@article{MTMT:33039097,
	title = {In Arabidopsis thaliana, RNA-Induced Silencing Complex-Loading of MicroRNAs Plays a Minor Regulatory Role During Photomorphogenesis Except for miR163},
	url = {https://m2.mtmt.hu/api/publication/33039097},
	author = {Lakatos, Lóránt and Groma, Gergely and Silhavy, Dániel and Nagy, Ferenc István},
	doi = {10.3389/fpls.2022.854869},
	journal-iso = {FRONT PLANT SCI},
	journal = {FRONTIERS IN PLANT SCIENCE},
	volume = {13},
	unique-id = {33039097},
	issn = {1664-462X},
	abstract = {The shift of dark-grown seedlings to the light leads to substantial reprogramming of gene expression, which results in dramatic developmental changes (referred to as de-etiolation or photomorphogenesis). MicroRNAs (miRNAs) regulate most steps of plant development, thus miRNAs might play important role in transcriptional reprogramming during de-etiolation. Indeed, miRNA biogenesis mutants show aberrant de-etiolation. Previous works showed that the total miRNA expression pattern (total miRNAome) is only moderately altered during photomorphogenesis. However, a recent study has shown that plant miRNAs are present in two pools, biologically active miRNAs loaded to RISC (RNA-induced silencing complex-loaded) form while inactive miRNAs accumulate in duplex form upon organ formation. To test if RISC-loading efficiency is changed during photomorphogenesis. we compared the total miRNAome and the RISC-loaded miRNAome of dark-grown and de-etiolated Arabidopsis thaliana seedlings. miRNA sequencing has revealed that although regulated RISC-loading is involved in the control of active miRNAome formation during de-etiolation, this effect is moderate. The total miRNAomes and the RISC-loaded miRNAomes of dark-grown and de-etiolated plants are similar indicating that most miRNAs are loaded onto RISC with similar efficiency in dark and light. Few miRNAs were loaded onto RISC with different efficiency and one miRNA, miR163, was RISC-loaded much more effectively in light than in dark. Thus, our results suggest that although RISC-loading contributes significantly to the control of the formation of organ-specific active miRNA pools, it plays a limited role in the regulation of active miRNA pool formation during de-etiolation. Regulated RISC-loading strongly modifies the expression of miRNA163, could play a role in the fine-tuning of a few other miRNAs, and do not modify the expression of most miRNAs.},
	keywords = {EXPRESSION; EFFICIENT; miRNA; miRNA; BIOGENESIS; Arabidopsis thaliana; PHOTOMORPHOGENESIS; ARGONAUTE1; SERRATE; miRNAome; reprogramming of gene expression; efficiency of AGO loading},
	year = {2022},
	eissn = {1664-462X},
	orcid-numbers = {Nagy, Ferenc István/0000-0002-6157-9269}
}

@article{MTMT:32640714,
	title = {Elongation factor TFIIS is essential for heat stress adaptation in plants},
	url = {https://m2.mtmt.hu/api/publication/32640714},
	author = {Szádeczky-Kardoss, István and Szaker, Henrik Mihály and Verma, Radhika and Darkó, Éva and Pettkó-Szandtner, Aladár and Silhavy, Dániel and Csorba, Tibor},
	doi = {10.1093/nar/gkac020},
	journal-iso = {NUCLEIC ACIDS RES},
	journal = {NUCLEIC ACIDS RESEARCH},
	volume = {50},
	unique-id = {32640714},
	issn = {0305-1048},
	year = {2022},
	eissn = {1362-4962},
	pages = {1927-1950},
	orcid-numbers = {Szaker, Henrik Mihály/0000-0001-8340-8287}
}

@article{MTMT:31997619,
	title = {The role of RST1 and RIPR proteins in plant RNA quality control systems},
	url = {https://m2.mtmt.hu/api/publication/31997619},
	author = {Auth, Mariann and Nyikó, Tünde and Auber, Andor and Silhavy, Dániel},
	doi = {10.1007/s11103-021-01145-9},
	journal-iso = {PLANT MOL BIOL},
	journal = {PLANT MOLECULAR BIOLOGY},
	volume = {106},
	unique-id = {31997619},
	issn = {0167-4412},
	abstract = {To keep mRNA homeostasis, the RNA degradation, quality control and silencing systems should act in balance in plants. Degradation of normal mRNA starts with deadenylation, then deadenylated transcripts are degraded by the SKI-exosome 3 '-5 ' and/or XRN4 5 '-3 ' exonucleases. RNA quality control systems identify and decay different aberrant transcripts. RNA silencing degrades double-stranded transcripts and homologous mRNAs. It also targets aberrant and silencing prone transcripts. The SKI-exosome is essential for mRNA homeostasis, it functions in normal mRNA degradation and different RNA quality control systems, and in its absence silencing targets normal transcripts. It is highly conserved in eukaryotes, thus recent reports that the plant SKI-exosome is associated with RST1 and RIPR proteins and that, they are required for SKI-exosome-mediated decay of silencing prone transcripts were unexpected. To clarify whether RST1 and RIPR are essential for all SKI-exosome functions or only for the elimination of silencing prone transcripts, degradation of different reporter transcripts was studied in RST1 and RIPR inactivated Nicotiana benthamiana plants. As RST1 and RIPR, like the SKI-exosome, were essential for Non-stop and No-go decay quality control systems, and for RNA silencing- and minimum ORF-mediated decay, we propose that RST1 and RIPR are essential components of plant SKI-exosome supercomplex. Key message The RST1 and RIPR proteins are required for the degradation of aberrant transcripts lacking a stop codon and the 5 ' cleavage fragments of no-go decay, RNA silencing and minimum ORF.},
	year = {2021},
	eissn = {1573-5028},
	pages = {271-284},
	orcid-numbers = {Silhavy, Dániel/0000-0002-3370-7067}
}

@article{MTMT:31612927,
	title = {Expression of the translation termination factor eRF1 is autoregulated by translational readthrough and 3'UTR intron-mediated NMD inNeurospora crassa},
	url = {https://m2.mtmt.hu/api/publication/31612927},
	author = {Kurilla, Anita and Szőke, Anita and Auber, Andor and Káldi, Krisztina and Silhavy, Dániel},
	doi = {10.1002/1873-3468.13918},
	journal-iso = {FEBS LETT},
	journal = {FEBS LETTERS},
	volume = {594},
	unique-id = {31612927},
	issn = {0014-5793},
	abstract = {Eukaryotic release factor 1 (eRF1) is a translation termination factor that binds to the ribosome at stop codons. The expression of eRF1 is strictly controlled, since its concentration defines termination efficiency and frequency of translational readthrough. Here, we show that eRF1 expression inNeurospora crassais controlled by an autoregulatory circuit that depends on the specific 3'UTR structure oferf1mRNA. The stop codon context oferf1promotes readthrough that protects the mRNA from its 3'UTR-induced nonsense-mediated mRNA decay (NMD). High eRF1 concentration leads to inefficient readthrough, thereby allowing NMD-mediatederf1degradation. We propose that eRF1 expression is controlled by similar autoregulatory circuits in many fungi and seed plants and discuss the evolution of autoregulatory systems of different translation termination factors.},
	year = {2020},
	eissn = {1873-3468},
	pages = {3504-3517},
	orcid-numbers = {Szőke, Anita/0000-0003-0593-2088; Káldi, Krisztina/0000-0002-5724-0182; Silhavy, Dániel/0000-0002-3370-7067}
}

@article{MTMT:31386132,
	title = {Bulbous perennials precisely detect the length of winter and adjust flowering dates},
	url = {https://m2.mtmt.hu/api/publication/31386132},
	author = {Jánosi, Imre Miklós and Silhavy, Dániel and Tamás, Júlia and Csontos, Péter},
	doi = {10.1111/nph.16740},
	journal-iso = {NEW PHYTOL},
	journal = {NEW PHYTOLOGIST},
	volume = {228},
	unique-id = {31386132},
	issn = {0028-646X},
	year = {2020},
	eissn = {1469-8137},
	pages = {1535-1547},
	orcid-numbers = {Jánosi, Imre Miklós/0000-0002-3705-5748; Silhavy, Dániel/0000-0002-3370-7067}
}

@article{MTMT:31281263,
	title = {RNA Helicases from the DEA(D/H)-Box Family Contribute to Plant NMD Efficiency},
	url = {https://m2.mtmt.hu/api/publication/31281263},
	author = {Sulkowska, Aleksandra and Auber, Andor and Sikorski, Pawel J. and Silhavy, Dániel and Auth, Mariann and Sitkiewicz, Ewa and Jean, Viviane and Merret, Remy and Bousquet-Antonelli, Cecile and Kufel, Joanna},
	doi = {10.1093/pcp/pcz186},
	journal-iso = {PLANT CELL PHYSIOL},
	journal = {PLANT AND CELL PHYSIOLOGY},
	volume = {61},
	unique-id = {31281263},
	issn = {0032-0781},
	abstract = {Nonsense-mediated mRNA decay (NMD) is a conserved eukaryotic RNA surveillance mechanism that degrades aberrantm RNAs comprising a premature translation termination codon. The adenosine triphosphate (ATP)-dependent RNA helicase up-frameshift 1 (UPF1) is a major NMD factor in all studied organisms; however, the complexity of this mechanism has not been fully characterized in plants. To identify plant NMD factors, we analyzed UPF1-interacting proteins using tandem affinity purification coupled to mass spectrometry.Canonical members of the NMD pathway were found along with numerous NMD candidate factors, including conserved DEA(D/H)-box RNA helicase homologs of human DDX3, DDX5 and DDX6, translation initiation factors, ribosomal proteins and transport factors. Our functional studies revealed that depletion of DDX3 helicases enhances the accumulation of NMD target reporterm RNAs but does not result in increased protein levels. In contrast, silencing of DDX6 group leads to decreased accumulation of the NMD substrate. The inhibitory effect of DDX6-like helicases on NMD was confirmed by transient over-expression of RH12 helicase. These results indicate that DDX3 and DDX6 helicases in plants have a direct and opposing contribution to NMD and act as functional NMD factors.},
	keywords = {PROTEINS; COMPLEX; DEGRADATION; ENDOPLASMIC-RETICULUM; UPF1; STRESS GRANULES; Plant Sciences; Nonsense-mediated decay; PROCESSING BODIES; P-bodies; nonsense-mediated mRNA decay; RNA quality control; DEA(D/H)-box RNA helicases; ABERRANT MESSENGER-RNA},
	year = {2020},
	eissn = {1471-9053},
	pages = {144-157},
	orcid-numbers = {Sulkowska, Aleksandra/0000-0003-0595-8536}
}

@article{MTMT:30982110,
	title = {Nectar- and stigma exudate-specific expression of an acidic chitinase could partially protect certain apple cultivars against fire blight disease},
	url = {https://m2.mtmt.hu/api/publication/30982110},
	author = {Kurilla, Anita and Tóth, Tímea and Dorgai, L. and Darula, Zsuzsanna and Lakatos, Tamás and Silhavy, Dániel and Kerényi, Zoltán and Dallmann, G.},
	doi = {10.1007/s00425-019-03303-2},
	journal-iso = {PLANTA},
	journal = {PLANTA},
	volume = {251},
	unique-id = {30982110},
	issn = {0032-0935},
	year = {2020},
	eissn = {1432-2048},
	orcid-numbers = {Tóth, Tímea/0000-0002-5943-1791; Lakatos, Tamás/0000-0003-0405-3532}
}

@article{MTMT:30450590,
	title = {Characterization of Eukaryotic Release Factor 3 (eRF3) Translation Termination Factor in Plants},
	url = {https://m2.mtmt.hu/api/publication/30450590},
	author = {Auber, Andor and Nyikó, Tünde and Merai, Zsuzsanna and Silhavy, Dániel},
	doi = {10.1007/s11105-018-1128-5},
	journal-iso = {PLANT MOL BIOL REP},
	journal = {PLANT MOLECULAR BIOLOGY REPORTER},
	volume = {36},
	unique-id = {30450590},
	issn = {0735-9640},
	abstract = {Eukaryotic translation termination is mediated by two conserved interacting release factors, eRF1 and eRF3. eRF1 recognizes the stop codon and promotes the hydrolysis of the polypeptide chain, while eukaryotic eRF3 stimulates eRF1 release activity in the presence of GTP. It is widely believed that translation termination is highly conserved in eukaryotes. However, recent results that eRF1 is present in multiple, partially redundant copies in plants and that eRF1 expression is controlled by a complex, plant-specific autoregulatory circuit suggest that regulation of translation termination might be especially complex in plants. Surprisingly, very little is known about translation termination in plant, for instance, the eRF3 termination factor has not been analyzed in plants yet. Thus, we wanted to identify and characterize the eRF3 translation termination factor in plants. By combining a range of transient and transgenic assay here, we identified plant eRF3 and showed that it directly interacts with eRF1. In contrast to eRF1, plant eRF3 is not autoregulated, while eRF3 and eRF1 expressions are connected. We also demonstrated that eRF3 interacts with the core NMD factor, UPF1, and the expression of eRF3 is NMD regulated in certain plant species suggesting that in addition to the normal translation termination, eRF3 could be connected to plant nonsense-mediated decay (NMD). Finally, it appears that the plant termination factors are present in physiologically different concentrations, while eRF1 concentration limits the efficiency of both translation termination and NMD, eRF3 is present in non-limiting concentration.},
	keywords = {NMD; Translation termination complex; eRF3; Cross-regulation},
	year = {2018},
	eissn = {1572-9818},
	pages = {858-869},
	orcid-numbers = {Auber, Andor/0000-0001-8432-3760}
}

@article{MTMT:3420895,
	title = {The No-go decay system degrades plant mRNAs that contain a long A-stretch in the coding region},
	url = {https://m2.mtmt.hu/api/publication/3420895},
	author = {Szádeczky-Kardoss, István and Gal, L and Auber, Andor and Taller, János and Silhavy, Dániel},
	doi = {10.1016/j.plantsci.2018.07.008},
	journal-iso = {PLANT SCI},
	journal = {PLANT SCIENCE},
	volume = {275},
	unique-id = {3420895},
	issn = {0168-9452},
	abstract = {RNA quality control systems identify and degrade aberrant mRNAs, thereby preventing the accumulation of faulty proteins. Non-stop decay (NSD) and No-go decay (NGD) are closely related RNA quality control systems that act during translation. NSD degrades mRNAs lacking a stop codon, while NGD recognizes and decays mRNAs that contain translation elongation inhibitory structures. NGD has been intensively studied in yeast and animals but it has not been described in plants yet. In yeast, NGD is induced if the elongating ribosome is stalled by a strong inhibitory structure. Then, the mRNA is cleaved by an unknown nuclease and the cleavage fragments are degraded. Here we show that NGD also operates in plant. We tested several potential NGD cis-elements and found that in plants, unlike in yeast, only long A-stretches induce NGD. These long A-stretches trigger endonucleolytic cleavage, and then the 5' fragments are degraded in a Pelota-, HBS1- and SKI2- dependent manner, while XRN4 eliminates the 3' fragment. We also show that plant NGD operates gradually, the longer the A stretch, the more efficient the cleavage. Our data suggest that mechanistically NGD is conserved in eukaryotes, although the NGD inducing cis-elements could be different. Moreover, we found that Arabidopsis AtPelota1 functions in both NGD and NSD, while AtPelota2 represses these quality control systems. The function of plant NGD will be discussed.},
	keywords = {COMPLEX; YEAST; DISSOCIATION; DEGRADATION; TRANSLATION; QUALITY-CONTROL; RIBOSOME; PROFILING REVEALS; SILENCING SUPPRESSOR; DOUBLE-STRANDED RNAS; Prevention of silencing amplification; Ribosome stalling; Pelota2 dominant-negative mutant; Long A-stretch; No-go decay},
	year = {2018},
	eissn = {1873-2259},
	pages = {19-27},
	orcid-numbers = {Auber, Andor/0000-0001-8432-3760}
}

@article{MTMT:3370402,
	title = {The nonstop decay and the RNA silencing systems operate cooperatively in plants},
	url = {https://m2.mtmt.hu/api/publication/3370402},
	author = {Szádeczky-Kardoss, István and Csorba, Tibor and Auber, Andor and Schamberger, Anita and Nyikó, Tünde and Taller, János and Orbán, Tamás I. and Burgyán, József and Silhavy, Dániel},
	doi = {10.1093/nar/gky279},
	journal-iso = {NUCLEIC ACIDS RES},
	journal = {NUCLEIC ACIDS RESEARCH},
	volume = {46},
	unique-id = {3370402},
	issn = {0305-1048},
	abstract = {Translation-dependent mRNA quality control systems protect the protein homeostasis of eukaryotic cells by eliminating aberrant transcripts and stimulating the decay of their protein products. Although these systems are intensively studied in animals, little is known about the translation-dependent quality control systems in plants. Here, we characterize the mechanism of nonstop decay (NSD) system in Nicotiana benthamiana model plant. We show that plant NSD efficiently degrades nonstop mRNAs, which can be generated by premature polyadenylation, and stop codon-less transcripts, which are produced by endonucleolytic cleavage. We demonstrate that in plants, like in animals, Pelota, Hbs1 and SKI2 proteins are required for NSD, supporting that NSD is an ancient and conserved eukaryotic quality control system. Relevantly, we found that NSD and RNA silencing systems cooperate in plants. Plant silencing predominantly represses target mRNAs through endonucleolytic cleavage in the coding region. Here we show that NSD is required for the elimination of 5' cleavage product of mi- or siRNA-guided silencing complex when the cleavage occurs in the coding region. We also show that NSD and nonsense-mediated decay (NMD) quality control systems operate independently in plants.},
	year = {2018},
	eissn = {1362-4962},
	pages = {4632-4648},
	orcid-numbers = {Auber, Andor/0000-0001-8432-3760; Orbán, Tamás I./0000-0002-3424-3428}
}