@article{MTMT:34154576,
	title = {Epitomics: Analysis of Plasma C9 Epitope Heterogeneity in the Plasma of Lung Cancer Patients and Control Subjects},
	url = {https://m2.mtmt.hu/api/publication/34154576},
	author = {Tornyi, Ilona and Lazar, Jozsef and Pettkó-Szandtner, Aladár and Hunyadi-Gulyás Éva, Csilla and Takács, László Kristóf},
	doi = {10.3390/ijms241814359},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {24},
	unique-id = {34154576},
	issn = {1661-6596},
	abstract = {The human proteome is more complex than the genetic code predicts it to be. Epitomics, or protein epitome profiling, is a tool for understanding sub-protein level variation. With the ultimate goal to explore C9 proteoforms and their relevance to lung cancer, here we report plasma C9 epitope-associated molecular heterogeneity in plasma samples of lung cancer patients and control subjects. We show three C9 epitopes (BSI0449, BSI0581, BSI0639) with markedly different association with lung cancer (“unaltered”, “upregulated” and “downregulated”). In order to exclude confounding effects, we show first that the three epitope-defining mAbs recognize C9 in purified form and in the natural context, in the human plasma. Then, we present data demonstrating the lack of major epitope interdependence or overlap. The next experiments represent a quest toward the understanding of the molecular basis of apparent disparate association with lung cancer. Using immunochemistry, SDS PAGE and LC-MS/MS technologies, we demonstrate that epitope-specific immunoprecipitates of plasma C9 seem identical regarding peptide sequence. However, we found epitope-specific posttranslational modification and coprecipitated protein composition differences with respect to control and lung cancer plasma. Epitope profiling enabled the classification of hypothetical C9 proteoforms through differential association with lung cancer.},
	year = {2023},
	eissn = {1422-0067}
}

@article{MTMT:33846356,
	title = {Reconsidering Dogmas about the Growth of Bacterial Populations},
	url = {https://m2.mtmt.hu/api/publication/33846356},
	author = {Ughy, Bettina and Nagyapáti, Sarolta and Lajkó, Dézi Bianka and Letoha, Tamas and Prohaszka, Adam and Deeb, Dima and Dér, András and Pettkó-Szandtner, Aladár and Szilák, László},
	doi = {10.3390/cells12101430},
	journal-iso = {CELLS-BASEL},
	journal = {CELLS},
	volume = {12},
	unique-id = {33846356},
	abstract = {The growth of bacterial populations has been described as a dynamic process of continuous reproduction and cell death. However, this is far from the reality. In a well fed, growing bacterial population, the stationary phase inevitably occurs, and it is not due to accumulated toxins or cell death. A population spends the most time in the stationary phase, where the phenotype of the cells alters from the proliferating ones, and only the colony forming unit (CFU) decreases after a while, not the total cell concentration. A bacterial population can be considered as a virtual tissue as a result of a specific differentiation process, in which the exponential-phase cells develop to stationary-phase cells and eventually reach the unculturable form. The richness of the nutrient had no effect on growth rate or on stationary cell density. The generation time seems not to be a constant value, but it depended on the concentration of the starter cultures. Inoculations with serial dilutions of stationary populations reveal a so-called minimal stationary cell concentration (MSCC) point, up to which the cell concentrations remain constant upon dilutions; that seems to be universal among unicellular organisms.},
	year = {2023},
	eissn = {2073-4409},
	orcid-numbers = {Letoha, Tamas/0000-0002-6035-4009; Prohaszka, Adam/0000-0002-2390-2387}
}

@article{MTMT:33630992,
	title = {Syndecan-4 Mediates the Cellular Entry of Adeno-Associated Virus 9},
	url = {https://m2.mtmt.hu/api/publication/33630992},
	author = {Hudák, Anett and Roach, Matthew and Pusztai, Dávid and Pettkó-Szandtner, Aladár and Letoha, Annamária and Szilák, László and Azzouz, Mimoun and Letoha, Tamás},
	doi = {10.3390/ijms24043141},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {24},
	unique-id = {33630992},
	issn = {1661-6596},
	abstract = {Due to their low pathogenicity, immunogenicity, and long-term gene expression, adeno-associated virus (AAV) vectors emerged as safe and efficient gene delivery tools, over-coming setbacks experienced with other viral gene delivery systems in early gene therapy trials. Among AAVs, AAV9 can translocate through the blood-brain barrier (BBB), making it a promising gene delivery tool for transducing the central nervous system (CNS) via systemic administration. Recent reports on the shortcomings of AAV9-mediated gene delivery into the CNS require reviewing the molecular base of AAV9 cellular biology. A more detailed understanding of AAV9’s cellular entry would eradicate current hurdles and enable more efficient AAV9-based gene therapy approaches. Syndecans, the transmembrane family of heparan-sulfate proteoglycans, facilitate the cellular uptake of various viruses and drug delivery systems. Utilizing human cell lines and syndecan-specific cellular assays, we assessed the involvement of syndecans in AAV9’s cellular entry. The ubiquitously expressed isoform, syndecan-4 proved its superiority in facilitating AAV9 internalization among syndecans. Introducing syndecan-4 into poorly transducible cell lines enabled robust AAV9-dependent gene transduction, while its knockdown reduced AAV9’s cellular entry. Attachment of AAV9 to syndecan-4 is mediated not just by the polyanionic heparan-sulfate chains but also by the cell-binding domain of the extracellular syndecan-4 core protein. Co-immunoprecipitation assays and affinity proteomics also confirmed the role of syndecan-4 in the cellular entry of AAV9. Overall, our findings highlight the universally expressed syndecan-4 as a significant contributor to the cellular internalization of AAV9 and provide a molecular-based, rational explanation for the low gene delivery potential of AAV9 into the CNS.},
	year = {2023},
	eissn = {1422-0067},
	orcid-numbers = {Letoha, Tamás/0000-0002-6035-4009}
}

@article{MTMT:33560404,
	title = {Widely conserved AHL transcription factors are essential for NCR gene expression and nodule development in Medicago},
	url = {https://m2.mtmt.hu/api/publication/33560404},
	author = {ZHANG, Senlei and Wang, Ting and Lima, Rui and Pettkó-Szandtner, Aladár and Kereszt, Attila and Downie, J. Allan and Kondorosi, Éva},
	doi = {10.1038/s41477-022-01326-4},
	journal-iso = {NAT PLANTS},
	journal = {NATURE PLANTS},
	volume = {9},
	unique-id = {33560404},
	issn = {2055-026X},
	abstract = {Symbiotic nitrogen fixation by Rhizobium bacteria in the cells of legume root nodules alleviates the need for nitrogen fertilizers. Nitrogen fixation requires the endosymbionts to differentiate into bacteroids which can be reversible or terminal. The latter is controlled by the plant, it is more beneficial and has evolved in multiple clades of the Leguminosae family. The plant effectors of terminal differentiation in inverted repeat-lacking clade legumes (IRLC) are nodule-specific cysteine-rich (NCR) peptides, which are absent in legumes such as soybean where there is no terminal differentiation of rhizobia. It was assumed that NCR s co-evolved with specific transcription factors, but our work demonstrates that expression of NCR genes does not require NCR -specific transcription factors. Introduction of the Medicago truncatula NCR169 gene under its own promoter into soybean roots resulted in its nodule-specific expression, leading to bacteroid changes associated with terminal differentiation. We identified two AT-Hook Motif Nuclear Localized (AHL) transcription factors from both M. truncatula and soybean nodules that bound to AT-rich sequences in the NCR169 promoter inducing its expression. Whereas mutation of NCR169 arrested bacteroid development at a late stage, the absence of MtAHL1 or MtAHL2 completely blocked bacteroid differentiation indicating that they also regulate other NCR genes required for the development of nitrogen-fixing nodules. Regulation of NCR s by orthologous transcription factors in non-IRLC legumes opens up the possibility of increasing the efficiency of nitrogen fixation in legumes lacking NCR s.},
	year = {2023},
	eissn = {2055-0278},
	pages = {280-288},
	orcid-numbers = {Downie, J. Allan/0000-0003-1011-4960; Kondorosi, Éva/0000-0002-4065-8515}
}

@article{MTMT:33127391,
	title = {A systems biological analysis of the ATF4-GADD34-CHOP regulatory triangle upon endoplasmic reticulum stress},
	url = {https://m2.mtmt.hu/api/publication/33127391},
	author = {Márton, Margita and Bánhegyi, Gábor and Gyöngyösi, Norbert and Kálmán, Eszter Éva and Pettkó-Szandtner, Aladár and Káldi, Krisztina and Kapuy, Orsolya},
	doi = {10.1002/2211-5463.13484},
	journal-iso = {FEBS OPEN BIO},
	journal = {FEBS OPEN BIO},
	volume = {12},
	unique-id = {33127391},
	issn = {2211-5463},
	abstract = {Endoplasmic reticulum (ER) stress-dependent accumulation of incorrectly folded proteins leads to activation of the unfolded protein response. The role of the unfolded protein response (UPR) is to avoid cell damage and restore the homeostatic state by autophagy; however, excessive ER stress results in apoptosis. Here we investigated the ER stress-dependent feedback loops inside one of the UPR branches by focusing on PERK-induced ATF4 and its two targets, called CHOP and GADD34. Our goal was to qualitatively describe the dynamic behavior of the system by exploring the key regulatory motifs using both molecular and theoretical biological techniques. Using the HEK293T cell line as a model system, we confirmed that the life-or-death decision is strictly regulated. We investigated the dynamic characteristics of the crucial elements of the PERK pathway at both the RNA and protein level upon tolerable and excessive levels of ER stress. Of particular note, inhibition of GADD34 or CHOP resulted in various phenotypes upon high levels of ER stress. Our computer simulations suggest the existence of two new feedback loops inside the UPR. First, GADD34 seems to have a positive effect on ATF4 activity, while CHOP inhibits it. We claim that these newly described feedback loops ensure the fine-tuning of the ATF4-dependent stress response mechanism of the cell. © 2022 The Authors. FEBS Open Bio published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.},
	keywords = {Systems biology; Endoplasmic reticulum stress; Unfolded protein response; FEEDBACK LOOP; ATF4-GADD34-CHOP; PERK pathway},
	year = {2022},
	eissn = {2211-5463},
	pages = {2065-2082},
	orcid-numbers = {Márton, Margita/0000-0002-3530-9695; Bánhegyi, Gábor/0000-0001-7559-0066; Kálmán, Eszter Éva/0000-0002-5839-3420; Káldi, Krisztina/0000-0002-5724-0182; Kapuy, Orsolya/0000-0002-8484-4504}
}

@article{MTMT:33114978,
	title = {A Novel BRET-Based GAP assay reveals phosphorylation-dependent regulation of the RAC-specific GTPase activating protein ARHGAP25},
	url = {https://m2.mtmt.hu/api/publication/33114978},
	author = {Wisniewski, Éva and Czárán, Domonkos Tamás and Kovács, Fanni and Bahurek, Enikő and Németh, Afrodité and Sasvári, Péter and Szanda, Gergő and Pettkó-Szandtner, Aladár and Klement, Éva and Ligeti, Erzsébet and Csépányi-Kömi, Roland},
	doi = {10.1096/fj.202200689R},
	journal-iso = {FASEB J},
	journal = {FASEB JOURNAL},
	volume = {36},
	unique-id = {33114978},
	issn = {0892-6638},
	year = {2022},
	eissn = {1530-6860},
	orcid-numbers = {Wisniewski, Éva/0000-0001-8698-6867; Szanda, Gergő/0000-0002-1308-7593; Ligeti, Erzsébet/0000-0001-6374-729X; Csépányi-Kömi, Roland/0000-0001-6825-7142}
}

@article{MTMT:33050457,
	title = {Biodistribution and Cellular Internalization of Inactivated SARS-CoV-2 in Wild-Type Mice},
	url = {https://m2.mtmt.hu/api/publication/33050457},
	author = {Hudak, Anett and Morgan, Gareth and Bacovsky, Jaromir and Patai, Roland and Polgár, Tamás Ferenc and Letoha, Annamaria and Pettkó-Szandtner, Aladár and Vizler, Csaba and Szilák, László and Letoha, Tamás},
	doi = {10.3390/ijms23147609},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {23},
	unique-id = {33050457},
	issn = {1661-6596},
	abstract = {Despite the growing list of identified SARS-CoV-2 receptors, the human angiotensin-converting enzyme 2 (ACE2) is still viewed as the main cell entry receptor mediating SARS-CoV-2 internalization. It has been reported that wild-type mice, like other rodent species of the Muridae family, cannot be infected with SARS-CoV-2 due to differences in their ACE2 receptors. On the other hand, the consensus heparin-binding motif of SARS-CoV-2's spike protein, PRRAR, enables the attachment to rodent heparan sulfate proteoglycans (HSPGs), including syndecans, a transmembrane HSPG family with a well-established role in clathrin- and caveolin-independent endocytosis. As mammalian syndecans possess a relatively conserved structure, we analyzed the cellular uptake of inactivated SARS-CoV-2 particles in in vitro and in vivo mice models. Cellular studies revealed efficient uptake into murine cell lines with established syndecan-4 expression. After intravenous administration, inactivated SARS-CoV-2 was taken up by several organs in vivo and could also be detected in the brain. Internalized by various tissues, inactivated SARS-CoV-2 raised tissue TNF-alpha levels, especially in the heart, reflecting the onset of inflammation. Our studies on in vitro and in vivo mice models thus shed light on unknown details of SARS-CoV-2 internalization and help broaden the understanding of the molecular interactions of SARS-CoV-2.},
	keywords = {MECHANISMS; PROTEIN; MEMBRANE; IMMUNODEFICIENCY-VIRUS TYPE-1; ENDOCYTOSIS; Proteoglycans; Heparan Sulfate Proteoglycans; CELLULAR UPTAKE; Syndecans; Syndecans; Biochemistry & Molecular Biology; COVID-19; SARS-CoV-2; ARGININE-RICH PEPTIDES},
	year = {2022},
	eissn = {1422-0067},
	orcid-numbers = {Letoha, Tamás/0000-0002-6035-4009}
}

@article{MTMT:32824513,
	title = {Effector-mediated relocalization of a maize lipoxygenase protein triggers susceptibility to Ustilago maydis},
	url = {https://m2.mtmt.hu/api/publication/32824513},
	author = {Saado, Indira and Chia, Khong-Sam and Betz, Ruben and Alcantara, Andre and Pettkó-Szandtner, Aladár and Navarrete, Fernando and D'Auria, John C. and Kolomiets, Michael V and Melzer, Michael and Feussner, Ivo and Djamei, Armin},
	doi = {10.1093/plcell/koac105},
	journal-iso = {PLANT CELL},
	journal = {PLANT CELL},
	volume = {34},
	unique-id = {32824513},
	issn = {1040-4651},
	abstract = {As the gall-inducing smut fungus Ustilago maydis colonizes maize (Zea mays) plants, it secretes a complex effector blend that suppresses host defense responses, including production of reactive oxygen species (ROS) and redirects host metabolism to facilitate colonization. We show that the U. maydis effector ROS burst interfering protein 1 (Rip1), which is involved in pathogen-associated molecular pattern (PAMP)-triggered suppression of host immunity, is functionally conserved in several other monocot-infecting smut fungi. We also have identified a conserved C-terminal motif essential for Rip1-mediated PAMP-triggered suppression of the ROS burst. The maize susceptibility factor lipoxygenase 3 (Zmlox3) bound by Rip1 was relocalized to the nucleus, leading to partial suppression of the ROS burst. Relocalization was independent of its enzymatic activity, revealing a distinct function for ZmLox3. Most importantly, whereas Zmlox3 maize mutant plants showed increased resistance to U. maydis wild-type strains, rip1 deletion strains infecting the Zmlox3 mutant overcame this effect. This could indicate that Rip1-triggered host resistance depends on ZmLox3 to be suppressed and that lox3 mutation-based resistance of maize to U. maydis requires functional Rip1. Together, our results reveal that Rip1 acts in several cellular compartments to suppress immunity and that targeting of ZmLox3 by Rip1 is responsible for the suppression of Rip1-dependent reduced susceptibility of maize to U. maydis. The fungal effector Rip1, which inhibits pattern-triggered immunity, relocalizes maize lipoxygenase 3 to the plant nucleus, suppressing ROS burst responses in the host that are triggered by pathogen recognition.},
	keywords = {STRUCTURAL BASIS; PLANT; Defense; SUBCELLULAR-LOCALIZATION; Biochemistry & Molecular Biology; Plant Sciences; 5-Lipoxygenase; Pathogen effectors; INCREASED RESISTANCE; OXYLIPIN PATHWAYS; 9-LIPOXYGENASE},
	year = {2022},
	eissn = {1532-298X},
	pages = {2785-2805},
	orcid-numbers = {D'Auria, John C./0000-0002-4865-3938; Kolomiets, Michael V/0000-0003-1038-9534; Melzer, Michael/0000-0002-5213-4030; Feussner, Ivo/0000-0002-9888-7003}
}

@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:32475639,
	title = {The DREAM complex represses growth in response to DNA damage in Arabidopsis},
	url = {https://m2.mtmt.hu/api/publication/32475639},
	author = {Lang, L. and Pettkó-Szandtner, Aladár and Elbasi, H.T. and Takatsuka, H. and Nomoto, Y. and Zaki, A. and Dorokhov, S. and De, Jaeger G. and Eeckhout, D. and Ito, M. and Magyar, Zoltán and Bögre, L. and Heese, M. and Schnittger, A.},
	doi = {10.26508/lsa.202101141},
	journal-iso = {LIFE SCI ALLIANCE},
	journal = {LIFE SCIENCE ALLIANCE},
	volume = {4},
	unique-id = {32475639},
	abstract = {The DNA of all organisms is constantly damaged by physiological processes and environmental conditions. Upon persistent damage, plant growth and cell proliferation are reduced. Based on previous findings that RBR1, the only Arabidopsis homolog of the mammalian tumor suppressor gene retinoblastoma, plays a key role in the DNA damage response in plants, we unravel here the network of RBR1 interactors under DNA stress conditions. This led to the identification of homologs of every DREAM component in Arabidopsis, including previously not recognized homologs of LIN52. Interestingly, we also discovered NAC044, a mediator of DNA damage response in plants and close homolog of the major DNA damage regulator SOG1, to directly interact with RBR1 and the DREAM component LIN37B. Consistently, not only mutants in NAC044 but also the double mutant of the two LIN37 homologs and mutants for the DREAM component E2FB showed reduced sensitivities to DNA-damaging conditions. Our work indicates the existence of multiple DREAM complexes that work in conjunction with NAC044 to mediate growth arrest after DNA damage. © 2021 Rockefeller University Press. All rights reserved.},
	year = {2021},
	eissn = {2575-1077}
}