation and primary metabolism, providing novel contributions to our understanding of the evolutionary history of legumes. In this study, we present a complex characterization of two narrow-leafed lupin gene families—glutamine synthetase (GS) and phosphoenolpyruvate carboxylase (PEPC). We combine a comparative analysis of gene structures and a synteny-based approach with phylogenetic reconstruction and reconciliation of the gene family and species history in order to examine events underlying the extant diversity of both families. Employing the available evidence, we show the impact of duplications on the initial complement of the analyzed gene families within the genistoid clade and posit that the function of duplicates has been largely retained. In terms of a broader perspective, our results concerning GS and PEPC gene families corroborate earlier findings pointing to key whole genome duplication/triplication event(s) affecting the genistoid lineage.
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5
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Rychel-Bielska S, Plewiński P, Kozak B, Galek R, Ksia Żkiewicz M. Photoperiod and Vernalization Control of Flowering-Related Genes: A Case Study of the Narrow-Leafed Lupin ( Lupinus angustifolius L.). FRONTIERS IN PLANT SCIENCE 2020; 11:572135. [PMID: 33193508 DOI: 10.3389/fpls.2020.572135/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/24/2020] [Indexed: 05/18/2023]
Abstract
Narrow-leafed lupin (Lupinus angustifolius L.) is a moderate-yielding legume crop known for its high grain protein content and contribution to soil improvement. It is cultivated under photoperiods ranging from 9 to 17 h, as a spring-sown (in colder locations) or as an autumn-sown crop (in warmer regions). Wild populations require a prolonged cold period, called vernalization, to induce flowering. The key achievement of L. angustifolius domestication was the discovery of two natural mutations (named Ku and Jul) conferring vernalization independence. These mutations are overlapping deletion variants in the promoter of LanFTc1, a homolog of the Arabidopsis thaliana FLOWERING LOCUS T (FT) gene. The third deletion, named here as Pal, was recently found in primitive germplasm. In this study, we genotyped L. angustifolius germplasm that differs in domestication status and geographical origin for LanFTc1 alleles, which we then phenotyped to establish flowering time and vernalization responsiveness. The Ku and Jul lines were vernalization-independent and early flowering, wild (ku) lines were vernalization-dependent and late flowering, whereas the Pal line conferred intermediate phenotype. Three lines representing ku, Pal, and Ku alleles were subjected to gene expression surveys under 8- and 16-h photoperiods. FT homologs (LanFTa1, LanFTa2, LanFTc1, and LanFTc2) and some genes selected by recent expression quantitative trait loci mapping were analyzed. Expression profiles of LanFTc1 and LanAGL8 (AGAMOUS-like 8) matched observed differences in flowering time between genotypes, highlighted by high induction after vernalization in the ku line. Moreover, these genes revealed altered circadian clock control in Pal line under short days. LanFD (FD) and LanCRLK1 (CALCIUM/CALMODULIN-REGULATED RECEPTOR-LIKE KINASE 1) were negatively responsive to vernalization in Ku and Pal lines but positively responsive or variable in ku, whereas LanUGT85A2 (UDP-GLUCOSYL TRANSFERASE 85A2) was significantly suppressed by vernalization in all lines. Such a pattern suggests the opposite regulation of these gene pairs in the vernalization pathway. LanCRLK1 and LanUGT85A2 are homologs of A. thaliana genes involved in the FLOWERING LOCUS C (FLC) vernalization pathway. Lupins, like many other legumes, do not have any FLC homologs. Therefore, candidate genes surveyed in this study, namely LanFTc1, LanAGL8, LanCRLK1, and LanUGT85A2, may constitute anchors for further elucidation of molecular components contributing to vernalization response in legumes.
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Affiliation(s)
- Sandra Rychel-Bielska
- Department of Genetics, Plant Breeding and Seed Production, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Piotr Plewiński
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Bartosz Kozak
- Department of Genetics, Plant Breeding and Seed Production, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Renata Galek
- Department of Genetics, Plant Breeding and Seed Production, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Michał Ksia Żkiewicz
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
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Książkiewicz M, Yang H. Molecular Marker Resources Supporting the Australian Lupin Breeding Program. COMPENDIUM OF PLANT GENOMES 2020. [DOI: 10.1007/978-3-030-21270-4_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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7
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Plewiński P, Książkiewicz M, Rychel-Bielska S, Rudy E, Wolko B. Candidate Domestication-Related Genes Revealed by Expression Quantitative Trait Loci Mapping of Narrow-Leafed Lupin ( Lupinus angustifolius L.). Int J Mol Sci 2019; 20:ijms20225670. [PMID: 31726789 PMCID: PMC6888189 DOI: 10.3390/ijms20225670] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/08/2019] [Accepted: 11/09/2019] [Indexed: 12/12/2022] Open
Abstract
The last century has witnessed rapid domestication of the narrow-leafed lupin (Lupinus angustifolius L.) as a grain legume crop, exploiting discovered alleles conferring low-alkaloid content (iucundus), vernalization independence (Ku and Julius), and reduced pod shattering (lentus and tardus). In this study, a L. angustifolius mapping population was subjected to massive analysis of cDNA ends (MACE). The MACE yielded 4185 single nucleotide polymorphism (SNP) markers for linkage map improvement and 30,595 transcriptomic profiles for expression quantitative trait loci (eQTL) mapping. The eQTL highlighted a high number of cis- and trans-regulated alkaloid biosynthesis genes with gene expression orchestrated by a regulatory agent localized at iucundus locus, supporting the concept that ETHYLENE RESPONSIVE TRANSCRIPTION FACTOR RAP2-7 may control low-alkaloid phenotype. The analysis of Ku shed light on the vernalization response via FLOWERING LOCUS T and FD regulon in L. angustifolius, providing transcriptomic evidence for the contribution of several genes acting in C-repeat binding factor (CBF) cold responsiveness and in UDP-glycosyltransferases pathways. Research on lentus selected a DUF1218 domain protein as a candidate gene controlling the orientation of the sclerified endocarp and a homolog of DETOXIFICATION14 for purplish hue of young pods. An ABCG transporter was identified as a hypothetical contributor to sclerenchyma fortification underlying tardus phenotype.
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Nováková E, Zablatzká L, Brus J, Nesrstová V, Hanáček P, Kalendar R, Cvrčková F, Majeský Ľ, Smýkal P. Allelic Diversity of Acetyl Coenzyme A Carboxylase accD/ bccp Genes Implicated in Nuclear-Cytoplasmic Conflict in the Wild and Domesticated Pea ( Pisum sp.). Int J Mol Sci 2019; 20:E1773. [PMID: 30974846 PMCID: PMC6480052 DOI: 10.3390/ijms20071773] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/04/2019] [Accepted: 04/08/2019] [Indexed: 01/09/2023] Open
Abstract
Reproductive isolation is an important component of species differentiation. The plastid accD gene coding for the acetyl-CoA carboxylase subunit and the nuclear bccp gene coding for the biotin carboxyl carrier protein were identified as candidate genes governing nuclear-cytoplasmic incompatibility in peas. We examined the allelic diversity in a set of 195 geographically diverse samples of both cultivated (Pisum sativum, P. abyssinicum) and wild (P. fulvum and P. elatius) peas. Based on deduced protein sequences, we identified 34 accD and 31 bccp alleles that are partially geographically and genetically structured. The accD is highly variable due to insertions of tandem repeats. P. fulvum and P. abyssinicum have unique alleles and combinations of both genes. On the other hand, partial overlap was observed between P. sativum and P. elatius. Mapping of protein sequence polymorphisms to 3D structures revealed that most of the repeat and indel polymorphisms map to sequence regions that could not be modeled, consistent with this part of the protein being less constrained by requirements for precise folding than the enzymatically active domains. The results of this study are important not only from an evolutionary point of view but are also relevant for pea breeding when using more distant wild relatives.
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Affiliation(s)
- Eliška Nováková
- Department of Botany, Faculty of Sciences, Palacký University, 78371 Olomouc, Czech Republic.
| | - Lenka Zablatzká
- Department of Botany, Faculty of Sciences, Palacký University, 78371 Olomouc, Czech Republic.
| | - Jan Brus
- Department of Geoinformatics, Faculty of Sciences, Palacký University, 78371 Olomouc, Czech Republic.
| | - Viktorie Nesrstová
- Department of Mathematical Analysis and Applications of Mathematics, Palacký University, 78371 Olomouc, Czech Republic.
| | - Pavel Hanáček
- Department of Plant Biology, Faculty of Agronomy, Mendel University, 61300 Brno, Czech Republic.
| | - Ruslan Kalendar
- National Center for Biotechnology, Astana 010000, Kazakhstan.
- Department of Agricultural Sciences, Viikki Plant Science Centre and Helsinki Sustainability Centre, University of Helsinki, FI-00014 Helsinki, Finland.
| | - Fatima Cvrčková
- Department of Experimental Plant Biology, Faculty of Sciences, Charles University, 12844 Prague, Czech Republic.
| | - Ľuboš Majeský
- Department of Botany, Faculty of Sciences, Palacký University, 78371 Olomouc, Czech Republic.
| | - Petr Smýkal
- Department of Botany, Faculty of Sciences, Palacký University, 78371 Olomouc, Czech Republic.
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