All types of small RNAs in plants, piwi-interacting RNAs (piRNAs) in animals and a subset of siRNAs in Drosophila and C. elegans are subject to HEN1 mediated 3’ terminal 2’-O-methylation. This modification plays a pivotal role in protecting small RNAs from 3’ uridylation, trimming and degradation. In Arabidopsis, HESO1 is a major enzyme that uridylates small RNAs to trigger their degradation. However, U-tail is still present in null hen1 heso1 mutants, suggesting the existence of (an) enzymatic activities redundant with HESO1. Here, we report that UTP: RNA uridylyltransferase (URT1) is a functional paralog of HESO1. URT1 interacts with AGO1 and plays a predominant role in miRNA uridylation when HESO1 is absent. Uridylation of miRNA is globally abolished in a hen1 heso1 urt1 triple mutant, accompanied by an extensive increase of 3’-to-5’ trimming. In contrast, disruption of URT1 appears not to affect the heterochromatic siRNA uridylation. This indicates the involvement of additional nucleotidyl transferases in the siRNA pathway. Analysis of miRNA tailings in the hen1 heso1 urt1 triple mutant also reveals the existence of previously unknown enzymatic activities that can add non-uridine nucleotides. Importantly, we show HESO1 may also act redundantly with URT1 in miRNA uridylation when HEN1 is fully competent. Taken together, our data not only reveal a synergistic action of HESO1 and URT1 in the 3’ uridylation of miRNAs, but also independent activities of multiple terminal nucleotidyl transferases in the 3’ tailing of small RNAs and an antagonistic relationship between uridylation and trimming. Our results may provide further insight into the mechanisms of small RNA 3’ end modification and stability control.

DNA methylation aberrations have been implicated in acquired resistance to platinum drugs in ovarian cancer. In this study, we elucidated an epigenetic signature associated with platinum drug resensitization that may offer utility in predicting the outcomes of patients who are coadministered a DNA methyltransferase inhibitor. The ovarian cancer specimens we analyzed were derived from a recent clinical trial that compared the responses of patients with recurrent platinum-resistant ovarian cancer who received carboplatin plus the DNA methyltransferase inhibitor guadecitabine or a standard-of-care chemotherapy regimen selected by the treating physician. Tumor biopsies or malignant ascites were collected from patients before treatment (day 1, cycle 1) or after treatment (after 2 cycles) for epigenomic and transcriptomic profiling using the Infinium HumanMethylation450 BeadChip (HM450). We defined 94 gene promoters that were hypomethylated significantly by guadecitabine, with 1,659 genes differentially expressed in pretreatment versus posttreatment tumors. Pathway analysis revealed that the experimental regimen significantly altered immune reactivation and DNA repair pathways. Progression-free survival correlated with baseline expression levels of 1,155 genes involved in 25 networks. In functional investigations in ovarian cancer cells, engineered upregulation of certain signature genes silenced by promoter methylation (, , and others) restored platinum drug sensitivity. Overall, our findings illuminate how inhibiting DNA methylation can sensitize ovarian cancer cells to platinum drugs, in large part by altering gene expression patterns related to DNA repair and immune activation, with implications for improving the personalized care and survival outcomes of ovarian cancer patients. Epigenomic targeting may improve therapeutic outcomes in platinum-resistant and recurrent ovarian cancer in part by effects on DNA repair and antitumor immune responses. .

Manganese (Mn) is an essential catalytic metal in the Mn-cluster that oxidizes water to produce oxygen during photosynthesis. However, the transport protein(s) responsible for Mn import into the chloroplast remains unknown. Here, we report the characterization of Arabidopsis CMT1 (Chloroplast Manganese Transporter 1), an evolutionarily conserved protein in the Uncharacterized Protein Family 0016 (UPF0016), that is required for manganese accumulation into the chloroplast. CMT1 is expressed primarily in green tissues, and its encoded product is localized in the inner envelope membrane of the chloroplast. Disruption of CMT1 in the T-DNA insertional mutant cmt1-1 resulted in stunted plant growth, defective thylakoid stacking, and severe reduction of photosystem II complexes and photosynthetic activity. Consistent with reduced oxygen evolution capacity, the mutant chloroplasts contained less manganese than the wild-type ones. In support of its function as a Mn transporter, CMT1 protein supported the growth and enabled Mn accumulation in the yeast cells of Mn-uptake deficient mutant (Δsmf1). Taken together, our results indicate that CMT1 functions as an inner envelope Mn transporter responsible for chloroplast Mn uptake.

We present a computational study of tissue transcriptomic data of 14 cancer types to address: what may drive cancer cell division? Our analyses point to that persistent disruption of the intracellular pH by Fenton reactions may be at the root of cancer development. Specifically, we have statistically demonstrated that Fenton reactions take place in cancer cytosol and mitochondria across all the 14 cancer types, based on cancer tissue gene-expression data integrated via the Michaelis–Menten equation. In addition, we have shown that (i) Fenton reactions in cytosol of the disease cells will continuously increase their pH, to which the cells respond by generating net protons to keep the pH stable through a combination of synthesizing glycolytic ATPs and consuming them by nucleotide syntheses, which may drive cell division to rid of the continuously synthesized nucleotides; and (ii) Fenton reactions in mitochondria give rise to novel ways for ATP synthesis with electrons ultimately coming from H2O2, largely originated from immune cells. A model is developed to link these to cancer development, where some mutations may be selected to facilitate cell division at rates dictated by Fenton reactions.

In the Caenorhabditis elegans germline, fem-3 Binding Factor (FBF) partners with LST-1 to maintain stem cells. A crystal structure of an FBF-2/LST-1/RNA complex revealed that FBF-2 recognizes a short RNA motif different from the characteristic 9-nt FBF binding element, and compact motif recognition coincided with curvature changes in the FBF-2 scaffold. Previously, we engineered FBF-2 to favor recognition of shorter RNA motifs without curvature change (Bhat et al., 2019). In vitro selection of RNAs bound by FBF-2 suggested sequence specificity in the central region of the compact element. This bias, reflected in the crystal structure, was validated in RNA-binding assays. FBF-2 has the intrinsic ability to bind to this shorter motif. LST-1 weakens FBF-2 binding affinity for short and long motifs, which may increase target selectivity. Our findings highlight the role of FBF scaffold flexibility in RNA recognition and suggest a new mechanism by which protein partners refine target site selection.

Fungal pathogens cause various diseases for plant and animal hosts. Despite the extensive impact of fungi on human health and life, the threats posed by emerging fungal pathogens are poorly understood. Specifically, there exist few fungal virulence gene databases, which prevent effective bioinformatics studies on fungal pathogens. Therefore, we constructed a comprehensive online database of known fungal virulence factors, which collected 2058 pathogenic genes produced by 228 fungal strains from 85 genera. This database creates a pivotal platform capable of stimulating and facilitating further bench studies on fungal pathogens.Database URL: http://sysbio.unl.edu/DFVF/

2015). The intrinsically disordered protein BKI1 is essential for inhibiting BRI1 signaling in plants. Mol. Plant.

A number of proposals have been made in the past century regarding what may drive sporadic cancers to initiate and develop. Yet the problem remains largely unsolved as none of the proposals have been widely accepted as cancer-initiation drivers. We propose here a driver model for the initiation and early development of solid cancers associated with inflammation-induced chronic hypoxia and reactive oxygen species (ROS) accumulation. The model consists of five key elements: (i)human cells tend to have a substantial gap between ATP demand and supply during chronic hypoxia, which would inevitably lead to increased uptake of glucose and accumulation of its metabolites; (ii) the accumulation of these metabolites will cast mounting pressure on the cells and ultimately result in the production and export of hyaluronic acid; (iii) the exported hyaluronic acid will be degraded into fragments of various sizes, serving as tissue-repair signals, including signals for cell proliferation, cell survival and angiogenesis, which lead to the initial proliferation of the underlying cells; (iv) cell division provides an exit for the accumulated glucose metabolites using them towards macromolecular synthesis for the new cell, and hence alleviate the pressure from the metabolite accumulation; and (v) this process continues as long as the hypoxic condition persists. In tandem, genetic mutations may be selected to make cell divisions and hence survival more sustainable and efficient, also increasingly more uncontrollable. This model also applies to some hereditary cancers as their key mutations, such as BRCA for breast cancer, generally lead to increased ROS and ultimately to repression of mitochondrial activities and up-regulation of glycolysis, as well as hypoxia; hence the energy gap, glucose-metabolite accumulation, hyaluronic acid production and continuous cell division for survival.The most popular theories about cancer and cancer drivers in the past century include: (i) Warburg's theory as summarized by him in 1966 1 : "Cancer . . . has countless secondary causes; But there is only one prime cause, (which) is the replacement of respiration of oxygen in normal body cells by a fermentation of sugar"; (ii) the genomic mutation theory of cancer, including mutations that lead to the formation of oncogenes and loss of function in tumor suppressor genes, which has been the most popular in the past four decades; and (iii) microbe-induced cancers such as cervical cancers induced by the infection of human papilloma virus 2 or liver cancer induced by hepatitis viruses. 3 Among these major proposals, Warburg's proposal has been most intriguing and has received considerable renewed interests in the past few years. 4,5 However, the proposal clearly lacks key information that connects the observed energy-metabolism reprogramming to cell proliferation, hence it remains as a proposal rather than a testable model. Various genetic mutation-centric driver models have been proposed since the first discoveries of oncogenes by Bishop and Varmus 6 and t...