Small RNAs in Plant Immunity and Virulence of Filamentous Pathogens

Gene silencing guided by small RNAs governs a broad range of cellular processes in eukaryotes. Small RNAs are important components of plant immunity because they contribute to pathogen-triggered transcription reprogramming and directly target pathogen RNAs. Recent research suggests that silencing of pathogen genes by plant small RNAs occurs not only during viral infection but also in nonviral pathogens through a process termed host-induced gene silencing, which involves trans-species small RNA trafficking. Similarly, small RNAs are also produced by eukaryotic pathogens and regulate virulence. This review summarizes the small RNA pathways in both plants and filamentous pathogens, including fungi and oomycetes, and discusses their role in host-pathogen interactions. We highlight secondarysmall interfering RNAs of plants as regulators of immune receptor gene expression and executors of host-induced gene silencing in invading pathogens. The current status and prospects of trans-species gene silencing at the host-pathogen interface are discussed.

P–389 The relationship between serum hormone profiles and missed abortion in humans

Study question

Are circulating profiles of metabolic-related hormones also associated with the missed abortion (MA) in humans?

Summary answer

Serum levels of fatty acid-binding protein–4 (FABP4) and fibroblast growth factor 21 (FGF21) are positively associated with MA.

What is known already

A cluster of endocrine hormones, including FABP4, FGF21, adiponectin, lipocalin–2 (LCN2), exhibit pleiotropic effects on regulating systematic metabolism. Serum levels of them are associated with gestational obesity and diabetes and affect pregnancy outcomes, however, the relationship between their circulating profiles and MA is under-investigated.

Study design, size, duration

78 patients with MA and 86 healthy pregnant subjects matching on maternal age and body mass index (BMI) were nested from a prospective cohort in the Chinese population.

Participants/materials, setting, methods

Fasting serum samples from all participants were collected to test their serum levels of FGF21, FABP4, adiponectin, and LCN2 by enzyme-linked immunosorbent assay method (ELISA).

Main results and the role of chance

There were no significant differences in circulating profiles of adiponectin and LCN2 between MA patients and healthy pregnant subjects. By contrast, circulating levels of FGF21 and FABP4 were significantly and independently elevated in patients with MA relative to control cases even after adjusting confounding factors (for FGF21: MA: 28.96 ± 2.17 ng/ml; HP: 19.18 ± 1.12 ng/ml, P < 0.001, for FABP4: MA: 152.50 ± 9.31 pg/ml; HP: 90.86 ± 4.14 pg/ml, P < 0.001). Linear regression analysis showed, FGF21 raised every 10 pg/ml contributed to a 24% (95% CI: 15% - 34%) increase in the risk of MA, whereas the OR of FABP4 for the risk of MA was 1.052 (95% CI: 1.022 –1.088). Furthermore, using serum FGF21 level or FABP4 levels discriminated MA from healthy controls with an area under the operating characteristic’s curve (AUROC) of 0.81 (95% CI 0.76–0.92) and 0.70 (95% CI 0.62 - 0.78), respectively.

Limitations, reasons for caution

The study is limited by the sample size. In addition, our results were based-on Chinese population, whether it could be observed in other ethics group remain to be investigated. Meanwhile, the cause-effect relationship between increased serum FGF21 level and MA remains to be explored.

Wider implications of the findings: Our data would suggest that serum levels of FGF21 and FABP4 are associated with MA. Moreover, circulating FGF21 levels may serve as a potential diagnostic biomarker for the recognition of M.

Trial registration number

IRB Ref. No.: KY201913

Improved Whole-Genome Sequence of Phytophthora capsici Generated by Long-Read Sequencing

The soilborne oomycete Phytophthora capsici is the most destructive pathogen of vegetable crops and is responsible for substantial economic losses worldwide. Here, we present an improved genome assembly of P. capsici generated by Oxford Nanopore long-read sequencing (for de novo assembly) and Illumina short-read sequencing (for polishing). The genome of P. capsici is 100.5 Mb in length (GC content = 50.8%) and contains 26,069 predicted protein-coding genes. The whole genome of P. capsici is assembled into 194 scaffolds, 90% of which are larger than 300 kb. The N₅₀ scaffold length and maximum scaffold length are 1.0 and 4.1 Mb, respectively. The whole-genome sequence of P. capsici will broaden our knowledge of this pathogen and enhance our understanding of the molecular basis of its pathogenicity, which will facilitate the development of effective management strategies.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Mutations in chronic myelomonocytic leukemia and their prognostic relevance

Chronic myelomonocytic leukemia (CMML) is a hematologic malignancy that overlaps with myeloproliferative neoplasms (MPN) and myelodysplastic syndromes (MDS) and tends to transform into acute myeloid leukemia (AML). Among cases of CMML, > 90% have gene mutations, primarily involving TET2 (~ 60%), ASXL1 (~ 40%), SRSF2 (~ 50%), and the RAS pathways (~ 30%). These gene mutations are associated with both the clinical phenotypes and the prognosis of CMML, special CMML variants and pre-phases of CMML. Cytogenetic abnormalities and the size of genome are also associated with prognosis. Meanwhile, cases with ASXL1, DNMT3A, NRAS, SETBP1, CBL and RUNX1 mutations may have inferior prognoses, but only ASXL1 mutations were confirmed to be independent predictors of the patient outcome and were included in three prognostic models. Novel treatment targets related to the various gene mutations are emerging. Therefore, this review provides new insights to explore the correlations among gene mutations, clinical phenotypes, prognosis, and novel drugs in CMML.

Improving the productivity of Candida glycerinogenes in the fermentation of ethanol from non-detoxified sugarcane bagasse hydrolysate by a hexose transporter mutant

AIMS

In this study, we attempted to increase the productivity of Candida glycerinogenes yeast for ethanol production from non-detoxified sugarcane bagasse hydrolysates (NDSBH) by identifying the hexose transporter in this yeast that makes a high contribution to glucose consumption, and by adding additional copies of this transporter and enhancing its membrane localisation stability (MLS).

METHODS AND RESULTS

Based on the knockout and overexpression of key hexose transporter genes and the characterisation of their promoter properties, we found that Cghxt4 and Cghxt6 play major roles in the early and late stages of fermentation, respectively, with Cghxt4 contributing most to glucose consumption. Next, subcellular localisation analysis revealed that a common mutation of two ubiquitination sites (K9 and K538) in Cghxt4 improved its MLS. Finally, we overexpressed this Cghxt4 mutant (Cghxt4.2A) using a strong promoter, P_CgGAP , which resulted in a significant increase in the ethanol productivity of C. glycerinogenes in the NDSBH medium. Specifically, the recombinant strain showed 18 and 25% higher ethanol productivity than the control in two kinds of YP-NDSBH medium (YP-NDSBH1_G160 and YP-NDSBH2_G160 ), respectively.

CONCLUSIONS

The hexose transporter mutant Cghxt4.2A (Cghxt4^K9A,K538A ) with multiple copies and high MLS was able to significantly increase the ethanol productivity of C. glycerinogenes in NDSBH.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our results provide a promising strategy for constructing efficient strains for ethanol production.

Genome-Wide Identification and Characterization of Wheat 14-3-3 Genes Unravels the Role of TaGRF6-A in Salt Stress Tolerance by Binding MYB Transcription Factor

14-3-3 proteins are a large multigenic family of general regulatory factors (GRF) ubiquitously found in eukaryotes and play vital roles in the regulation of plant growth, development, and response to stress stimuli. However, so far, no comprehensive investigation has been performed in the hexaploid wheat. In the present study, A total of 17 potential 14-3-3 gene family members were identified from the Chinese Spring whole-genome sequencing database. The phylogenetic comparison with six 14-3-3 families revealed that the majority of wheat 14-3-3 genes might have evolved as an independent branch and grouped into ε and non-ε group using the phylogenetic comparison. Analysis of gene structure and motif indicated that 14-3-3 protein family members have relatively conserved exon/intron arrangement and motif composition. Physical mapping showed that wheat 14-3-3 genes are mainly distributed on chromosomes 2, 3, 4, and 7. Moreover, most 14-3-3 members in wheat exhibited significantly down-regulated expression in response to alkaline stress. VIGS assay and protein-protein interaction analysis further confirmed that TaGRF6-A positively regulated slat stress tolerance by interacting with a MYB transcription factor, TaMYB64. Taken together, our findings provide fundamental information on the involvement of the wheat 14-3-3 family in salt stress and further investigating their molecular mechanism.

Incidence and associated predictors of adverse pregnancy outcomes of maternal syphilis in China, 2016-19: a Cox regression analysis

OBJECTIVE

This study aimed to investigate the incidence and associated predictors of adverse pregnancy outcomes (APOs) among pregnant women infected with syphilis.

DESIGN

Cox regression analysis.

SETTING

China.

POPULATION OR SAMPLE

Pregnant women who were tested for and diagnosed with syphilis during the index pregnancy and delivered at a gestational age ≥28 weeks between 2016 and 2019.

METHODS

Data were extracted from China's Information System of Prevention of Mother-to-Child Transmission of Syphilis Management. Descriptive analysis provided profiles and pregnancy outcomes of maternal syphilis, as well as the incidence of APOs. Log-rank tests and Cox proportional hazard models were used to investigate factors influencing APOs in infected mothers with singleton births.

MAIN OUTCOME MEASURES

The incidence of APOs and the hazard ratios of associated predictors using Cox proportional hazard model.

RESULTS

Syphilis treatment data were available from 83.86% of diagnosed women. Including deliveries from the total study population, 13.33% experienced APOs. Cox regression indicated that APOs were more likely in women tested and diagnosed in the late trimester, at delivery or postpartum. Women who accepted non-standardised treatment and who received standardised treatment had less risk of APOs.

CONCLUSIONS

China has made huge progress over the last decades in the prevention of mother-to-child transmission of syphilis, but the incidence of APOs among pregnant women infected with syphilis remains high. It is essential to further strengthen access to early detection and standardised treatment of infected women to reduce the risk of APOs.

TWEETABLE ABSTRACT

Access to early detection and standardised treatment reduces the risk of APOs due to maternal syphilis.

Establishment of a novel virus-induced virulence effector assay for the identification of virulence effectors of plant pathogens using a PVX-based expression vector

Plant pathogens deliver virulence effectors into plant cells to modulate plant immunity and facilitate infection. Although species-specific virulence effector screening approaches have been developed for several pathogens, these assays do not apply to pathogens that cannot be cultured and/or transformed outside of their hosts. Here, we established a rapid and parallel screening assay, called the virus-induced virulence effector (VIVE) assay, to identify putative effectors in various plant pathogens, including unculturable pathogens, using a virus-based expression vector. The VIVE assay uses the potato virus X (PVX) vector to transiently express candidate effector genes of various bacterial and fungal pathogens into Nicotiana benthamiana leaves. Using the VIVE assay, we successfully identified Avh148 as a potential virulence effector of Phytophthora sojae. Plants infected with PVX carrying Avh148 showed strong viral symptoms and high-level Avh148 and viral RNA accumulation. Analysis of P. sojae Avh148 deletion mutants and soybean hairy roots overexpressing Avh148 revealed that Avh148 is required for full pathogen virulence. In addition, the VIVE assay was optimized in N. benthamiana plants at different developmental stages across a range of Agrobacterium cell densities. Overall, we identified six novel virulence effectors from seven pathogens, thus demonstrating the broad effectiveness of the VIVE assay in plant pathology research.

Genome-Wide Mining of Wheat DUF966 Gene Family Provides New Insights Into Salt Stress Responses

Domain of unknown function (DUF) proteins constitute a great deal of families of functionally uncharacterized proteins in eukaryotes. The DUF966 gene family is found in monocotyledons, dicotyledons, mosses, and other species. However, little is known about the functions of DUF966 genes in wheat (Triticum aestivum L.). In this study, we identified and characterized the TaDUF966 gene family members in wheat by in silico analysis. A total of 28 TaDUF966 proteins were identified in wheat. Phylogenetic analysis divided these proteins into two groups (Groups I and II). Proteins in each group showed a highly conserved DUF966 domain and conserved motif distribution, implying their functional conservation. Analysis of gene expression profiling data showed that some TaDUF966 genes were induced by salt stress. We further confirmed the role of TaDUF966-9B in salt stress using virus induced gene silencing (VIGS) assay. Compared with the empty vector control, the TaDUF966-9B knockdown plants exhibited severe leaf curling at 10 days post-inoculation with BSMV under salt stress, suggesting that TaDUF966 genes play a vital role in salt stress tolerance in wheat. Taken together, these results expand our knowledge of the evolution of the DUF966 gene family in wheat and promote the potential application of these genes in wheat genetic improvement.

[Establishment and primary clinical application of metabolic evaluation database of urolithiasis]

Objective: To establish the metabolic evaluation database of urolithiasis, perform metabolic evaluation, and provide instructions for treatment and prevention of urolithiasis. Methods: This metabolic evaluation database was developed by JAVA and was established by Oracle11g database and Browser/Server framework. We extracted the clinical data of all patients who had complete information, and analyzed their risk factors of stone formation, stone-related medical history, blood and urine tests results and 24-hour urine analysis. Results: A total of 360 patients diagnosed as urolithiasis were included in this research. Male to female ratio was 1.9∶1, and the urolithiasis was first diagnosed at (35.5±13.5) years old. Family history was positive in 39.7% of patients. Metabolic syndrome occurred in 35.0% of patients. Overweight or obesity occurred in 73.2% and 50.0% of male patients, respectively. Abdominal obesity in 62.3% and 56.1% of male and female patients, respectively. Among all patients, 67.5% had high urine sodium, 53.6% had hypercalciuria, 41.1% had hypocitraturia, 29.7% had hyperuricosuria, 22.5% had hypomagnesuria, 15.8% had hyperoxaluria, 11.7% had hyperphosphoraturia, and 36.4% had low urinary volume. Conclusions: The prevalence of overweight or obesity, abdominal obesity, hypertension, diabetes, and metabolic syndrome in stone patients were significantly higher than those in general population. The number of 24-hour urinary abnormalities was positively associated with body mass index. The interventions on high urinary sodium, low urinary volume, obesity and metabolic syndrome were important to the treatment of urolithiasis. This database would facilitate the metabolic evaluation, provide evidence for the treatment and prevention of urolithiasis, and lay foundation for finding important controllable risk factors of urinary stone.

Altered resting-state functional connectivity between subregions in the thalamus and cortex in migraine without aura

BACKGROUND AND PURPOSE

Migraine is a complex and disabling neurological disorder, the exact neurological mechanisms of which remain unclear. The thalamus is considered to be the hub of the central processing and integration of nociceptive information, as well as the modulation of these processes.

METHODS

A total of 48 migraineurs without aura (MWoAs) during the interictal phase and 48 age- and sex-matched healthy controls underwent resting-state functional magnetic resonance imaging scans. We utilized masked independent component analysis and seed-based functional connectivity (FC) to investigate whether MWoAs exhibited abnormal FC between subregions in the thalamus and the cortex regions.

RESULTS

The MWoAs showed significantly weaker FC between the anterior dorsal thalamic nucleus and left precuneus. Additionally, MWoAs exhibited significantly reduced FC between the ventral posterior nucleus (VPN) and left precuneus, right inferior parietal lobule (R-IPL) and right middle frontal gyrus. Furthermore, the FC Z-scores between the VPN and R-IPL were negatively correlated with pain intensity in MWoAs. The disease duration of patients was negatively correlated with the FC Z-scores between the VPN and R-IPL.

CONCLUSION

These altered thalamocortical connectivity patterns may contribute to multisensory integration abnormalities, deficits in pain attention, cognitive evaluation and pain modulation. Pain sensitivity and disease duration are closely tied to abnormal FC between the VPN and R-IPL. Remarkably, recurrent headache attacks might contribute to this maladaptive functional plasticity closely related to pain intensity.

High-Throughput Sequencing-Based Identification of Arabidopsis miRNAs Induced by Phytophthora capsici Infection

MicroRNAs (miRNAs) are a group of small non-coding endogenous RNAs. In plants, miRNAs play vital functions in regulating growth, development, and stress response. However, the role of miRNAs in Arabidopsis-Phytophthora capsici (P. capsici) model pathosystem is poorly understood. Here, we used a high-throughput sequencing approach to identify pathogen-responsive miRNAs using 15 small RNA (sRNA) libraries prepared from Arabidopsis thaliana leaves collected at 0, 3, 6, 12, and 24 h post-inoculation with P. capsici. A total of 293 known miRNAs and 6 potential novel sRNAs (miRNAs or siRNAs) were identified, of which 33 miRNAs were differentially expressed at four different infection stages. To verify the reliability of the sRNA-seq results, we investigated the expression of five sRNAs upregulated throughout the four infection stages and their potential target genes using northern blot analysis and/or stem-loop quantitative real-time polymerase chain reaction (qRT-PCR). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that the potential target genes of the differentially expressed miRNAs, both conserved and novel, were enriched in pathways such as starch and sugar metabolism, spliceosome, and plant-pathogen interaction, indicating that the splicing machinery and pathogenesis-related (PR) proteins play important roles in the response to P. capsici infection. Taken together, these results provide novel insights into the molecular mechanisms of pathogenesis by P. capsici. Additionally, these results will serve as a strong foundation for further in-depth analysis of miRNAs involved in the resistance to Phytophthora species in other crops.

Screening and Identification of RNA Silencing Suppressors from Secreted Effectors of Plant Pathogens

RNA silencing is an evolutionarily conserved, sequence-specific gene regulation mechanism in eukaryotes. Several plant pathogens have evolved proteins with the ability to inhibit the host plant RNA silencing pathway. Unlike virus effector proteins, only several secreted effector proteins have showed the ability to suppress RNA silencing in bacterial, oomycete, and fungal pathogens, and the molecular functions of most effectors remain largely unknown. Here, we describe in detail a slightly modified version of the co-infiltration assay that could serve as a general method for observing RNA silencing and for characterizing effector proteins secreted by plant pathogens. The key steps of the approach are choosing the healthy and fully developed leaves, adjusting the bacteria culture to the appropriate optical density (OD) at 600 nm, and observing green fluorescent protein (GFP) fluorescence at the optimum time on the infiltrated leaves in order to avoid omitting effectors with weak suppression activity. This improved protocol will contribute to rapid, accurate, and extensive screening of RNA silencing suppressors and serve as an excellent starting point for investigating the molecular functions of these proteins.

OsNAC2 integrates auxin and cytokinin pathways to modulate rice root development

The rice root system is important for growth. The crosstalk between auxin and cytokinin mediates root initiation and elongation. However, it remains unclear how the transcriptional network upstream of the auxin and cytokinin signalling pathways determines root development. Here, we observed that the knockdown of OsNAC2, which encodes a NAC transcription factor, increased the primary root length and the number of crown roots. OsNAC2 predominantly expressed in primary root tips, crown roots and lateral root primordia, implying it influences root development. Molecular analyses revealed that the expressions of auxin- and cytokinin-responsive genes were affected in OsNAC2-overexpressing (OsNAC2-OX; ON7 and ON11), RNA interference (OsNAC2-RNAi; RNAi25 and RNAi31) and CRISPR/Cas9 plants. Additionally, OsNAC2 can directly bind to the promoters of IAA inactivation-related genes (GH3.6 and GH3.8), an IAA signalling-related gene (OsARF25), and a cytokinin oxidase gene (OsCKX4). Furthermore, genetic analysis of ON11/osgh3.6 and RNAi31/osckx4 homozygote confirmed that OsCKX4 and OsGH3.6 functioned downstream of OsNAC2. The mRNA levels of CROWN ROOTLESS (CRL) genes and cyclin-dependent protein kinase (CDK) genes increased in OsNAC2-RNAi and OsNAC2-cas9 lines while reduced in OsNAC2-OX lines. Thus, we describe that OsNAC2 functions as an upstream integrator of auxin and cytokinin signals that affect CRL and CDK production to regulate cell division during root development. This novel auxin-OsNAC2-cytokinin model should provide a new insight into the understanding of NAC TFs and crosstalk of auxin and cytokinin pathway, and can be potentially applied in agriculture to enhance rice yields by genetic approaches.

Genomic analyses reveal selection footprints in rice landraces grown under on-farm conservation conditions during a short-term period of domestication

Traditional rice landraces grown under on-farm conservation conditions by indigenous farmers are extremely important for future crop improvement. However, little is known about how the natural selection and agriculture practices of indigenous farmers interact to shape and change the population genetics of rice landraces grown under on-farm conservation conditions during the domestication. In this study, we sequenced DNA from 108 core on-farm conserved rice landraces collected from the ethnic minority regions of Yunnan, China, including 56 accessions collected in 1980 and 52 accessions collected in 2007 and obtained 2,771,245 of credible SNPs. Our findings show that most genetic diversity was retained during the 27 years of domestication by on-farm conservation. However, SNPs with marked allele frequency differences were found in some genome regions, particularly enriched in genic regions, indicating changes in genic regions may have played a much more prominent role in the short-term domestication of 27 years. We identified 186 and 183 potential selective-sweep regions in the indica and japonica genomes, respectively. We propose that on-farm conserved rice landraces during the short-term domestication had a highly polygenic basis with many loci responding to selection rather than a few loci with critical changes in response to selection. Moreover, loci affecting important agronomic traits and biotic or abiotic stress responses have been particularly targeted in selection. A genome-wide association study identified 90 significant signals for six traits, 13 of which were in regions of selective sweeps. Moreover, we observed a number of significant and interesting associations between loci and environmental factors, which implies adaptation to local environment. Our results provide insights into short-term evolutionary processes and shed light on the underlying mechanisms of on-farm conservation.

Long noncoding RNA ABHD11-AS1 predicts the prognosis of pancreatic cancer patients and serves as a promoter by activating the PI3K-AKT pathway

OBJECTIVE

Accumulating evidence showed aberrant expressions of long non-coding RNAs (lncRNAs) strongly correlated to the development of cancers, including pancreatic cancer (PC). Whether lncRNA ABHD11-AS1 (ABHD11-AS1) is involved in PC remains to be elucidated. Thus, we aimed to evaluate the effects of ABHD11-AS1 on PC and the underlying molecular mechanism.

PATIENTS AND METHODS

RT-PCR was used to detect the expression level of ABHD11-AS1 in both PC tissue and cell lines. Then, the correlation of ABHD11-AS1 expression with clinicopathological features and prognosis was studied. Cell proliferation, apoptosis, migration and invasion abilities were detected by MTT, flow cytometry, and transwell assays. We further investigated the effect of abnormal ABHD11-AS1 expression through the PI3K/AKT and EMT pathway by Western blot assays in treated PC cells.

RESULTS

We found that the expression of ABHD11-AS1 was significantly increased in both PC tissues and cell lines. The clinical analysis revealed that a high level of ABHD11-AS1 expression was correlated with distant metastasis, TNM stage, and tumor differentiation. The Kaplan-Meier analysis showed that high ABHD11-AS1 expression levels predicted poorer survival. Moreover, univariate and multivariate analyses confirmed that the expression of ABHD11-AS1 was an independent and significant factor associated with poor overall survival rates. Loss-of-function experiments showed that the knockdown of ABHD11-AS1 suppressed PC cell proliferation, migration, invasion, and EMT in vitro. Mechanistically, the knockdown of ABHD11-AS1 decreased phospho(p) AKT and phospho(p) PI3K expression, but did not affect the AKT and PI3K expression in PC cells CONCLUSIONS: This study suggested that ABHD11-AS1 may potentially function as a valuable prognostic biomarker and a therapeutic target for PC patients.

High-Throughput Sequencing-Based Identification of Arabidopsis miRNAs Induced by Phytophthora capsici Infection

MicroRNAs (miRNAs) are a group of small non-coding endogenous RNAs. In plants, miRNAs play vital functions in regulating growth, development, and stress response. However, the role of miRNAs in Arabidopsis-Phytophthora capsici (P. capsici) model pathosystem is poorly understood. Here, we used a high-throughput sequencing approach to identify pathogen-responsive miRNAs using 15 small RNA (sRNA) libraries prepared from Arabidopsis thaliana leaves collected at 0, 3, 6, 12, and 24 h post-inoculation with P. capsici. A total of 293 known miRNAs and 6 potential novel sRNAs (miRNAs or siRNAs) were identified, of which 33 miRNAs were differentially expressed at four different infection stages. To verify the reliability of the sRNA-seq results, we investigated the expression of five sRNAs upregulated throughout the four infection stages and their potential target genes using northern blot analysis and/or stem-loop quantitative real-time polymerase chain reaction (qRT-PCR). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that the potential target genes of the differentially expressed miRNAs, both conserved and novel, were enriched in pathways such as starch and sugar metabolism, spliceosome, and plant-pathogen interaction, indicating that the splicing machinery and pathogenesis-related (PR) proteins play important roles in the response to P. capsici infection. Taken together, these results provide novel insights into the molecular mechanisms of pathogenesis by P. capsici. Additionally, these results will serve as a strong foundation for further in-depth analysis of miRNAs involved in the resistance to Phytophthora species in other crops.

Pyrophosphate-fructose 6-phosphate 1-phosphotransferase (PFP1) regulates starch biosynthesis and seed development via heterotetramer formation in rice (Oryza sativa L.)

Pyrophosphate-fructose 6-phosphate 1-phosphotransferase (PFP1) reversibly converts fructose 6-phosphate and pyrophosphate to fructose 1, 6-bisphosphate and orthophosphate during glycolysis, and has diverse functions in plants. However, mechanisms underlying the regulation of starch metabolism by PFP1 remain elusive. This study addressed the function of PFP1 in rice floury endosperm and defective grain filling. Compared with the wild type, pfp1-3 exhibited remarkably low grain weight and starch content, significantly increased protein and lipid content, and altered starch physicochemical properties and changes in embryo development. Map-based cloning revealed that pfp1-3 is a novel allele and encodes the regulatory β-subunit of PFP1 (PFP1β). Measurement of nicotinamide adenine dinucleotide (NAD+) showed that mutation of PFP1β markedly decreased its enzyme activity. PFP1β and three of four putative catalytic α-subunits of PFP1, PFP1α1, PFP1α2, and PFP1α4, interacted with each other to form a heterotetramer. Additionally, PFP1β, PFP1α1 and PFP1α2 also formed homodimers. Furthermore, transcriptome analysis revealed that mutation of PFP1β significantly altered expression of many essential enzymes in starch biosynthesis pathways. Concentrations of multiple lipid and glycolytic intermediates and trehalose metabolites were elevated in pfp1-3 endosperm, indicating that PFP1 modulates endosperm metabolism, potentially through reversible adjustments to metabolic fluxes. Taken together, these findings provide new insights into seed endosperm development and starch biosynthesis and will help in the breeding of rice cultivars with higher grain yield and quality.

A genome-wide DNA methylation signature for SETD1B-related syndrome

SETD1B is a component of a histone methyltransferase complex that specifically methylates Lys-4 of histone H3 (H3K4) and is responsible for the epigenetic control of chromatin structure and gene expression. De novo microdeletions encompassing this gene as well as de novo missense mutations were previously linked to syndromic intellectual disability (ID). Here, we identify a specific hypermethylation signature associated with loss of function mutations in the SETD1B gene which may be used as an epigenetic marker supporting the diagnosis of syndromic SETD1B-related diseases. We demonstrate the clinical utility of this unique epi-signature by reclassifying previously identified SETD1B VUS (variant of uncertain significance) in two patients.