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Yang Z, Zhang H, Tan X, Wei Z, Wen C, Sun Z, Sun B, Chen J. Insights Into the Effect of Rice Stripe Virus P2 on Rice Defense by Comparative Proteomic Analysis. Front Microbiol 2022; 13:897589. [PMID: 35747367 PMCID: PMC9209781 DOI: 10.3389/fmicb.2022.897589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/09/2022] [Indexed: 11/29/2022] Open
Abstract
Rice stripe virus (RSV) has a serious effect on rice production. Our previous research had shown that RSV P2 plays important roles in RSV infection, so in order to further understand the effect of P2 on rice, we used Tandem Mass Tag (TMT) quantitative proteomics experimental system to analyze the changes of protein in transgenic rice expressing P2 for the first time. The results of proteomics showed that a total of 4,767 proteins were identified, including 198 up-regulated proteins and 120 down-regulated proteins. Functional classification results showed that differentially expressed proteins (DEPs) were mainly localized in chloroplasts and mainly involved in the metabolic pathways. Functional enrichment results showed that DEPs are mainly involved in RNA processing and splicing. We also verified the expression of several DEPs at the mRNA level and the interaction of a transcription factor (B7EPB8) with RSV P2. This research is the first time to use proteomics technology to explore the mechanism of RSV infection in rice with the RSV P2 as breakthrough point. Our findings provide valuable information for the study of RSV P2 and RSV infection mechanism.
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Affiliation(s)
- Zihang Yang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Hehong Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Xiaoxiang Tan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Zhongyan Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Caiyi Wen
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Zongtao Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Bingjian Sun
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
- *Correspondence: Bingjian Sun,
| | - Jianping Chen
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
- Jianping Chen,
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Schvartzman C, Fresia P, Murchio S, Mujica MV, Dalla-Rizza M. RNAi in Piezodorus guildinii (Hemiptera: Pentatomidae): Transcriptome Assembly for the Development of Pest Control Strategies. FRONTIERS IN PLANT SCIENCE 2022; 13:804839. [PMID: 35432425 PMCID: PMC9011191 DOI: 10.3389/fpls.2022.804839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Red-banded stink bug Piezodorus guildinii (P. guildinii) has been described as the most damaging stink bug regarding soybean crops, leading to seed injury, low germination percentages, and foliar retention, at low population densities. In recent years, RNA interference (RNAi), a conserved eukaryote silencing mechanism has been explored to develop species-selective pesticides. In this work, we evaluated RNAi in P. guildinii to develop new pest-control strategies. For this, we assembled and annotated a P. guildinii transcriptome from a pool of all developmental stages. Analysis of this transcriptome led to the identification of 56 genes related to the silencing process encompassing siRNA, miRNA, and piRNA pathways. To evaluate the functionality of RNAi machinery, P. guildinii adults were injected with 28 ng/mg of body weight of double stranded RNA (dsRNA) targeting vATPase A. A mortality of 35 and 51.6% was observed after 7 and 14 days, respectively, and a downregulation of vATPase A gene of 84% 72 h post-injection. In addition, Dicer-2 and Argonaute-2 genes, core RNAi proteins, were upregulated 1.8-fold 48 h after injection. These findings showed for the first time that RNAi is functional in P. guildinii and the silencing of essential genes has a significant effect in adult viability. Taken together, the work reported here shows that RNAi could be an interesting approach for the development of red-banded stink bug control strategies.
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Affiliation(s)
- Claudia Schvartzman
- Unidad de Biotecnología, Instituto Nacional de Investigación Agropecuaria, Canelones, Uruguay
| | - Pablo Fresia
- Unidad Mixta Pasteur + INIA (UMPI), Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Sara Murchio
- Unidad de Biotecnología, Instituto Nacional de Investigación Agropecuaria, Canelones, Uruguay
| | - María Valentina Mujica
- Unidad de Protección Vegetal, Instituto Nacional de Investigación Agropecuaria, Canelones, Uruguay
| | - Marco Dalla-Rizza
- Unidad de Biotecnología, Instituto Nacional de Investigación Agropecuaria, Canelones, Uruguay
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3
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Gowda P, Reddy PH, Kumar S. Deregulated mitochondrial microRNAs in Alzheimer's disease: Focus on synapse and mitochondria. Ageing Res Rev 2022; 73:101529. [PMID: 34813976 PMCID: PMC8692431 DOI: 10.1016/j.arr.2021.101529] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/17/2021] [Accepted: 11/16/2021] [Indexed: 01/03/2023]
Abstract
Alzheimer's disease (AD) is the most common cause of dementia and is currently one of the biggest public health concerns in the world. Mitochondrial dysfunction in neurons is one of the major hallmarks of AD. Emerging evidence suggests that mitochondrial miRNAs potentially play important roles in the mitochondrial dysfunctions, focusing on synapse in AD progression. In this meta-analysis paper, a comprehensive literature review was conducted to identify and discuss the (1) role of mitochondrial miRNAs that regulate mitochondrial and synaptic functions; (2) the role of various factors such as mitochondrial dynamics, biogenesis, calcium signaling, biological sex, and aging on synapse and mitochondrial function; (3) how synapse damage and mitochondrial dysfunctions contribute to AD; (4) the structure and function of synapse and mitochondria in the disease process; (5) latest research developments in synapse and mitochondria in healthy and disease states; and (6) therapeutic strategies that improve synaptic and mitochondrial functions in AD. Specifically, we discussed how differences in the expression of mitochondrial miRNAs affect ATP production, oxidative stress, mitophagy, bioenergetics, mitochondrial dynamics, synaptic activity, synaptic plasticity, neurotransmission, and synaptotoxicity in neurons observed during AD. However, more research is needed to confirm the locations and roles of individual mitochondrial miRNAs in the development of AD.
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Affiliation(s)
- Prashanth Gowda
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - P. Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Neuroscience & Pharmacology, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Neurology, Departments of School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Public Health Department of Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX, USA.,Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Subodh Kumar
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
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4
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Chikungunya virus non-structural protein nsP3 interacts with Aedes aegypti DEAD-box helicase RM62F. Virusdisease 2021; 32:657-665. [PMID: 34901322 DOI: 10.1007/s13337-021-00734-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/22/2021] [Indexed: 10/20/2022] Open
Abstract
The non-structural proteins (nsPs) of the chikungunya virus (CHIKV) form the virus's replication complex. They are known to participate in several functions that allow efficient replication of the virus in diverse host systems. One such function is evading the host defense system such as RNA interference (RNAi). Two nsPs of CHIKV, namely, nsP2 and nsP3, were found to suppress the host/vector RNAi machinery and exhibit RNAi suppressor activity. The present study was undertaken to identify interacting partners of CHIKV-nsP3 in Aedes aegypti. We performed pull-down assays with the mass spectrometry approach and showed the interaction of CHIKV-nsP3 with several Aedes proteins. Further co-immunoprecipitation assays revealed that CHIKV-nsP3 interacts with RM62F, a DEAD-box containing RNA known to play roles in multiple gene regulatory processes such as alternative splicing, RNA release, and also is a component of Ago2-RISC complex. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-021-00734-y.
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5
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Poosapati S, Ravulapalli PD, Viswanathaswamy DK, Kannan M. Proteomics of Two Thermotolerant Isolates of Trichoderma under High-Temperature Stress. J Fungi (Basel) 2021; 7:1002. [PMID: 34946985 PMCID: PMC8704589 DOI: 10.3390/jof7121002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/22/2021] [Accepted: 11/22/2021] [Indexed: 11/22/2022] Open
Abstract
Several species of the soil borne fungus of the genus Trichoderma are known to be versatile, opportunistic plant symbionts and are the most successful biocontrol agents used in today's agriculture. To be successful in field conditions, the fungus must endure varying climatic conditions. Studies have indicated that a high atmospheric temperature coupled with low humidity is a major factor in the inconsistent performance of Trichoderma under field conditions. Understanding the molecular modulations associated with Trichoderma that persist and deliver under abiotic stress conditions will aid in exploiting the value of these organisms for such uses. In this study, a comparative proteomic analysis, using two-dimensional gel electrophoresis (2DE) and matrix-assisted laser desorption/time-of-flight (MALDI-TOF-TOF) mass spectrometry, was used to identify proteins associated with thermotolerance in two thermotolerant isolates of Trichoderma: T. longibrachiatum 673, TaDOR673 and T. asperellum 7316, TaDOR7316; with 32 differentially expressed proteins being identified. Sequence homology and conserved domains were used to identify these proteins and to assign a probable function to them. The thermotolerant isolate, TaDOR673, seemed to employ the stress signaling MAPK pathways and heat shock response pathways to combat the stress condition, whereas the moderately tolerant isolate, TaDOR7316, seemed to adapt to high-temperature conditions by reducing the accumulation of misfolded proteins through an unfolded protein response pathway and autophagy. In addition, there were unique, as well as common, proteins that were differentially expressed in the two isolates studied.
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Affiliation(s)
- Sowmya Poosapati
- Department of Plant Pathology, ICAR-Indian Institute of Oilseeds Research, Rajendranagar, Hyderabad 500030, India;
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Prasad Durga Ravulapalli
- Department of Plant Pathology, ICAR-Indian Institute of Oilseeds Research, Rajendranagar, Hyderabad 500030, India;
| | | | - Monica Kannan
- Proteomics Facility, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India;
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Pandey S, Prasad A, Sharma N, Prasad M. Linking the plant stress responses with RNA helicases. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 299:110607. [PMID: 32900445 DOI: 10.1016/j.plantsci.2020.110607] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 07/15/2020] [Accepted: 07/19/2020] [Indexed: 05/21/2023]
Abstract
RNA helicases are omnipresent plant proteins across all kingdoms and have been demonstrated to play an essential role in all cellular processes involving nucleic acids. Currently, these proteins emerged as a new tool for plant molecular biologists to modulate plant stress responses. Here, we review the crucial role of RNA helicases triggered by biotic, abiotic, and multiple stress conditions. In this review, the emphasis has been given on the role of these proteins upon viral stress. Further, we have explored RNA helicase mediated regulation of RNA metabolism, starting from ribosome biogenesis to its decay upon stress induction. We also highlighted the cross-talk between RNA helicase, phytohormones, and ROS. Different overexpression and transgenic studies have been provided in the text to indicate the stress tolerance abilities of these proteins.
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Affiliation(s)
- Saurabh Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ashish Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Namisha Sharma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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7
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Humphreys SC, Thayer MB, Campbell J, Chen WLK, Adams D, Lade JM, Rock BM. Emerging siRNA Design Principles and Consequences for Biotransformation and Disposition in Drug Development. J Med Chem 2020; 63:6407-6422. [PMID: 32352779 DOI: 10.1021/acs.jmedchem.9b01839] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
After two decades teetering at the intersection of laboratory tool and therapeutic reality, with two siRNA drugs now clinically approved, this modality has finally come into fruition. Consistent with other emerging modalities, initial proof-of-concept efforts concentrated on coupling pharmacologic efficacy with desirable safety profiles. Consequently, thorough investigations of siRNA absorption, distribution, metabolism, and excretion (ADME) properties are lacking. Advancing ADME knowledge will aid establishment of in vitro-in vivo correlations and pharmacokinetic-pharmacodynamic relationships to optimize candidate selection through discovery and translation. Here, we outline the emerging siRNA design principles and discuss the consequences for siRNA disposition and biotransformation. We propose a conceptual framework for siRNA ADME evaluation, contextualizing the site of biotransformation product formation with PK-PD modulation, and end with a discussion around safety and regulatory considerations and future directions for this modality.
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Affiliation(s)
- Sara C Humphreys
- Pharmacokinetics and Drug Metabolism Department, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California 94080, United States
| | - Mai B Thayer
- Pharmacokinetics and Drug Metabolism Department, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California 94080, United States
| | - Jabbar Campbell
- Neuroscience Department, Amgen Research, 360 Binney Street, Cambridge, Massachusetts 02141, United States
| | - Wen Li Kelly Chen
- Comparative Biology and Safety Sciences Department, Amgen Research, 360 Binney Street, Cambridge, Massachusetts 02141, United States
| | - Dan Adams
- Comparative Biology and Safety Sciences Department, Amgen Research, 360 Binney Street, Cambridge, Massachusetts 02141, United States
| | - Julie M Lade
- Pharmacokinetics and Drug Metabolism Department, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California 94080, United States
| | - Brooke M Rock
- Pharmacokinetics and Drug Metabolism Department, Amgen Research, 1120 Veterans Boulevard, South San Francisco, California 94080, United States
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8
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Loh HY, Norman BP, Lai KS, Rahman NMANA, Alitheen NBM, Osman MA. The Regulatory Role of MicroRNAs in Breast Cancer. Int J Mol Sci 2019; 20:E4940. [PMID: 31590453 PMCID: PMC6801796 DOI: 10.3390/ijms20194940] [Citation(s) in RCA: 187] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/21/2019] [Accepted: 08/23/2019] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules which function as critical post-transcriptional gene regulators of various biological functions. Generally, miRNAs negatively regulate gene expression by binding to their selective messenger RNAs (mRNAs), thereby leading to either mRNA degradation or translational repression, depending on the degree of complementarity with target mRNA sequences. Aberrant expression of these miRNAs has been linked etiologically with various human diseases including breast cancer. Different cellular pathways of breast cancer development such as cell proliferation, apoptotic response, metastasis, cancer recurrence and chemoresistance are regulated by either the oncogenic miRNA (oncomiR) or tumor suppressor miRNA (tsmiR). In this review, we highlight the current state of research into miRNA involved in breast cancer, with particular attention to articles published between the years 2000 to 2019, using detailed searches of the databases PubMed, Google Scholar, and Scopus. The post-transcriptional gene regulatory roles of various dysregulated miRNAs in breast cancer and their potential as therapeutic targets are also discussed.
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Affiliation(s)
- Hui-Yi Loh
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia.
| | - Brendan P Norman
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, UK.
| | - Kok-Song Lai
- Health Sciences Division, Abu Dhabi Women's College, Higher Colleges of Technology, Abu Dhabi 41012, UAE.
| | - Nik Mohd Afizan Nik Abd Rahman
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia.
| | - Noorjahan Banu Mohamed Alitheen
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia.
| | - Mohd Azuraidi Osman
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia.
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9
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Elbarbary RA, Miyoshi K, Hedaya O, Myers JR, Maquat LE. UPF1 helicase promotes TSN-mediated miRNA decay. Genes Dev 2017; 31:1483-1493. [PMID: 28827400 PMCID: PMC5588929 DOI: 10.1101/gad.303537.117] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 07/24/2017] [Indexed: 12/22/2022]
Abstract
While microRNAs (miRNAs) regulate the vast majority of protein-encoding transcripts, little is known about how miRNAs themselves are degraded. We recently described Tudor-staphylococcal/micrococcal-like nuclease (TSN)-mediated miRNA decay (TumiD) as a cellular pathway in which the nuclease TSN promotes the decay of miRNAs that contain CA and/or UA dinucleotides. While TSN-mediated degradation of either protein-free or AGO2-loaded miRNAs does not require the ATP-dependent RNA helicase UPF1 in vitro, we report here that cellular TumiD requires UPF1. Results from experiments using AGO2-loaded miRNAs in duplex with target mRNAs indicate that UPF1 can dissociate miRNAs from their mRNA targets, making the miRNAs susceptible to TumiD. miR-seq (deep sequencing of miRNAs) data reveal that the degradation of ∼50% of candidate TumiD targets in T24 human urinary bladder cancer cells is augmented by UPF1. We illustrate the physiological relevance by demonstrating that UPF1-augmented TumiD promotes the invasion of T24 cells in part by degrading anti-invasive miRNAs so as to up-regulate the expression of proinvasive proteins.
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Affiliation(s)
- Reyad A Elbarbary
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Keita Miyoshi
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Omar Hedaya
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Jason R Myers
- Genomics Research Center, University of Rochester, Rochester, New York 14642, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
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10
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Calo S, Nicolás FE, Lee SC, Vila A, Cervantes M, Torres-Martinez S, Ruiz-Vazquez RM, Cardenas ME, Heitman J. A non-canonical RNA degradation pathway suppresses RNAi-dependent epimutations in the human fungal pathogen Mucor circinelloides. PLoS Genet 2017; 13:e1006686. [PMID: 28339467 PMCID: PMC5384783 DOI: 10.1371/journal.pgen.1006686] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 04/07/2017] [Accepted: 03/13/2017] [Indexed: 11/21/2022] Open
Abstract
Mucorales are a group of basal fungi that includes the casual agents of the human emerging disease mucormycosis. Recent studies revealed that these pathogens activate an RNAi-based pathway to rapidly generate drug-resistant epimutant strains when exposed to stressful compounds such as the antifungal drug FK506. To elucidate the molecular mechanism of this epimutation pathway, we performed a genetic analysis in Mucor circinelloides that revealed an inhibitory role for the non-canonical RdRP-dependent Dicer-independent silencing pathway, which is an RNAi-based mechanism involved in mRNA degradation that was recently identified. Thus, mutations that specifically block the mRNA degradation pathway, such as those in the genes r3b2 and rdrp3, enhance the production of drug resistant epimutants, similar to the phenotype previously described for mutation of the gene rdrp1. Our genetic analysis also revealed two new specific components of the epimutation pathway related to the quelling induced protein (qip) and a Sad-3-like helicase (rnhA), as mutations in these genes prevented formation of drug-resistant epimutants. Remarkably, drug-resistant epimutant production was notably increased in M. circinelloides f. circinelloides isolates from humans or other animal hosts. The host-pathogen interaction could be a stressful environment in which the phenotypic plasticity provided by the epimutant pathway might provide an advantage for these strains. These results evoke a model whereby balanced regulation of two different RNAi pathways is determined by the activation of the RNAi-dependent epimutant pathway under stress conditions, or its repression when the regular maintenance of the mRNA degradation pathway operates under non-stress conditions. Mucormycosis is a fungal infection that is attracting the attention of both clinical and research communities because of the lack of effective antifungal treatments and its often fatal prognosis. Our previous studies revealed an RNAi-mediated epimutation mechanism that operates in the casual human fungal pathogens (Mucorales species) and which might underlie the lack of efficacy of some antifungal treatments. This epimutation mechanism represses the expression of antifungal drug target genes and thereby generates antifungal drug resistant strains. Here, we studied the regulation and identified new components of the epimutation pathway. We found that a newly identified mRNA degradation pathway, named the non-canonical RdRP-dependent Dicer-independent silencing pathway, exerts an inhibitory effect on the RNAi-mediated epimutation mechanism and operates during growth under non-stressful conditions. Interestingly, the RNAi-based epimutation mechanism is more active in M. circinelloides f. circinelloides isolates from human and other animal sources, suggesting that this mechanism may influence host-pathogen interactions. These results further our understanding of the mechanisms deployed by fungal pathogens to survive and adapt under stressful environmental conditions that may include the host niche.
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Affiliation(s)
- Silvia Calo
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Francisco E. Nicolás
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Murcia, Spain
| | - Soo Chan Lee
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Ana Vila
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Murcia, Spain
| | - Maria Cervantes
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Murcia, Spain
| | - Santiago Torres-Martinez
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Murcia, Spain
| | - Rosa M. Ruiz-Vazquez
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Murcia, Spain
| | - Maria E. Cardenas
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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11
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Beyond the survival and death of the deltamethrin-threatened pollen beetle Meligethes aeneus: An in-depth proteomic study employing a transcriptome database. J Proteomics 2016; 150:281-289. [PMID: 27705816 DOI: 10.1016/j.jprot.2016.09.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 09/10/2016] [Accepted: 09/28/2016] [Indexed: 12/18/2022]
Abstract
Insecticide resistance is an increasingly global problem that hampers pest control. We sought the mechanism responsible for survival following pyrethroid treatment and the factors connected to paralysis/death of the pollen beetle Meligethes aeneus through a proteome-level analysis using nanoLC coupled with Orbitrap Fusion™ Tribrid™ mass spectrometry. A tolerant field population of beetles was treated with deltamethrin, and the ensuing proteome changes were observed in the survivors (resistant), dead (paralyzed) and control-treated beetles. The protein database consisted of the translated transcriptome, and the resulting changes were manually annotated via BLASTP. We identified a number of high-abundance changes in which there were several dominant proteins, e.g., the electron carrier cytochrome b5, ribosomal proteins 60S RPL28, 40S RPS23 and RPS26, eIF4E-transporter, anoxia up-regulated protein, 2 isoforms of vitellogenin and pathogenesis-related protein 5. Deltamethrin detoxification was influenced by different cytochromes P450, which were likely boosted by increased cytochrome b5, but glutathione-S-transferase ε and UDP-glucuronosyltransferases also contributed. Moreover, we observed changes in proteins related to RNA interference, RNA binding and epigenetic modifications. The high changes in ribosomal proteins and associated factors suggest specific control of translation. Overall, we showed modulation of expression processes by epigenetic markers, alternative splicing and translation. Future functional studies will benefit. BIOLOGICAL SIGNIFICANCE Insects develop pesticide resistance, which has become one of the key issues in plant protection. This growing resistance increases the demand for pesticide applications and the development of new substances. Knowledge in the field regarding the resistance mechanism and its responses to pesticide treatment provides us the opportunity to propose a solution for this issue. Although the pollen beetle Meligethes aeneus was effectively controlled with pyrethroids for many years, there have been reports of increasing resistance. We show protein changes including production of isoforms in response to deltamethrin at the protein level. These results illustrate the insect's survival state as a resistant beetle and in its paralyzed state (evaluated as dead) relative to resistant individuals.
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Phetrungnapha A, Kondo H, Hirono I, Panyim S, Ongvarrasopone C. Molecular cloning and characterization of Mj-mov-10, a putative RNA helicase involved in RNAi of kuruma shrimp. FISH & SHELLFISH IMMUNOLOGY 2015; 44:241-247. [PMID: 25724627 DOI: 10.1016/j.fsi.2015.02.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 02/15/2015] [Accepted: 02/16/2015] [Indexed: 06/04/2023]
Abstract
Identification and characterization of the RNAi-related genes is the key to understanding RNAi mechanism in shrimp. In this study, we have identified and characterized a novel putative RNA helicase gene, Mj-mov-10 from the kuruma shrimp, Marsupenaeus japonicus and its implication in shrimp RNAi was demonstrated. The full-length Mj-mov-10 gene contained 3536bp, including 239 bp of 5'UTR, 2895 bp of the open reading frame (ORF) and 402bp of 3'UTR, respectively. An ORF of Mj-mov-10 could be translated to a 109-kDa protein which consists of a single helicase core domain containing seven signature motifs of the RNA helicase superfamily-1. Mj-MOV-10 protein shared 47% and 40% identity with mammalian MOV-10 and plant SDE3, respectively. Expression of Mj-mov-10 gene was significantly up-regulated upon dsRNA and white spot syndrome virus (WSSV) challenge. In vivo gene knockdown of Mj-mov-10 resulted in an increase of a susceptibility of shrimp to WSSV infection. Our results implied the functional significance of Mj-MOV-10 in dsRNA-mediated gene silencing and antiviral defense mechanism in shrimp.
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Affiliation(s)
- Amnat Phetrungnapha
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Hidehiro Kondo
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Minato, Tokyo, Japan
| | - Ikuo Hirono
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Minato, Tokyo, Japan
| | - Sakol Panyim
- Institute of Molecular Biosciences, Mahidol University, Phutthamonthon 4 Road, Salaya, Nakhon Pathom 73170, Thailand; Department of Biochemistry, Faculty of Science, Mahidol University, Rama VI Road, Phayathai, Bangkok 10400, Thailand
| | - Chalermporn Ongvarrasopone
- Institute of Molecular Biosciences, Mahidol University, Phutthamonthon 4 Road, Salaya, Nakhon Pathom 73170, Thailand.
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Nozaki K, Kagamu H, Shoji S, Igarashi N, Ohtsubo A, Okajima M, Miura S, Watanabe S, Yoshizawa H, Narita I. DDX3X induces primary EGFR-TKI resistance based on intratumor heterogeneity in lung cancer cells harboring EGFR-activating mutations. PLoS One 2014; 9:e111019. [PMID: 25343452 PMCID: PMC4208809 DOI: 10.1371/journal.pone.0111019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 09/26/2014] [Indexed: 11/19/2022] Open
Abstract
The specific mechanisms how lung cancer cells harboring epidermal growth factor receptor (EGFR) activating mutations can survive treatment with EGFR-tyrosine kinase inhibitors (TKIs) until they eventually acquire treatment-resistance genetic mutations are unclear. The phenotypic diversity of cancer cells caused by genetic or epigenetic alterations (intratumor heterogeneity) confers treatment failure and may foster tumor evolution through Darwinian selection. Recently, we found DDX3X as the protein that was preferentially expressed in murine melanoma with cancer stem cell (CSC)-like phenotypes by proteome analysis. In this study, we transfected PC9, human lung cancer cells harboring EGFR exon19 deletion, with cDNA encoding DDX3X and found that DDX3X, an ATP-dependent RNA helicase, induced CSC-like phenotypes and the epithelial-mesenchymal transition (EMT) accompanied with loss of sensitivity to EGFR-TKI. DDX3X expression was associated with upregulation of Sox2 and increase of cancer cells exhibiting CSC-like phenotypes, such as anchorage-independent proliferation, strong expression of CD44, and aldehyde dehydrogenase (ALDH). The EMT with switching from E-cadherin to N-cadherin was also facilitated by DDX3X. Either ligand-independent or ligand-induced EGFR phosphorylation was inhibited in lung cancer cells that strongly expressed DDX3X. Lack of EGFR signal addiction resulted in resistance to EGFR-TKI. Moreover, we found a small nonadherent subpopulation that strongly expressed DDX3X accompanied by the same stem cell-like properties and the EMT in parental PC9 cells. The unique subpopulation lacked EGFR signaling and was highly resistant to EGFR-TKI. In conclusion, our data indicate that DDX3X may play a critical role for inducing phenotypic diversity, and that treatment targeting DDX3X may overcome primary resistance to EGFR-TKI resulting from intratumor heterogeneity.
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Affiliation(s)
- Koichiro Nozaki
- Division of Respiratory Medicine, Department of Homeostatic Regulation and Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Hiroshi Kagamu
- Division of Respiratory Medicine, Department of Homeostatic Regulation and Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
- * E-mail:
| | - Satoshi Shoji
- Division of Respiratory Medicine, Department of Homeostatic Regulation and Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Natsue Igarashi
- Division of Respiratory Medicine, Department of Homeostatic Regulation and Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Aya Ohtsubo
- Division of Respiratory Medicine, Department of Homeostatic Regulation and Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Masaaki Okajima
- Division of Respiratory Medicine, Department of Homeostatic Regulation and Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Satoru Miura
- Division of Respiratory Medicine, Department of Homeostatic Regulation and Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Satoshi Watanabe
- Bioscience Medical Research Center, Niigata University Medical and Dental Hospital, Niigata, Japan
| | - Hirohisa Yoshizawa
- Bioscience Medical Research Center, Niigata University Medical and Dental Hospital, Niigata, Japan
| | - Ichiei Narita
- Division of Respiratory Medicine, Department of Homeostatic Regulation and Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
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14
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Khan A, Garbelli A, Grossi S, Florentin A, Batelli G, Acuna T, Zolla G, Kaye Y, Paul LK, Zhu JK, Maga G, Grafi G, Barak S. The Arabidopsis STRESS RESPONSE SUPPRESSOR DEAD-box RNA helicases are nucleolar- and chromocenter-localized proteins that undergo stress-mediated relocalization and are involved in epigenetic gene silencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:28-43. [PMID: 24724701 DOI: 10.1111/tpj.12533] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Revised: 04/03/2014] [Accepted: 04/08/2014] [Indexed: 05/03/2023]
Abstract
DEAD-box RNA helicases are involved in many aspects of RNA metabolism and in diverse biological processes in plants. Arabidopsis thaliana mutants of two DEAD-box RNA helicases, STRESS RESPONSE SUPPRESSOR1 (STRS1) and STRS2 were previously shown to exhibit tolerance to abiotic stresses and up-regulated stress-responsive gene expression. Here, we show that Arabidopsis STRS-overexpressing lines displayed a less tolerant phenotype and reduced expression of stress-induced genes confirming the STRSs as attenuators of Arabidopsis stress responses. GFP-STRS fusion proteins exhibited localization to the nucleolus, nucleoplasm and chromocenters and exhibited relocalization in response to abscisic acid (ABA) treatment and various stresses. This relocalization was reversed when stress treatments were removed. The STRS proteins displayed mis-localization in specific gene-silencing mutants and exhibited RNA-dependent ATPase and RNA-unwinding activities. In particular, STRS2 showed mis-localization in three out of four mutants of the RNA-directed DNA methylation (RdDM) pathway while STRS1 was mis-localized in the hd2c mutant that is defective in histone deacetylase activity. Furthermore, heterochromatic RdDM target loci displayed reduced DNA methylation and increased expression in the strs mutants. Taken together, our findings suggest that the STRS proteins are involved in epigenetic silencing of gene expression to bring about suppression of the Arabidopsis stress response.
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Affiliation(s)
- Asif Khan
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, 84990, Israel
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15
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Bakkali M. A bird's-eye view on the modern genetics workflow and its potential applicability to the locust problem. C R Biol 2013; 336:375-83. [PMID: 24018194 DOI: 10.1016/j.crvi.2013.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 07/19/2013] [Accepted: 07/23/2013] [Indexed: 01/16/2023]
Abstract
Genetics is an immense science and the current developments in its methods and techniques as well as the fast emerging tools make it one of the most powerful biological sciences. Indeed, from taxonomy and ecology to physiology and molecular biology, every biological science makes use of genetics techniques and methods at one time or another. In fact, development in genetics is such that it is now possible to characterize and analyze the expression of the whole set of genes of virtually every living organism, even if it is a non-model one. Locusts are notorious for the damage they cause to the ecosystems and economies of the areas affected by their recurrent population outbreaks. To prevent and deal with these outbreaks, we now count on both biological as well as chemical agents that are proving to be successful in reducing the damage that otherwise locust population outbreaks might cause. However, a better, efficient and environmentally friendly solution is still a hoped-for target. In my opinion, the ideal future pesticide should be both environmentally friendly, risk free and species-specific. To reach the knowledge needed for the development of such species-specific anti-locust agent, deep and accurate knowledge of the locusts' genetics and molecular biology is a must. Since genes and their expression levels lie at the bottom of every biological phenomenon, any species-specific solution to the locust problem requires a good knowledge of these organisms' genes as well as the quantitative and spatio-temporal dynamics of their expression. To reach such knowledge, collaborative work is needed as well as a clear workflow that, given the fast development in the genetics tools, is not always clear to all research groups. For this reason, here I describe a genetics workflow that should allow taking advantage of the most recent genetics tools and techniques to answer question relating to locust biology. My hope is that the adoption of this and other work strategies by different research groups, especially when the work is a collaborative one, would provide precious information on the biology and the biological phenomena that these economically important organisms exhibit.
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Affiliation(s)
- Mohammed Bakkali
- Departamento de Genetica, Facultad de Ciencias, Universidad de Granada, Fuentenueva S/N, 18071 Granada, Spain.
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16
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An emerging role for microRNAs in sexually dimorphic neurobiological systems. Pflugers Arch 2013; 465:655-67. [PMID: 23397171 DOI: 10.1007/s00424-013-1227-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 01/28/2013] [Indexed: 10/27/2022]
Abstract
Over the past 20 years, our understanding of the basic mechanisms of gene regulation has vastly expanded due to the unexpected roles of small regulatory RNAs, in particular microRNAs (miRNAs). miRNAs add another layer of complexity to the regulation of effector molecules for nearly every physiological process, making them excellent candidate molecules as therapeutic targets, biomarkers, and disease predictors. Hormonal contributions to mature miRNA expression, biosynthetic processing, and downstream functions have only just begun to be investigated. Elucidating the physiological consequences of miRNA sexual dimorphism, and their associated regulatory processes, may be key toward understanding both normal and pathological processes in the brain. This short review provides a basic overview of miRNA biosynthesis, their role in normal brain development, and potential links to neurological diseases. We conclude with a brief discussion of the current knowledge of sex-specific miRNA processes in both the brain and the heart to conceptually integrate the relevance of miRNAs with the overarching theme ("sex differences in health and disease: brain and heart connections") of this special topics issue.
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17
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Gargantini PR, Serradell MC, Torri A, Lujan HD. Putative SF2 helicases of the early-branching eukaryote Giardia lamblia are involved in antigenic variation and parasite differentiation into cysts. BMC Microbiol 2012. [PMID: 23190735 PMCID: PMC3566956 DOI: 10.1186/1471-2180-12-284] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background Regulation of surface antigenic variation in Giardia lamblia is controlled post-transcriptionally by an RNA-interference (RNAi) pathway that includes a Dicer-like bidentate RNase III (gDicer). This enzyme, however, lacks the RNA helicase domain present in Dicer enzymes from higher eukaryotes. The participation of several RNA helicases in practically all organisms in which RNAi was studied suggests that RNA helicases are potentially involved in antigenic variation, as well as during Giardia differentiation into cysts. Results An extensive in silico analysis of the Giardia genome identified 32 putative Super Family 2 RNA helicases that contain almost all the conserved RNA helicase motifs. Phylogenetic studies and sequence analysis separated them into 22 DEAD-box, 6 DEAH-box and 4 Ski2p-box RNA helicases, some of which are homologs of well-characterized helicases from higher organisms. No Giardia putative helicase was found to have significant homology to the RNA helicase domain of Dicer enzymes. Additionally a series of up- and down-regulated putative RNA helicases were found during encystation and antigenic variation by qPCR experiments. Finally, we were able to recognize 14 additional putative helicases from three different families (RecQ family, Swi2/Snf2 and Rad3 family) that could be considered DNA helicases. Conclusions This is the first comprehensive analysis of the Super Family 2 helicases from the human intestinal parasite G. lamblia. The relative and variable expression of particular RNA helicases during both antigenic variation and encystation agrees with the proposed participation of these enzymes during both adaptive processes. The putatives RNA and DNA helicases identified in this early-branching eukaryote provide initial information regarding the biological role of these enzymes in cell adaptation and differentiation.
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Affiliation(s)
- Pablo R Gargantini
- Laboratory of Biochemistry and Molecular Biology, School of Medicine, Catholic University of Córdoba, Córdoba X5004ASK, Argentina.
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18
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Abstract
Similar to proteins, RNA molecules must fold into the correct conformation and associate with protein complexes in order to be functional within a cell. RNA helicases rearrange RNA secondary structure and RNA-protein interactions in an ATP-dependent reaction, performing crucial functions in all aspects of RNA metabolism. In prokaryotes, RNA helicase activity is associated with roles in housekeeping functions including RNA turnover, ribosome biogenesis, translation and small RNA metabolism. In addition, RNA helicase expression and/or activity are frequently altered during cellular response to abiotic stress, implying they perform defined roles during cellular adaptation to changes in the growth environment. Specifically, RNA helicases contribute to the formation of cold-adapted ribosomes and RNA degradosomes, implying a role in alleviation of RNA secondary structure stabilization at low temperature. A common emerging theme involves RNA helicases acting as scaffolds for protein-protein interaction and functioning as molecular clamps, holding RNA-protein complexes in specific conformations. This review highlights recent advances in DEAD-box RNA helicase association with cellular response to abiotic stress in prokaryotes.
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Affiliation(s)
- George W Owttrim
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
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19
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Ambrus AM, Frolov MV. Mutation of the DEAD-box helicase belle downregulates the cyclin-dependent kinase inhibitor Dacapo. Cell Cycle 2010; 9:1016-20. [PMID: 20160476 DOI: 10.4161/cc.9.5.10953] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The retinoblastoma protein (pRB) negatively regulates cell proliferation by limiting the activity of the family of E2F transcription factors. In Drosophila, mutation of the DEAD-box helicase belle (bel) relieves an E2F/pRB induced G(1) cell cycle arrest; however, the mechanism of this rescue is unknown. Here, we show that the level of the cyclin-dependent kinase inhibitor Dacapo (Dap), homolog of mammalian p21/p27, is strongly reduced both in bel mutant cells in vivo and in tissue culture cells depleted of Bel by RNA interference. Interestingly, the loss of bel also partially alleviates an ectopically induced G(1) cell cycle arrest. Additionally, we show that Bel undergoes nucleocytoplasmic shuttling. Thus, inactivation of bel renders cells less sensitive to several anti-proliferative signals inducing G(1) arrest.
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Affiliation(s)
- Aaron M Ambrus
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
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