Interacting Proteins Research Articles

Effects Of Exercise On PPARγ Protein-protein Interaction In Subcutaneous Adipose Tissue Of High-fat Diet Rats

PPARγ is an important transcription factor in regulating the lipid metabolism of adipose tissue in exercise. However, the PPARγ-centered network is still unclear. PURPOSE: To explore the effects of exercise on the PPARγ protein-protein interaction network (PPI) in subcutaneous adipose tissue of high-fat diet rats. METHODS:24 4-week-old male SD rats were randomly divided into standard quiet group (C), high-fat quiet group (HC), high-fat training group (HE), each of eight. Rats of the C group were fed a normal diet (D12450B), while HC and HE groups were fed a high-fat diet (D12451). Rats in each group were subjected to 8 weeks of the experimental intervention. HE group also received the exercise intervention for 5 days every week and underwent 60%-70% VO2max intensity treadmill training for 50 minutes per day. After an 8-week intervention, the body weight of the rats was weighed, the body composition was measured by DEXA scanning. 3 rats from each group who completed the intervention process were randomly selected for the PPI work of PPARγ in subcutaneous adipose tissue, which consists of COIP-MS experiment and bioinformatics analysis. RESULTS:1.After the intervention, there was no significant difference in body weight among the three groups. However, the body fat percentage in the HC group was significantly higher than in the C group (43.71 ± 9.06% vs. 36.36 ± 6.19%, P < 0.01). And the body fat percentage in the HE group was significantly lower than the HC group (35.34 ± 2.99% vs. 43.71 ± 9.06%, P < 0.01).2. The protein expression of PPARγ in group H was significantly reduced vs. group C (0.59 ± 0.16 vs. 1.00 ± 0.00, P < 0.05); the total number of differential proteins was 33, 11 were up-regulated and 22 were down-regulated. The expression of PPARγ in the HE group was significantly increased vs. group H (0.94 ± 0.13 vs. 0.59 ± 0.16, P < 0.05); the total number of differential proteins was 25, 6 were up-regulated, and 19 were down-regulated. CONCLUSIONS:1. The 8-week high-fat diet may inhibit the body's inflammatory response by down-regulating the expression of PPARγ and its direct interaction protein Crp, and regulate lipid metabolism.2.In the 8-week high-fat diet rat model under the intervention of exercise, the differential protein function is enriched in amino acid metabolism, etc., and the energy metabolism process is closely related.

The introduction of an N-glycosylation site into prochymosin greatly enhances its production and secretion by Pichia pastoris

BackgroundN-glycosylation is one of the most important post-translational modifications. Many studies have shown that N-glycosylation has a significant effect on the secretion level of heterologous glycoproteins in yeast cells. However, there have been few studies reporting a clear and unified explanation for the intracellular mechanism that N-glycosylation affect the secretion of heterologous glycoproteins so far. Pichia pastoris is an important microbial cell factory producing heterologous protein. It is of great significance to study the effect of N-glycosylation on the secretion level of heterologous protein. Camel chymosin is a glycoprotein with higher application potential in cheese manufacturing industry. We have expressed camel prochymosin in P. pastoris GS115, but the lower secretion level limits its industrial application. This study attempts to increase the secretion level of prochymosin through N-glycosylation, and explore the molecular mechanism of N-glycosylation affecting secretion.ResultsAdding an N-glycosylation site at the 34th amino acid of the propeptide of prochymosin significantly increased its secretion in P. pastoris. N-glycosylation improved the thermostability of prochymosin without affecting the enzymatic activity. Immunoprecipitation coupled to mass spectrometry (IP-MS) analysis showed that compared with the wild prochymosin (chy), the number of proteins interacting with N-glycosylated mutant (chy34) decreased, and all differential interacting proteins (DIPs) were down-regulated in chy34-GS115 cell. The DIPs in endoplasmic reticulum were mainly concentrated in the misfolded protein pathway. Among the five DIPs in this pathway, overexpression of BiP significantly increased the secretion of chy. The knockout of the possible misfolded protein recognition elements, UDP-glycose:glycoprotein glucosyltransferase 1 and 2 (UGGT1/2) had no effect on the growth of yeast cells and the secretion of prochymosin.ConclusionsIn conclusion, N-glycosylation increased the secretion of prochymosin in P. pastoris trough the adjustment of intracellular interacted proteins. The results of our study may help to elucidate the molecular mechanism of N-glycosylation affecting secretion and provide a new research method to improve the secretion of heterologous glycoprotein in P. pastoris.

Ultrafast analysis of peptides by laser diode thermal desorption-triple quadrupole mass spectrometry.

The COVID-19 pandemic demonstrated the importance of high-throughput analysis for public health. Given the importance of surface viral proteins for interactions with healthy tissue, they are targets of interest for mass spectrometry-based analysis. For that reason, the possibility of detecting and quantifying peptides using a high-throughput technique, laser diode thermal desorption-triple quadrupole mass spectrometry (LDTD-QqQMS), was explored. Two peptides used as models for small peptides (leu-enkephalin and endomorphin-2) and four tryptic peptides (GVYYPDK, NIDGYFK, IADYNYK, and QIAPGQTGK) specific to the SARS-CoV-2 Spike protein were employed. Target peptides were analyzed individually in the positive mode by LDTD-QqQMS. Peptides were quantified by internal calibration using selected reaction monitoring transitions in pure solvents and in samples spiked with 20 μg mL-1 of a bovine serum albumin tryptic digest to represent real analysis conditions. Low-energy fragment ions (b and y ions) as well as high-energy fragment ions (c and x ions) and some of their corresponding water or ammonia losses were detected in the full mass spectra. Only for the smallest peptides, leu-enkephalin and endomorphin-2, were [M + H]+ ions observed. Product ion spectra confirmed that, with the experimental conditions used in the present study, LDTD transfers a considerable amount of energy to the target peptides. Quantitative analysis showed that it was possible to quantify peptides using LDTD-QqQMS with acceptable calibration curve linearity (R2 > 0.99), precision (RSD < 18.2%), and trueness (bias < 8.3%). This study demonstrated for the first time that linear peptides can be qualitatively and quantitatively analyzed using LDTD-QqQMS. Limits of quantification and dynamic ranges are still inadequate for clinical applications, but other applications where higher levels of proteins must be detected could be possible with LDTD. Given the high-throughput capabilities of LDTD-QqQMS (>15 000 samples in less than 43 h), more studies are needed to improve the sensitivity for peptide analysis of this technique.

Central Roles of STAT3-Mediated Signals in Onset and Development of Cancers: Tumorigenesis and Immunosurveillance.

Since the time of Rudolf Virchow in the 19th century, it has been well-known that cancer-associated inflammation contributes to tumor initiation and progression. However, it remains unclear whether a collapse of the balance between the antitumor immune response via the immunological surveillance system and protumor immunity due to cancer-related inflammation is responsible for cancer malignancy. The majority of inflammatory signals affect tumorigenesis by activating signal transducer and activation of transcription 3 (STAT3) and nuclear factor-κB. Persistent STAT3 activation in malignant cancer cells mediates extremely widespread functions, including cell growth, survival, angiogenesis, and invasion and contributes to an increase in inflammation-associated tumorigenesis. In addition, intracellular STAT3 activation in immune cells causes suppressive effects on antitumor immunity and leads to the differentiation and mobilization of immature myeloid-derived cells and tumor-associated macrophages. In many cancer types, STAT3 does not directly rely on its activation by oncogenic mutations but has important oncogenic and malignant transformation-associated functions in both cancer and stromal cells in the tumor microenvironment (TME). We have reported a series of studies aiming towards understanding the molecular mechanisms underlying the proliferation of various types of tumors involving signal-transducing adaptor protein-2 as an adaptor molecule that modulates STAT3 activity, and we recently found that AT-rich interactive domain-containing protein 5a functions as an mRNA stabilizer that orchestrates an immunosuppressive TME in malignant mesenchymal tumors. In this review, we summarize recent advances in our understanding of the functional role of STAT3 in tumor progression and introduce novel molecular mechanisms of cancer development and malignant transformation involving STAT3 activation that we have identified to date. Finally, we discuss potential therapeutic strategies for cancer that target the signaling pathway to augment STAT3 activity.

A cuproptosis and copper metabolism-related gene prognostic index for head and neck squamous cell carcinoma.

BackgroundThe purpose of this study was to identify the prognostic value of cuproptosis and copper metabolism–related genes, to clarify their molecular and immunological characteristics, and to elucidate their benefits in head and neck squamous cell carcinoma (HNSCC).MethodsThe details of human cuproptosis and copper metabolism–related genes were searched and filtered from the msigdb database and the latest literature. To identify prognostic genes associated with cuproptosis and copper metabolism, we used least absolute shrinkage and selection operator regression, and this coefficient was used to set up a prognostic risk score model. HNSCC samples were divided into two groups according to the median risk. Afterwards, the function and immune characteristics of these genes in HNSCC were analyzed.ResultsThe 14-gene signature was constructed to classify HNSCC patients into low-risk and high-risk groups according to the risk level. In the The Cancer Genome Atlas (TCGA) cohort, the overall survival (OS) rate of the high-risk group was lower than that of the low-risk group (P < 0.0001). The area under the curve of the time-dependent Receiver Operator Characteristic (ROC) curve assessed the good performance of the genetic signature in predicting OS and showed similar performance in the external validation cohort. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment assays and Protein-Protein Interaction (PPI) protein networks have been used to explore signaling pathways and potential mechanisms that were markedly active in patients with HNSCC. Furthermore, the 14 cuproptosis and copper metabolism-related genes were significantly correlated with the immune microenvironment, suggesting that these genes may be linked with the immune regulation and development of HNSCC.ConclusionsOur results emphasize the significance of cuproptosis and copper metabolism as a predictive biomarker for HNSCC, and its expression levels seem to be correlated with immune- related features; thus, they may be a possible biomarker for HNSCC prognosis.

Profiling of the Candidate Interacting Proteins of SELF-PRUNING 6A (SP6A) in Solanum tuberosum

SELF-PRUNING 6A (SP6A), a homolog of FLOWERING LOCUS T (FT), has been identified as tuberigen in potato. StSP6A is a mobile signal synthesized in leaves and transmitted to the stolon through phloem, and plays multiple roles in the growth and development of potato. However, the global StSP6A protein interaction network in potato remains poorly understood. In this study, BK-StSP6A was firstly used as the bait to investigate the StSP6A interaction network by screening the yeast two-hybrid (Y2H) library of potato, resulting in the selection of 200 independent positive clones and identification of 77 interacting proteins. Then, the interaction between StSP6A and its interactors was further confirmed by the Y2H and BiFC assays, and three interactors were selected for further expression analysis. Finally, the expression pattern of Flowering Promoting Factor 1.1 (StFPF1.1), No Flowering in Short Days 1 and 2 (StNFL1 and StNFL2) was studied. The three genes were highly expressed in flowers or flower buds. StFPF1.1 exhibited an expression pattern similar to that of StSP6A at the stolon swelling stages. StPHYF-silenced plants showed up-regulated expression of StFPF1.1 and StSP6A, while expression of StNFL1 and StNFL2 was down-regulated in the stolon. The identification of these interacting proteins lays a solid foundation for further functional studies of StSP6A.

Graph convolutional network based virus-human protein-protein interaction prediction for novel viruses

Computational identification of human-virus protein-protein interactions (PHIs) is a worthwhile step towards understanding infection mechanisms. Analysis of the PHI networks is important for the determination of pathogenic diseases. Prediction of these interactions is a popular problem since experimental detection of PHIs is both time-consuming and expensive. The available methods use biological features like amino acid sequences, molecular structure, or biological activities for prediction. Recent studies show that the topological properties of proteins in protein-protein interaction (PPI) networks increase the performance of the predictions. The basic network projections, random-walk-based models, or graph neural networks are used for generating topologically enriched (hybrid) protein embeddings. In this study, we propose a three-stage machine learning pipeline that generates and uses hybrid embeddings for PHI prediction. In the first stage, numerical features are extracted from the amino acid sequences using the Doc2Vec and Byte Pair Encoding method. The amino acid embeddings are used as node features while training a modified GraphSAGE model, which is an improved version of the graph convolutional network. Lastly, the hybrid protein embeddings are used for training a binary interaction classifier model that predicts whether there is an interaction between the given two proteins or not. The proposed method is evaluated with comprehensive experiments to test its functionality and compare it with the state-of-art methods. The experimental results on the benchmark dataset prove the efficiency of the proposed model by having a 3–23% better area under curve (AUC) score than its competitors.

Downregulation of Inflammatory Response via Nrf2/Trx1/TXNIP Axis in Oxidative Stress-Induced ARPE-19 Cells and Mouse Model of AMD.

Aim Chronic inflammation is crucial for age-related macular degeneration (AMD) pathogenesis. However, the mechanism involved in activating inflammation remains unclear. This study is aimed at investigating whether nuclear factor erythrocyte-associated factor 2 (Nrf2) negatively regulated the Nod-like receptor protein 3 (NLRP3) inflammasomes through the thioredoxin 1 (Trx1)/thioredoxin interaction protein (TXNIP) complex. Methods We determined the optimal hydrogen peroxide (H2O2) concentration, time, and changes in reactive oxygen species (ROS) levels. We also constructed animal models using blue LED irradiation. Then, the expression of Nrf2, TXNIP, Trx1, NLRP3, and inflammation-related factors and proteins, along with the changes in retinal thickness and functional status, was analyzed. Results The oxidative stress model was established after 1 h intervention with 100 μM H2O2. Nrf2 reduced ROS production, protected the ultrastructure of mitochondria, increased the thickness of the ONL layer, and increased the amplitude of a- and b-wave amplitudes in ERG. Trx1 knockdown increased the production of ROS, damaged the ultrastructure of mitochondria, reduced the thickness of the other ONL layer, and reduced the amplitudes of a- and b-waves in the electroretinogram (ERG). Thus, TXNIP in the cytoplasm activated the inflammasomes. Conclusions Nrf2 showed antioxidant and anti-inflammatory activity in the H2O2-induced cell stress model and blue LED-induced retinal light damage model. TXNIP transferred from the nucleus to the cytoplasm, activated NLRP3, and aggravated the retinal injury in both the cell stress model and the animal blue LED model. In contrast, Trx1 knockout promoted this process. This study revealed the possible role of the thioredoxin system in developing AMD while also providing newer insights for the future treatment of AMD.

Identification of Pri-miRNA Stem-Loop Interacting Proteins in Plants Using a Modified Version of the Csy4 CRISPR Endonuclease.

Regulation at the RNA level by RNA-binding proteins (RBPs) and microRNAs (miRNAs) is key to coordinating eukaryotic gene expression. In plants, the importance of miRNAs is highlighted by severe developmental defects in mutants impaired in miRNA biogenesis. MiRNAs are processed from long primary-microRNAs (pri-miRNAs) with internal stem-loop structures by endonucleolytic cleavage. The highly structured stem-loops constitute the basis for the extensive regulation of miRNA biogenesis through interaction with RBPs. However, trans-acting regulators of the biogenesis of specific miRNAs are largely unknown in plants. Therefore, we exploit an RNA-centric approach based on modified versions of the conditional CRISPR nuclease Csy4* to pull down interactors of the Arabidopsis pri-miR398b stem-loop (pri-miR398b-SL) in vitro. We designed three epitope-tagged versions of the inactive Csy4* for the immobilization of the protein together with the pri-miR398b-SL bait on high affinity matrices. After incubation with nucleoplasmic extracts from Arabidopsis and extensive washing, pri-miR398b-SL, along with its specifically bound proteins, were released by re-activating the cleavage activity of the Csy4* upon the addition of imidazole. Co-purified proteins were identified via quantitative mass spectrometry and data sets were compared. In total, we identified more than 400 different proteins, of which 180 are co-purified in at least two out of three independent Csy4*-based RNA pulldowns. Among those, the glycine-rich RNA-binding protein AtRZ-1a was identified in all pulldowns. To analyze the role of AtRZ-1a in miRNA biogenesis, we determined the miR398 expression level in the atrz-1a mutant. Indeed, the absence of AtRZ-1a caused a decrease in the steady-state level of mature miR398 with a concomitant reduction in pri-miR398b levels. Overall, we show that our modified Csy4*-based RNA pulldown strategy is suitable to identify new trans-acting regulators of miRNA biogenesis and provides new insights into the post-transcriptional regulation of miRNA processing by plant RBPs.

Additional Pathogenic Pathways in RBCK1 Deficiency

RBCK1 deficiency is a rare congenital autoinflammatory disease that causes inflammatory disruption on the molecular level. This deficiency has three major clinical manifestations: increased sensitivity to bacterial infections, autoinflammation syndrome, and the accumulation of amylopectin in skeletal muscle. The amylopectinosis causes myopathy and cardiomyopathy. The pathogenesis of the disease is poorly investigated and may include unnoticed relationships. We performed gene expression analysis on patients with RBCK1 deficiency and three other autoinflammatory diseases. The identification of differentially expressed genes revealed a large number of downregulated genes that are involved in the activation of essential metabolic and immune pathways, including NF-kB and Pi3k-Akt-mTOR. Signaling pathways were analysed using the KEGG (Kyoto Encyclopedia of Genes and Genomes) and Gene Ontology resource. Predicted protein-protein interactions were retrieved from the STRING (Search Tool for the Retrieval of Interacting proteins database). Besides the primary involvement of RBCK1 in disease pathology, several downregulated pathways aggravate symptoms of myopathy, cardiomyopathy, and bacterial disease. The studied pathways may serve as new targets for the development of compensatory therapies for patients with RBCK1 deficiency.

PbXND1 Results in a Xylem-Deficient Dwarf Phenotype through Interaction with PbTCP4 in Pear (Pyrus bretschneideri Rehd.).

Dwarfing is an important agronomic characteristic in fruit breeding. However, due to the lack of dwarf cultivars and dwarf stocks, the dwarfing mechanism is poorly understood in pears. In this research, we discovered that the dwarf hybrid seedlings of pear (Pyrus bretschneideri Rehd.), ‘Red Zaosu,’ exhibited a xylem-deficient dwarf phenotype. The expression level of PbXND1, a suppressor of xylem development, was markedly enhanced in dwarf hybrid seedlings and its overexpression in pear results in a xylem-deficient dwarf phenotype. To further dissect the mechanism of PbXND1, PbTCP4 was isolated as a PbXND1 interaction protein through the pear yeast library. Root transformation experiments showed that PbTCP4 promotes root xylem development. Dual-luciferase assays showed that PbXND1 interactions with PbTCP4 suppressed the function of PbTCP4. PbXND1 expression resulted in a small amount of PbTCP4 sequestration in the cytoplasm and thereby prevented it from activating the gene expression, as assessed by bimolecular fluorescence complementation and co-location analyses. Additionally, PbXND1 affected the DNA-binding ability of PbTCP4, as determined by utilizing an electrophoretic mobility shift assay. These results suggest that PbXND1 regulates the function of PbTCP4 principally by affecting the DNA-binding ability of PbTCP4, whereas the cytoplasmic sequestration of PbTCP4 is only a minor factor. Taken together, this study provides new theoretical support for the extreme dwarfism associated with the absence of xylem caused by PbXND1, and it has significant reference value for the breeding of dwarf varieties and dwarf rootstocks of the pear.

Characteristics and molecular identification of glyceraldehyde-3-phosphate dehydrogenases in poplar

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), an essential enzyme of the glycolysis metabolic pathway, plays a vital role in carbon metabolism, plant development, and stress resistance. As a kind of woody plant, poplars are widely cultivated for afforestation. Although the whole genome data of poplars have been published, little information is known about the GAPDH family of genes in poplar. This study performed a genome-wide identification of the poplar GAPDH family, and 13 determined PtGAPDH genes were identified from poplar genome. Phylogenetic tree showed that the PtGAPDH members were divided into PtGAPA/B, PtGAPC, PtGAPCp, and PtGAPN groups. A total of 13 PtGAPDH genes were distributed on eight chromosomes, 13 gene pairs belonging to segmented replication events were detected in poplar, and 23 collinearity gene pairs were determined between poplar and willow. The PtGAPDHcis-acting elements associated with growth and development as well as stress resistance revealed that PtGAPDHs might be involved in these processes. The phosphoglycerate kinase (PGK) and triose-phosphate isomerase (TPI) were predicted as the putative interaction proteins of PtGAPDHs. Gene ontology (GO) analysis showed that PtGAPDHs play a crucial role in the oxidation and reduction processes. PtGAPDH expression levels were induced by NaCl and PEG treatments, which implied that PtGAPDHs might be involved in stress response. Overexpression of PtGAPC1 significantly changed the contents of lipid and carbohydrate metabolites, which indicated that PtGAPC1 plays an essential role in metabolic regulation. This study highlights the characterizations and profiles of PtGAPDHs and reveals that PtGAPC1 is involved in the loop of lipid and carbohydrate metabolisms.

Revealing the Active Compounds and Mechanism of Banxia Xiexin Decoction Against Gastric Ulcer by Network Pharmacology and Molecular Docking

Gastric ulcer (GU) is a clinically common gastrointestinal disease with a long disease course that frequently reoccurs. Banxia Xiexin decoction (BXD), a traditional Chinese medicine prescription, has a prominent protective effect against GU. Nonetheless, the therapeutic mechanisms of BXD against GU remain elusive. In this study, a rat model of GU was established by gavage with 95% ethanol, and BXD significantly attenuated the inflammatory effect of GU in rats. An “active ingredient–target” interaction and GU protein–protein interaction networks were constructed based on system biology, which could screen out the crucial active ingredients. The target protein–protein interaction network for the BXD treatment of GU was constructed to identify the key target proteins with network topology parameters. The DAVID database was then used to perform Gene Ontology and Kyoto encyclopedia of genes and genomes enrichment analysis on the proteins targeted by BXD in the treatment of GU. Finally, molecular docking technology was used to study the interactions between key active ingredients and core target proteins. A total of 89 active ingredients of BXD were screened and 63 target proteins of BXD in the treatment of GU were identified. Through the analysis of protein–protein interaction and the active ingredient–target protein network diagram, it was found that tumor necrosis factor-α(TNF-α), AKT1, and PTGS2 may play a key role in the treatment of GU by BXD. Molecular docking showed that these 3 core target proteins had a good affinity with the main components of BXD, including baicalein, norwogonin, and skullcapflavone II. The mechanism of BXD against GU may involve the inhibition of inflammatory response and oxidative stress, involving signaling pathways such as TNF, hypoxia-inducible factor-1, and mitogen-activated protein kinase. Network pharmacology and molecular docking technology indicated the key active ingredients, target proteins, and signal pathways that may be the biological basis of BXD in the treatment of GU.

Long-Chain Acyl-CoA Synthetases Promote Poplar Resistance to Abiotic Stress by Regulating Long-Chain Fatty Acid Biosynthesis.

Long-chain acyl-CoA synthetases (LACSs) catalyze fatty acids (FAs) to form fatty acyl-CoA thioesters, which play essential roles in FA and lipid metabolisms and cuticle wax biosynthesis. Although LACSs from Arabidopsis have been intensively studied, the characterization and function of LACSs from poplar are unexplored. Here, 10 poplar PtLACS genes were identified from the poplar genome and distributed to eight chromosomes. A phylogenetic tree indicated that PtLACSs are sorted into six clades. Collinearity analysis and duplication events demonstrated that PtLACSs expand through segmental replication events and experience purifying selective pressure during the evolutionary process. Expression patterns revealed that PtLACSs have divergent expression changes in response to abiotic stress. Interaction proteins and GO analysis could enhance the understanding of putative interactions among protein and gene regulatory networks related to FA and lipid metabolisms. Cluster networks and long-chain FA (LCFA) and very long-chain FA (VLCFA) content analysis revealed the possible regulatory mechanism in response to drought and salt stresses in poplar. The present study provides valuable information for the functional identification of PtLACSs in response to abiotic stress metabolism in poplar.

Role of microbial secreted proteins in gut microbiota-host interactions.

The mammalian gut microbiota comprises a variety of commensals including potential probiotics and pathobionts, influencing the host itself. Members of the microbiota can intervene with host physiology by several mechanisms, including the secretion of a relatively well-reported set of metabolic products. Another microbiota influence mechanism is the use of secreted proteins (i.e., the secretome), impacting both the host and other community members. While widely reported and studied in pathogens, this mechanism remains understood to a lesser extent in commensals, and this knowledge is increasing in recent years. In the following minireview, we assess the current literature covering different studies, concerning the functions of secretable proteins from members of the gut microbiota (including commensals, pathobionts, and probiotics). Their effect on host physiology and health, and how these effects can be harnessed by postbiotic products, are also discussed.

Divergent Host-Microbe Interaction and Pathogenesis Proteins Detected in Recently Identified Liberibacter Species

ABSTRACTCandidatus (Ca.) Liberibacter taxa are economically important bacterial plant pathogens that are not culturable; however, genome-enabled insights can help us develop a deeper understanding of their host-microbe interactions and evolution. The draft genome of a recently identified Liberibacter taxa, Ca. Liberibacter capsica, was curated and annotated here with a total draft genome size of 1.1 MB with 1,036 proteins, which is comparable to other Liberibacter species with complete genomes. A total of 459 orthologous clusters were identified among Ca. L. capsica, Ca. L. asiaticus, Ca. L. psyllaurous, Ca. L. americanus, Ca. L. africanus, and L. crescens, and these genes within these clusters consisted of housekeeping and environmental response functions. We estimated the rates of molecular evolution for each of the 443 one-to-one ortholog clusters and found that all Ca. L. capsica orthologous pairs were under purifying selection when the synonymous substitutions per synonymous site (dS) were not saturated. These results suggest that these genes are largely maintaining their conserved functions. We also identified the most divergent single-copy orthologous proteins in Ca. L. capsica by analyzing the ortholog pairs that represented the highest nonsynonymous substitutions per nonsynonymous site (dN) values for each pairwise comparison. From these analyses, we found that 21 proteins which are known to be involved in pathogenesis and host-microbe interactions, including the Tad pilus complex, were consistently divergent between Ca. L. capsica and the majority of other Liberibacter species. These results further our understanding of the evolutionary genetics of Ca. L. capsica and, more broadly, the evolution of Liberibacter.IMPORTANCE “Candidatus” (Ca.) Liberibacter taxa are economically important plant pathogens vectored by insects; however, these host-dependent bacterial taxa are extremely difficult to study because they are unculturable. Recently, we identified a new Ca. Liberibacter lineage (Ca. Liberibacter capsica) from a rare insect metagenomic sample. In this current study, we report that the draft genome of Ca. Liberibacter capsica is similar in genome size and protein content compared to the other Ca. Liberibacter taxa. We provide evidence that many of their shared genes, which encode housekeeping and environmental response functions, are evolving under purifying selection, suggesting that these genes are maintaining similar functions. Our study also identifies 21 proteins that are rapidly evolving amino acid changes in Ca. Liberibacter capsica compared to the majority of other Liberibacter taxa. Many of these proteins represent key genes involved in Liberibacter-host interactions and pathogenesis and are valuable candidate genes for future studies.

Genome Sequence Resource of Albifimbria verrucaria Causing the Leaf Spot Disease of the Spinach Plant Spinacia oleracea.

Genome Sequence Resource of Albifimbria verrucaria Causing the Leaf Spot Disease of the Spinach Plant Spinacia oleracea.

A novel nonsense variant in ARID1B causing simultaneous RNA decay and exon skipping is associated with Coffin-Siris syndrome

Coffin-Siris syndrome (CSS) is a congenital disorder that is characterized by an absent/hypoplastic fifth distal phalanx, psychomotor developmental delay, and coarse facial features. One of the causative genes, ARID1B (AT-rich interactive domain-containing protein 1B), encodes components of the BAF chromatin remodeling complexes. Here, we report a case of a 3-year 8-month-old male with a novel nonsense variant (NM_001374820.1:c.4282C > T, p.(Gln1428*)) in the ARID1B gene, which was identified with whole-exome sequencing. He showed clinical symptoms of cleft soft palate, distinctive facial features (flat nasal bridge, thick eyebrows, and long eyelashes), right cryptorchidism, and hypertrichosis that partially overlapped with CSS. One of the most characteristic features of CSS is absent/hypoplastic fifth distal phalanx. He showed no obvious clinical finding in the lengths of his fingers or in the formation of his fingernails. However, radiographic analyses of the metacarpophalangeal bones revealed shortening of all the distal phalanges and fifth middle phalanges, suggesting brachydactyly. We performed mRNA analyses and revealed that both nonsense-mediated decay and nonsense-associated altered splicing were simultaneously caused by the c.4282C > T nonsense variant. The proband’s clinical manifestations fit the previously reported criteria of disease for CSS or intellectual disability with ARID1B variant. Altogether, we suggest that c.4282C > T is a pathogenic variant that causes this clinical phenotype.

ARID1A has prognostic value in acute myeloid leukemia and promotes cell proliferation via TGF-β1/SMAD3 signaling.

Previous studies have shown that the gene AT-rich interactive domain-containing protein 1A (ARID1A) is a subunit of SWI/SNF chromatin remodeling complex that acts as a tumor suppressor gene in several cancers and plays a vital role in tumorigenesis. However, its biological functions in acute myeloid leukemia (AML) are still unclear. Here, we tried to elaborate the expression of ARID1A in patients with AML, in leukemia cells, as well as the molecular mechanisms. Our results indicated that the expression of ARID1A was significantly downregulated in the bone marrow of patients with AML and relapsed patients compared with healthy subjects and patients in complete remission. Meantime, receiver operating characteristic curve analysis showed that the expression of ARID1A could be used to discriminate between patients with AML and patients in complete remission. We further constructed a knockdown cell model to determine the regulatory mechanisms of ARID1A in AML cells. We found that the decreased expression of ARID1A promoted cell proliferation, suppressed cellular apoptosis, and impeded cell cycle arrest via TGF-β1/SMAD3 signaling pathway. These results revealed that the reduced expression of ARID1A promoted cell proliferation via the TGF-β1/SMAD3 cascade and served as a prognostic biomarker for AML and therapeutic targets.

Overexpression VaPYL9 improves cold tolerance in tomato by regulating key genes in hormone signaling and antioxidant enzyme

BackgroundAbscisic acid (ABA) has been reported in controlling plant growth and development, and particularly dominates a role in resistance to abiotic stress. The Pyrabactin Resistance1/PYR1-Like /Regulatory Components of ABA receptors (PYR1/PYL/RCAR) gene family, of which the PYL9 is a positive regulator related to stress response in ABA signaling transduction. Although the family has been identified in grape, detailed VaPYL9 function in cold stress remains unknown.ResultsIn order to explore the cold tolerance mechanism in grape, VaPYL9 was cloned from Vitis amurensis. The subcellular localization showed that VaPYL9 was mainly expressed in the plasma membrane. Yeast two-hybrid (Y2H) showed VaPCMT might be a potential interaction protein of VaPYL9. Through the overexpression of VaPYL9 in tomatoes, results indicated transgenic plants had higher antioxidant enzyme activities and proline content, lower malondialdehyde (MDA) and H2O2 content, and improving the ability to scavenge reactive oxygen species than wild-type (WT). Additionally, ABA content and the ratio of ABA/IAA kept a higher level than WT. Quantitative real-time PCR (qRT-PCR) showed that VaPYL9, SlNCED3, SlABI5, and antioxidant enzyme genes (POD, SOD, CAT) were up-regulated in transgenic tomatoes. Transcriptome sequencing (RNA-seq) found that VaPYL9 overexpression caused the upregulation of key genes PYR/PYL, PYL4, MAPK17/18, and WRKY in transgenic tomatoes under cold stress.ConclusionOverexpression VaPYL9 enhances cold resistance of transgenic tomatoes mediated by improving antioxidant enzymes activity, reducing membrane damages, and regulating key genes in plant hormones signaling and antioxidant enzymes.