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Genomics Mar 2021Here, 38 wheat PYL genes (TaPYLs) belonging to 13 homoeologous groups were identified using the genome-search method, with 26 and 12 PYL genes identified in Triticum...
Here, 38 wheat PYL genes (TaPYLs) belonging to 13 homoeologous groups were identified using the genome-search method, with 26 and 12 PYL genes identified in Triticum dicoccoides and Aegilops tauschii, respectively. Phylogenetic relationship, conserved domain and molecular evolution analysis revealed that PYL genes showed highly conservative between wheat and theprogenitors. Interaction network and miRNA target prediction found that TaPYLs could interact with the important components of ABA signaling pathway and Tae-miR966b-3p might be a hub regulator mediating wheat ABA signal network. Furthermore, the tissue-specific and stress-responsive TaPYLs were detected through RNA-seq analysis. Expressions of 10 TaPYLs were validated by QPCR analysis and the homoeologous genes showed significantly differential expression, suggesting subfunctionalization of them has occurred. Finally, 3D structures of the TaPYL proteins were predicted by homology modeling. This study lays the foundation for further functional study of PYL genes for development and stress tolerance improvement in wheat and beyond.
Topics: Conserved Sequence; Evolution, Molecular; Exons; Introns; Multigene Family; Plant Proteins; Protein Domains; Triticum
PubMed: 33321205
DOI: 10.1016/j.ygeno.2020.12.017 -
RNA Biology Jan 2023The genomic arrangement of most picornavirus of the family shares a similar monocistronic genomic pattern and a defining organizational feature. A defining feature of... (Review)
Review
The genomic arrangement of most picornavirus of the family shares a similar monocistronic genomic pattern and a defining organizational feature. A defining feature of picornavirus is the presence of evolutionarily conserved and highly-structured RNA elements in untranslated regions (UTRs) at the genome' 5'and 3' ends, essential for viral replication and translation. Given the diversity and complexity of RNA structure and the limitations of molecular biology techniques, the functional characterization and biological significance of UTRs remain to be fully elucidated, especially for 5' UTR. Here, we summarize the current knowledge of the 5' UTR of picornavirus. This review focuses on the structural characterization and the biological function of the RNA secondary and tertiary structures in the 5' UTR of picornavirus. Understanding the role of the 5' UTR of picornavirus can provide a deep insight into the viral replication cycle and pathogenic mechanisms.
Topics: 5' Untranslated Regions; Ribosomes; Nucleic Acid Conformation; Picornaviridae; RNA, Viral; 3' Untranslated Regions
PubMed: 37534989
DOI: 10.1080/15476286.2023.2240992 -
EMBO Reports Apr 2012Transcription is a complex process that integrates the state of the cell and its environment to generate adequate responses for cell fitness and survival. Recent... (Review)
Review
Transcription is a complex process that integrates the state of the cell and its environment to generate adequate responses for cell fitness and survival. Recent microscopy experiments have been able to monitor transcription from single genes in individual cells. These observations have revealed two striking features: transcriptional activity can vary markedly from one cell to another, and is subject to large changes over time, sometimes within minutes. How the chromatin structure, transcription machinery assembly and signalling networks generate such patterns is still unclear. In this review, we present the techniques used to investigate transcription from single genes, introduce quantitative modelling tools, and discuss transcription mechanisms and their implications for gene expression regulation.
Topics: Animals; Gene Expression Regulation; Genes; Humans; Models, Genetic; Stochastic Processes; Transcription, Genetic
PubMed: 22410830
DOI: 10.1038/embor.2012.31 -
Trends in Genetics : TIG Mar 2013Many bacterial and archaeal lineages have a history of extensive and ongoing horizontal gene transfer and loss, as evidenced by the large differences in genome content... (Review)
Review
Many bacterial and archaeal lineages have a history of extensive and ongoing horizontal gene transfer and loss, as evidenced by the large differences in genome content even among otherwise closely related isolates. How ecologically cohesive populations might evolve and be maintained under such conditions of rapid gene turnover has remained controversial. Here we synthesize recent literature demonstrating the importance of habitat and niche in structuring horizontal gene transfer. This leads to a model of ecological speciation via gradual genetic isolation triggered by differential habitat-association of nascent populations. Further, we hypothesize that subpopulations can evolve through local gene-exchange networks by tapping into a gene pool that is adaptive towards local, continuously changing organismic interactions and is, to a large degree, responsible for the observed rapid gene turnover. Overall, these insights help to explain how bacteria and archaea form populations that display both ecological cohesion and high genomic diversity.
Topics: Archaea; Bacteria; Ecosystem; Evolution, Molecular; Gene Transfer, Horizontal; Genes, Bacterial; Genotype; Multigene Family
PubMed: 23332119
DOI: 10.1016/j.tig.2012.12.006 -
Microbiology Spectrum Oct 2016This article provides an overview of sexual reproduction in the ascomycetes, a phylum of fungi that is named after the specialized sacs or "asci" that hold the sexual... (Review)
Review
This article provides an overview of sexual reproduction in the ascomycetes, a phylum of fungi that is named after the specialized sacs or "asci" that hold the sexual spores. They have therefore also been referred to as the Sac Fungi due to these characteristic structures that typically contain four to eight ascospores. Ascomycetes are morphologically diverse and include single-celled yeasts, filamentous fungi, and more complex cup fungi. The sexual cycles of many species, including those of the model yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe and the filamentous saprobes Neurospora crassa, Aspergillus nidulans, and Podospora anserina, have been examined in depth. In addition, sexual or parasexual cycles have been uncovered in important human pathogens such as Candida albicans and Aspergillus fumigatus, as well as in plant pathogens such as Fusarium graminearum and Cochliobolus heterostrophus. We summarize what is known about sexual fecundity in ascomycetes, examine how structural changes at the mating-type locus dictate sexual behavior, and discuss recent studies that reveal that pheromone signaling pathways can be repurposed to serve cellular roles unrelated to sex.
Topics: Ascomycota; Genes, Fungal; Genes, Mating Type, Fungal; Reproduction, Asexual
PubMed: 27763253
DOI: 10.1128/microbiolspec.FUNK-0005-2016 -
Genes To Cells : Devoted To Molecular &... Jun 1996In one scenario of gene evolution, exon shuffling has a fundamental role in increasing gene diversity. As DNA sequences accumulate in the databases, the picture of the... (Review)
Review
In one scenario of gene evolution, exon shuffling has a fundamental role in increasing gene diversity. As DNA sequences accumulate in the databases, the picture of the intron/exon structures of genes becomes more and more clear. We discuss in this review some features of this picture that suggest that introns have been present since the early stages of evolution, and that exon shuffling was a fundamental process in the construction of ancient as well as modern genes.
Topics: Animals; Evolution, Molecular; Exons; Genetic Variation; Humans; Introns; Models, Genetic; Molecular Structure; Phylogeny; Proteins; RNA
PubMed: 9078380
DOI: 10.1046/j.1365-2443.1996.d01-264.x -
Cold Spring Harbor Perspectives in... Jun 2010A common ancestor to the three p53 family members of human genes p53, p63, and p73 is first detected in the evolution of modern-day sea anemones, in which both... (Review)
Review
A common ancestor to the three p53 family members of human genes p53, p63, and p73 is first detected in the evolution of modern-day sea anemones, in which both structurally and functionally it acts to protect the germ line from genomic instabilities in response to stresses. This p63/p73 common ancestor gene is found in almost all invertebrates and first duplicates to produce a p53 gene and a p63/p73 ancestor in cartilaginous fish. Bony fish contain all three genes, p53, p63, and p73, and the functions of these three transcription factors diversify in the higher vertebrates. Thus, this gene family has preserved its structural features and functional activities for over one billion years of evolution.
Topics: Animals; Biological Evolution; Gene Expression Regulation; Humans; Multigene Family; Protein Structure, Tertiary; Tumor Suppressor Proteins
PubMed: 20516129
DOI: 10.1101/cshperspect.a001198 -
WormBook : the Online Review of C.... Oct 2014In the early stage of the C. elegans sequencing project, the ab initio gene prediction program Genefinder was used to find protein-coding genes. Subsequently,... (Review)
Review
In the early stage of the C. elegans sequencing project, the ab initio gene prediction program Genefinder was used to find protein-coding genes. Subsequently, protein-coding genes structures have been actively curated by WormBase using evidence from all available data sources. Most coding loci were identified by the Genefinder program, but the process of gene curation results in a continual refinement of the details of gene structure, involving the correction and confirmation of intron splice sites, the addition of alternate splicing forms, the merging and splitting of incorrect predictions, and the creation and extension of 5' and 3' ends. The development of new technologies results in the availability of further data sources, and these are incorporated into the evidence used to support the curated structures. Non-coding genes are more difficult to curate using this methodology, and so the structures for most of these have been imported from the literature or from specialist databases of ncRNA data. This article describes the structure and curation of transcribed regions of genes.
Topics: Animals; Caenorhabditis elegans; Genes, Helminth; Transcription, Genetic
PubMed: 25368915
DOI: 10.1895/wormbook.1.65.2 -
PloS One 2022Despite its high and direct impact on nearly all biological processes, the underlying structure of gene-gene interaction networks is investigated so far according to...
Despite its high and direct impact on nearly all biological processes, the underlying structure of gene-gene interaction networks is investigated so far according to pair connections. To address this, we explore the gene interaction networks of the yeast Saccharomyces cerevisiae beyond pairwise interaction using the structural balance theory (SBT). Specifically, we ask whether essential and nonessential gene interaction networks are structurally balanced. We study triadic interactions in the weighted signed undirected gene networks and observe that balanced and unbalanced triads are over and underrepresented in both networks, thus beautifully in line with the strong notion of balance. Moreover, we note that the energy distribution of triads is significantly different in both essential and nonessential networks compared to the shuffled networks. Yet, this difference is greater in the essential network regarding the frequency as well as the energy of triads. Additionally, results demonstrate that triads in the essential gene network are more interconnected through sharing common links, while in the nonessential network they tend to be isolated. Last but not least, we investigate the contribution of all-length signed walks and its impact on the degree of balance. Our findings reveal that interestingly when considering longer cycles, not only, both essential and nonessential gene networks are more balanced compared to their corresponding shuffled networks, but also, the nonessential gene network is more balanced compared to the essential network.
Topics: Gene Regulatory Networks; Genes, Essential; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins
PubMed: 35353818
DOI: 10.1371/journal.pone.0258596 -
The FEBS Journal Nov 2005The platelet-derived growth factor (PDGF) family was for more than 25 years assumed to consist of only PDGF-A and -B. The discovery of the novel family members PDGF-C... (Review)
Review
The platelet-derived growth factor (PDGF) family was for more than 25 years assumed to consist of only PDGF-A and -B. The discovery of the novel family members PDGF-C and PDGF-D triggered a search for novel activities and complementary fine tuning between the members of this family of growth factors. Since the expansion of the PDGF family, more than 60 publications on the novel PDGF-C and PDGF-D have been presented, highlighting similarities and differences to the classical PDGFs. In this paper we review the published data on the PDGF family covering structural (gene and protein) similarities and differences among all four family members, with special focus on PDGF-C and PDGF-D expression and functions. Little information on the protein structures of PDGF-C and -D is currently available, but the PDGF-C protein may be structurally more similar to VEGF-A than to PDGF-B. PDGF-C contributes to normal development of the heart, ear, central nervous system (CNS), and kidney, while PDGF-D is active in the development of the kidney, eye and brain. In adults, PDGF-C is active in the kidney and the central nervous system. PDGF-D also plays a role in the lung and in periodontal mineralization. PDGF-C is expressed in Ewing family sarcoma and PDGF-D is linked to lung, prostate and ovarian cancers. Both PDGF-C and -D play a role in progressive renal disease, glioblastoma/medulloblastoma and fibrosis in several organs.
Topics: Alternative Splicing; Amino Acid Motifs; Amino Acid Sequence; Animals; Codon, Initiator; Codon, Terminator; Cysteine; Dimerization; Disulfides; Exons; Humans; Introns; Lymphokines; Mice; Mice, Knockout; Models, Molecular; Molecular Sequence Data; Platelet-Derived Growth Factor; Promoter Regions, Genetic; Protein Binding; Protein Processing, Post-Translational; Protein Sorting Signals; Protein Structure, Secondary; Protein Structure, Tertiary; Receptors, Platelet-Derived Growth Factor; Sequence Homology, Amino Acid
PubMed: 16279938
DOI: 10.1111/j.1742-4658.2005.04989.x