PKR senses nuclear and mitochondrial signals by interacting with endogenous double-stranded RNAs

Yoosik KIM,Joha PARK,Sujin KIM,Min A KIM,Myeong-Gyun KANG,Chulhwan KWAK,Minjeong KANG,Baekgyu KIM,Hyun-Woo RHEE,V. Narry KIM 한국생물공학회 2018 한국생물공학회 학술대회 Vol.2018 No.4

PKR Senses Nuclear and Mitochondrial Signals by Interacting with Endogenous Double-Stranded RNAs

Kim, Yoosik,Park, Joha,Kim, Sujin,Kim, MinA,Kang, Myeong-Gyun,Kwak, Chulhwan,Kang, Minjeong,Kim, Baekgyu,Rhee, Hyun-Woo,Kim, V. Narry Elsevier 2018 Molecular cell Vol.71 No.6

<P><B>Summary</B></P> <P>Protein kinase RNA-activated (PKR) induces immune response by sensing viral double-stranded RNAs (dsRNAs). However, growing evidence suggests that PKR can also be activated by endogenously expressed dsRNAs. Here, we capture these dsRNAs by formaldehyde-mediated crosslinking and immunoprecipitation sequencing and find that various noncoding RNAs interact with PKR. Surprisingly, the majority of the PKR-interacting RNA repertoire is occupied by mitochondrial RNAs (mtRNAs). MtRNAs can form intermolecular dsRNAs owing to bidirectional transcription of the mitochondrial genome and regulate PKR and eIF2α phosphorylation to control cell signaling and translation. Moreover, PKR activation by mtRNAs is counteracted by PKR phosphatases, disruption of which causes apoptosis from PKR overactivation even in uninfected cells. Our work unveils dynamic regulation of PKR even without infection and establishes PKR as a sensor for nuclear and mitochondrial signaling cues in regulating cellular metabolism.</P> <P><B>Highlights</B></P> <P> <UL> <LI> fCLIP-seq reveals PKR-interacting endogenously expressed dsRNAs </LI> <LI> PKR binds to various noncoding RNAs such as retrotransposons and satellite RNAs </LI> <LI> MtRNAs can form intermolecular dsRNAs and strongly interact with PKR </LI> <LI> MtRNAs can regulate PKR phosphorylation and signaling, especially under stress </LI> </UL> </P> <P><B>Graphical Abstract</B></P> <P>[DISPLAY OMISSION]</P>

PABP Cooperates with the CCR4-NOT Complex to Promote mRNA Deadenylation and Block Precocious Decay

Yi, Hyerim,Park, Joha,Ha, Minju,Lim, Jaechul,Chang, Hyeshik,Kim, V. Narry Elsevier 2018 Molecular cell Vol.70 No.6

<P><B>Summary</B></P> <P>Multiple deadenylases are known in vertebrates, the PAN2-PAN3 (PAN2/3) and CCR4-NOT (CNOT) complexes, and PARN, yet their differential functions remain ambiguous. Moreover, the role of poly(A) binding protein (PABP) is obscure, limiting our understanding of the deadenylation mechanism. Here, we show that CNOT serves as a predominant nonspecific deadenylase for cytoplasmic poly(A)<SUP>+</SUP> RNAs, and PABP promotes deadenylation while preventing premature uridylation and decay. PAN2/3 selectively trims long tails (>∼150 nt) with minimal effect on transcriptome, whereas PARN does not affect mRNA deadenylation. CAF1 and CCR4, catalytic subunits of CNOT, display distinct activities: CAF1 trims naked poly(A) segments and is blocked by PABPC, whereas CCR4 is activated by PABPC to shorten PABPC-protected sequences. Concerted actions of CAF1 and CCR4 delineate the ∼27 nt periodic PABPC footprints along shortening tail. Our study unveils distinct functions of deadenylases and PABPC, re-drawing the view on mRNA deadenylation and regulation.</P> <P><B>Highlights</B></P> <P> <UL> <LI> The human CCR4-NOT complex is a predominant nonspecific deadenylase </LI> <LI> PAN2/3 trims excessively long tails with minimal impact on mRNA stability </LI> <LI> CAF1 trims PABPC-free A tails while CCR4 removes PABPC-bound A tails </LI> <LI> PABPC facilitates mRNA deadenylation while preventing precocious uridylation and decay </LI> </UL> </P> <P><B>Graphical Abstract</B></P> <P>[DISPLAY OMISSION]</P>

엽과비 조절이 무가온 하우스 하례조생 감귤의 비대 및 과실품질에 미치는 영향

강석범 ( Seok-beom Kang ),좌재호 ( Jae-ho Joha ),문영일 ( Young-eel Moon ),이혜진 ( Hae-jin Lee ),한승갑 ( Seung-gap Han ),박경진 ( Kyung-jin Park ),김상숙 ( Sang-suk Kim ),최영훈 ( Young-hun Choi ) 한국환경농학회 2018 한국환경농학회지 Vol.37 No.3

BACKGROUND: Recently, the need for a method to cultivate ‘Haryejosaeng’ Satsuma mandarin has been increasing. However, there is limited information available as this is a new Satsuma mandarin cultivar, which was bred by the RDA in 2004. Many farmers who cultivate this cultivar follow the cultivation method similar to that used for ‘Miyagawa’ Satsuma mandarin, and suffer low production of optimum-sized fruits. METHODS AND RESULTS: This study was conducted to find out the optimum ratio of leaf-to-fruit for the stable production of high quality ‘Haryejosaeng’ Satsuma mandarin fruits in a non-heated plastic film house. Seven-year-old ‘Haryejosaeng’ Satsuma mandarin trees were used in the study. Before the treatment, the leaf- to-fruit ratio ranged from 5.7 to 17.9. The treatments included 10, 20, 30, and 40 leaves per fruit. The fruits were removed if over fruiting was observed at day 60 after full bloom. We investigated the fruit size and quality on the day of harvest. Flowering and fruiting patterns in each treatment were recorded for the following year. In the experiments, the flower-to-leaf ratio was 1.12 to 1.74. As the leaf-to-fruit ratio decreased, the fruit size and weight also decreased. Contrarily, the higher the ratio of leaf-to-fruit, the higher fruit size and weight were. It was noted that the ratio of 20:1 was ideal to produce the M grade optimum-sized Satsuma mandarin fruits on the day of harvest. However, higher ratio might result in fruits weighting above 100 g. There was no difference among the treatments in terms of fruit quality, such as total soluble solid contents, titratable acid, and color. In the subsequent years, flowering and fruiting in the treatments were lowered when the leaf number per fruit was 10, but they were improved when the leaf number per fruit was above 20. CONCLUSION: Based on the above results, the optimum ratio of leaf-to-fruit was found to be 20:1 for flowering and fruiting of ‘Haryejosaeng’ Satsuma mandarin. It is important that optimum ratio of leaf-to-fruit is set as a standard to produce good grade and quality of ‘Haryejosaeng’ Satsuma mandarin fruits.

TALEN-based knockout library for human microRNAs

Kim, Young-Kook,Wee, Gabbine,Park, Joha,Kim, Jongkyu,Baek, Daehyun,Kim, Jin-Soo,Kim, V Narry Nature Publishing Group, a division of Macmillan P 2013 Nature structural & molecular biology Vol.20 No.12

Various technical tools have been developed to probe the functions of microRNAs (miRNAs), yet their application has been limited by low efficacy and specificity. To overcome the limitations, we used transcription activator–like effector nucleases (TALENs) to knock out human miRNA genes. We designed and produced a library of 540 pairs of TALENs for 274 miRNA loci, focusing on potentially important miRNAs. The knockout procedure takes only 2–4 weeks and can be applied to any cell type. As a case study, we generated knockout cells for two related miRNAs, miR-141 and miR-200c, which belong to the highly conserved miR-200 family. Interestingly, miR-141 and miR-200c, despite their overall similarity, suppress largely nonoverlapping groups of targets, thus suggesting that functional miRNA-target interaction requires strict seed-pairing. Our study illustrates the potency of TALEN technology and provides useful resources for miRNA research.

Microprocessor depends on hemin to recognize the apical loop of primary microRNA

Nguyen, Tuan ,Anh,Park, Joha,Dang, Thi ,Lieu,Choi, Yeon-Gil,Kim, V ,Narry Oxford University Press 2018 Nucleic acids research Vol.46 No.11

<P><B>Abstract</B></P><P>Microprocessor, which consists of a ribonuclease III DROSHA and its cofactor DGCR8, initiates microRNA (miRNA) maturation by cleaving primary miRNA transcripts (pri-miRNAs). We recently demonstrated that the DGCR8 dimer recognizes the apical elements of pri-miRNAs, including the UGU motif, to accurately locate and orient Microprocessor on pri-miRNAs. However, the mechanism underlying the selective RNA binding remains unknown. In this study, we find that hemin, a ferric ion-containing porphyrin, enhances the specific interaction between the apical UGU motif and the DGCR8 dimer, allowing Microprocessor to achieve high efficiency and fidelity of pri-miRNA processing <I>in vitro</I>. Furthermore, by generating a DGCR8 mutant cell line and carrying out rescue experiments, we discover that hemin preferentially stimulates the expression of miRNAs possessing the UGU motif, thereby conferring differential regulation of miRNA maturation. Our findings reveal the molecular action mechanism of hemin in pri-miRNA processing and establish a novel function of hemin in inducing specific RNA-protein interaction.</P>

Prostate calcifications: A case series supporting the microbial biofilm theory

Tommaso Cai,Francesco Tessarolo,Iole Caola,Federico Piccoli,Giandomenico Nollo,Patrizio Caciagli,Sandra Mazzoli,Alessandro Palmieri,Paolo Verze,Gianni Malossini,Vincenzo Mirone,Truls E. Bjerklund Joha 대한비뇨의학회 2018 Investigative and Clinical Urology Vol.59 No.3

Purpose: Prostate calcifications are a common finding during transrectal prostate ultrasound in both healthy subjects and patients, but their etiopathogenesis and clinical significance are not fully understood. We aimed to establish a new methodology for evaluating the role of microbial biofilms in the genesis of prostate calcifications. Materials and Methods: Ten consecutive patients who had undergone radical prostatectomy were enrolled in this study. All of the patients presented with prostate calcifications during transrectal ultrasound evaluation before surgery and underwent Meares-Stamey tests and clinical evaluation with the National Institutes of Health Chronic Prostatitis Symptom Index and the International Prostate Symptom Score. At the time of radical prostatectomy, the prostate specimen, after removal, was analyzed with ultrasonography under sterile conditions in the operating room. Core biopsy specimens were taken from the site of prostate calcification and subjected to ultrastructural and microbiological analysis. Results: The results of the Meares-Stamey test showed only 1 of 10 patients (10%) with positive cultures for Escherichia coli. Two of five patients (40%) had positive cultures from prostate biopsy specimens. Enterococcus faecalis, Enterococcus raffinosus, and Citrobacter freundii were isolated. Ultrastructural analysis of the prostate biopsy specimens showed prostate calcifications in 6 of 10 patients (60%), and a structured microbial biofilm in 1 patient who had positive cultures for E. faecalis and E. raffinosus. Conclusions: Although the findings are supported by a low number of patients, this study highlights the validity of the proposed methodology for investigating the role of bacterial biofilms in the genesis of prostate calcification.