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Plant Biotechnology Journal Dec 2023Numerous staple crops exhibit polyploidy and are difficult to genetically modify. However, recent advances in genome sequencing and editing have enabled polyploid genome...
Numerous staple crops exhibit polyploidy and are difficult to genetically modify. However, recent advances in genome sequencing and editing have enabled polyploid genome engineering. The hexaploid black nightshade species Solanum nigrum has immense potential as a beneficial food supplement. We assembled its genome at the scaffold level. After functional annotations, we identified homoeologous gene sets, with similar sequence and expression profiles, based on comparative analyses of orthologous genes with close diploid relatives Solanum americanum and S. lycopersicum. Using CRISPR-Cas9-mediated mutagenesis, we generated various mutation combinations in homoeologous genes. Multiple mutants showed quantitative phenotypic changes based on the genotype, resulting in a broad-spectrum effect on the quantitative traits of hexaploid S. nigrum. Furthermore, we successfully improved the fruit productivity of Boranong, an orphan cultivar of S. nigrum suggesting that engineering homoeologous genes could be useful for agricultural improvement of polyploid crops.
Topics: Base Sequence; Chromosome Mapping; Mutation; Phenotype; Crops, Agricultural; Polyploidy; Genome, Plant; Gene Editing
PubMed: 37530518
DOI: 10.1111/pbi.14141 -
Nature Communications Nov 2023Transposable elements (TEs) comprise ~85% of the common wheat genome, which are highly diverse among subgenomes, possibly contribute to polyploid plasticity, but the...
Transposable elements (TEs) comprise ~85% of the common wheat genome, which are highly diverse among subgenomes, possibly contribute to polyploid plasticity, but the causality is only assumed. Here, by integrating data from gene expression cap analysis and epigenome profiling via hidden Markov model in common wheat, we detect a large proportion of enhancer-like elements (ELEs) derived from TEs producing nascent noncoding transcripts, namely ELE-RNAs, which are well indicative of the regulatory activity of ELEs. Quantifying ELE-RNA transcriptome across typical developmental stages reveals that TE-initiated ELE-RNAs are mainly from RLG_famc7.3 specifically expanded in subgenome A. Acquisition of spike-specific transcription factor binding likely confers spike-specific expression of RLG_famc7.3-initiated ELE-RNAs. Knockdown of RLG_famc7.3-initiated ELE-RNAs resulted in global downregulation of spike-specific genes and abnormal spike development. These findings link TE expansion to regulatory specificity and polyploid developmental plasticity, highlighting the functional impact of TE-driven regulatory innovation on polyploid evolution.
Topics: DNA Transposable Elements; Triticum; Gene Expression Regulation; Polyploidy; Transcriptome; RNA
PubMed: 37978184
DOI: 10.1038/s41467-023-42771-9 -
Critical shifts in lipid metabolism promote megakaryocyte differentiation and proplatelet formation.Nature Cardiovascular Research Sep 2023During megakaryopoiesis, megakaryocytes (MK) undergo cellular morphological changes with strong modification of membrane composition and lipid signaling. Here we adopt a...
During megakaryopoiesis, megakaryocytes (MK) undergo cellular morphological changes with strong modification of membrane composition and lipid signaling. Here we adopt a lipid-centric multiomics approach to create a quantitative map of the MK lipidome during maturation and proplatelet formation. Data reveal that MK differentiation is driven by an increased fatty acyl import and lipid synthesis, resulting in an anionic membrane phenotype. Pharmacological perturbation of fatty acid import and phospholipid synthesis blocked membrane remodeling and directly reduced MK polyploidization and proplatelet formation resulting in thrombocytopenia. The anionic lipid shift during megakaryopoiesis was paralleled by lipid-dependent relocalization of the scaffold protein CKIP-1 and recruitment of the kinase CK2α to the plasma membrane, which seems to be essential for sufficient platelet biogenesis. Overall, this study provides a framework to understand how the MK lipidome is altered during maturation and the impact of MK membrane lipid remodeling on MK kinase signaling involved in thrombopoiesis.
PubMed: 38075556
DOI: 10.1038/s44161-023-00325-8 -
International Journal of Molecular... Oct 2023Alternative splicing (AS) is a gene regulatory mechanism modulating gene expression in multiple ways. AS is prevalent in all eukaryotes including plants. AS generates... (Review)
Review
Alternative splicing (AS) is a gene regulatory mechanism modulating gene expression in multiple ways. AS is prevalent in all eukaryotes including plants. AS generates two or more mRNAs from the precursor mRNA (pre-mRNA) to regulate transcriptome complexity and proteome diversity. Advances in next-generation sequencing, omics technology, bioinformatics tools, and computational methods provide new opportunities to quantify and visualize AS-based quantitative trait variation associated with plant growth, development, reproduction, and stress tolerance. Domestication, polyploidization, and environmental perturbation may evolve novel splicing variants associated with agronomically beneficial traits. To date, pre-mRNAs from many genes are spliced into multiple transcripts that cause phenotypic variation for complex traits, both in model plant and field crops. Cataloguing and exploiting such variation may provide new paths to enhance climate resilience, resource-use efficiency, productivity, and nutritional quality of staple food crops. This review provides insights into AS variation alongside a gene expression analysis to select for novel phenotypic diversity for use in breeding programs. AS contributes to heterosis, enhances plant symbiosis (mycorrhiza and rhizobium), and provides a mechanistic link between the core clock genes and diverse environmental clues.
Topics: Alternative Splicing; Plant Breeding; RNA Splicing; Arabidopsis; Crops, Agricultural; RNA Precursors
PubMed: 37894886
DOI: 10.3390/ijms242015205 -
Plant Communications Nov 2023Plants adapted to challenging environments offer fascinating models of evolutionary change. Importantly, they also give information to meet our pressing need to develop... (Review)
Review
Plants adapted to challenging environments offer fascinating models of evolutionary change. Importantly, they also give information to meet our pressing need to develop resilient, low-input crops. With mounting environmental fluctuation-including temperature, rainfall, and soil salinity and degradation-this is more urgent than ever. Happily, solutions are hiding in plain sight: the adaptive mechanisms from natural adapted populations, once understood, can then be leveraged. Much recent insight has come from the study of salinity, a widespread factor limiting productivity, with estimates of 20% of all cultivated lands affected. This is an expanding problem, given increasing climate volatility, rising sea levels, and poor irrigation practices. We therefore highlight recent benchmark studies of ecologically adaptive salt tolerance in plants, assessing macro- and microevolutionary mechanisms, and the recently recognized role of ploidy and the microbiome on salinity adaptation. We synthesize insight specifically on naturally evolved adaptive salt-tolerance mechanisms, as these works move substantially beyond traditional mutant or knockout studies, to show how evolution can nimbly "tweak" plant physiology to optimize function. We then point to future directions to advance this field that intersect evolutionary biology, abiotic-stress tolerance, breeding, and molecular plant physiology.
Topics: Salt Tolerance; Soil; Crops, Agricultural
PubMed: 36883005
DOI: 10.1016/j.xplc.2023.100571 -
Advanced Science (Weinheim,... Nov 2023Prokaryotic genomes are generally organized in haploid. In synthetic biological research, efficient chassis cells must be constructed to produce bio-based products....
Prokaryotic genomes are generally organized in haploid. In synthetic biological research, efficient chassis cells must be constructed to produce bio-based products. Here, the essential division of the ftsZ gene to create functional polyploid E. coli is regulated. The artificial polyploid E. coli containing 2-4 chromosomes is confirmed through PCR amplification, terminator localization, and flow cytometry. The polyploid E. coli exhibits a larger cell size, and its low pH tolerance and acetate resistance are stronger than those of haploid E. coli. Transcriptome analysis shows that the genes of the cell's main functional pathways are significantly upregulated in the polyploid E. coli. These advantages of the polyploid E. coli results in the highest reported L-threonine yield (160.3 g L ) in fed-batch fermentation to date. In summary, an easy and convenient method for constructing polyploid E. coli and demonstrated its application in L-threonine production is developed. This work provides a new approach for creating an excellent host strain for biochemical production and studying the evolution of prokaryotes and their chromosome functions.
Topics: Escherichia coli; Metabolic Engineering; Threonine; Fermentation
PubMed: 37749873
DOI: 10.1002/advs.202302417 -
Frontiers in Plant Science 2023Grapevines are economically important woody perennial crops widely cultivated for their fruits that are used for making wine, grape juice, raisins, and table grapes.... (Review)
Review
Grapevines are economically important woody perennial crops widely cultivated for their fruits that are used for making wine, grape juice, raisins, and table grapes. However, grapevine production is constantly facing challenges due to climate change and the prevalence of pests and diseases, causing yield reduction, lower fruit quality, and financial losses. To ease the burden, continuous crop improvement to develop superior grape genotypes with desirable traits is imperative. Polyploidization has emerged as a promising tool to generate genotypes with novel genetic combinations that can confer desirable traits such as enhanced organ size, improved fruit quality, and increased resistance to both biotic and abiotic stresses. While previous studies have shown high polyploid induction rates in spp., rigorous screening of genotypes among the produced polyploids to identify those exhibiting desired traits remains a major bottleneck. In this perspective, we propose the integration of the genomic selection approach with omics data to predict genotypes with desirable traits among the vast unique individuals generated through polyploidization. This integrated approach can be a powerful tool for accelerating the breeding of grapevines to develop novel and improved grapevine varieties.
PubMed: 38034577
DOI: 10.3389/fpls.2023.1248978 -
Plants (Basel, Switzerland) Nov 2023Polyploidy is a significant evolutionary process in plants that involves the duplication of genomic content and has been recognized as a key mechanism driving plant...
Polyploidy is a significant evolutionary process in plants that involves the duplication of genomic content and has been recognized as a key mechanism driving plant diversification and adaptation. In natural populations, polyploids frequently arise from unreduced gametes, which subsequently fuse with reduced or unreduced gametes, resulting in triploid or tetraploid offspring, respectively. L. is a diploid species, but recent work using artificially induced polyploidy has demonstrated its potential advantages in an agricultural setting. Further, recent work has identified that some elite clonal cultivars, vis. Mac1, are triploid, with no indication that they were artificially produced. The current study was conducted to determine if polyploidy is a naturally occurring phenomenon in cannabis and to estimate the frequency of this phenomenon across populations. To do this, the presence of natural triploid individuals was evaluated in 13 seedling populations of cannabis using a flow cytometry analysis. Among the examined populations, natural triploids were identified in 10 groups with an average frequency of approximately 0.5%. The highest frequency of natural triploids was observed in a self-pollinated population at 2.3%. This research demonstrates that polyploidy is a naturally occurring event in cannabis and triploids are present at an average of approximately 0.5%, or 1 in 200 plants. These data shed light on the natural variation in ploidy within cannabis populations and contribute valuable insights to the understanding of cannabis genetics and breeding practices.
PubMed: 38068564
DOI: 10.3390/plants12233927 -
Trends in Genetics : TIG Oct 2023Angiosperm diversity arises from trait flexibility and repeated evolutionary radiations, but the role of genomic characters in these radiations remains unclear. In this... (Review)
Review
Angiosperm diversity arises from trait flexibility and repeated evolutionary radiations, but the role of genomic characters in these radiations remains unclear. In this opinion article, we discuss how genome size can influence angiosperm diversification via its intricate link with cell size, tissue packing, and physiological processes which, in turn, influence the macroevolution of functional traits. We propose that integrating genome size, functional traits, and phylogenetic data across a wide range of lineages allows us to test whether genome size decrease consistently leads to increased trait flexibility, while genome size increase constrains trait evolution. Combining theories from molecular biology, functional ecology and macroevolution, we provide a framework to better understand the role of genome size in trait evolution, evolutionary radiations, and the global distribution of angiosperms.
Topics: Phylogeny; Biological Evolution; Magnoliopsida; Genome Size; Ecology
PubMed: 37582671
DOI: 10.1016/j.tig.2023.07.006 -
Translational Oncology Jan 2024Adipocytes are derived from pluripotent mesenchymal stem cells and can develop into several cell types including adipocytes, myocytes, chondrocytes, and osteocytes.... (Review)
Review
Adipocytes are derived from pluripotent mesenchymal stem cells and can develop into several cell types including adipocytes, myocytes, chondrocytes, and osteocytes. Adipocyte differentiation is regulated by a variety of transcription factors and signaling pathways. Various epigenetic factors, particularly histone modifications, play key roles in adipocyte differentiation and have indispensable functions in altering chromatin conformation. Histone acetylases and deacetylases participate in the regulation of protein acetylation, mediate transcriptional and post-translational modifications, and directly acetylate or deacetylate various transcription factors and regulatory proteins. The adipocyte differentiation of stem cells plays a key role in various metabolic diseases. Cancer stem cells(CSCs) play an important function in cancer metastasis, recurrence, and drug resistance, and have the characteristics of stem cells. They are expressed in various cell lineages, including adipocytes. Recent studies have shown that cancer stem cells that undergo epithelial-mesenchymal transformation can undergo adipocytic differentiation, thereby reducing the degree of malignancy. This opens up new possibilities for cancer treatment. This review summarizes the regulation of acetylation during adipocyte differentiation, involving the functions of histone acetylating and deacetylating enzymes as well as non-histone acetylation modifications. Mechanistic studies on adipogenesis and acetylation during the differentiation of cancer cells into a benign cell phenotype may help identify new targets for cancer treatment.
PubMed: 37935080
DOI: 10.1016/j.tranon.2023.101815