Regulatory Network In Response Research Articles

Phosphorylation of ZmAL14 by ZmSnRK2.2 regulates drought resistance through derepressing ZmROP8 expression.

Drought stress has negative effects on crop growth and production. Characterization of transcription factors that regulate the expression of drought-responsive genes is critical for understanding the transcriptional regulatory networks in response to drought, which facilitates the improvement of crop drought tolerance. Here, we identified an Alfin-like (AL) family gene ZmAL14 that negatively regulates drought resistance. Overexpression of ZmAL14 exhibits susceptibility to drought while mutation of ZmAL14 enhances drought resistance. An abscisic acid (ABA)-activated protein kinase ZmSnRK2.2 interacts and phosphorylates ZmAL14 at T38 residue. Knockout of ZmSnRK2.2 gene decreases drought resistance of maize. A dehydration-induced Rho-like small guanosine triphosphatase gene ZmROP8 is directly targeted and repressed by ZmAL14. Phosphorylation of ZmAL14 by ZmSnRK2.2 prevents its binding to the ZmROP8 promoter, thereby releasing the repression of ZmROP8 transcription. Overexpression of ZmROP8 stimulates peroxidase activity and reduces hydrogen peroxide accumulation after drought treatment. Collectively, our study indicates that ZmAL14 is a negative regulator of drought resistance, which can be phosphorylated by ZmSnRK2.2 through the ABA signaling pathway, thus preventing its suppression on ZmROP8 transcription during drought stress response.

Crosstalk between long non-coding RNAs and miRNAs regulates transferase activities in response to salt stress in Pistachio (Pistacia vera L.)

Long non-coding RNA (lncRNA) molecules are important regulators of a broad spectrum of biological processes, including adaptation to diverse stresses in plants. However, how plant lncRNAs function during salt stress conditions is largely unknown. In our study, we identified 48 conserved mature Pistacia vera L. (P. vera) miRNAs among pistachio miRNA precursors and used RNA sequencing data to predict and validate the interaction relationship between lncRNAs and miRNAs. We indicated that the regulatory networks of pve-miRNA-lncRNA-mRNAs were more complex in the salt-tolerant (Ghazvini) compared to the salt-sensitive (Sarakhs) pistachio cultivar under NaCl treatment. We also found that 7 and 8 salt-responsive lncRNAs play a role as competing endogenous target mimics (eTMs) for 7 pve-miRNA families in Ghazvini (mir164, mir169, mir397, and mir827) and Sarakhs (mir156, mir159, mir169, and mir482), respectively. The GO-term enrichment analysis showed that protein-coding target genes of pve-miRNAs that regulated with target mimic relationship mainly enriched in transferase activity include: 7-deoxyloganetin glucosyltransferase, Arginine N-methyltransferase, Glutathione transferase, Flavonol sulfotransferase, and Beta-glucuronosyltransferase. Their activity regulates alkaloids and polysulfated flavonols biosynthesis, sequesters sodium, improves antioxidant capacity and controls epigenetic elements in Ghazvini under salt treatment. In Sarakhs, the analysis of GO-term enrichment in pve-miRNAs protein-coding target genes of lncRNA-related mimic relationship enriched in response to wounding, cell death, and jasmonic acid biosynthetic process. Compared to Sarakhs, Ghazvini had a more effective ceRNA network for regulating transferase enzymes and specific transcription factors including MYB, WRKY, and ABR1 in response to salt stress, which led to more salt tolerance in the Ghazvini cultivar. The present study provides new information about the complex lncRNA-miRNA-mRNA regulatory networks in response to plant stress conditions in pistachio. Furthermore, our findings can be used for different breeding programs and the introduction of salt-tolerant pistachio rootstocks.

Engineering pluripotent stem cells with synthetic biology for regenerative medicine.

Pluripotent stem cells (PSCs), characterized by self-renewal and capacity of differentiating into three germ layers, are the programmable building blocks of life. PSC-derived cells and multicellular systems, particularly organoids, exhibit great potential for regenerative medicine. However, this field is still in its infancy, partly due to limited strategies to robustly and precisely control stem cell behaviors, which are tightly regulated by inner gene regulatory networks in response to stimuli from the extracellular environment. Synthetic receptors and genetic circuits are powerful tools to customize the cellular sense-and-response process, suggesting their underlying roles in precise control of cell fate decision and function reconstruction. Herein, we review the progress and challenges needed to be overcome in the fields of PSC-based cell therapy and multicellular system generation, respectively. Furthermore, we summarize several well-established synthetic biology tools and their applications in PSC engineering. Finally, we highlight the challenges and perspectives of harnessing synthetic biology to PSC engineering for regenerative medicine.

Joint Analysis of Small RNA and mRNA Sequencing Unveils miRNA-Mediated Regulatory Network in Response to Methyl Jasmonate in Apocynum venetum L.

Apocynum venetum L. is a natural fiber and medicinal plant species with significant economic value. Jasmonic acid is an endogenous growth regulatory substance present in higher plants that participate in plant growth, development, and defense. As important endogenous single-stranded RNA molecules, microRNA (miRNA) plays an important role in the post-transcriptional regulation of plant genes. A combination of miRNA and mRNA sequencing techniques was used to systematically identify the methyl jasmonate miRNAs and mRNAs in A. venetum. Up to 135 conserved and 26 species-specific miRNAs have been identified in A. venetum. These miRNAs mainly target genes that encode transcription factors and enzymes. The expression levels of 23 miRNAs, including miR398 and miR482, significantly changed after MeJA treatment. A total of 1778 genes were differentially expressed under MeJA treatment, of which 825 were upregulated and 953 were downregulated. The main biological processes enriched in these differentially expressed genes were redox balance, secondary metabolism, photosynthesis, and plant hormone signal transduction. Joint analysis of the miRNAs and mRNA revealed that MeJA-responsive miRNAs function by forming regulatory modules, including miR398-CSD, miR482-NBS-LRR, miR156-SPL10, and miR164-NAC056, which further regulate multiple biological processes, including redox balance, disease resistance, and morphogenesis in A. venetum. This study provides important information to understand the biological roles of miRNAs in A. venetum.

Integrated transcriptomics and proteomics assay identifies the role of FCGR1A in maintaining sperm fertilization capacity during semen cryopreservation in sheep.

Semen cryopreservation is a promising technology employed in preserving high-quality varieties in animal husbandry and is also widely applied in the human sperm bank. However, the compromised qualities, such as decreased sperm motility, damaged membrane structure, and reduced fertilization competency, have significantly hampered the efficient application of this technique. Therefore, it is imperative to depict various molecular changes found in cryopreserved sperm and identify the regulatory network in response to the cryopreservation stress. In this study, semen was collected from three Chinese Merino rams and divided into untreated (fresh semen, FS) and programmed freezing (programmed freezing semen, PS) groups. After measuring different quality parameters, the ultra-low RNA-seq and tandem mass tag-based (TMT) proteome were conducted in both the groups. The results indicated that the motility (82.63% ± 3.55% vs. 34.10% ± 2.90%, p < 0.05) and viability (89.46% ± 2.53% vs. 44.78% ± 2.29%, p < 0.05) of the sperm in the FS group were significantly higher compared to those in the PS group. In addition, 45 upregulated and 291 downregulated genes, as well as 30 upregulated and 48 downregulated proteins, were found in transcriptomics and proteomics data separately. Moreover, three integrated methods, namely, functional annotation and enrichment analysis, Pearson's correlation analysis, and two-way orthogonal partial least squares (O2PLS) analysis, were used for further analysis. The results suggested that various differentially expressed genes and proteins (DEGs and DEPs) were mainly enriched in leishmaniasis and hematopoietic cell lineage, and Fc gamma receptor Ia (FCGR1A) was significantly downregulated in cryopreserved sperm both at mRNA and protein levels in comparison with the fresh counterpart. In addition, top five genes (FCGR1A, HCK, SLX4, ITGA3, and BET1) and 22 proteins could form a distinct network in which genes and proteins were significantly correlated (p < 0.05). Interestingly, FCGR1A also appeared in the top 25 correlation list based on O2PLS analysis. Hence, FCGR1A was selected as the most potential differentially expressed candidate for screening by the three integrated multi-omics analysis methods. In addition, Pearson's correlation analysis indicated that the expression level of FCGR1A was positively correlated with sperm motility and viability. A subsequent experiment was conducted to identify the biological role of FCGR1A in sperm function. The results showed that both the sperm viability (fresh group: 87.65% ± 4.17% vs. 75.8% ± 1.15%, cryopreserved group: 48.15% ± 0.63% vs. 42.45% ± 2.61%, p < 0.05) and motility (fresh group: 83.27% ± 4.15% vs. 70.41% ± 1.07%, cryopreserved group: 45.31% ± 3.28% vs. 35.13% ± 2.82%, p < 0.05) were significantly reduced in fresh and frozen sperm when FCGR1A was blocked. Moreover, the cleavage rate of embryos fertilized by FCGR1A-blocked sperm was noted to be significantly lower in both fresh (95.28% ± 1.16% vs. 90.44% ± 1.56%, p < 0.05) and frozen groups (89.8% ± 1.50% vs. 82.53% ± 1.53%, p < 0.05). In conclusion, our results revealed that the downregulated membrane protein FCGR1A can potentially contribute to the reduced sperm fertility competency in the cryopreserved sheep sperm.

Effects of Dietary Cystine and Tyrosine Supplementation on Melanin Synthesis in the Pacific Oyster (Crassostrea gigas).

Melanogenesis is a multistep process to produce melanin for dark pigmentation in skin coloration. Previous studies in vertebrates demonstrated that cystine and tyrosine amino acids are involved in the melanin synthesis. However, very little is known about the melanogenesis in bivalve. In this study, cystine supplementation for 30days significantly upregulated the expression of CgB-aat1, CgCbs and CgTyr and pheomelanin content in the Pacific oyster Crassostrea gigas. Transmission electron microscope (TEM) results revealed more melanosomes in the connective tissue and melanin granules were secreted in epithelium of mantle. In contrast, tyrosine supplementation had no clear effect on melanogenesis except the gene expression changes of CgB-aat1 and CgCbs. In addition, prolonged supplementation of cystine or tyrosine for 60days had a negative impact on melanogenesis. Indeed, after 60days, expression of most of the melanin synthesis-related genes under study was decreased, and melanin content was significantly reduced, indicating that cystine and tyrosine might inhibit production of eumelanin and pheomelanin, respectively. In addition, in vitro analysis using primary cell culture from mantle tissue indicated that incubation with cystine, tyrosine, or B-AAT1 polypeptide, CBS/TYR recombinant proteins induced the increase of CgB-aat1 and CgCbs expression in a dose-dependent manner, suggesting the presence of a regulatory network in response to cystine and tyrosine amino acids intakes in pheomelanin synthesis-related gene expression. Taken together, these data indicate that cystine-CgB-aat1-CgCbs-CgTyr axis is a potential regulator of the pheomelanin biosynthesis pathway, and thus plays an important role in the mantle pigmentation in C. gigas. This work provides a new clue for selective cultivation of oyster strains with specific shell colors in bivalve breeding.

Genome-wide identification, classification, and expression analysis of heat shock transcription factor family in switchgrass (Panicum virgatum L.)

Switchgrass is one of the most promising bioenergy crops and is generally cultivated in arid climates and poor soils. Heat shock transcription factors (Hsfs) are key regulators of plant responses to abiotic and biotic stressors. However, their role and mechanism of action in switchgrass have not been elucidated. Hence, this study aimed to identify the Hsf family in switchgrass and understand its functional role in heat stress signal transduction and heat tolerance by using bioinformatics and RT-PCR analysis. Forty-eight PvHsfs were identified and divided into three main classes based on their gene structure and phylogenetic relationships: HsfA, HsfB, and HsfC. The results of the bioinformatics analysis showed a DNA-binding domain (DBD) at the N-terminal in PvHsfs, and they were not evenly distributed on all chromosomes except for chromosomes 8 N and 8 K. Many cis-elements related to plant development, stress responses, and plant hormones were identified in the promoter sequence of each PvHsf. Segmental duplication is the primary force underlying Hsf family expansion in switchgrass. The results of the expression pattern of PvHsfs in response to heat stress showed that PvHsf03 and PvHsf25 might play critical roles in the early and late stages of switchgrass response to heat stress, respectively, and HsfB mainly showed a negative response to heat stress. Ectopic expression of PvHsf03 in Arabidopsis significantly increased the heat resistance of seedlings. Overall, our research lays a notable foundation for studying the regulatory network in response to deleterious environments and for further excavating tolerance genes in switchgrass.

The ERF-VII transcription factor AvERF75 positively regulates the waterlogging tolerance by interacting with AvLOB41 in kiwifruit (Actinidia valvata)

The ethylene-responsive VII (ERF-VII) transcription factors are crucial in regulating plant waterlogging tolerance. However, the positive role of ERF-VII genes in kiwifruit waterlogging tolerance is rarely reported. In this study, we cloned the AvERF75 gene from the waterlogging-tolerant genotype KR5 (Actinidia valvata) and explored its roles in response to waterlogging stress. Subcellular localization showed AvERF75 protein was localized in cytoplasm and nucleus, and transactivation assays indicated it exhibited transactivation activity. Overexpression of AvERF75 significantly improved the waterlogging tolerance of transgenic plants (both tobacco and kiwifruit) by scavenging ROS. furthermore, we identified AvLOB41 as an interacting partner of AvERF75 protein by Y2H screening and BiFC assay. Taken together, this study confirms the positive role of AvERF75 in regulating waterlogging tolerance and reveals a new regulatory network in response to waterlogging stress.

The transcriptional mechanism responding to air particulate matter in Laurus nobilis (L.)

Air levels of particulate matter (PM) are dangerously increasing in urban environment due to high levels of industrialization. The use of plants to reduce pollutants is well-known although molecular mechanisms underlying this phenomenon have been scarcely investigated. The aim of this work was to shed lights into the molecular physiological responses of leaves of a typical plant ornamental species (Laurus nobilis L.), to identify key PM-modulated genes of early leaf responses and to optimize phylloremediation strategies in polluted areas. The transcriptome and the PM accumulation in leaf tissues were analysed in plants grown in pots for three months under two different areas: rural and traffic. Differentially expressed genes in common between different pairwise comparisons were highly effective in discriminating leaves at high PM levels after three months of exposure. Thirty of these genes showed contrasting trend of expression between rural and traffic conditions. Higher PM levels highlighted significant repression of genes and gene set categories involved in cell wall and membrane modification. In addition, a repression of genes involved in photosynthesis reactions, glycolysis, gluconeogenesis, TCA, fermentation was observed. Some key members of C2H2, WRKYs and CCAAT-HAP2 were induced as well as downstream defense response genes. The results allowed to develop a general model of gene regulatory networks in response to particulate matter in plants and innovative biotechnological approaches for phylloremediation strategies.

Chromatin accessibility dynamics insight into crosstalk between regulatory landscapes in poplar responses to multiple treatments.

Perennial trees develop and coordinate endogenous response signaling pathways, including their crosstalk and convergence, to cope with various environmental stresses which occur simultaneously in most cases. These processes are involved in gene transcriptional regulations that depend on dynamic interactions between regulatory proteins and corresponding chromatin regions, but the mechanisms remain poorly understood in trees. In this study, we detected chromatin regulatory landscapes of poplar under abscisic acid, methyl jasmonate, salicylic acid and sodium chloride (NaCl) treatment, through integrating ATAC-seq and RNA-seq data. Our results showed that the degree of chromatin accessibility for a given gene is closely related to its expression level. However, unlike the gene expression that shows treatment-specific response patterns, changes in chromatin accessibility exhibit high similarities under these treatments. We further proposed and experimentally validated that a homologous gene copy of RESPONSIVE TO DESICCATION 26 mediates the crosstalk between jasmonic acid and NaCl signaling pathways by directly regulating the stress-responsive genes and that circadian clock-related transcription factors like REVEILLE8 play a central role in response of poplar to these treatments. Overall, our study provides a chromatin insight into the molecular mechanism of transcription regulatory networks in response to different environmental stresses and raises the key roles of the circadian clock of poplar to adapt to adverse environments.

Extracytoplasmic sigma factor AlgU contributes to fitness of Pseudomonas aeruginosa PGPR2 during corn root colonization.

In bacteria, sigma factors are crucial in determining the plasticity of core RNA polymerase (RNAP) while promoter recognition during transcription initiation. This process is modulated through an intricate regulatory network in response to environmental cues. Previously, an extracytoplasmic function (ECF) sigma factor, AlgU, was identified to positively influence the fitness of Pseudomonas aeruginosa PGPR2 during corn root colonization. In this study, we report that the inactivation of the algU gene encoded by PGPR2_23995 hampers the root colonization ability of PGPR2. An insertion mutant in the algU gene was constructed by allele exchange mutagenesis. The mutant strains displayed threefold decreased root colonization efficiency compared with the wild-type strain when inoculated individually and in the competition assay. The mutant strain was more sensitive to osmotic and antibiotic stresses and showed higher resistance to oxidative stress. On the other hand, the mutant strain showed increased biofilm formation on the abiotic surface, and the expression of the pelB and pslA genes involved in the biofilm matrix formation were up-regulated. In contrast, the expression of algD, responsible for alginate production, was significantly down-regulated in the mutant strain, which is directly regulated by the AlgU sigma factor. The mutant strain also displayed altered motility. The expression of RNA binding protein RsmA was also impeded in the mutant strain. Further, the transcript levels of genes associated with the type III secretion system (T3SS) were analyzed, which revealed a significant down-regulation in the mutant strain. These results collectively provide evidence for the regulatory role of the AlgU sigma factor in modulating gene expression during root colonization.

Characterization of the gene expression profile response to drought stress in Haloxylon using PacBio single-molecule real-time and Illumina sequencing.

Haloxylon ammodendron and Haloxylon persicum are important drought-tolerant plants in northwest China. The whole-genome sequencing of H. ammodendron and H. persicum grown in their natural environment is incomplete, and their transcriptional regulatory network in response to drought environment remains unclear. To reveal the transcriptional responses of H. ammodendron and H. persicum to an arid environment, we performed single-molecule real-time (SMRT) and Illumina RNA sequencing. In total, 20,246,576 and 908,053 subreads and 435,938 and 210,334 circular consensus sequencing (CCS) reads were identified by SMRT sequencing of H. ammodendron and H. persicum, and 15,238 and 10,135 unigenes, respectively, were successfully obtained. In addition, 9,794 and 7,330 simple sequence repeats (SSRs) and 838 and 71 long non-coding RNAs were identified. In an arid environment, the growth of H. ammodendron was restricted; plant height decreased significantly; basal and branch diameters became thinner and hydrogen peroxide (H2O2) content and peroxidase (POD) activity were increased. Under dry and wet conditions, 11,803 and 15,217 differentially expressed genes (DEGs) were identified in H. ammodendron and H. persicum, respectively. There were 319 and 415 DEGs in the signal transduction pathways related to drought stress signal perception and transmission, including the Ca2+ signal pathway, the ABA signal pathway, and the MAPK signal cascade. In addition, 217 transcription factors (TFs) and 398 TFs of H. ammodendron and H. persicum were differentially expressed, including FAR1, MYB, and AP2/ERF. Bioinformatic analysis showed that under drought stress, the expression patterns of genes related to active oxygen [reactive oxygen species (ROS)] scavenging, functional proteins, lignin biosynthesis, and glucose metabolism pathways were altered. Thisis the first full-length transcriptome report concerning the responses of H. ammodendron and H. persicum to drought stress. The results provide a foundation for further study of the adaptation to drought stress. The full-length transcriptome can be used in genetic engineering research.

Integrated analysis of miRNA and mRNA expression profiles in response to gut microbiota depletion in the abdomens of female Bactrocera dorsalis.

Insect gut microbiota has been reported to participate in regulating host multiple biological processes including metabolism and reproduction. However, the corresponding molecular mechanisms remain largely unknown. Recent studies suggest that microRNAs (miRNAs) are involved in complex interactions between the gut microbiota and the host. Here, we used next-generation sequencing technology to characterize miRNA and mRNA expression profiles and construct the miRNA-gene regulatory network in response to gut microbiota depletion in the abdomens of female Bactrocera dorsalis. A total of 3016 differentially expressed genes (DEGs) and 18 differentially expressed miRNAs (DEMs) were identified. Based on the integrated analysis of miRNA and mRNA sequencing data, 229 negatively correlated miRNA-gene pairs were identified from the miRNA-mRNA network. Gene ontology enrichment analysis indicated that DEMs could target several genes involved in the metabolic process, oxidation-reduction process, oogenesis, and insulin signaling pathway. Finally, real-time quantitative polymerase chain reaction further verified the accuracy of RNA sequencing results. In conclusion, our study provides the profiles of miRNA and mRNA expressions under antibiotics treatment and provides an insight into the roles of miRNAs and their target genes in the interaction between the gut microbiota and its host.

The Toggle Switch Model for Gene Expression Change during the Prenatal-to-Postnatal Transition in Mammals.

The prenatal-to-postnatal transition is a pivotal process in the life cycle whereby an organism shifts from responding to intrauterine cues to undergoing extrauterine stresses with many physiological adaptations. However, the molecular basis underlying the evolutionarily conserved physiological adaptations remains elusive. Here, we analyze the transcriptomes of seven organs across developmental time points from five mammalian species by constructing computational coexpression networks and report a developmental shift of gene expression at the perinatal stage. The low-to-high and high-to-low expressed genes tightly coalesce in the functional categories and gene regulatory pathways that implicate the physiological adaptions during the prenatal-to-postnatal transition, including lipid metabolism, circadian rhythm, immune response, cell cycle, and cell division. The low-to-high and high-to-low expressed genes around the perinatal stage tend to form the mutually inhibitory toggle switch gene pairs linking the gene regulatory networks in response to the environmental changes. We thus propose the toggle switch model for the developmental shift of gene expression as a mechanic framework to investigate how the physiological adaptations occur during the prenatal-to-postnatal transition.

Integrative Analysis of the lncRNA-Associated ceRNA Regulatory Network Response to Hypoxia in Alveolar Type II Epithelial Cells of Tibetan Pigs.

The function of alveolar type II epithelial (ATII) cells is severely hampered by oxygen deficiency, and understanding the regulatory mechanisms controlling responses to hypoxia may assist in relieving injury induced by hypoxia. In this study, we cultured ATII cells from Tibetan pigs and Landrace pigs under hypoxic and normoxic environments to screen for differentially expressed (DE) lncRNAs, DEmiRNAs, and construct their associated ceRNA regulatory networks in response to hypoxia. Enrichment analysis revealed that target genes of DElncRNAs of Tibetan pigs and Landrace pig between the normoxic (TN, LN) and hypoxic (TL, LL) groups significantly enriched in the proteoglycans in cancer, renal cell carcinoma, and erbB signaling pathways, while the target genes of DEmiRNAs were significantly enriched in the axon guidance, focal adhesion, and mitogen-activated protein kinase (MAPK) signaling pathways. Hypoxia induction was shown to potentially promote apoptosis by activating the focal adhesion/PI3K-Akt/glycolysis pathway. The ssc-miR-20b/MSTRG.57127.1/ssc-miR-7-5p axis potentially played a vital role in alleviating hypoxic injury by regulating ATII cell autophagy under normoxic and hypoxic conditions. MSTRG.14861.4-miR-11971-z-CCDC12, the most affected axis, regulated numerous RNAs and may thus regulate ATII cell growth in Tibetan pigs under hypoxic conditions. The ACTA1/ssc-miR-30c-3p/MSTRG.23871.1 axis is key for limiting ATII cell injury and improving dysfunction and fibrosis mediated by oxidative stress in Landrace pigs. Our findings provide a deeper understanding of the lncRNA/miRNA/mRNA regulatory mechanisms of Tibetan pigs under hypoxic conditions.

Comprehensive Transcriptomic Analysis of Heterotrophic Nitrifying Bacterium Klebsiella sp. TN-10 in Response to Nitrogen Stress.

Klebsiella sp. TN-10, a heterotrophic nitrifying bacterium, showed excellent nitrification ability under nitrogen stress. The strain was cultured under different nitrogen stress levels, including ammonium sulfate 0.5, 2.5, and 5 g/L, and samples were titled group-L, group-M, and group-H, respectively. In these three groups, the removed total nitrogen was 70.28, 118.33, and 157.18 mg/L after 12 h of cultivation, respectively. An RNA-Seq transcriptome analysis was used to describe key regulatory networks in response to nitrogen stress. The GO functional enrichment and KEGG enrichment analyses showed that differentially expressed genes (DEGs) participated in more pathways under higher nitrogen stress (group-H). Carbohydrate metabolism and amino acid metabolism were the most abundant subcategories, which meant these pathways were significantly influenced by nitrogen stress and could be related to nitrogen removal. In the nitrogen cycle, up-regulated gene2311 (narK, encodes major facilitator superfamily transporter) may accelerate the entry of nitrogen into the cells and subsequently contribute to the nitrogen utilization. In addition, the up-regulation of gene2312 (narG), gene2313 (narH), and gene2315 (narH) may accelerate denitrification pathways and facilitate nitrogen removal. The results presented in this study may play a pivotal role in understanding the regulation networks of the nitrifying bacterium TN-10 under nitrogen stress.

Acute hypoxia and reoxygenation induces oxidative stress, glycometabolism, and oxygen transport change in red swamp crayfish (Procambarus clarkii): Application of transcriptome profiling in assessment of hypoxia

Red swamp crayfish (Procambarus clarkii), an economically and ecologically important crustacean, frequently encounter hypoxic environments in burrows or aquatic habitats. However, hepatopancreas oxidative stress and molecular regulatory network under hypoxia in crayfish has not been clearly established. To determine oxidative stress changes during hypoxia/reoxygenation in crayfish, we assessed the enzymatic activities of CAT, SOD, GST, and GPx as well as the hepatopancreas mRNA levels of Cu/Zn-sod, cat, Mu-gst, and gpx1. The mRNA levels of the aforementioned genes and activity of the enzyme increased gradually and peaked at 6.5 h of hypoxic stress (1.0 ± 0.1 mg/L) and then dropped during reoxygenation (7.0 ± 0.2 mg/L), suggesting that they protect from oxidative stress. Hepatopancreas transcriptomic analysis of changes in key genes and regulatory networks in response to hypoxia identified 4643 DEGs (differentially expressed genes), of which 2012 were upregulated, whereas 2631 downregulated. These genes are enriched in signaling cascades linked to glucose metabolism (e.g., glycolysis/gluconeogenesis, AMPK, and insulin signaling pathways) as well as oxygen transport (e.g., HIF-1, MAPK and PI3K-Akt signaling pathways). Genes associated with glucose metabolism (e.g., gapdh, pyk, and pck) and oxygen transport (e.g., egln, gapdh, and pdk1) were also identified. Our findings indicate that the red swamp crayfish may utilize “glycolysis/gluconeogenesis” to maintain responsive and active functions and “HIF-1″ to obtain more oxygen under hypoxia.

Transcriptional regulatory networks in response to drought stress and rewatering in maize (Zea mays L.).

Drought severely affects the growth and development of maize, but there is a certain degree of compensation effect after rewatering. This study intends to elaborate the response mechanism of maize at the physiological and molecular level as well as excavating potential genes with strong drought resistance and recovery ability. Physiological indexes analysis demonstrated that stomata conductance, transpiration rate, photosynthesis rate, antioxidant enzymes, and proline levels in maize were significantly altered in response to drought for 60 and 96h and rewatering for 3days. At 60h, 96h, and R3d, we detected 3095, 1941, and 5966 differentially expressed genes (DEGs) and 221, 226, and 215 differentially expressed miRNAs. Weighted correlation network analysis (WGCNA) showed that DEGs responded to maize drought and rewatering through participating in photosynthesis, proline metabolism, ABA signaling, and oxidative stress. Joint analysis of DEGs, miRNA, and target genes showed that zma-miR529, miR5072, zma-miR167e, zma-miR167f, zma-miR167j, miR397, and miR6214 were involved to regulate SBPs, MYBs, ARFs, laccases, and antioxidant enzymes, respectively. Hundreds of differentially expressed DNA methylation-related 24-nt siRNA clusters overlap with DEGs, indicating that DNA methylation is involved in responses under drought stress. These results provide new insights into the molecular mechanisms of drought tolerance, and may identify new targets for breeding drought-tolerant maize lines.

Genome-wide identification and analysis of WRKY gene family in maize provide insights into regulatory network in response to abiotic stresses

BackgroundThe WRKY transcription factor family plays significant roles in biotic and abiotic stress responses, which has been associated with various biological processes in higher plants. However, very little is known regarding the structure and function of WRKY genes in maize.ResultsIn this study, a total of 140 ZmWRKY proteins encoded by 125 ZmWRKY genes were eventually identified in maize. On the basis of features of molecular structure and a comparison of phylogenetic relationships of WRKY transcription factor families from Arabidopsis, rice and maize, all 140 ZmWRKY proteins in maize were divided into three main groups (Groups I, II and III) and the Group II was further classified into five subgroups. The characteristics of exon-intron structure of these putative ZmWRKY genes and conserved protein motifs of their encoded ZmWRKY proteins were also presented respectively, which was in accordance with the group classification results. Promoter analysis suggested that ZmWRKY genes shared many abiotic stress-related elements and hormone-related elements. Gene duplication analysis revealed that the segmental duplication and purifying selection might play a significant role during the evolution of the WRKY gene family in maize. Using RNA-seq data, transcriptome analysis indicated that most of ZmWRKY genes displayed differential expression patterns at different developmental stages of maize. Further, by quantitative real-time PCR analysis, twenty-one ZmWRKY genes were confirmed to respond to two different abiotic stress treatments, suggesting their potential roles in various abiotic stress responses. In addition, RNA-seq dataset was used to conduct weighted gene co-expression network analysis (WGCNA) in order to recognize gene subsets possessing similar expression patterns and highly correlated with each other within different metabolic networks. Further, subcellular localization prediction, functional annotation and interaction analysis of ZmWRKY proteins were also performed to predict their interactions and associations involved in potential regulatory network.ConclusionsTaken together, the present study will serve to present an important theoretical basis for further exploring function and regulatory mechanism of ZmWRKY genes in the growth, development, and adaptation to abiotic stresses in maize.

Dynamic changes in gene-to-gene regulatory networks in response to SARS-CoV-2 infection

The current pandemic of SARS-CoV-2 has caused extensive damage to society. The characterization of SARS-CoV-2 profiles has been addressed by researchers globally with the aim of resolving this disruptive crisis. This investigation process is indispensable to understand how SARS-CoV-2 behaves in human host cells. However, little is known about the systematic molecular mechanisms involved in the effects of SARS-CoV-2 infection on human host cells. Here, we present gene-to-gene regulatory networks in response to SARS-CoV-2 using a Bayesian network. We examined the dynamic changes in the SARS-CoV-2-purturbated networks established by our proposed framework for gene network analysis, thus revealing that interferon signaling gradually switched to the subsequent inflammatory cytokine signaling cascades. Furthermore, we succeeded in capturing a COVID-19 patient-specific network in which transduction of these signals was concurrently induced. This enabled us to explore the local regulatory systems influenced by SARS-CoV-2 in host cells more precisely at an individual level. Our panel of network analyses has provided new insights into SARS-CoV-2 research from the perspective of cellular systems.