Plant disease resistance genes (R genes) encode proteins that function to monitor signals indicating pathogenic infection, thus playing a critical role in the plant's defense system. Although many ...studies have been performed to explore the functional details of these important genes, their origin and evolutionary history remain unclear.
In this study, focusing on the largest group of R genes, the nucleotide-binding site–leucinerich repeat (NBS-LRR) genes, we conducted an extensive genome-wide survey of 38 representative model organisms and obtained insights into the evolutionary stage and timing of NBS-LRR genes.
Our data show that the two major domains, NBS and LRR, existed before the split of prokaryotes and eukaryotes but their fusion was observed only in land plant lineages. The Toll/interleukin-1 receptor (TIR) class of NBS-LRR genes probably had an earlier origin than its nonTIR counterpart. The similarities of the innate immune systems of plants and animals are likely to have been shaped by convergent evolution after their independent origins.
Our findings start to unravel the evolutionary history of these important genes from the perspective of comparative genomics and also highlight the important role of reorganizing pre-existing building blocks in generating evolutionary novelties.
Sulfur oxidation is an essential component of the earth's sulfur cycle.
spp. can oxidize various reduced inorganic sulfur compounds (RISCs) with high efficiency to obtain electrons for their ...autotrophic growth. Strains in this genus have been widely applied in bioleaching and biological desulfurization. Diverse sulfur-metabolic pathways and corresponding regulatory systems have been discovered in these acidophilic sulfur-oxidizing bacteria. The sulfur-metabolic enzymes in
spp. can be categorized as elemental sulfur oxidation enzymes (sulfur dioxygenase, sulfur oxygenase reductase, and Hdr-like complex), enzymes in thiosulfate oxidation pathways (tetrathionate intermediate thiosulfate oxidation (S
I) pathway, the sulfur oxidizing enzyme (Sox) system and thiosulfate dehydrogenase), sulfide oxidation enzymes (sulfide:quinone oxidoreductase) and sulfite oxidation pathways/enzymes. The two-component systems (TCSs) are the typical regulation elements for periplasmic thiosulfate metabolism in these autotrophic sulfur-oxidizing bacteria. Examples are RsrS/RsrR responsible for S
I pathway regulation and TspS/TspR for Sox system regulation. The proposal of sulfur metabolic and regulatory models provide new insights and overall understanding of the sulfur-metabolic processes in
spp. The future research directions and existing barriers in the bacterial sulfur metabolism are also emphasized here and the breakthroughs in these areas will accelerate the research on the sulfur oxidation in
spp. and other sulfur oxidizers.
Mutation rates vary within genomes, but the causes of this remain unclear. As many prior inferences rely on methods that assume an absence of selection, potentially leading to artefactual results, we ...call mutation events directly using a parent-offspring sequencing strategy focusing on Arabidopsis and using rice and honey bee for replication. Here we show that mutation rates are higher in heterozygotes and in proximity to crossover events. A correlation between recombination rate and intraspecific diversity is in part owing to a higher mutation rate in domains of high recombination/diversity. Implicating diversity per se as a cause, we find an ∼3.5-fold higher mutation rate in heterozygotes than in homozygotes, with mutations occurring in closer proximity to heterozygous sites than expected by chance. In a genome that is a patchwork of heterozygous and homozygous domains, mutations occur disproportionately more often in the heterozygous domains. If segregating mutations predispose to a higher local mutation rate, clusters of genes dominantly under purifying selection (more commonly homozygous) and under balancing selection (more commonly heterozygous), might have low and high mutation rates, respectively. Our results are consistent with this, there being a ten times higher mutation rate in pathogen resistance genes, expected to be under positive or balancing selection. Consequently, we do not necessarily need to evoke extremely weak selection on the mutation rate to explain why mutational hot and cold spots might correspond to regions under positive/balancing and purifying selection, respectively.
Abstract
We propose an effective protocol for the implementation of nonadiabatic geometric quantum gates of cat-state qubits in Kerr-nonlinear resonators driven by two-photon squeezing drives. ...Coupling the Kerr-nonlinear resonators with an auxiliary qutrit with proper coupling strengths, the selective transition of the auxiliary qutrit is realized. The selective transition can be exploited in the implementation of a set of useful quantum gates, including the phase gates, the NOT gates, the controlled-phase gates, the controlled NOT gates, and the Toffoli gates. Numerical simulations show the implementations of different types of gates are robust against systematic errors, random noise, and decoherence. Therefore, the protocol may be helpful for robust and scalable quantum computation based on cat-state qubits.
In response to hypoxic succinate accumulates in arthritis synovium, however, the implication is little known. This study aims to investigate whether succinate could act as a metabolic signal linking ...metabolic alternation with angiogenesis in arthritis synovium.
The interaction between elevated succinate and VEGF production was examined in endothelial cells. Succinate production, HIF-1α induction and angiogenesis in the hypoxic synovium of collagen-induced arthritis rats were also investigated.
Intracellular succinate promoted VEGF production and induced angiogenic response dependent on HIF-1α induction in endothelial cells. Luciferase reporter assay showed that succinate increased VEGF expression through gene promoter activation dependent on HIF-1α induction. Intracellular succinate released into intercellular space, where extracellular succinate activated succinate receptor G-protein-coupled receptor 91 (GPR91) and induced VEGF production, further exacerbating angiogenesis. In addition, TGF-β1 treatment increased succinate production due to the reversal of succinate dehydrogenase (SDH) activation, and consistently, SDH inhibitor dimethyl malonate reduced angiogenesis in the arthritis synovium.
More than an intermediate, succinate functioned as a signaling molecule to link metabolic reprograming with angiogenesis. Intracellular succinate induced angiogenesis through HIF-1α induction, while extracellular succinate acted on GPR91 activation, working together to disturb energy metabolism and exacerbate inflammation and angiogenesis in arthritis synovium. Our work suggested that suppression of SDH could prevent succinate accumulation and inhibit angiogenesis via blocking HIF-1α/VEGF axis. This finding not only provides a novel insight into angiogenesis, but also reveals a potential therapeutical strategy to attenuate revascularization in arthritis.
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•Succinate acts as a metabolic signal linking metabolic alternation and angiogenesis;•Succinate induces angiogenesis through metabolic remodeling and HIF-1α/VEGF axis;•Suppression of SDH could prevent succinate accumulation and inhibit angiogenesis.
We show that the genomes of maize, sorghum, and brachypodium contain genes that, when transformed into rice, confer resistance to rice blast disease. The genes are resistance genes (R genes) that ...encode proteins with nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains (NBS–LRR proteins). By using criteria associated with rapid molecular evolution, we identified three rapidly evolving R -gene families in these species as well as in rice, and transformed a randomly chosen subset of these genes into rice strains known to be sensitive to rice blast disease caused by the fungus Magnaporthe oryzae . The transformed strains were then tested for sensitivity or resistance to 12 diverse strains of M. oryzae . A total of 15 functional blast R genes were identified among 60 NBS – LRR genes cloned from maize, sorghum, and brachypodium; and 13 blast R genes were obtained from 20 NBS – LRR paralogs in rice. These results show that abundant blast R genes occur not only within species but also among species, and that the R genes in the same rapidly evolving gene family can exhibit an effector response that confers resistance to rapidly evolving fungal pathogens. Neither conventional evolutionary conservation nor conventional evolutionary convergence supplies a satisfactory explanation of our findings. We suggest a unique mechanism termed “constrained divergence,” in which R genes and pathogen effectors can follow only limited evolutionary pathways to increase fitness. Our results open avenues for R -gene identification that will help to elucidate R -gene vs. effector mechanisms and may yield new sources of durable pathogen resistance.
Summary
Plant resistance genes (R genes) harbor tremendous allelic diversity, constituting a robust immune system effective against microbial pathogens. Nevertheless, few functional R genes have been ...identified for even the best‐studied pathosystems. Does this limited repertoire reflect specificity, with most R genes having been defeated by former pests, or do plants harbor a rich diversity of functional R genes, the composite behavior of which is yet to be characterized? Here, we survey 332 NBS‐LRR genes cloned from five resistant Oryza sativa (rice) cultivars for their ability to confer recognition of 12 rice blast isolates when transformed into susceptible cultivars. Our survey reveals that 48.5% of the 132 NBS‐LRR loci tested contain functional rice blast R genes, with most R genes deriving from multi‐copy clades containing especially diversified loci. Each R gene recognized, on average, 2.42 of the 12 isolates screened. The abundant R genes identified in resistant genomes provide extraordinary redundancy in the ability of host genotypes to recognize particular isolates. If the same is true for other pathogens, many extant NBS‐LRR genes retain functionality. Our success at identifying rice blast R genes also validates a highly efficient cloning and screening strategy.
Significance Statement
Resistance genes (R‐genes) provide protection against pathogens, but relatively few have been characterized. Here we surveyed the rice genome and identified 98 R‐genes capable of recognizing one or more isolates of rice blast, nearly twice the number previously identified against any pathogen. These results provide the most comprehensive picture to date of the architecture of resistance and overturn the perception that most R‐genes in genomes are relics that have been overcome by pathogens.
Along with the emergence of green plants on this planet one billion years ago, the nucleotide binding site leucine-rich repeat (NLR) gene family originated and diverged into at least three ...subclasses. Two of them, with either characterized N-terminal toll/interleukin-1 receptor (TIR) or coiled-coil (CC) domain, serve as major types of immune receptor of effector-triggered immunity (ETI) in plants, whereas the one having a N-terminal Resistance to powdery mildew8 (RPW8) domain, functions as signal transfer component to them. In this review, we briefly summarized the history of identification of diverse NLR subclasses across Viridiplantae lineages during the establishment of NLR category, and highlighted recent advances on the evolution of NLR genes and several key downstream signal components under the background of ecological adaption.
•Much about NLR diversity and function are known in angiosperms but unknown in other plant lineages.•Plant NLR gene expansion and contraction are largely driven by ecological adaption.•Origin and divergence of EDS1 gene family reshaped seed plants ETI system.•NLR genes co-evolve with several key signal components.
Most disease resistance genes in plants encode NBS-LRR proteins. However, in woody species, little is known about the evolutionary history of these genes. Here, we identified 459 and 330 respective ...NBS-LRRs in grapevine and poplar genomes. We subsequently investigated protein motif composition, phylogenetic relationships and physical locations. We found significant excesses of recent duplications in perennial species, compared with those of annuals, represented by rice and Arabidopsis. Consequently, we observed higher nucleotide identity among paralogs and a higher percentage of NBS-encoding genes positioned in numerous clusters in the grapevine and poplar. These results suggested that recent tandem duplication played a major role in NBS-encoding gene expansion in perennial species. These duplication events, together with a higher probability of recombination revealed in this study, could compensate for the longer generation time in woody perennial species e.g. duplication and recombination could serve to generate novel resistance specificities. In addition, we observed extensive species-specific expansion in TIR-NBS-encoding genes. Non-TIR-NBS-encoding genes were poly- or paraphyletic, i.e. genes from three or more plant species were nested in different clades, suggesting different evolutionary patterns between these two gene types.
We present the ElasTool package, an automated toolkit for calculating the second-order elastic constants (SOECs) of any two- (2D) and three-dimensional (3D) crystal systems. ElasTool uses three kinds ...of strain-matrix sets, i.e., the high-efficiency strain-matrix sets (OHESS), the universal linear-independent coupling strains (ULICS), and the all-single-element strain-matrix sets (ASESS), to calculate the SOECs automatically. ElasTool can efficiently compute both zero- and high-temperature elastic constants. We describe in detail the theoretical background and computational method of elastic constants, the package structure, the installation, and run, the input/output files, the controlling parameters, and two representative examples of how to use the ElasTool package. ElasTool is useful for either the exploration of materials' elastic properties or high-throughput new materials screening and design. ElasTool is freely available on GitHub: https://github.com/elastool
Program Title: ElasTool
CPC Library link to program files:https://doi.org/10.17632/ktvmxrdhpz.1
Code Ocean capsule:https://codeocean.com/capsule/1893813
Licensing provisions: GNU General Public License, version 3
Programming language: Python 3
External routines: NumPy 1, Spglib 2, ASE 3, Pandas 4
Nature of problem: The stress-strain method of elastic constants calculation depends on accurate stresses calculated with first-principles methods, such as the density functional theory (DFT). Compared to the energy-strain method, the stress-strain approach needs a smaller number of strain sets to solve the equation sets needed to deduce the elastic constants; it is also more straightforward to implement. However, accurate stresses take a lot of time to compute within DFT. Thus, a smaller number of strain sets and more efficient strain sets are urgently needed to improve the computational efficiency of elastic constants. An automated solution coupled with DFT is necessary for the exploration of materials' elastic properties and high-throughput new materials screening and design.
Solution method: The solution to improve the computational efficiency of the stress-strain method is to decrease the number of strain-matrix sets and optimize the strain-matrix sets. We coupled our previously proposed high-efficiency strain-matrix sets (OHESS) with DFT and automated the processes of calculating the elastic tensor using the stress-strain method in the ElasTool package. ElasTool can also adopt the all-single-element strain-matrix sets (ASESS) and the universal linear-independent coupling strains (ULICS) approaches. It can deal with both zero- and high-temperature elastic constants of any crystal systems belonging to 2D or 3D. Having obtained the elastic moduli, ElasTool also gives other essential mechanical and elastic properties of materials such as Young's modulus, bulk modulus, elastic anisotropy, Debye temperature, and the sound velocities.
Additional comments including restrictions and unusual features: Currently, this package interfaces with Vienna Ab initio Simulation Package (VASP) code as the stress tensors calculator. 5-7 Extension to other electronic structures is straightforward.
1https://numpy.org/2https://atztogo.github.io/spglib/3https://wiki.fysik.dtu.dk/ase/4https://pandas.pydata.org/5https://www.vasp.at/6G. Kresse, J. Furthmüller, Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set, Phys. Rev. B 54 (1996) 11169.7G. Kresse, D. Joubert, From ultrasoft pseudopotentials to the projector augmented-wave method, Phys. Rev. B 59 (1999) 1758.
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