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Hada A, Patil BL, Bajpai A, Kesiraju K, Dinesh-Kumar S, Paraselli B, Sreevathsa R, Rao U. Micro RNA-induced gene silencing strategy for the delivery of siRNAs targeting Meloidogyne incognita in a model plant Nicotiana benthamiana. Pest Manag Sci 2021; 77:3396-3405. [PMID: 33786977 DOI: 10.1002/ps.6384] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/23/2021] [Accepted: 03/31/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Occurrence of multiple biotic stresses on crop plants result in drastic yield losses which may have severe impact on the food security. It is a challenge to design strategies for simultaneous management of these multiple stresses. Hence, establishment of innovative approaches that aid in their management is critical. Here, we have introgressed a micro RNA-induced gene silencing (MIGS) based combinatorial gene construct containing seven target gene sequences of cotton leaf curl disease (CLCuD), cotton leaf hopper (Amrasca biguttula biguttula), cotton whitefly (Bemisia tabaci) and root-knot nematode (Meloidogyne incognita). RESULTS Stable transgenic lines of Nicotiana benthamiana were generated with the T-DNA harboring Arabidopsis miR173 target site fused to fragments of Sec23 and ecdysone receptor (EcR) genes of cotton leaf hopper and cotton whitefly. It also contained C2/replication associated protein (C2/Rep) and C4 (movement protein) along with βC1 gene of betasatellite to target CLCuD, and two FMRFamide-like peptide (FLP) genes, Mi-flp14 and Mi-flp18 of M. incognita. These transgenic plants were assessed for the amenability of MIGS approach for pest control by efficacy evaluation against M. incognita. Results showed successful production of small interfering RNA (siRNA) through the tasiRNA (trans-acting siRNA) pathway in the transgenic plants corresponding to Mi-flp18 gene. Furthermore, we observed reduced Mi-flp14 and Mi-flp18 transcripts (up to 2.37 ± 0.12-fold) in females extracted from transgenic plants. The average number of galls, total endoparasites, egg masses and number of eggs per egg mass reduced were in the range 27-62%, 39-70%, 38-65% and 34-49%, respectively. More importantly, MIGS transgenic plants showed 80% reduction in the nematode multiplication factor (MF). CONCLUSION This study demonstrates successful validation of the MIGS approach in the model plant, N. benthamiana for efficacy against M. incognita, as a prelude to translation to cotton. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Alkesh Hada
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Basavaprabhu L Patil
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
- Division of Basic Sciences, ICAR-Indian Institute of Horticultural Research, Bengaluru, India
| | - Akansha Bajpai
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Karthik Kesiraju
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Savithramma Dinesh-Kumar
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California Davis, Davis, CA, USA
| | | | | | - Uma Rao
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Ellison EE, Nagalakshmi U, Gamo ME, Huang PJ, Dinesh-Kumar S, Voytas DF. Author Correction: Multiplexed heritable gene editing using RNA viruses and mobile single guide RNAs. Nat Plants 2021; 7:99. [PMID: 33328598 DOI: 10.1038/s41477-020-00837-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Evan E Ellison
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN, USA
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, USA
- Plant and Microbial Biology Graduate Program, University of Minnesota, St. Paul, MN, USA
| | - Ugrappa Nagalakshmi
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, USA
| | - Maria Elena Gamo
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN, USA
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, USA
| | - Pin-Jui Huang
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, USA
| | - Savithramma Dinesh-Kumar
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, USA
| | - Daniel F Voytas
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN, USA.
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN, USA.
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, USA.
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Ellison EE, Nagalakshmi U, Gamo ME, Huang PJ, Dinesh-Kumar S, Voytas DF. Multiplexed heritable gene editing using RNA viruses and mobile single guide RNAs. Nat Plants 2020; 6:620-624. [PMID: 32483329 DOI: 10.1038/s41477-020-0670-y] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 04/22/2020] [Indexed: 05/20/2023]
Abstract
An in planta gene editing approach was developed wherein Cas9 transgenic plants are infected with an RNA virus that expresses single guide RNAs (sgRNAs). The sgRNAs are augmented with sequences that promote cell-to-cell mobility. Mutant progeny are recovered in the next generation at frequencies ranging from 65 to 100%; up to 30% of progeny derived from plants infected with a virus expressing three sgRNAs have mutations in all three targeted loci.
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Affiliation(s)
- Evan E Ellison
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN, USA
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, USA
- Plant and Microbial Biology Graduate Program, University of Minnesota, St. Paul, MN, USA
| | - Ugrappa Nagalakshmi
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, USA
| | - Maria Elena Gamo
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN, USA
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, USA
| | - Pin-Jui Huang
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, USA
| | - Savithramma Dinesh-Kumar
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, USA
| | - Daniel F Voytas
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN, USA.
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN, USA.
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, USA.
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Michelmore R, Coaker G, Bart R, Beattie G, Bent A, Bruce T, Cameron D, Dangl J, Dinesh-Kumar S, Edwards R, Eves-van den Akker S, Gassmann W, Greenberg JT, Hanley-Bowdoin L, Harrison RJ, Harvey J, He P, Huffaker A, Hulbert S, Innes R, Jones JDG, Kaloshian I, Kamoun S, Katagiri F, Leach J, Ma W, McDowell J, Medford J, Meyers B, Nelson R, Oliver R, Qi Y, Saunders D, Shaw M, Smart C, Subudhi P, Torrance L, Tyler B, Valent B, Walsh J. Foundational and Translational Research Opportunities to Improve Plant Health. Mol Plant Microbe Interact 2017; 30:515-516. [PMID: 28398839 PMCID: PMC5810936 DOI: 10.1094/mpmi-01-17-0010-cr] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Reader Comments | Submit a Comment The white paper reports the deliberations of a workshop focused on biotic challenges to plant health held in Washington, D.C. in September 2016. Ensuring health of food plants is critical to maintaining the quality and productivity of crops and for sustenance of the rapidly growing human population. There is a close linkage between food security and societal stability; however, global food security is threatened by the vulnerability of our agricultural systems to numerous pests, pathogens, weeds, and environmental stresses. These threats are aggravated by climate change, the globalization of agriculture, and an over-reliance on nonsustainable inputs. New analytical and computational technologies are providing unprecedented resolution at a variety of molecular, cellular, organismal, and population scales for crop plants as well as pathogens, pests, beneficial microbes, and weeds. It is now possible to both characterize useful or deleterious variation as well as precisely manipulate it. Data-driven, informed decisions based on knowledge of the variation of biotic challenges and of natural and synthetic variation in crop plants will enable deployment of durable interventions throughout the world. These should be integral, dynamic components of agricultural strategies for sustainable agriculture.
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Affiliation(s)
- Richard Michelmore
- 1 The Genome Center and Departments of Plant Sciences, Molecular & Cellular Biology, and Medical Microbiology & Immunology, University of California, Davis, CA, U.S.A
| | - Gitta Coaker
- 2 Department of Plant Pathology, University of California, Davis, CA, U.S.A
| | | | | | - Andrew Bent
- 5 University of Wisconsin, Madison, WI, U.S.A
| | | | | | - Jeffery Dangl
- 8 University of North Carolina, Chapel Hill, NC, U.S.A
| | | | - Rob Edwards
- 10 University of Newcastle, Newcastle upon Tyne, U.K
| | | | | | | | | | | | | | - Ping He
- 17 Texas A&M University, College Station, TX, U.S.A
| | | | - Scot Hulbert
- 19 Washington State University, Pullman, WA, U.S.A
| | - Roger Innes
- 20 Indiana University, Bloomigton, IN, U.S.A
| | | | | | | | | | - Jan Leach
- 24 Colorado State University, Fort Collins, CO, U.S.A
| | - Wenbo Ma
- 22 University of California, Riverside, CA, U.S.A
| | | | | | | | | | | | - Yiping Qi
- 29 East Carolina University, Greenville, NC, U.S.A
| | | | | | | | | | - Lesley Torrance
- 33 University of St. Andrews and James Hutton Institute, Fife, U.K
| | - Bret Tyler
- 34 Oregon State University, Corvallis, OR, U.S.A.; and
| | | | - John Walsh
- 35 University of Warwick, Wellesbourne, U.K
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Lemos M, Xiao Y, Bjornson M, Wang JZ, Hicks D, Souza AD, Wang CQ, Yang P, Ma S, Dinesh-Kumar S, Dehesh K. The plastidial retrograde signal methyl erythritol cyclopyrophosphate is a regulator of salicylic acid and jasmonic acid crosstalk. J Exp Bot 2016; 67:1557-66. [PMID: 26733689 PMCID: PMC4762391 DOI: 10.1093/jxb/erv550] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The exquisite harmony between hormones and their corresponding signaling pathways is central to prioritizing plant responses to simultaneous and/or successive environmental trepidations. The crosstalk between jasmonic acid (JA) and salicylic acid (SA) is an established effective mechanism that optimizes and tailors plant adaptive responses. However, the underlying regulatory modules of this crosstalk are largely unknown. Global transcriptomic analyses of mutant plants (ceh1) with elevated levels of the stress-induced plastidial retrograde signaling metabolite 2-C-methyl-D-erythritol cyclopyrophosphate (MEcPP) revealed robustly induced JA marker genes, expected to be suppressed by the presence of constitutively high SA levels in the mutant background. Analyses of a range of genotypes with varying SA and MEcPP levels established the selective role of MEcPP-mediated signal(s) in induction of JA-responsive genes in the presence of elevated SA. Metabolic profiling revealed the presence of high levels of the JA precursor 12-oxo-phytodienoic acid (OPDA), but near wild type levels of JA in the ceh1 mutant plants. Analyses of coronatine-insensitive 1 (coi1)/ceh1 double mutant plants confirmed that the MEcPP-mediated induction is JA receptor COI1 dependent, potentially through elevated OPDA. These findings identify MEcPP as a previously unrecognized central regulatory module that induces JA-responsive genes in the presence of high SA, thereby staging a multifaceted plant response within the environmental context.
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Affiliation(s)
- Mark Lemos
- Department of Plant Biology, University of California Davis, Davis, CA 95616, USA
| | - Yanmei Xiao
- Department of Plant Biology, University of California Davis, Davis, CA 95616, USA
| | - Marta Bjornson
- Department of Plant Biology, University of California Davis, Davis, CA 95616, USA Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
| | - Jin-Zheng Wang
- Department of Plant Biology, University of California Davis, Davis, CA 95616, USA
| | - Derrick Hicks
- Department of Plant Biology, University of California Davis, Davis, CA 95616, USA
| | - Amancio de Souza
- Department of Plant Biology, University of California Davis, Davis, CA 95616, USA
| | - Chang-Quan Wang
- Department of Plant Biology, University of California Davis, Davis, CA 95616, USA
| | - Panyu Yang
- Department of Plant Biology, University of California Davis, Davis, CA 95616, USA
| | - Shisong Ma
- Department of Plant Biology, University of California Davis, Davis, CA 95616, USA
| | - Savithramma Dinesh-Kumar
- Department of Plant Biology, University of California Davis, Davis, CA 95616, USA Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Katayoon Dehesh
- Department of Plant Biology, University of California Davis, Davis, CA 95616, USA
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6
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Ali Z, Abul-faraj A, Li L, Ghosh N, Piatek M, Mahjoub A, Aouida M, Piatek A, Baltes NJ, Voytas DF, Dinesh-Kumar S, Mahfouz MM. Efficient Virus-Mediated Genome Editing in Plants Using the CRISPR/Cas9 System. Mol Plant 2015; 8:1288-91. [PMID: 25749112 DOI: 10.1016/j.molp.2015.02.011] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 02/13/2015] [Accepted: 02/14/2015] [Indexed: 05/17/2023]
Affiliation(s)
- Zahir Ali
- Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Aala Abul-faraj
- Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Lixin Li
- Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Neha Ghosh
- Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Marek Piatek
- Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Ali Mahjoub
- Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Mustapha Aouida
- Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Agnieszka Piatek
- Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Nicholas J Baltes
- Department of Genetics, Cell Biology and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel F Voytas
- Department of Genetics, Cell Biology and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Magdy M Mahfouz
- Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.
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7
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Ma S, Dinesh-Kumar S. SGR-based Reporter to Assay Plant Transcription Factor-promoter Interactions. Bio Protoc 2014. [DOI: 10.21769/bioprotoc.1214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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8
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Lee HY, Bowen CH, Popescu GV, Kang HG, Kato N, Ma S, Dinesh-Kumar S, Snyder M, Popescu SC. Arabidopsis RTNLB1 and RTNLB2 Reticulon-like proteins regulate intracellular trafficking and activity of the FLS2 immune receptor. Plant Cell 2011; 23:3374-91. [PMID: 21949153 PMCID: PMC3203430 DOI: 10.1105/tpc.111.089656] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 08/26/2011] [Accepted: 09/12/2011] [Indexed: 05/18/2023]
Abstract
Receptors localized at the plasma membrane are critical for the recognition of pathogens. The molecular determinants that regulate receptor transport to the plasma membrane are poorly understood. In a screen for proteins that interact with the FLAGELIN-SENSITIVE2 (FLS2) receptor using Arabidopsis thaliana protein microarrays, we identified the reticulon-like protein RTNLB1. We showed that FLS2 interacts in vivo with both RTNLB1 and its homolog RTNLB2 and that a Ser-rich region in the N-terminal tail of RTNLB1 is critical for the interaction with FLS2. Transgenic plants that lack RTNLB1 and RTNLB2 (rtnlb1 rtnlb2) or overexpress RTNLB1 (RTNLB1ox) exhibit reduced activation of FLS2-dependent signaling and increased susceptibility to pathogens. In both rtnlb1 rtnlb2 and RTNLB1ox, FLS2 accumulation at the plasma membrane was significantly affected compared with the wild type. Transient overexpression of RTNLB1 led to FLS2 retention in the endoplasmic reticulum (ER) and affected FLS2 glycosylation but not FLS2 stability. Removal of the critical N-terminal Ser-rich region or either of the two Tyr-dependent sorting motifs from RTNLB1 causes partial reversion of the negative effects of excess RTNLB1 on FLS2 transport out of the ER and accumulation at the membrane. The results are consistent with a model whereby RTNLB1 and RTNLB2 regulate the transport of newly synthesized FLS2 to the plasma membrane.
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Affiliation(s)
- Hyoung Yool Lee
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853
| | | | - George Viorel Popescu
- National Institute for Laser, Plasma, and Radiation Physics, Magurele 077125 Bucharest, Romania
| | - Hong-Gu Kang
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853
| | - Naohiro Kato
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Shisong Ma
- College of Biological Sciences, University of California, Davis, California 95616
| | | | - Michael Snyder
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Sorina Claudia Popescu
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853
- Address correspondence to
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Klionsky DJ, Abeliovich H, Agostinis P, Agrawal DK, Aliev G, Askew DS, Baba M, Baehrecke EH, Bahr BA, Ballabio A, Bamber BA, Bassham DC, Bergamini E, Bi X, Biard-Piechaczyk M, Blum JS, Bredesen DE, Brodsky JL, Brumell JH, Brunk UT, Bursch W, Camougrand N, Cebollero E, Cecconi F, Chen Y, Chin LS, Choi A, Chu CT, Chung J, Clarke PGH, Clark RSB, Clarke SG, Clavé C, Cleveland JL, Codogno P, Colombo MI, Coto-Montes A, Cregg JM, Cuervo AM, Debnath J, Demarchi F, Dennis PB, Dennis PA, Deretic V, Devenish RJ, Di Sano F, Dice JF, Difiglia M, Dinesh-Kumar S, Distelhorst CW, Djavaheri-Mergny M, Dorsey FC, Dröge W, Dron M, Dunn WA, Duszenko M, Eissa NT, Elazar Z, Esclatine A, Eskelinen EL, Fésüs L, Finley KD, Fuentes JM, Fueyo J, Fujisaki K, Galliot B, Gao FB, Gewirtz DA, Gibson SB, Gohla A, Goldberg AL, Gonzalez R, González-Estévez C, Gorski S, Gottlieb RA, Häussinger D, He YW, Heidenreich K, Hill JA, Høyer-Hansen M, Hu X, Huang WP, Iwasaki A, Jäättelä M, Jackson WT, Jiang X, Jin S, Johansen T, Jung JU, Kadowaki M, Kang C, Kelekar A, Kessel DH, Kiel JAKW, Kim HP, Kimchi A, Kinsella TJ, Kiselyov K, Kitamoto K, Knecht E, Komatsu M, Kominami E, Kondo S, Kovács AL, Kroemer G, Kuan CY, Kumar R, Kundu M, Landry J, Laporte M, Le W, Lei HY, Lenardo MJ, Levine B, Lieberman A, Lim KL, Lin FC, Liou W, Liu LF, Lopez-Berestein G, López-Otín C, Lu B, Macleod KF, Malorni W, Martinet W, Matsuoka K, Mautner J, Meijer AJ, Meléndez A, Michels P, Miotto G, Mistiaen WP, Mizushima N, Mograbi B, Monastyrska I, Moore MN, Moreira PI, Moriyasu Y, Motyl T, Münz C, Murphy LO, Naqvi NI, Neufeld TP, Nishino I, Nixon RA, Noda T, Nürnberg B, Ogawa M, Oleinick NL, Olsen LJ, Ozpolat B, Paglin S, Palmer GE, Papassideri I, Parkes M, Perlmutter DH, Perry G, Piacentini M, Pinkas-Kramarski R, Prescott M, Proikas-Cezanne T, Raben N, Rami A, Reggiori F, Rohrer B, Rubinsztein DC, Ryan KM, Sadoshima J, Sakagami H, Sakai Y, Sandri M, Sasakawa C, Sass M, Schneider C, Seglen PO, Seleverstov O, Settleman J, Shacka JJ, Shapiro IM, Sibirny A, Silva-Zacarin ECM, Simon HU, Simone C, Simonsen A, Smith MA, Spanel-Borowski K, Srinivas V, Steeves M, Stenmark H, Stromhaug PE, Subauste CS, Sugimoto S, Sulzer D, Suzuki T, Swanson MS, Tabas I, Takeshita F, Talbot NJ, Tallóczy Z, Tanaka K, Tanaka K, Tanida I, Taylor GS, Taylor JP, Terman A, Tettamanti G, Thompson CB, Thumm M, Tolkovsky AM, Tooze SA, Truant R, Tumanovska LV, Uchiyama Y, Ueno T, Uzcátegui NL, van der Klei I, Vaquero EC, Vellai T, Vogel MW, Wang HG, Webster P, Wiley JW, Xi Z, Xiao G, Yahalom J, Yang JM, Yap G, Yin XM, Yoshimori T, Yu L, Yue Z, Yuzaki M, Zabirnyk O, Zheng X, Zhu X, Deter RL. Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes. Autophagy 2008; 4:151-75. [PMID: 18188003 PMCID: PMC2654259 DOI: 10.4161/auto.5338] [Citation(s) in RCA: 1821] [Impact Index Per Article: 113.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Research in autophagy continues to accelerate,(1) and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.(2,3) There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.
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Affiliation(s)
- Daniel J Klionsky
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109-2216, USA.
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Abstract
Although research in this area is still in a stage of infancy, it seems likely that the lysosomal degradation pathway of autophagy plays an evolutionarily conserved role in antiviral immunity. The interferon-inducible, antiviral PKR signaling pathway positively regulates autophagy, and both mammalian and plant autophagy genes restrict viral replication and protect against virus-induced cell death. Given this role of autophagy in innate immunity, it is not surprising that viruses have evolved numerous strategies to inhibit host autophagy. Different viral gene products can either modulate autophagy regulatory signals or directly interact with components of the autophagy execution machinery. Moreover, certain RNA viruses have managed to “co-apt” the autophagy pathway, selectively utilizing certain components of the dynamic membrane rearrangement system to promote their own replication inside the host cytoplasm. In addition to this newly emerging role of autophagy in innate immunity, autophagy plays an important role in many other fundamental biological processes, including tissue homeostasis, differentiation and development, cell growth control, and the prevention of aging. Accordingly, the inhibition of host autophagy by viral gene products has important implications not only for understanding mechanisms of immune evasion, but also for understanding novel mechanisms of viral pathogenesis. It will be interesting to dissect the role of viral inhibition of autophagy in acute, persistent, and latent viral replication, as well as in the pathogenesis of cancer and other medical diseases.
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