TY - THES AU - Lima, Rui TI - A gümőspecifikus ciszteinben gazdag NCR peptidek evolúciója és funkcionális analízise PB - Szegedi Tudományegyetem PY - 2023 SP - 99 DO - 10.14232/phd.11682 UR - https://m2.mtmt.hu/api/publication/33762364 ID - 33762364 LA - Hungarian DB - MTMT ER - TY - JOUR AU - Nyerki, Emil AU - Kalmár, Tibor AU - Schütz, Oszkár AU - Lima, Rui AU - Neparáczki, Endre AU - Török, Tibor AU - Maróti, Zoltán TI - correctKin. an optimized method to infer relatedness up to the 4th degree from low-coverage ancient human genomes TS - an optimized method to infer relatedness up to the 4th degree from low-coverage ancient human genomes JF - GENOME BIOLOGY J2 - GENOME BIOL VL - 24 PY - 2023 IS - 1 PG - 21 SN - 1474-7596 DO - 10.1186/s13059-023-02882-4 UR - https://m2.mtmt.hu/api/publication/33677647 ID - 33677647 AB - Kinship analysis from very low-coverage ancient sequences has been possible up to the second degree with large uncertainties. We propose a new, accurate, and fast method, correctKin, to estimate the kinship coefficient and the confidence interval using low-coverage ancient data. We perform simulations and also validate correctKin on experimental modern and ancient data with widely different genome coverages (0.12×–11.9×) using samples with known family relations and known/unknown population structure. Based on our results, correctKin allows for the reliable identification of relatedness up to the 4th degree from variable/low-coverage ancient or badly degraded forensic whole genome sequencing data. LA - English DB - MTMT ER - TY - JOUR AU - ZHANG, Senlei AU - Wang, Ting AU - Lima, Rui AU - Pettkó-Szandtner, Aladár AU - Kereszt, Attila AU - Downie, J. Allan AU - Kondorosi, Éva TI - Widely conserved AHL transcription factors are essential for NCR gene expression and nodule development in Medicago JF - NATURE PLANTS J2 - NAT PLANTS VL - 9 PY - 2023 IS - 2 SP - 280 EP - 288 PG - 9 SN - 2055-026X DO - 10.1038/s41477-022-01326-4 UR - https://m2.mtmt.hu/api/publication/33560404 ID - 33560404 N1 - Funding Agency and Grant Number: International Balzan Foundation; Hungarian National Research, Development and Innovation Office [K128486]; Hungarian Academy of Sciences; China Scholarship Council fellowship; Frontline Research project [KKP129924] Funding text: We thank X. Li from the Huazhong Agricultural University for providing seeds of G. max cv. Williams 82 and for providing aid with the screening of target proteins in soybean. This work was supported by the Frontline Research project (KKP129924) and the Balzan Prize (2018) from the International Balzan Foundation to E.K.; OTKA grant (K128486) from the Hungarian National Research, Development and Innovation Office to A.K.; a visiting fellowship from the Hungarian Academy of Sciences to J. A. D; and the China Scholarship Council fellowship to S.Z. and T.W. AB - 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. LA - English DB - MTMT ER - TY - JOUR AU - Lima, Rui AU - Rathod, Balaji Baburao AU - Tiricz, Hilda AU - Howan, Dian Herlinda Octorina AU - Al Bouni, Mohamad Anas AU - Jenei, Sándor AU - Tímár, Edit AU - Endre, Gabriella AU - Tóth, Gábor AU - Kondorosi, Éva TI - Legume Plant Peptides as Sources of Novel Antimicrobial Molecules Against Human Pathogens JF - FRONTIERS IN MOLECULAR BIOSCIENCES J2 - FRONT MOL BIOSCI VL - 9 PY - 2022 PG - 12 SN - 2296-889X DO - 10.3389/fmolb.2022.870460 UR - https://m2.mtmt.hu/api/publication/32917591 ID - 32917591 N1 - Funding Agency and Grant Number: Hungarian National Office for Research, Development and Innovation (NKFIH) [KKP129924]; Balzan research grant Funding text: Research has been supported by the Hungarian National Office for Research, Development and Innovation (NKFIH) Frontline Research project KKP129924 and the Balzan research grant to EK. AB - Antimicrobial peptides are prominent components of the plant immune system acting against a wide variety of pathogens. Legume plants from the inverted repeat lacking clade (IRLC) have evolved a unique gene family encoding nodule-specific cysteine-rich NCR peptides acting in the symbiotic cells of root nodules, where they convert their bacterial endosymbionts into non-cultivable, polyploid nitrogen-fixing cells. NCRs are usually 30-50 amino acids long peptides having a characteristic pattern of 4 or 6 cysteines and highly divergent amino acid composition. While the function of NCRs is largely unknown, antimicrobial activity has been demonstrated for a few cationic Medicago truncatula NCR peptides against bacterial and fungal pathogens. The advantages of these plant peptides are their broad antimicrobial spectrum, fast killing modes of actions, multiple bacterial targets, and low propensity to develop resistance to them and no or low cytotoxicity to human cells. In the IRLC legumes, the number of NCR genes varies from a few to several hundred and it is possible that altogether hundreds of thousands of different NCR peptides exist. Due to the need for new antimicrobial agents, we investigated the antimicrobial potential of 104 synthetic NCR peptides from M. truncatula, M. sativa, Pisum sativum, Galega orientalis and Cicer arietinum against eight human pathogens, including ESKAPE bacteria. 50 NCRs showed antimicrobial activity with differences in the antimicrobial spectrum and effectivity. The most active peptides eliminated bacteria at concentrations from 0.8 to 3.1 mu M. High isoelectric point and positive net charge were important but not the only determinants of their antimicrobial activity. Testing the activity of shorter peptide derivatives against Acinetobacter baumannii and Candida albicans led to identification of regions responsible for the antimicrobial activity and provided insight into their potential modes of action. This work provides highly potent lead molecules without hemolytic activity on human blood cells for novel antimicrobial drugs to fight against pathogens. LA - English DB - MTMT ER - TY - JOUR AU - Lima, Rui AU - Kylarová, Salome AU - Mergaert, Peter AU - Kondorosi, Éva TI - Unexplored Arsenals of Legume Peptides With Potential for Their Applications in Medicine and Agriculture. JF - FRONTIERS IN MICROBIOLOGY J2 - FRONT MICROBIOL VL - 11 PY - 2020 SN - 1664-302X DO - 10.3389/fmicb.2020.01307 UR - https://m2.mtmt.hu/api/publication/31374676 ID - 31374676 N1 - Journal Article; Review Institute of Plant Biology, Biological Research Centre, Szeged, Hungary Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France Export Date: 9 July 2020 Correspondence Address: Kondorosi, E.; Institute of Plant Biology, Biological Research CentreHungary; email: eva.kondorosi@gmail.com Chemicals/CAS: colistin, 1066-17-7, 1264-72-8; cysteine, 4371-52-2, 52-89-1, 52-90-4; gamma interferon, 82115-62-6 Funding details: Nemzeti Kutatási Fejlesztési és Innovációs Hivatal, NKFI, GINOP 2.3.2-15-2016-00015 I-KOM, KKP129924 Funding text 1: Funding. This work was supported by the Hungarian National Office for Research, Development and Innovation (NKFIH) GINOP 2.3.2-15-2016-00014 Evomer, GINOP 2.3.2-15-2016-00015 I-KOM and the Frontline Research project KKP129924 and the Balzan research grant to ?K. Institute of Plant Biology, Biological Research Centre, Szeged, Hungary Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France Cited By :1 Export Date: 22 October 2020 Correspondence Address: Kondorosi, E.; Institute of Plant Biology, Biological Research CentreHungary; email: eva.kondorosi@gmail.com Institute of Plant Biology, Biological Research Centre, Szeged, Hungary Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France Cited By :1 Export Date: 9 February 2021 Correspondence Address: Kondorosi, E.; Institute of Plant Biology, Hungary; email: eva.kondorosi@gmail.com Institute of Plant Biology, Biological Research Centre, Szeged, Hungary Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France Cited By :3 Export Date: 26 April 2021 Correspondence Address: Kondorosi, E.; Institute of Plant Biology, Hungary; email: eva.kondorosi@gmail.com Institute of Plant Biology, Biological Research Centre, Szeged, Hungary Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France Cited By :3 Export Date: 1 May 2021 Correspondence Address: Kondorosi, E.; Institute of Plant Biology, Hungary; email: eva.kondorosi@gmail.com AB - During endosymbiosis, bacteria live intracellularly in the symbiotic organ of their host. The host controls the proliferation of endosymbionts and prevents their spread to other tissues and organs. In Rhizobium-legume symbiosis the major host effectors are secreted nodule-specific cysteine-rich (NCR) peptides, produced exclusively in the symbiotic cells. NCRs have evolved in the Inverted Repeat Lacking Clade (IRLC) of the Leguminosae family. They are secreted peptides that mediate terminal differentiation of the endosymbionts, forming polyploid, non-cultivable cells with increased membrane permeability. NCRs form an extremely large family of peptides, which have four or six conserved cysteines but otherwise highly diverse amino acid sequences, resulting in a wide variety of anionic, neutral and cationic peptides. In vitro, many synthetic NCRs have strong antimicrobial activities against both Gram-negative and Gram-positive bacteria, including the ESKAPE strains and pathogenic fungi. The spectra and minimal bactericidal and anti-fungal concentrations of NCRs differ, indicating that, in addition to their charge, the amino acid composition and sequence also play important roles in their antimicrobial activity. NCRs attack the bacteria and fungi at the cell envelope and membrane as well as intracellularly, forming interactions with multiple essential cellular machineries. NCR-like peptides with similar symbiotic functions as the NCRs also exist in other branches of the Leguminosae family. Thus, legumes provide countless and so far unexplored sources of symbiotic peptides representing an enormous resource of pharmacologically interesting molecules. LA - English DB - MTMT ER - TY - JOUR AU - Jenei, Sándor AU - Tiricz, Hilda AU - Szolomájer, János AU - Tímár, Edit AU - Klement, Éva AU - Al Bouni, Mohamad Anas AU - Lima, Rui AU - Kata, Diána AU - Harmati, Mária AU - Buzás, Krisztina AU - Földesi, Imre AU - Tóth, Gábor AU - Endre, Gabriella AU - Kondorosi, Éva TI - Potent Chimeric Antimicrobial Derivatives of the Medicago truncatula NCR247 Symbiotic Peptide JF - FRONTIERS IN MICROBIOLOGY J2 - FRONT MICROBIOL VL - 11 PY - 2020 PG - 10 SN - 1664-302X DO - 10.3389/fmicb.2020.00270 UR - https://m2.mtmt.hu/api/publication/31281264 ID - 31281264 N1 - Funding Agency and Grant Number: Hungarian National Office for Research, Development and Innovation (NKFIH) [GINOP 2.3.2-15-2016-00014 Evomer, GINOP 2.3.2-15-2016-00015 I-KOM, GINOP-2.3.2-15-2016-00001, GINOP-2.3.2-15-2016-00020]; ERCEuropean Research Council (ERC) [269067]; NKFIH Frontline Research project [KKP129924]; Balzan research grant; [TUDFO/47138-1/2019-ITM FIKP]; [20391-3/2018/FEKUSTRAT] Funding text: Research has been supported by the Hungarian National Office for Research, Development and Innovation (NKFIH) through the grants GINOP 2.3.2-15-2016-00014 Evomer and GINOP 2.3.2-15-2016-00015 I-KOM, GINOP-2.3.2-15-2016-00001, GINOP-2.3.2-15-2016-00020; and by the ERC Advanced Grant 269067 "SymBiotics," the NKFIH Frontline Research project KKP129924 and the Balzan research grant to EKo; as well as by grants TUDFO/47138-1/2019-ITM FIKP and 20391-3/2018/FEKUSTRAT to GT. Institute of Plant Biology, Biological Research Centre, Szeged, Hungary Department of Medical Chemistry, University of Szeged, Szeged, Hungary Institute of Biochemistry, Biological Research Centre, Szeged, Hungary Department of Laboratory Medicine, University of Szeged, Szeged, Hungary Department of Oral Biology and Experimental Dental Research, University of Szeged, Szeged, Hungary MTA-SZTE Biomimetic Systems Research Group, University of Szeged, Szeged, Hungary Cited By :2 Export Date: 9 February 2021 Correspondence Address: Endre, G.; Institute of Plant Biology, Hungary; email: endre.gabriella@brc.hu Institute of Plant Biology, Biological Research Centre, Szeged, Hungary Department of Medical Chemistry, University of Szeged, Szeged, Hungary Institute of Biochemistry, Biological Research Centre, Szeged, Hungary Department of Laboratory Medicine, University of Szeged, Szeged, Hungary Department of Oral Biology and Experimental Dental Research, University of Szeged, Szeged, Hungary MTA-SZTE Biomimetic Systems Research Group, University of Szeged, Szeged, Hungary Cited By :3 Export Date: 1 May 2021 Correspondence Address: Endre, G.; Institute of Plant Biology, Hungary; email: endre.gabriella@brc.hu AB - In Rhizobium-legume symbiosis, the bacteria are converted into nitrogen-fixing bacteroids. In many legume species, differentiation of the endosymbiotic bacteria is irreversible, culminating in definitive loss of their cell division ability. This terminal differentiation is mediated by plant peptides produced in the symbiotic cells. In Medicago truncatula more than similar to 700 nodule-specific cysteine-rich (NCR) peptides are involved in this process. We have shown previously that NCR247 and NCR335 have strong antimicrobial activity on various pathogenic bacteria and identified interaction of NCR247 with many bacterial proteins, including FtsZ and several ribosomal proteins, which prevent bacterial cell division and protein synthesis. In this study we designed and synthetized various derivatives of NCR247, including shorter fragments and various chimeric derivatives. The antimicrobial activity of these peptides was tested on the ESKAPE bacteria; Enterococcus faecalis, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli as a member of Enterobacteriaceae and in addition Listeria monocytogenes and Salmonella enterica. The 12 amino acid long C-terminal half of NCR247, NCR247C partially retained the antimicrobial activity and preserved the multitarget interactions with partners of NCR247. Nevertheless NCR247C became ineffective on S. aureus, P. aeruginosa, and L. monocytogenes. The chimeric derivatives obtained by fusion of NCR247C with other peptide fragments and particularly with a truncated mastoparan sequence significantly increased bactericidal activity and altered the antimicrobial spectrum. The minimal bactericidal concentration of the most potent derivatives was 1.6 mu M, which is remarkably lower than that of most classical antibiotics. The killing activity of the NCR247-based chimeric peptides was practically instant. Importantly, these peptides had no hemolytic activity or cytotoxicity on human cells. The properties of these NCR derivatives make them promising antimicrobials for clinical use. LA - English DB - MTMT ER - TY - JOUR AU - Farkas, Attila AU - Maróti, Gergely AU - Dürgő, Hajnalka AU - Györgypál, Zoltán AU - Lima, Rui AU - Medzihradszky F., Katalin AU - Kereszt, Attila AU - Mergaert, P AU - Kondorosi, Éva TI - Medicago truncatula symbiotic peptide NCR247 contributes to bacteroid differentiation through multiple mechanisms JF - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA J2 - P NATL ACAD SCI USA VL - 111 PY - 2014 IS - 14 SP - 5183 EP - 5188 PG - 6 SN - 0027-8424 DO - 10.1073/pnas.1404169111 UR - https://m2.mtmt.hu/api/publication/2583121 ID - 2583121 N1 - Cited By :100 Export Date: 3 August 2022 CODEN: PNASA AB - Symbiosis between rhizobia soil bacteria and legume plants results in the formation of root nodules where plant cells are fully packed with nitrogen fixing bacteria. In the host cells, the bacteria adapt to the intracellular environment and gain the ability for nitrogen fixation. Depending on the host plants, the symbiotic fate of bacteria can be either reversible or irreversible. In Medicago and related legume species, the bacteria undergo a host-directed multistep differentiation process culminating in the formation of elongated and branched polyploid bacteria with definitive loss of cell division ability. The plant factors are nodule-specific symbiotic peptides. Approximately 600 of them are nodule-specific cysteine-rich (NCR) peptides produced in the rhizobium-infected plant cells. NCRs are targeted to the endosymbionts, and concerted action of different sets of peptides governs different stages of endosymbiont maturation, whereas the symbiotic function of individual NCRs is unknown. This study focused on NCR247, a cationic peptide exhibiting in vitro antimicrobial activities. We show that NCR247 acts in those nodule cells where bacterial cell division is arrested and cell elongation begins. NCR247 penetrates the bacteria and forms complexes with many bacterial proteins. Interaction with FtsZ required for septum formation is one of the host interventions for inhibiting bacterial cell division. Complex formation with the ribosomal proteins affects translation and contributes to altered proteome and physiology of the endosymbiont. Binding to the chaperone GroEL amplifies the NCR247-modulated biological processes. We show that GroEL1 of Sinorhizobium meliloti is required for efficient infection, terminal differentiation, and nitrogen fixation. LA - English DB - MTMT ER - TY - JOUR AU - Tiricz, Hilda AU - Szűcs, Attila AU - Farkas, Attila AU - Pap, Bernadett AU - Lima, Rui AU - Maróti, Gergely AU - Kondorosi, Éva AU - Kereszt, Attila TI - Antimicrobial Nodule-Specific Cysteine-Rich Peptides Induce Membrane Depolarization-Associated Changes in the Transcriptome of Sinorhizobium meliloti. JF - APPLIED AND ENVIRONMENTAL MICROBIOLOGY J2 - APPL ENVIRON MICROB VL - 79 PY - 2013 IS - 21 SP - 6737 EP - 6746 PG - 10 SN - 0099-2240 DO - 10.1128/AEM.01791-13 UR - https://m2.mtmt.hu/api/publication/2448433 ID - 2448433 AB - Leguminous plants establish symbiosis with nitrogen-fixing alpha- and betaproteobacteria, collectively called rhizobia, which provide combined nitrogen to support plant growth. Members of the inverted repeat-lacking clade of legumes impose terminal differentiation on their endosymbiotic bacterium partners with the help of the nodule-specific cysteine-rich (NCR) peptide family composed of close to 600 members. Among the few tested NCR peptides, cationic ones had antirhizobial activity measured by reduction or elimination of the CFU and uptake of the membrane-impermeable dye propidium iodide. Here, the antimicrobial spectrum of two of these peptides, NCR247 and NCR335, was investigated, and their effect on the transcriptome of the natural target Sinorhizobium meliloti was characterized. Both peptides were able to kill quickly a wide range of Gram-negative and Gram-positive bacteria; however, their spectra were only partially overlapping, and differences were found also in their efficacy on given strains, indicating that the actions of NCR247 and NCR335 might be similar though not identical. Treatment of S. meliloti cultures with either peptide resulted in a quick downregulation of genes involved in basic cellular functions, such as transcription-translation and energy production, as well as upregulation of genes involved in stress and oxidative stress responses and membrane transport. Similar changes provoked mainly in Gram-positive bacteria by antimicrobial agents were coupled with the destruction of membrane potential, indicating that it might also be a common step in the bactericidal actions of NCR247 and NCR335. LA - English DB - MTMT ER -