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Background: We studied patterns of molecular adaptation in the wild Mediterranean legume Medicago truncatula. We focused on two phenotypic traits that are not functionally linked: flowering time and perception of symbiotic microbes. Phenology is an important fitness component, especially for annual plants, and many instances of molecular adaptation have been reported for genes involved in flowering pathways. While perception of symbiotic microbes is also integral to adaptation in many plant species, very few reports of molecular adaptation exist for symbiotic genes. Here we used data from 57 individuals and 53 gene fragments to quantify the overall strength of both positive and purifying selection in M. truncatula and asked if footprints of positive selection can be detected at key genes of rhizobia recognition pathways.
Results: We examined nucleotide variation among 57 accessions from natural populations in 53 gene fragments: 5 genes involved in nitrogen-fixing bacteria recognition, 11 genes involved in flowering, and 37 genes used as control loci. We detected 1757 polymorphic sites yielding an average nucleotide diversity (pi) of 0.003 per site. Non-synonymous variation is under sizable purifying selection with 90% of amino-acid changing mutations being strongly selected against. Accessions were structured in two groups consistent with geographical origins. Each of these two groups harboured an excess of rare alleles, relative to expectations of a constant-sized population, suggesting recent population expansion. Using coalescent simulations and an approximate Bayesian computation framework we detected several instances of genes departing from selective neutrality within each group and showed that the polymorphism of two nodulation and four flowering genes has probably been shaped by recent positive selection.
Conclusion: We quantify the intensity of purifying selection in the M. truncatula genome and show that putative footprints of natural selection can be detected at different time scales in both flowering and symbiotic pathways.
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http://dx.doi.org/10.1186/1471-2148-11-229 | DOI Listing |
Angew Chem Int Ed Engl
December 2024
Chinese Academy of Sciences Fujian Institute of Research on the Structure of Matter, The State Key Laboratory of Structural Chemistry, 155 Yangqiao Road West, 350002, Fuzhou, CHINA.
Macrocycles represent one important class of functional molecules, and dynamic macrocycles with the potential of cleavability, adaptability, and topological conversion are challenging. Herein we report photoswitchable allosteric and topological control of dynamic covalent macrocycles and further the use in guest binding and mechanically interlocked molecules. The manipulation of competing ring-chain equilibria and bond formation/scission within reaction systems enabled light-induced structural regulation over dithioacetal and thioacetal dynamic bonds, accordingly realizing bidirectional switching between crown ether-like covalent macrocycles and their linear counterparts.
View Article and Find Full Text PDFAutoimmun Rev
December 2024
Department of Clinical Immunology, PLA Specialized Research Institute of Rheumatology & Immunology, Xijing Hospital and National Translational Science Center for Molecular Medicine, Fourth Military Medical University, Shaanxi, China. Electronic address:
Citrullination, a post-translational modification that changes arginine to citrulline in proteins, is vital for immune response modulation and cell signaling. Catalyzed by peptidyl arginine deiminases (PADs), citrullination is linked to various diseases, particularly autoimmune disorders like rheumatoid arthritis (RA). Citrullinated proteins can trigger the production of anti-citrullinated protein antibodies (ACPAs), included in RA classification criteria.
View Article and Find Full Text PDFMol Biol Evol
December 2024
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
The origin of genes from non-coding sequences is a long-term and fundamental biological question. However, how de novo genes originate and integrate into the existing pathways to regulate phenotypic variations is largely unknown. Here, we selected seven genes from 782 de novo genes for functional exploration based on transcriptional and translational evidence.
View Article and Find Full Text PDFJ Cell Mol Med
December 2024
Laboratoire d'Oncologie Moléculaire, Département de Chimie, Université du Québec à Montréal, Montreal, Quebec, Canada.
The Hippo pathway plays a tumorigenic role in highly angiogenic glioblastoma (GBM), whereas little is known about clinically relevant Hippo pathway inhibitors' ability to target adaptive mechanisms involved in GBM chemoresistance. Their molecular impact was investigated here in vitro against an alternative process to tumour angiogenesis termed vasculogenic mimicry (VM) in GBM-derived cell models. In silico analysis of the downstream Hippo signalling members YAP1, TAZ and TEAD1 transcript levels in low-grade glioblastoma (LGG) and GBM tumour tissues was performed using GEPIA.
View Article and Find Full Text PDFAnal Chem
December 2024
Instituto de Biomedicina y Genética Molecular, Unidad de Excelencia, University of Valladolid-CSIC, Valladolid 47003, Spain.
Lipid rafts are liquid-ordered domains in which specific enzymes and receptors are located. These membrane platforms play crucial roles in a variety of signaling pathways. Alterations in the lipid environment, such as those elicited by oxidative stress, can lead to important functional disruptions in membrane proteins.
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