Identification of Novel Regulators of Leaf Senescence Using a Deep Learning Model.

Deep learning has emerged as a powerful tool for investigating intricate biological processes in plants by harnessing the potential of large-scale data. Gene regulation is a complex process that transcription factors (TFs), cooperating with their target genes, participate in through various aspects of biological processes. Despite its significance, the study of gene regulation has primarily focused on a limited number of notable instances, leaving numerous aspects and interactions yet to be explored comprehensively. Here, we developed DEGRN (Deep learning on Expression for Gene Regulatory Network), an innovative deep learning model designed to decipher gene interactions by leveraging high-dimensional expression data obtained from bulk RNA-Seq and scRNA-Seq data in the model plant Arabidopsis. DEGRN exhibited a compared level of predictive power when applied to various datasets. Through the utilization of DEGRN, we successfully identified an extensive set of 3,053,363 high-quality interactions, encompassing 1430 TFs and 13,739 non-TF genes. Notably, DEGRN's predictive capabilities allowed us to uncover novel regulators involved in a range of complex biological processes, including development, metabolism, and stress responses. Using leaf senescence as an example, we revealed a complex network underpinning this process composed of diverse TF families, including bHLH, ERF, and MYB. We also identified a novel TF, named MAF5, whose expression showed a strong linear regression relation during the progression of senescence. The mutant maf5 showed early leaf decay compared to the wild type, indicating a potential role in the regulation of leaf senescence. This hypothesis was further supported by the expression patterns observed across four stages of leaf development, as well as transcriptomics analysis. Overall, the comprehensive coverage provided by DEGRN expands our understanding of gene regulatory networks and paves the way for further investigations into their functional implications.

BMSCs-derived Exosome CISH Alleviates Myocardial Infarction by Inactivating the NF-κB Pathway to Stimulate Macrophage M2 Polarization.

Current myocardial infarction (MI) treatments are suboptimal, necessitating deeper pathogenesis understanding of MI. This research explored how exosomes (Exo) derived from bone marrow mesenchymal stem cells (BMSCs) contribute to MI mitigation and their therapeutic potential. Isolated BMSCs was identified by microscope, flow cytometry, alizarin red and oil red O staining. Exo were identified by TEM, NTA and western blot. HE staining, masson staining, and cardiac function parameters were used to assess the cardiac function in MI mice. TUNEL staining, western blot and qRT-PCR were used to detect apoptosis, inflammatory factors and M1/M2 markers. The NF-κB pathway activation was detected through western blot assays. Immunofluorescence, qRT-PCR, western blot, and flow cytometry were employed to evaluate macrophage polarization. MI mice showed cardiac injury, increased apoptosis and inflammation, while BMSCs-Exo treatment alleviated these effects. In MI mice, the macrophage M1 polarization was increased and the NF-κB pathway was activated, whereas BMSCs-Exo treatment reversed these changes. Furthermore, CISH expression was reduced in MI mice, but was elevated with BMSCs-Exo treatment. In vitro, LPS shifted RAW264.7 cells to M1 phenotype and activated the NF-κB pathway, yet BMSCs-Exo shifted them to M2 phenotype and inhibited the NF-κB pathway. Mechanistically, BMSCs-Exo induced macrophage M2 polarization by transmitting CISH to inhibit NF-κB activation. BMSCs-Exo mitigates MI by transmitting CISH to inhibit the NF-κB pathway, promoting macrophages to M2 type. This implies BMSCs-Exo could be a useful treatment for MI, and CISH could be a potential therapy target.

Natural variation in Fatty Acid 9 is a determinant of fatty acid and protein content.

Soybean is one of the most economically important crops worldwide and an important source of unsaturated fatty acids and protein for the human diet. Consumer demand for healthy fats and oils is increasing, and the global demand for vegetable oil is expected to double by 2050. Identification of key genes that regulate seed fatty acid content can facilitate molecular breeding of high-quality soybean varieties with enhanced fatty acid profiles. Here, we analysed the genetic architecture underlying variations in soybean seed fatty acid content using 547 accessions, including mainly landraces and cultivars from northeastern China. Through fatty acid profiling, genome re-sequencing, population genomics analyses, and GWAS, we identified a SEIPIN homologue at the FA9 locus as an important contributor to seed fatty acid content. Transgenic and multiomics analyses confirmed that FA9 was a key regulator of seed fatty acid content with pleiotropic effects on seed protein and seed size. We identified two major FA9 haplotypes in 1295 resequenced soybean accessions and assessed their phenotypic effects in a field planting of 424 accessions. Soybean accessions carrying FA9H2 had significantly higher total fatty acid contents and lower protein contents than those carrying FA9H1 . FA9H2 was absent in wild soybeans but present in 13% of landraces and 26% of cultivars, suggesting that it may have been selected during soybean post-domestication improvement. FA9 therefore represents a useful genetic resource for molecular breeding of high-quality soybean varieties with specific seed storage profiles.

Exosomes Derived From Mesenchymal Stem Cells Pretreated With Ischemic Rat Heart Extracts Promote Angiogenesis via the Delivery of DMBT1.

Mesenchymal stem cell-derived exosomes (MSC-Exos) have been shown to promote angiogenesis. Treating MSCs with ischemic rat brain extracts was sufficient to augment their benefits in stroke. However, no similar analyses of ischemic heart extracts have been performed to date. We aim to determine whether MSC-Exos derived from MSCs pretreated with ischemic rat heart extract were able to promote angiogenesis and to clarify underlying mechanisms. ELISA (enzyme-linked immunosorbent assay) of heart extracts revealed a significant increase of vascular endothelial growth factor (VEGF) at 24 h post-MI (myocardial infarction) modeling, and time-dependent decreases in hypoxia inducible factor-1α (HIF-1α). MTT and wound healing assays revealed human umbilical vein endothelial cells (HUVECs) migration and proliferation increased following MSCE-Exo treatment (exosomes derived from MSC pretreated with ischemic heart extracts of 24 h post-MI) relative to MSCN-Exo treatment (exosomes derived from MSC pretreated with normal heart extracts). Proteomic analyses of MSCE-Exo and MSCN-Exo were conducted to screen for cargo proteins promoting angiogenesis. Result revealed several angiogenesis-related proteins were upregulated in MSCE-Exo, including DMBT1 (deleted in malignant brain tumors 1). When DMBT1 was silenced in MSCs, HUVECs with MSCDMBT1 RNAi-Exo treatment exhibited impaired proliferative and migratory activity and reductions of DMBT1, p-Akt, ß-catenin, and VEGF. To explore how ischemic heart extracts took effects, ELISA was conducted showing a significant increase of IL-22 at 24 h post-MI modeling. P-STAT3, IL22RA1, DMBT1, and VEGF proteins were increased in MSCE relative to MSCN, and VEGF and DMBT1 were increased in MSCE-Exos. Together, these suggest that IL-22 upregulation in ischemic heart extracts can increase DMBT1 in MSCs. Exosomes derived from those MSCs deliver DMBT1 to HUVECs, thereby enhancing their migratory and proliferative activity.

CRF07_BC is associated with slow HIV disease progression in Chinese patients.

HIV subtypes convey important epidemiological information and possibly influence the rate of disease progression. In this study, HIV disease progression in patients infected with CRF01_AE, CRF07_BC, and subtype B was compared in the largest HIV molecular epidemiology study ever done in China. A national data set of HIV pol sequences was assembled by pooling sequences from public databases and the Beijing HIV laboratory network. Logistic regression was used to assess factors associated with the risk of AIDS at diagnosis ([AIDSAD], defined as a CD4 count < 200 cells/µL) in patients with HIV subtype B, CRF01_AE, and CRF07_BC. Of the 20,663 sequences, 9,156 (44.3%) were CRF01_AE. CRF07_BC was responsible for 28.3% of infections, followed by B (13.9%). In multivariable analysis, the risk of AIDSAD differed significantly according to HIV subtype (OR for CRF07_BC vs. B: 0.46, 95% CI 0.39─0.53), age (OR for ≥ 65 years vs. < 18 years: 4.3 95% CI 1.81─11.8), and transmission risk groups (OR for men who have sex with men vs. heterosexuals: 0.67 95% CI 0.6─0.75). These findings suggest that HIV diversity in China is constantly evolving and gaining in complexity. CRF07_BC is less pathogenic than subtype B, while CRF01_AE is as pathogenic as B.

Lovastatin Inhibits RhoA to Suppress Canonical Wnt/ß-Catenin Signaling and Alternative Wnt-YAP/TAZ Signaling in Colon Cancer.

Statins are first-line drugs used to control patient lipid levels, but there is recent evidence that statin treatment can lower colorectal cancer (CRC) incidence by 50% and prolong CRC patient survival through mechanisms that are poorly understood. In this study, we found that the treatment of APCmin mice by the mevalonate pathway inhibitor lovastatin significantly reduced the number of colonic masses and improved hypersplenism and peripheral anemia. Furthermore, reverse transcription polymerase chain reaction (RT-PCR) analysis of colonic mass tissues showed a potent inhibitory effect in both Wnt/ß-catenin signaling and YAP/TAZ signaling in the lovastatin treatment group. The results of our transcriptomic analyses in RKO indicated that lovastatin regulated several proliferation-related signaling pathways. Moreover, lovastatin suppressed important genes and proteins related to the canonical Wnt/ß-catenin and alternative Wnt-YAP/TAZ signaling pathways in RKO and SW480 cells, and these effects were rescued by mevalonic acid (MVA), as confirmed through a series of Western blotting, RT-PCR, and reporter assays. Given that statins suppress oncogenic processes primarily through the inhibition of Rho GTPase in the mevalonate pathway, we speculate that lovastatin can inhibit certain Rho GTPases to suppress both canonical Wnt/ß-catenin signaling and alternative Wnt-YAP/TAZ signaling. In RKO cells, lovastatin showed similar inhibitory properties as the RhoA inhibitor CCG1423, being able to inhibit ß-catenin, TAZ, and p-LATS1 protein activity. Our results revealed that lovastatin inhibited RhoA activity, thereby suppressing the downstream canonical Wnt/ß-catenin and alternative Wnt-YAP/TAZ pathways in colon cancer cells. These inhibitory properties suggest the promise of statins as a treatment for CRC. Altogether, the present findings support the potential clinical use of statins in non-cardiovascular contexts and highlight novel targets for anticancer treatments.

The Bionic High-Cushioning Midsole of Shoes Inspired by Functional Characteristics of Ostrich Foot.

The sole is a key component of the interaction between foot and ground in daily activities, and its cushioning performance plays a crucial role in protecting the joints of lower limbs from impact injuries. Based on the excellent cushioning performance of the ostrich foot and inspired by the structure and material assembly features of the ostrich foot's metatarsophalangeal skeletal-tendon and the ostrich toe pad-fascia, a functional bionic cushioning unit for the midsole (including the forefoot and heel) area of athletic shoes was designed using engineering bionic technology. The bionic cushioning unit was then processed based on the bionic design model, and the shoe soles were tested with six impact energies ranging from 3.3 J to 11.6 J for a drop hammer impact and compared with the conventional control sole of the same size. The results indicated that the bionic forefoot area absorbed 9.83-34.95% more impact and 10.65-43.84% more energy than the conventional control forefoot area, while the bionic heel area absorbed 26.34-44.29% more impact and 28.1-51.29% more energy than the conventional control heel area when the controlled impact energy varied from 3.3 J to 11.6 J. The cushioning performance of the bionic cushioning sole was generally better than that of the conventional control sole, and the cushioning and energy-absorption performances of the heel bionic cushioning unit were better than those of the forefoot bionic cushioning unit. This study provides innovative reference and research ideas for the design and development of sports shoes with good cushioning performance.

A multilayered cross-species analysis of GRAS transcription factors uncovered their functional networks in plant adaptation to the environment.

Introduction: Environmental stress is both a major force of natural selection and a prime factor affecting crop qualities and yields. The impact of the GRAS [gibberellic acid-insensitive (GAI), repressor of GA1-3 mutant (RGA), and scarecrow (SCR)] family on plant development and the potential to resist environmental stress needs much emphasis. Objectives: This study aims to investigate the evolution, expansion, and adaptive mechanisms of GRASs of important representative plants during polyploidization. Methods: We explored the evolutionary characteristics of GRASs in 15 representative plant species by systematic biological analysis of the genome, transcriptome, metabolite, protein complex map and phenotype. Results: The GRAS family was systematically identified from 15 representative plant species of scientific and agricultural importance. The detection of gene duplication types of GRASs in all species showed that the widespread expansion of GRASs in these species was mainly contributed by polyploidization events. Evolutionary analysis reveals that most species experience independent genome-wide duplication (WGD) events and that interspecies GRAS functions may be broadly conserved. Polyploidy-related Chenopodium quinoa GRASs (CqGRASs) and Arabidopsis thaliana GRASs (AtGRASs) formed robust networks with flavonoid pathways by crosstalk with auxin and photosynthetic pathways. Furthermore, Arabidopsis thaliana population transcriptomes and the 1000 Plants (OneKP) project confirmed that GRASs are components of flavonoid biosynthesis, which enables plants to adapt to the environment by promoting flavonoid accumulation. More importantly, the GRASs of important species that may potentially improve important agronomic traits were mapped through TAIR and RARGE-II publicly available phenotypic data. Determining protein interactions and target genes contributes to determining GRAS functions. Conclusion: The results of this study suggest that polyploidy-related GRASs in multiple species may be a target for improving plant growth, development, and environmental adaptation.

Genomic characterization of a new CRF01_AE/CRF07_BC case from a MSM patient in Guangdong, China.

The CRF01_AE and CRF07_BC clades dominate the human immunodeficiency virus (HIV) epidemics in China. Both clades have been identified in the men who have sex with men (MSM) population in Guangdong province, raising a serious concern of possible complex recombination events ahead. Here, we report the first case of CRF01_AE/CRF07_BC recombinant sampled from a MSM patient in southern China. The genomic structure of this case is a mosaic with some regions resembling the CRF01_AE and CRF07_BC clades. Our phylogenetic analyses show that the two parental lineages of this recombinant virus were mainly found in the MSM population. This case has a different genomic composition compared with other recombinants descended from the same parental clades CRF01_AE and CRF07_BC. Our finding suggests that the MSM populations have become a hotspot for expanding viral diversity through the viral recombination mechanism. Therefore, further epidemiologic surveillance and monitoring should be conducted within the MSM populations to help advance our knowledge of viral transmission mechanisms. Additionally, these measures will serve to enhance the control and prevention of HIV/acquired immunodeficiency syndrome in China.

Forelimb joints contribute to locomotor performance in reindeer (Rangifer tarandus) by maintaining stability and storing energy.

Reindeer (Rangifer tarandus) have lengthy seasonal migrations on land and their feet possess excellent locomotor characteristics that can adapt to complex terrains. In this study, the kinematics and vertical ground reaction force (GRF) of reindeer forelimb joints (interphalangeal joint b, metacarpophalangeal joint c, and wrist joint d) under walk, trot 1, and trot 2 were measured using a motion tracking system and Footscan pressure plates. Significant differences among different locomotor activities were observed in the joint angles, but not in changes of the joint angles (α b , α c , α d ) during the stance phase. Peak vertical GRF increased as locomotor speed increased. Net joint moment, power, and work at the forelimb joints were calculated via inverse dynamics. The peak joint moment and net joint power related to the vertical GRF increased as locomotor speed increased. The feet absorbed and generated more energy at the joints. During different locomotor activities, the contribution of work of the forelimbs changed with both gait and speed. In the stance phase, the metacarpophalangeal joint absorbed more energy than the other two joints while trotting and thus performed better in elastic energy storage. The joint angles changed very little (∼5°) from 0 to 75% of the stance phase, which reflected the stability of reindeer wrist joints. Compared to typical ungulates, reindeer toe joints are more stable and the stability and energy storage of forelimb joints contribute to locomotor performance in reindeer.

Correction: Exosomal miR-25-3p from mesenchymal stem cells alleviates myocardial infarction by targeting pro-apoptotic proteins and EZH2.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Correction: Exosomal miR-25-3p from mesenchymal stem cells alleviates myocardial infarction by targeting proapoptotic proteins and EZH2.

Since online publication of this article, the authors noticed that an incorrect image was used during the compilation of Fig. 2a, which was caused during manuscript preparation. The correct Fig. 2a is shown below.

LncRNA SOX2OT/Smad3 feedback loop promotes myocardial fibrosis in heart failure.

Long noncoding RNA SOX2OT is associated with myocardial fibrosis (MF) in heart failure (HF). This article aims to investigate the role of SOX2OT in MF. We constructed HF mouse models by subcutaneous injection of isoprenaline (ISO). Cardiac fibroblasts (CFs) were treated with ISO to induce MF.Hematoxylin-eosin, Masson, and Sirius-red staining were used to identify myocardial injury and collagen deposition in heart tissues. The relationship among SOX2OT, miR-138-5p, TGF-ß1, and Smad3 were evaluated by chromatin immunoprecipitation and luciferase reporter assay. The gene and protein expression were verified by quantitative real-time PCR and western blot. We found that SOX2OT was up-regulated in HF mice and ISO-induced CFs. SOX2OT knockdown reduced myocardial injury and collagen deposition in HF mice. The expression of collagen I, α-SMA, TGF-ß1, and p-Smad3 were inhibited by SOX2OT down-regulation in HF mice and ISO-induced CFs. Furthermore, TGF-ß1 was a target gene of miR-138-5p and indirectly regulated by SOX2OT. SOX2OT promoted MF in HF by activating TGF-ß1/Smad3, and then Smad3 interacted with the SOX2OT promoter and formed a positive feedback loop. In conclusion, our work verifies that SOX2OT/Smad3 feedback loop promotes MF in HF. Thus, SOX2OT is potentially a novel therapeutic target for MF in HF.

Comprehensive multiomics analysis reveals key roles of NACs in plant growth and development and its environmental adaption mechanism by regulating metabolite pathways.

Abnormal environmental conditions induce polyploidization and exacerbate vulnerability to agricultural production. Polyploidization is a pivotal event for plant adaption to stress and the expansion of transcription factors. NACs play key roles in plant stress resistance and growth and development, but the adaptive mechanism of NACs during plant polyploidization remain to be explored. Here, we identified and analyzed NACs from 15 species and found that the expansion of NACs was contributed by polyploidization. The regulatory networks were systematically analyzed based on polyomics. NACs might influence plant phenotypes and were correlated with amino acids acting as nitrogen source, indicating that NACs play a vital role in plant development. More importantly, in quinoa and Arabidopsis thaliana, NACs enabled plants to resist stress by regulating flavonoid pathways, and the universality was further confirmed by the Arabidopsis population. Our study provides a cornerstone for future research into improvement of important agronomic traits by transcription factors in a changing global environment.

Spatial Divergence of PHR-PHT1 Modules Maintains Phosphorus Homeostasis in Soybean Nodules.

Maintaining phosphorus (Pi) homeostasis in nodules is the key to nodule development and nitrogen fixation, an important source of nitrogen for agriculture and ecosystems. PHOSPHATE-TRANSPORTER1 (PHT1) and its regulator PHOSPHATE-STARVATION-RESPONSE1 (PHR1), which constitute the PHR1-PHT1 module, play important roles in maintaining Pi homeostasis in different organs. However, the PHR1-PHT1 module and its functions in nodules remain unknown. We identified one PHT1 (GmPHT1;11) and four PHR1 (GmPHR1) homologs in soybean (Glycine max) plants, which displayed specific expression patterns in different tissues in nodules, similar to previously reported GmPHT1;1 and GmPHT1;4 Through the integration of different approaches, GmPHR-GmPHT1 modules were confirmed. Combining our results and previous reports, we established multiple GmPHR-GmPHT1 modules acting in the infected or noninfected tissues in nodules. A single GmPHR had more than one GmPHT1 target, and vice versa. Therefore, overlapping and cross-talking modules monitored the wave of available Pi to maintain Pi homeostasis in nodules, which sequentially regulated nodule initiation and development. High levels of GmPHT1;11 enhanced Pi accumulation in nodules, increased nodule size, but decreased nodule number. Nitrogenase activity was also enhanced by GmPHT1;11 Our findings uncover GmPHR-GmPHT1 modules in nodules, which expands our understanding of the mechanism of maintaining Pi homeostasis in soybean plants.

Study on bio-inspired feet based on the cushioning and shock absorption characteristics of the ostrich foot.

As the main actuator of high-speed running, the ostrich feet are highly capable of cushioning and shock absorption. In this study, based on the elastic modulus scales and assembly order of the 3rd toe soft tissues and the functions of the metatarsophalangeal (MTP) joint, we designed fourteen bio-inspired feet. The impact process on loose sand was simulated on the finite element software Abaqus. Also the stress distributions and deformations of each component of the bio-inspired feet were clarified. With the peak acceleration as the index, the cushioning performances of the bio-inspired feet were compared on both loose sand and solid ground through height-variable impact tests. The 15-15-15 HA (hardness unit) bio-inspired foot showed lower peak acceleration and thereby better cushioning performance, but larger deformation, less-uniform stress distribution and thereby lower stability than the 15-35-55 HA bio-inspired foot. In fact, the silicon rubbers with different hardness degrees (which simulate the elasticity modulus scales of the digital cushions, fascia and skin) and the spring mechanism (which simulates the functions of the MTP joint) work as an "integrated system" of cushioning and shock absorption.

Exosomal miR-25-3p from mesenchymal stem cells alleviates myocardial infarction by targeting pro-apoptotic proteins and EZH2.

Mesenchymal stem cell (MSC) therapy is a promising approach against myocardial infarction (MI). Studies have demonstrated that MSCs can communicate with other cells by secreting exosomes. In the present study, we aimed to identify exosomal microRNAs that might contribute to MSC-mediated cardioprotective effects. Primary cardiomyocytes were deprived of oxygen and glucose to mimic MI in vitro. For the animal model of MI, the left anterior descending artery was ligated for 1 h, followed by reperfusion for 12 h. MSC-derived exosomes were used to treat primary cardiomyocytes or mice. Cardioprotection-related microRNAs were determined, followed by target gene identification and functional studies with quantitative PCR, western blotting, MTT assay, flow cytometry assay, chromatin immunoprecipitation and dual-luciferase assay. We found that MSC co-culture reduced OGD-induced cardiomyocyte apoptosis and inflammatory responses. Cardioprotection was also observed upon treatment with MSC-derived exosomes in vitro and in vivo. In line with this, exosome uptake led to a significant increase in miR-25-3p in cardiomyocytes. Depletion of miR-25-3p in MSCs abolished the protective effects of exosomes. Mechanistically, miR-25-3p directly targeted the pro-apoptotic genes FASL and PTEN and reduced their protein levels. Moreover, miR-25-3p decreased the levels of EZH2 and H3K27me3, leading to derepression of the cardioprotective gene eNOS as well as the anti-inflammatory gene SOCS3. Inhibition of EZH2 or overexpression of miR-25-3p in cardiomyocytes was sufficient to confer cardioprotective effects in vitro and in vivo. We concluded that exosomal miR-25-3p from MSCs alleviated MI by targeting pro-apoptotic proteins and EZH2.

Genetic Diversity and Drug Resistance of HIV-1 CRF55_01B in Guangdong, China.

BACKGROUND: HIV-1 CRF55_01B was first reported in 2013. At present, no report is available regarding this new clade's polymorphisms in its functionally critical regions protease and reverse transcriptase. OBJECTIVE: To identify the diversity difference in protease and reverse transcriptase between CRF55_01B and its parental clades CRF01_AE and subtype B; and to investigate CRF55_01B's drug resistance mutations associated with the protease inhibition and reverse transcriptase inhibition. METHODS: HIV-1 RNA was extracted from plasma derived from a MSM population. The reverse transcription and nested PCR amplification were performed following our in-house PCR procedure. Genotyping and drug resistant-associated mutations and polymorphisms were identified based on polygenetic analyses and the usage of the HIV Drug Resistance Database, respectively. RESULTS: A total of 9.24 % of the identified CRF55_01B sequences bear the primary drug resistance. CRF55_01B contains polymorphisms I13I/V, G16E and E35D that differ from those in CRF01_AE. Among the 11 polymorphisms in the RT region, seven were statistically different from CRF01_AE's. Another three polymorphisms, R211K (98.3%), F214L (98.3%), and V245A/E (98.3 %.), were identified in the RT region and they all were statistically different with that of the subtype B. The V179E/D mutation, responsible for 100% potential low-level drug resistance, was found in all CRF55_01B sequences. Lastly, the phylogenetic analyses demonstrated 18 distinct clusters that account for 35% of the samples. CONCLUSION: CRF55_01B's pol has different genetic diversity comparing to its counterpart in CRF55_01B's parental clades. CRF55_01B has a high primary drug resistance presence and the V179E/D mutation may confer more vulnerability to drug resistance.

RNA Sequencing-Associated Study Identifies GmDRR1 as Positively Regulating the Establishment of Symbiosis in Soybean.

In soybean (Glycine max)-rhizobium interactions, the type III secretion system (T3SS) of rhizobium plays a key role in regulating host specificity. However, the lack of information on the role of T3SS in signaling networks limits our understanding of symbiosis. Here, we conducted an RNA sequencing analysis of three soybean chromosome segment substituted lines, one female parent and two derived lines with different chromosome-substituted segments of wild soybean and opposite nodulation patterns. By analyzing chromosome-linked differentially expressed genes in the substituted segments and quantitative trait loci (QTL)-assisted selection in the substituted-segment region, genes that may respond to type III effectors to mediate plant immunity-related signaling were identified. To narrow down the number of candidate genes, QTL assistant was used to identify the candidate region consistent with the substituted segments. Furthermore, one candidate gene, GmDRR1, was identified in the substituted segment. To investigate the role of GmDRR1 in symbiosis establishment, GmDRR1-overexpression and RNA interference soybean lines were constructed. The nodule number increased in the former compared with wild-type soybean. Additionally, the T3SS-regulated effectors appeared to interact with the GmDDR1 signaling pathway. This finding will allow the detection of T3SS-regulated effectors involved in legume-rhizobium interactions.

Light- and temperature-entrainable circadian clock in soybean development.

In plants, the spatiotemporal expression of circadian oscillators provides adaptive advantages in diverse species. However, the molecular basis of circadian clock in soybean is not known. In this study, we used soybean hairy roots expression system to monitor endogenous circadian rhythms and the sensitivity of circadian clock to environmental stimuli. We discovered in experiments with constant light and temperature conditions that the promoters of clock genes GmLCLb2 and GmPRR9b1 drive a self-sustained, robust oscillation of about 24-h in soybean hairy roots. Moreover, we demonstrate that circadian clock is entrainable by ambient light/dark or temperature cycles. Specifically, we show that light and cold temperature pulses can induce phase shifts of circadian rhythm, and we found that the magnitude and direction of phase responses depends on the specific time of these two zeitgeber stimuli. We obtained a quadruple mutant lacking the soybean gene GmLCLa1, LCLa2, LCLb1, and LCLb2 using CRISPR, and found that loss-of-function of these four GmLCL orthologs leads to an extreme short-period circadian rhythm and late-flowering phenotype in transgenic soybean. Our study establishes that the morning-phased GmLCLs genes act constitutively to maintain circadian rhythmicity and demonstrates that their absence delays the transition from vegetative growth to reproductive development.