Type III-A CRISPR-Cas Csm Complexes: Assembly,Periodic RNA Cleavage,DNase Activity Regulation,and Autoimmunity

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Soil microbiome mediates positive plant diversity‐productivity relationships in late successional grassland species

Which processes drive the productivity benefits of biodiversity remain a critical, but unanswered question in ecology. We tested whether the soil microbiome mediates the diversity‐productivity relationships among late successional plant species. We found that productivity increased with plant richness in diverse soil communities, but not with low‐diversity mixtures of arbuscular mycorrhizal fungi or in pasteurised soils. Diversity‐interaction modelling revealed that pairwise interactions among species best explained the positive diversity‐productivity relationships, and that transgressive overyielding resulting from positive complementarity was only observed with the late successional soil microbiome, which was both the most diverse and exhibited the strongest community differentiation among plant species. We found evidence that both dilution/suppression from host‐specific pathogens and microbiome‐mediated resource partitioning contributed to positive diversity‐productivity relationships and overyielding. Our results suggest that re‐establishment of a diverse, late successional soil microbiome may be critical to the restoration of the functional benefits of plant diversity following anthropogenic disturbance.     

Delineation of critical amino acids in activation function 1 of progesterone receptor for recruitment of transcription coregulators

The activation functions AF1 and AF2 of nuclear receptors mediate the recruitment of coregulators in gene regulation. AF1 is mapped to the highly variable and intrinsically unstructured N terminal domain and AF2 lies in the conserved ligand binding domain. The unstructured nature of AF1 offers structural plasticity and hence functional versatility in gene regulation. However, little is known about the key functional residues of AF1 that mediates its interaction with coregulators. This study focuses on the progesterone receptor (PR) and reports the identification of K464, K481 and R492 (KKR) as the key functional residues of PR AF1. The KKR are monomethylated and function cooperatively. The combined mutations of KKR to QQQ render PR isoform B (PRB) hyperactive, whereas KKR to FFF mutations abolishes as much as 80% of PR activity. Furthermore, the hyperactive QQQ mutation rescues the loss of PR activity due to E911A mutation in AF2. The study also finds that the magnitudes of the mutational effect differ in different cell types as a result of differential effects on the functional interaction with coregulators. Furthermore, KKR provides the interface for AF1 to physically interact with p300 and SRC-1, and with AF2 at E911. Intriguingly, the inactive FFF mutant interacts strikingly stronger with both SRC-1 and AF2 than wt PRB. We propose a tripartite model to describe the dynamic interactions between AF1, AF2 and SRC-1 with KKR of AF1 and E911 of AF2 as the interface. An overly stable interaction would hamper the dynamics of disassembly of the receptor complex.     

Contributions of the C-terminal domain to poly(A)-specific ribonuclease (PARN) stability and self-association

Poly(A)-specific ribonuclease (PARN) catalyzes the degradation of mRNA poly(A) tail to regulate translation efficiency and mRNA decay in higher eukaryotic cells. The full-length PARN is a multi-domain protein containing the catalytic nuclease domain, the R3H domain, the RRM domain and the C-terminal intrinsically unstructured domain (CTD). The roles of the three well-structured RNA-binding domains have been extensively studied, while little is known about CTD. In this research, the impact of CTD on PARN stability and aggregatory potency was studied by comparing the thermal inactivation and denaturation behaviors of full-length PARN with two N-terminal fragments lacking CTD. Our results showed that K⁺ induced additional regular secondary structures and enhanced PARN stability against heat-induced inactivation, unfolding and aggregation. CTD prevented PARN from thermal inactivation but promoted thermal aggregation to initiate at a temperature much lower than that required for inactivation and unfolding. Blue-shift of Trp fluorescence during thermal transitions suggested that heat treatment induced rearrangements of domain organizations. CTD amplified the stabilizing effect of K⁺, implying the roles of CTD was mainly achieved by electrostatic interactions. These results suggested that CTD might dynamically interact with the main body of the molecule and release of CTD promoted self-association via electrostatic interactions.     

Opposing effects of plant growth regulators via clonal integration on apical and basal performance in alligator weed

植物生长调节剂通过克隆整合对空心莲子草顶端和基部生长的不同作用 入侵植物不仅对全球生物多样性造成了巨大的威胁,同时也严重影响了农业生产与粮食安全。克隆整合使得相连植株进行资源共享,能促进入侵植物的生长从而获得优势。然而,入侵杂草 在植物调节剂(plant growth regulators, PGRs)影响下的克隆整合作用则很少有报道。PGRs被广泛应用于 农作物生产上,并能通过土壤淋溶、侵蚀和径流作用,影响分布在作物附近的农田杂草的生长。本 研究采用两种PGRs赤霉素(gibberellins, GA)和多效唑(paclobutrazol,PAC)处理恶性入侵杂草空心莲子草 (Alternanthera philoxeroides)基端,并保持或者通过剪切达到控制基端与顶端的连通,从而探究克隆整合作用在空心莲子草响应两种农业常用PGRs中的作用。研究结果表明,GA和PAC对空心莲子草生长的作用相反。GA通过克隆整合作用显著促进顶端植株的地上生长。相反地,PAC显著抑制基端和顶端的地 上生长,但是能够通过克隆整合作用显著促进基端和顶端的地下生长。这些研究结果解释了克隆整合作用能促进PGRs对空心莲子草生长的促进作用,这很可能是外来杂草能够成功入侵人为干扰较多的农业生态系统的重要原因之一。     

Residue-level prediction of DNA-binding sites and its application on DNA-binding protein predictions

Protein-DNA interactions are crucial to many cellular activities such as expression-control and DNA-repair. These interactions between amino acids and nucleotides are highly specific and any aberrance at the binding site can render the interaction completely incompetent. In this study, we have three aims focusing on DNA-binding residues on the protein surface: to develop an automated approach for fast and reliable recognition of DNA-binding sites; to improve the prediction by distance-dependent refinement; use these predictions to identify DNA-binding proteins. We use a support vector machines (SVM)-based approach to harness the features of the DNA-binding residues to distinguish them from non-binding residues. Features used for distinction include the residue's identity, charge, solvent accessibility, average potential, the secondary structure it is embedded in, neighboring residues, and location in a cationic patch. These features collected from 50 proteins are used to train SVM. Testing is then performed on another set of 37 proteins, much larger than any testing set used in previous studies. The testing set has no more than 20% sequence identity not only among its pairs, but also with the proteins in the training set, thus removing any undesired redundancy due to homology. This set also has proteins with an unseen DNA-binding structural class not present in the training set. With the above features, an accuracy of 66% with balanced sensitivity and specificity is achieved without relying on homology or evolutionary information. We then develop a post-processing scheme to improve the prediction using the relative location of the predicted residues. Balanced success is then achieved with average sensitivity, specificity and accuracy pegged at 71.3%, 69.3% and 70.5%, respectively. Average net prediction is also around 70%. Finally, we show that the number of predicted DNA-binding residues can be used to differentiate DNA-binding proteins from non-DNA-binding proteins with an accuracy of 78%. Results presented here demonstrate that machine-learning can be applied to automated identification of DNA-binding residues and that the success rate can be ameliorated as more features are added. Such functional site prediction protocols can be useful in guiding consequent works such as site-directed mutagenesis and macromolecular docking.     

A loop of coagulation factor VIIa influencing macromolecular substrate specificity

Coagulation factor VIIa (FVIIa) belongs to a family of proteases being part of the stepwise, self-amplifying blood coagulation cascade. To investigate the impact of the mutation Met(298{156})Lys in FVIIa, we replaced the Gly(283{140})-Met(298{156}) loop with the corresponding loop of factor Xa. The resulting variant exhibited increased intrinsic activity, concurrent with maturation of the active site, a less accessible N-terminus, and, interestingly, an altered macromolecular substrate specificity reflected in an increased ability to cleave factor IX (FIX) and a decreased rate of FX activation compared to that of wild-type FVIIa. In complex with tissue factor, activation of FIX, but not of FX, returned to normal. Deconvolution of the loop graft in order to identify important side chain substitutions resulted in the mutant Val(158{21})Asp/Leu(287{144})Thr/Ala(294{152})Ser/Glu(296{154}) Ile/Met(298{156})Lys-FVIIa with almost the same activity and specificity profile. We conclude that a lysine residue in position 298{156} of FVIIa requires a hydrophilic environment to be fully accommodated. This position appears critical for substrate specificity among the proteases of the blood coagulation cascade due to its prominent position in the macromolecular exosite and possibly via its interaction with the corresponding position in the substrate (i.e. FIX or FX).     

Fourteen polymorphic microsatellite loci in the field gudgeon,Gnathopogon elongatus elongatus

We isolated and characterized 14 polymorphic microsatellite loci for the field gudgeon, Gnathopogon elongatus elongatus, a popular freshwater species in streams including agricultural canals in Japan. The number of observed alleles for each locus ranged from 9 to 24, and the values of observed and expected heterozygosities ranged from 0.750 to 1.000 and from 0.832 to 0.953, respectively. These microsatellite markers will be useful for studies of population genetic structure and genetic variability of the field gudgeon.     

Soil multitrophic network complexity enhances the link between biodiversity and multifunctionality in agricultural systems

Belowground biodiversity supports multiple ecosystem functions and services that humans rely on. However, there is a dearth of studies exploring the determinants of the biodiversity–ecosystem function (BEF) relationships, particularly in intensely managed agricultural ecosystems. Here, we reported significant and positive relationships between soil biodiversity of multiple organism groups and multiple ecosystem functions in 228 agricultural fields, relating to crop yield, nutrient provisioning, element cycling, and pathogen control. The relationships were influenced by the types of organisms that soil phylotypes with larger sizes or at higher trophic levels, for example, invertebrates or protist predators, appeared to exhibit weaker or no BEF relationships when compared to those with smaller sizes or at lower trophic levels, for example, archaea, bacteria, fungi, and protist phototrophs. Particularly, we highlighted the role of soil network complexity, reflected by co-occurrence patterns among multitrophic-level organisms, in enhancing the link between soil biodiversity and ecosystem functions. Our results represent a significant advance in forecasting the impacts of belowground multitrophic organisms on ecosystem functions in agricultural systems, and suggest that soil multitrophic network complexity should be considered a key factor in enhancing ecosystem productivity and sustainability under land-use intensification.     

First report of the invasive crop pest Stenocranus pacificus (Hemiptera: Delphacidae) in temperate Asia

Numerous delphacid planthopper species are major pests of economically important and widely cultivated crops (i.e. rice, corn, and sugarcane). These insects have the potential to become serious crop pests in areas where they have either naturally migrated or been newly introduced. The white-bellied planthopper, Stenocranus pacificus Kirkaldy, 1907, originally known from tropical South Pacific islands, appeared in tropical and subtropical Asia in the early years of the 21st century. Since then, S. pacificus has become a serious pest of corn in some Southeast Asian countries, although it also feeds on rice, sugarcane, sorghum, and other grasses. Here, we report the presence of S. pacificus in mainland Japan, representing the first record of this species in temperate Asia. Seven male and 17 female adult individuals collected in Kumamoto Prefecture in 2019 and 2020 were identified as S. pacificus based on their morphological characteristics and mitochondrial COI sequences. In addition, molecular phylogenetic analysis showed that S. pacificus formed a distinct clade from other Stenocranus species, indicating uncertainty in its generic assignment. Although crop damage by S. pacificus has not yet been reported from temperate regions, given its wide range of plant hosts and the potential for future range expansions, damaged crops in Asia, including in temperate regions, should be monitored for the presence of this species.