Biology subjects

Yang, J.

Publications and source records attributed to Yang, J..

At least 901 records · Page 50Linked to original sources

bioRxiv2020

Genomic selection to optimize doubled haploid-based hybrid breeding in maize

Crop improvement, as a long-term endeavor, requires continuous innovations in technique from multiple perspectives. Doubled haploid (DH) technology for pure inbred production, which shaves years off of the conventional selfing approach, has been widely used for breeding. However, the final success rate of in vivo maternal DH production is determined by four factors: haploids induction, haploids identification, chromosome doubling, and successful selfing of the fertile haploid plants to produce DH seeds. Traits in each of these steps, if they can be accurately predicted using genomic selection methods, will help adjust the DH production protocol and simplify the logistics and save costs. Here, a hybrid population (N=158) was generated based on an incomplete half diallel design using 27 elite inbred lines. These hybrids were induced to create F1-derived haploid families. The hybrid materials, as well as the 27 inbreds, the inbred-derived haploids (N=200), and the F1-derived haploids (N=5,000) were planted in the field to collect four DH-production traits, three yield-related traits, and three developmental traits. Quantitative genetics analysis suggested that in both diploids and haploid families, most of the developmental traits showed high heritability, while the DH-production and developmental traits exhibited intermediate levels of heritability. By employing different genomic selection models, our results showed that the prediction accuracy ranged from 0.52 to 0.59 for the DH-production traits, 0.50 to 0.68 for the yield-related traits, and 0.44 to 0.87 for the developmental traits. Further analysis using index selection achieved the highest prediction accuracy when considering both DH production efficiency and the agronomic trait performance. Furthermore, the long-term responses through simulation confirmed that index selection would increase the genetic gain for targeted agronomic traits while maintaining the DH production efficiency. Therefore, our study provides an optimization strategy to integrate GS technology for DH-based hybrid breeding.

genetics↗

bioRxiv2020

Interaction network of SARS-CoV-2 with host receptome through spike protein

Host cellular receptors are key determinants of virus tropism and pathogenesis. Virus utilizes multiple receptors for attachment, entry, or specific host responses. However, other than ACE2, little is known about SARS-CoV-2 receptors. Furthermore, ACE2 cannot easily interpret the multi-organ tropisms of SARS-CoV-2 nor the clinical differences between SARS-CoV-2 and SARS-CoV. To identify host cell receptors involved in SARS-CoV-2 interactions, we performed genomic receptor profiling to screen almost all human membrane proteins, with SARS-CoV-2 capsid spike (S) protein as the target. Twelve receptors were identified, including ACE2. Most receptors bind at least two domains on S protein, the receptor-binding-domain (RBD) and the N-terminal-domain (NTD), suggesting both are critical for virus-host interaction. Ectopic expression of ASGR1 or KREMEN1 is sufficient to enable entry of SARS-CoV-2, but not SARS-CoV and MERS-CoV. Analyzing single-cell transcriptome profiles from COVID-19 patients revealed that virus susceptibility in airway epithelial ciliated and secretory cells and immune macrophages highly correlates with expression of ACE2, KREMEN1 and ASGR1 respectively, and ACE2/ASGR1/KREMEN1 (ASK) together displayed a much better correlation than any individual receptor. Based on modeling of systemic SARS-CoV-2 host interactions through S receptors, we revealed ASK correlation with SARS-CoV-2 multi-organ tropism and provided potential explanations for various COVID-19 symptoms. Our study identified a panel of SARS-CoV-2 receptors with diverse binding properties, biological functions, and clinical correlations or implications, including ASGR1 and KREMEN1 as the alternative entry receptors, providing insights into critical interactions of SARS-CoV-2 with host, as well as a useful resource and potential drug targets for COVID-19 investigation.

microbiology↗

bioRxiv2020

Extreme stiffness of neuronal synapses and implications for synaptic adhesion and plasticity

Synapses play a critical role in neural circuits, and they are potential sites for learning and memory. Maintenance of synaptic adhesion is critical for neural circuit function, however, biophysical mechanisms that help maintain synaptic adhesion are not clear. Studies with various cell types demonstrated the important role of stiffness in cellular adhesions. Although synaptic stiffness could also play a role in synaptic adhesion, stiffnesses of synapses are difficult to characterize due to their small size and challenges in verifying synapse identity and function. To address these challenges, we have developed an experimental platform that combines atomic force microscopy, fluorescence microscopy, and transmission electron microscopy. Here, using this platform, we report that functional, mature, excitatory synapses had an average elastic modulus of approximately 200 kPa, two orders of magnitude larger than that of the brain tissue, suggesting stiffness might have a role in synapse function. Similar to various functional and anatomical features of neural circuits, synaptic stiffness had a lognormal-like distribution, hinting a possible regulation of stiffness by processes involved in neural circuit function. In further support of this possibility, we observed that synaptic stiffness was correlated with spine size, a quantity known to correlate with synaptic strength. Using established stages of the long-term potentiation timeline and theoretical models of adhesion cluster dynamics, we developed a biophysical model of the synapse that not only explains extreme stiffness of synapses, their statistical distribution, and correlation with spine size, but also offers an explanation to how early biomolecular and structural changes during functional potentiation could lead to strengthening of synaptic adhesion. According to this model, synaptic stiffness serves as an indispensable physical messenger, feeding information back to synaptic adhesion molecules to facilitate maintenance of synaptic adhesion.

biophysics↗

bioRxiv2020

Munc13 binds and recruits SNAP25 to chaperone SNARE complex assembly

Synaptic vesicle fusion is mediated by membrane-bridging complexes formed by SNARE proteins - VAMP2 on the vesicle and Syntaxin-1/SNAP25 on the pre-synaptic membrane. Accumulating evidence suggest that chaperones Munc18-1 and Munc13-1 co-operatively catalyze SNARE assembly via an intermediate template complex containing Syntaxin-1 and VAMP2. How SNAP25 is chaperoned into this nascent complex remains a mystery. Here we report that Munc13-1 recruits SNAP25 to initiate the ternary SNARE complex assembly by direct binding, as judged by bulk FRET spectroscopy and single-molecule optical tweezer studies. Detailed structure-function analyses show that the binding is mediated by the Munc13-1 MUN domain and is specific for the SNAP25 linker region that connects the two SNARE motifs. Consequently, freely diffusing SNAP25 molecules on phospholipid bilayers are concentrated and presumably bound in ~1:1 stoichiometry by the self-assembled Munc13-1 nanoclusters. Our data suggests that Munc13-1s capacity to bind all three synaptic SNARE proteins likely underlie its chaperone function.

neuroscience↗

bioRxiv2020

Neonatal LPS exposure results in ATP8A2 down-regulation in the prefrontal cortex and depressive-like behaviors in mice through increasing IFN-γ level

Neonatal lipopolysaccharide (LPS) exposure can cause depressive-like behaviors in rodents involving elevated interferon (IFN)-{gamma}. Studies have linked down-regulation of prefrontal cortex (PFC) ATPase phospholipid transporting 8A2(ATP8A2) expression to depressive-like behaviors. In non-neuronal cells, IFN-{gamma} could reduce ATP8A2 expression. We therefore hypothesized that neonatal LPS exposure might induce PFC ATP8A2 down-regulation by increasing IFN-{gamma} level. Here, C57BL6/J mice of both sexes received 3-dose-injections of LPS (50g/kg bodyweight, i.p.) on postnatal day (PND)5, PND7 and PND9. LPS-treated mice showed a transiently decreased PFC ATP8A2 expression. Moreover, a negative correlation of PFC ATP8A2 expression was found with IFN-{gamma} level. Using neutralizing mAb, IFN-{gamma} was identified as the key mediator of LPS-induced PFC ATP8A2 decrease. Besides, neutralizing IFN-{gamma} during neonatal LPS exposure attenuated the depressive-like behaviors in adulthood. In sum, neonatal LPS exposure reduced ATP8A2 level in PFC in mice via increasing IFN-{gamma} level, maybe associated with mechanism underlying LPS-induced brain and behavior impairments.

neuroscience↗

bioRxiv2020

Varying intestinal absorption curves of glucose and fat with different plasma insulin curves in different positions

It has been shown that posture could affect the rehabilitation of some diseases, and even affect the physiological metabolism and function of certain systems of the human body, including gastrointestinal absorption of glucose. Studies attributed the different gastrointestinal absorption rate in different positions to the varying rate of gastric emptying in different positions. However, it is still unknown whether the absorption rate of nutrients from the intestine varies in different positions. To verify this hypothesis, the present study was conducted using rats as subjects. After injection of glucose or chyme of safflower oil into the upper segment of jejunum of rats, curves of plasma glucose or triglyceride were drawed to evaluate and compare the potential influences on intestinal absorption by postures. We found varying intestinal absorption curves of glucose and fat with different plasma insulin curves in different positions. To be specific, the right lateral decubitus resulted in the most sharp curves, whereas the supine position the most obtuse curves with a delayed peak, both in case of glucose and fat absorption. These findings contribute to understand the position-related absorption kinetics of substances in the intestinal tract. According to this study, posture may be important for the prevention and nursing intervention of some diseases related to metabolic kinetics of glucose and lipids. It may also be important for the absorption and transport of lipophilic drugs through the mesentery lymphatic vessels.

physiology↗

bioRxiv2020

Rhizosphere Microbiomes in a Historical Maize/Soybean Rotation System respond to Host Species and Nitrogen Fertilization at Genus and Sub-genus Levels

Root associated microbes are key players in plant health, disease resistance, and nitrogen (N) use efficiency. It remains largely unclear how the interplay of biological and environmental factors affects rhizobiome dynamics in agricultural systems. Here, we quantified the composition of rhizosphere and bulk soil microbial communities associated with maize (Zea mays L.) and soybean (Glycine max L.) in a long-term crop rotation study under conventional fertilization and low N regimes. Over two growing seasons, we evaluated the effects of environmental conditions and several treatment factors on the abundance of rhizosphere and soil colonizing microbial taxa. Time of sampling, host plant species and N fertilization had major effects on microbiomes, while no effect of crop rotation was observed. Using variance partitioning as well as 16S sequence information, we further defined a set of 82 microbial genera and sub-genus groups that show distinct responses to treatment factors. We identified taxa that are highly specific to either maize or soybean rhizospheres, as well as taxa that are sensitive to N fertilization in plant rhizospheres and bulk soil. This study provides insights to harness the full potential of soil microbes in maize and soybean agricultural systems through plant breeding and field management.

plant biology↗

bioRxiv2020

Different activation signatures in the primary sensorimotor and higher-level regions for haptic three-dimensional curved surface exploration

Haptic object perception begins with continuous exploratory contacts, and the human brain needs to accumulate sensory information continuously over time. However, it is still unclear how the primary sensorimotor cortex (PSC) interacts with these higher-level regions during haptic exploration across time. This functional magnetic resonance imaging (fMRI) study investigates time-dependent haptic object processing by examining brain activity during haptic 3D curve and roughness estimation. For this experiment, we designed sixteen haptic stimuli (4 kinds of curve x 4 kinds of roughness) for the haptic curve and roughness estimation tasks. Twenty participants were asked to move their right index and middle fingers along with the surface twice and to estimate one of the two features--roughness or curvature--dependent on the task instruction. We found that the brain activity in several higher-level regions (e.g., bilateral posterior parietal cortex) linearly increased with curvature through the haptic exploration phase. Surprisingly, we found that the contralateral PSC was parametrically modulated by the number of curves only during the late exploration phase, but not during the early exploration phase. In contrast, we found no similar parametric modulation activity patterns for haptic roughness estimation in either the contralateral PSC or in the higher-level regions. Together, our findings suggest that haptic 3D object perception is processed across the cortical hierarchy, while the contralateral PSC interacts with other higher-level regions across time in a manner that is dependent upon object features. HighlightsO_LIWe observed the brain activity of haptic object perception using parametric stimuli. C_LIO_LIHaptic curve estimation showed parametric modulation across the cortical hierarchy. C_LIO_LICurve parametric modulation in the sensorimotor cortex showed time dependency. C_LIO_LIRoughness parametric modulation showed very little dependency in any regions of the brain. C_LIO_LIThese findings reflect the nature of time-dependent haptic object processing in the brain. C_LI

neuroscience↗

bioRxiv2020

A valid protective immune response elicited in rhesus macaques by an inactivated vaccine is capable of defending against SARS-CoV-2 infection

With the relatively serious global epidemic outbreak of SARS-CoV-2 infection, public concerns focus on not only clinical therapeutic measures and public quarantine for this disease but also the development of vaccines. The technical design of our SARS-CoV-2 inactivated vaccine provides a viral antigen that enables the exposure of more than one structural protein based upon the antibody composition of COVID-19 patients convalescent serum. This design led to valid immunity with increasing neutralizing antibody titers and a CTL response detected post-immunization of this vaccine by two injections in rhesus macaques. Further, this elicited immunoprotection in macaques enables not only to restrain completely viral replication in tissues of immunized animals, compared to the adjuvant control and those immunized by an RBD peptide vaccine, but also to significantly alleviate inflammatory lesion in lung tissues in histo-pathologic detection, compared to the adjuvant control with developed interstitial pneumonia. The data obtained from these macaques immunized with the inactivated vaccine or RBD peptide vaccine suggest that immunity with a clinically protective effect against SARS-CoV-2 infection should include not only specific neutralizing antibodies but also specific CTL responses against at least the S and N antigens.

immunology↗

bioRxiv2020

Time-course transcriptome landscape of achene development in lettuce

Lettuce (Lactuca sativa L.), which belongs to the large Asteraceae (Compositae) family, breeds by sexual reproduction and produce seeds. Actually, lettuce seeds are achenes, which are defined as fruits. However, few studies have described the morphological characteristics of the lettuce achenes, and genes essential for achene development are largely unknown in lettuce. To investigate the gene activity during achene development and determine the possible mechanisms that influence achene development in lettuce, we performed a time-course transcriptome analysis of lettuce achenes. A total of 23,790 expressed genes were detected at the five achene development stages. We investigated the gene expression patterns during achene development and identified the enriched biological processes at the corresponding stages. Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses revealed a variety of transcriptomic similarities and differentiation at different achene development stages. Further, transcription factors and phytohormones were found to play important roles during achene development. Finally, we proposed a working model to illustrate the gene expression modules and possible molecular mechanism underlying achene development. Our time-course transcriptome data also provides a foundation for future functional studies to reveal the genetic control of achene development in lettuce.

plant biology↗

bioRxiv2020

SvFUL2, an A-class MADS-box transcription factor, is necessary for inflorescence determinacy in model panicoid cereal, Setaria viridis

Inflorescence architecture in cereal crops directly impacts yield potential through regulation of seed number and harvesting ability. Extensive architectural diversity found in inflorescences of grass species is due to spatial and temporal activity and determinacy of meristems, which control the number and arrangement of branches and flowers, and underlie plasticity. Timing of the floral transition is also intimately associated with inflorescence development and architecture, yet little is known about the intersecting pathways and how they are rewired during development. Here, we show that a single mutation in a gene encoding an AP1 A-class MADS-box transcription factor significantly delays flowering time and disrupts multiple levels of meristem determinacy in panicles of the C4 model panicoid grass, Setaria viridis. Previous reports of A-class genes in cereals have revealed extensive functional redundancy, and in panicoid grasses, no associated inflorescence phenotypes have been described. In S. viridis, perturbation of SvFul2, both through chemical mutagenesis and CRISPR/Cas9-based gene editing, converted a normally determinate inflorescence habit to an indeterminate one, and also repressed determinacy in axillary branch and floral meristems. Our analysis of gene networks connected to disruption of SvFul2 identified regulatory hubs at the intersect of floral transition and inflorescence determinacy, providing insights into the optimization of cereal crop architecture.

plant biology↗

bioRxiv2020

A Transcriptional Switch Governing Fibroblast Plasticity Underlies Reversibility of Chronic Heart Disease

In diseased organs, stress-activated signaling cascades alter chromatin, triggering broad shifts in transcription and cell state that exacerbate pathology. Fibroblast activation is a common stress response that worsens lung, liver, kidney and heart disease, yet its mechanistic basis remains poorly understood1,2. Pharmacologic inhibition of the BET family of transcriptional coactivators alleviates cardiac dysfunction and associated fibrosis, providing a tool to mechanistically interrogate maladaptive fibroblast states and modulate their plasticity as a potential therapeutic approach3-8. Here, we leverage dynamic single cell transcriptomic and epigenomic interrogation of heart tissue with and without BET inhibition to reveal a reversible transcriptional switch underlying stress-induced fibroblast activation. Transcriptomes of resident cardiac fibroblasts demonstrated robust and rapid toggling between the quiescent fibroblast and activated myofibroblast state in a manner that directly correlated with BET inhibitor exposure and cardiac function. Correlation of single cell chromatin accessibility with cardiac function revealed a novel set of reversibly accessible DNA elements that correlated with disease severity. Among the most dynamic elements was an enhancer regulating the transcription factor MEOX1, which was specifically expressed in activated myofibroblasts, occupied putative regulatory elements of a broad fibrotic gene program, and was required for TGF{beta}-induced myofibroblast activation. CRISPR interference of the most dynamic cis-element within the enhancer, marked by nascent transcription, prevented TGF{beta}-induced activation of Meox1. These findings identify MEOX1 as a central regulator of stress-induced myofibroblast activation associated with cardiac dysfunction. The plasticity and specificity of the BET-dependent regulation of MEOX1 in endogenous tissue fibroblasts provides new trans- and cis- targets for treating fibrotic disease.

molecular biology↗

bioRxiv2020

The discovery of a recombinant SARS2-like CoV strain provides insights into SARS and COVID-2019 pandemics

In December 2019, the world awoke to a new zoonotic strain of coronavirus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). In the present study, we identified key recombination regions and mutation sites cross the SARS-CoV-2, SARS-CoV and SARS-like CoV clusters of betacoronavirus subgroup B. Based on the analysis of these recombination events, we proposed that the Spike protein of SARS-CoV-2 may have more than one specific receptor for its function. In addition, we reported--for the first time--a recombination event of ORF8 at the whole-gene level in a bat and ultimately determined that ORF8 enhances the viral replication. In conjunction with our previous discoveries, we found that receptor binding abilities, junction furin cleavage sites (FCSs), strong first ribosome binding sites (RBSs) and enhanced ORF8s are main factors contributing to transmission, virulence and host adaptability of CoVs. Junction FCSs and enhanced ORF8s increase the efficiencies in viral entry into cells and replication, respectively while strong first RBSs enhance the translational initiation. The strong recombination ability of CoVs integrated these factors to generate multiple recombinant strains, two of which evolved into SARS-CoV and SARS-CoV-2 by nature selection, resulting in the SARS and COVID-19 pandemics.

bioinformatics↗

bioRxiv2020

Pseudogene-mediated DNA demethylation leads to oncogene activation

Despite being one of the leading causes of cancer-related deaths, there is an unmet clinical need for hepatocellular carcinoma (HCC) patients. The lack of effective treatment is, at least in part, due to our lack of understanding of the molecular pathogenesis of this disease. Oncofetal protein SALL4 is re-activated in patients with aggressive HCC along with other solid tumors and hematologic malignancies. This study identifies a previously unrecognized mechanism of SALL4 reactivation which is mediated by pseudogene-induced demethylation. Using a locus-specific demethylating technology, we identified the critical CpG region for SALL4 expression. We showed that SALL4 pseudogene 5 hypomethylates this region through interaction with DNMT1, resulting in SALL4 upregulation. Intriguingly, pseudogene 5 is significantly upregulated in a hepatitis B virus (HBV) model prior to SALL4 induction, and both are increased in HBV-HCC patients. Our results suggest that pseudogene-mediated demethylation represents a unique mechanism of oncogene activation in cancer. SignificanceOur study provides a mechanistic link between HBV infection, activation of the oncogene SALL4, and HCC. We reveal a previously undescribed capability of a pseudogene to epigenetically activate an oncogene by demethylation in a locus-specific manner.

cancer biology↗

bioRxiv2020

A simple and efficient metric quantifying druggable property of chemical small molecules

One big class of drugs are chemical small molecules (CSMs), but the majority of CSMs are in very low druggable potential. Therefore, it is quite important to predict drug-related properties (druggable properties) for candidate CSMs. Currently, although a number of druggable properties (e.g. logP and pKa) can be calculated by in silico methods, the identification of druggable CSMs is still at high risk and new quantitative metrics for the druggable potential of CSMs are increasingly needed. Here, we presented normalized bond energy (NBE), a new metric for the above purpose. By applying NBE to the DrugBank CSMs whose properties are largely known, we revealed that NBE is able to describe a number of critical druggable properties including logP, pKa, membrane permeability, blood-brain barrier penetration, and human intestinal absorption. Moreover, given that the human endogenous metabolites could be served as an important resource for drug discovery, we applied NBE to the metabolites in the Human Metabolome Database. As a result, NBE shows a significant difference in metabolites from various body fluids and is correlated with some important properties including melting point and water solubility.

bioinformatics↗

bioRxiv2020

The genome analysis of Tripterygium wilfordii reveals TwCYP712K1 and TwCYP712K2 responsible for oxidation of friedelin in celastrol biosynthesis pathway

ABSTRACTTripterygium wilfordii is a Traditional Chinese Medicine (TCM) from family Celastraceae and celastrol is one of the strongest active ingredients belonging to friedelane-type pentacyclic triterpenoid, which has a large clinical application value of anti-tumor, immunosuppression, and obesity treatment. The first committed biosynthesis step of celastrol is the cyclization of 2, 3-oxidosqualene to friedelin, catalyzed by the oxidosqualene cyclase, while the rest of this pathway is still unclear. In this study, we reported a reference genome assembly of T. wilfordii with high-quality annotation by using a hybrid sequencing strategy (Nanopore, Bionano, Illumina HiSeq, and Pacbio), which obtained a 340.12 Mb total size and contig N50 reached 3.09 Mb. In addition, we successfully anchored 91.02% sequences into 23 pseudochromosomes using Hi-C technology and the super-scaffold N50 reached 13.03 Mb. Based on integration genome, transcriptom and metabolite analyses, as well as in vivo and in vitro enzyme assays, two CYP450 genes, TwCYP712K1 and TwCYP712K2 have been proven for C-29 position oxidation of friedelin to produce polpunonic acid, which clarifies the second biosynthesis step of celastrol. Syntenic analysis revealed that TwCYP712K1 and TwCYP712K2 derived from the common ancestor. These results have provided insight into illustrating pathways for both celastrol and other bioactive compounds found in this plant.Competing Interest StatementThe authors have declared no competing interest.View Full Text

plant biology↗

bioRxiv2020

PCAT: An integrated portal for genomic and preclinical testing data of pediatric cancer patient-derived xenograft models

Although cancer is the leading cause of disease-related mortality in children, the relative rarity of pediatric cancers poses a significant challenge for developing novel therapeutics to further improve prognosis. Patient-derived xenograft (PDX) models, which are usually developed from high-risk tumors, are a useful platform to study molecular driver events, identify biomarkers, and prioritize therapeutic agents. Here we develop PDX for Childhood Cancer Therapeutics (PCAT), a new integrated portal for pediatric cancer PDX models. Distinct from previously reported PDX portals, PCAT is focused on pediatric cancer models and provides intuitive interfaces for querying and data mining. The current release comprises 324 models and their associated clinical and genomic data, including gene expression, mutation, and copy number alteration. Importantly, PCAT curates preclinical testing results for 68 models and 79 therapeutic agents manually collected from individual agent testing studies published since 2008. To facilitate comparisons of patterns between patient tumors and PDX models, PCAT curates clinical and molecular data of patient tumors from the TARGET project. In addition, PCAT provides access to gene fusions identified in nearly 1,000 TARGET samples. PCAT was built using R-shiny and MySQL. The portal can be accessed at http://pcat.zhenglab.info or http://www.pedtranscriptome.org.

genomics↗

bioRxiv2020

PacC-dependent adaptation and modulation of host cellular pH controls hemibiotrophic invasive growth and disease development by the rice blast fungus

Many of the worlds most serious crop diseases are caused by hemibiotrophic fungi. These pathogens have evolved the ability to colonize living plant cells, suppressing plant immunity responses, before switching to necrotrophic growth, in which host cells die, providing the energy to fuel sporulation and spread of the fungus. How hemibiotrophic pathogens switch between these two lifestyles remains poorly understood. Here, we report that the devastating rice blast fungus, Magnaporthe oryzae, manipulates host cellular pH to regulate hemibiotrophy. During infection by M. oryzae, host plant cells are alkalinized to pH 7.8 during biotrophic growth, but later acidified to pH 6.5 during necrotrophy. Using a forward genetic screen, we identified alkaline-sensitive mutants of M. oryzae that were blocked in biotrophic proliferation and impaired in induction of host cell acidification and necrotrophy. These mutants defined components of the PacC-dependent ambient pH signal transduction pathway in M. oryzae. We report that PacC exists as a full-length repressor, PacC559, and a truncated transcriptional activator, PacC222, which localize to the fungal nucleus during biotrophic growth and to the cytoplasm during necrotrophy. During biotrophy, PacC222 directly activates genes associated with nutrient acquisition and fungal virulence, while PacC559 represses genes associated with saprophytic mycelial growth and sporulation, which are subsequently de-repressed during necrotrophy. When considered together, our results indicate that temporal regulation of hemibiotrophy by M. oryzae requires PacC-dependent sensing and manipulation of host cellular pH. Author SummaryCrop diseases caused by fungi represent some of the most serious threats to global food security. Many fungal pathogens have evolved the ability to invade living plant tissue and suppress host immunity, before switching to a completely different mode of growth, in which they are able to kill host plant cells. This lifestyle- called hemibiotrophy -is exemplified by the blast fungus, Magnaporthe oryzae, which causes devastating diseases of rice, wheat and many other grasses. We found that during infection by M. oryzae, host cells initially have an alkaline pH, when the fungus is growing in living tissue, but pH rapidly becomes acidic, as host tissue is killed. We identified mutants of the blast fungus that were sensitive to alkaline pH and this enabled us to identify the signal transduction pathway by which the fungus responds to changes in ambient pH. We found that mutants in the pH response pathway were blocked in invasive fungal growth and could not cause acidification of host tissue. Consequently, they are unable to cause blast disease. We characterized the central regulator of this pathway, the PacC transcription factor, which unusually can act as both a repressor and an activator of fungal gene expression. During biotrophic invasive growth, PacC activates many genes previously reported to be required for virulence, including several associated with nutrient acquisition, and at the same time represses genes associated with vegetative growth and sporulation. The PacC signaling pathway is therefore necessary for regulating the switch in fungal lifestyle associated with causing blast disease.

microbiology↗