TY - JOUR AU - Vedelek, Viktor AU - Jankovics, Ferenc AU - Zádori, János AU - Sinka, Rita TI - Mitochondrial Differentiation during Spermatogenesis: Lessons from Drosophila melanogaster JF - INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES J2 - INT J MOL SCI VL - 25 PY - 2024 IS - 7 PG - 25 SN - 1661-6596 DO - 10.3390/ijms25073980 UR - https://m2.mtmt.hu/api/publication/34772438 ID - 34772438 N1 - Funding Agency and Grant Number: National Research, Development and Innovation Office Funding text: No Statement Available AB - Numerous diseases can arise as a consequence of mitochondrial malfunction. Hence, there is a significant focus on studying the role of mitochondria in cancer, ageing, neurodegenerative diseases, and the field of developmental biology. Mitochondria could exist as discrete organelles in the cell; however, they have the ability to fuse, resulting in the formation of interconnected reticular structures. The dynamic changes between these forms correlate with mitochondrial function and mitochondrial health, and consequently, there is a significant scientific interest in uncovering the specific molecular constituents that govern these transitions. Moreover, the specialized mitochondria display a wide array of variable morphologies in their cristae formations. These inner mitochondrial structures are closely associated with the specific functions performed by the mitochondria. In multiple cases, the presence of mitochondrial dysfunction has been linked to male sterility, as it has been observed to cause a range of abnormal spermatogenesis and sperm phenotypes in different species. This review aims to elucidate the dynamic alterations and functions of mitochondria in germ cell development during the spermatogenesis of Drosophila melanogaster. LA - English DB - MTMT ER - TY - GEN AU - Gulyás, Gábor AU - Kakuk, Balázs AU - Dörmő, Ákos AU - Járay, Tamás Flórián AU - Prazsák, István AU - Csabai, Zsolt AU - Miksa, Máté Henkrich AU - Boldogkői, Zsolt AU - Tombácz, Dóra TI - Cross-Comparison of Gut Metagenomic Profiling Strategies PY - 2024 UR - https://m2.mtmt.hu/api/publication/34670012 ID - 34670012 LA - English DB - MTMT ER - TY - JOUR AU - Prazsák, István AU - Tombácz, Dóra AU - Fülöp, Ádám AU - Torma, Gábor AU - Gulyás, Gábor AU - Dörmő, Ákos AU - Kakuk, Balázs AU - McKenzie, Spires Lauren AU - Toth, Zsolt AU - Boldogkői, Zsolt TI - KSHV 3.0. A State-of-the-Art Annotation of the Kaposi’s Sarcoma-Associated Herpesvirus Transcriptome Using Cross-Platform Sequencing TS - A State-of-the-Art Annotation of the Kaposi’s Sarcoma-Associated Herpesvirus Transcriptome Using Cross-Platform Sequencing JF - MSYSTEMS J2 - MSYSTEMS VL - 9 PY - 2024 IS - 2 PG - 19 SN - 2379-5077 DO - 10.1128/msystems.01007-23 UR - https://m2.mtmt.hu/api/publication/34430917 ID - 34430917 LA - English DB - MTMT ER - TY - JOUR AU - Lee, See-Chi AU - Naik, Nenavath Gopal AU - Tombácz, Dóra AU - Gulyás, Gábor AU - Kakuk, Balázs AU - Boldogkői, Zsolt AU - Hall, Kevin AU - Papp, Bernadett AU - Boulant, Steeve AU - Toth, Zsolt TI - Hypoxia and HIF-1α promote lytic de novo KSHV infection JF - JOURNAL OF VIROLOGY J2 - J VIROL VL - 97 PY - 2023 IS - 11 PG - 18 SN - 0022-538X DO - 10.1128/jvi.00972-23 UR - https://m2.mtmt.hu/api/publication/34402081 ID - 34402081 AB - The impact of different stress conditions on the oncogenic Kaposi's sarcoma-associated herpesvirus (KSHV) primary infection that can occur in vivo remains largely unknown. We hypothesized that KSHV can establish a latency or lytic cycle following de novo infection, depending on the conditions of the cellular environment. Previous studies showed that hypoxia is a natural stress condition that promotes lytic reactivation and contributes to KSHV pathogenesis, but its effect on de novo KSHV infection is unknown. To test the effect of hypoxia on KSHV infection, we infected cells under normoxia and hypoxia, performed a comparative analysis of viral gene expression and viral replication, and tested chromatinization of the KSHV genome during infection. We found that hypoxia induces viral lytic gene expression and viral replication following de novo infection in several biologically relevant cell types, in which the virus normally establishes latency under normoxia. We also found that hypoxia reduces the level of repressive heterochromatin and promotes the formation of a transcriptionally permissive chromatin on the incoming viral DNA during infection. We demonstrate that silencing hypoxia-inducible factor-1 alpha (HIF-1 alpha) during hypoxia abrogates lytic KSHV infection, while the overexpression of HIF-1 alpha under normoxia is sufficient to drive lytic KSHV infection. Also, we determined that the DNA-binding domain and the N-terminal but not the C-terminal transactivation domain of HIF-1 alpha are required for HIF-1 alpha-induced lytic gene expression. Altogether, our data indicate that HIF-1 alpha accumulation, which can be induced by hypoxia, prevents the establishment of latency and promotes lytic KSHV infection following primary infection. LA - English DB - MTMT ER - TY - GEN AU - Torma, Gábor AU - Tombácz, Dóra AU - Almsarrhad, Islam AU - Csabai, Zsolt AU - Nagy, Gergely Ármin AU - Kakuk, Balázs AU - Gulyás, Gábor AU - Lauren, McKenzie Spires AU - Ishaan, Gupta AU - Fülöp, Ádám AU - Dörmő, Ákos AU - Prazsák, István AU - Mizik, Máté Levente AU - Dani, Virág Éva AU - Csányi, Viktor AU - Zoltán, Zádori AU - Zsolt, Toth AU - Boldogkői, Zsolt TI - Novel Herpesvirus Transcripts with Putative Regulatory Roles in DNA Replication and Global Transcription PY - 2023 PG - 37 UR - https://m2.mtmt.hu/api/publication/34186518 ID - 34186518 LA - English DB - MTMT ER - TY - JOUR AU - Torma, Gábor AU - Tombácz, Dóra AU - Csabai, Zsolt AU - Almsarrhad, Islam AU - Nagy, Gergely Ármin AU - Kakuk, Balázs AU - Gulyás, Gábor AU - Spires, Lauren McKenzie AU - Gupta, Ishaan AU - Fülöp, Ádám AU - Dörmő, Ákos AU - Prazsák, István AU - Mizik, Máté Levente AU - Dani, Virág Éva AU - Csányi, Viktor AU - Harangozó, Ákos AU - Zádori, Zoltán AU - Toth, Zsolt AU - Boldogkői, Zsolt TI - Identification of herpesvirus transcripts from genomic regions around the replication origins JF - SCIENTIFIC REPORTS J2 - SCI REP VL - 13 PY - 2023 IS - 1 PG - 25 SN - 2045-2322 DO - 10.1038/s41598-023-43344-y UR - https://m2.mtmt.hu/api/publication/34171230 ID - 34171230 N1 - Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary MTA -SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary Department of Oral Biology, University of Florida College of Dentistry, Gainesville, FL, United States Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi, India HUN-REN Veterinary Medical Research Institute HU, Budapest, Hungary Export Date: 16 November 2023 Correspondence Address: Boldogkői, Z.; Department of Medical Biology, Hungary; email: boldogkoi.zsolt@med.u-szeged.hu AB - Long-read sequencing (LRS) techniques enable the identification of full-length RNA molecules in a single run eliminating the need for additional assembly steps. LRS research has exposed unanticipated transcriptomic complexity in various organisms, including viruses. Herpesviruses are known to produce a range of transcripts, either close to or overlapping replication origins (Oris) and neighboring genes related to transcription or replication, which possess confirmed or potential regulatory roles. In our research, we employed both new and previously published LRS and short-read sequencing datasets to uncover additional Ori-proximal transcripts in nine herpesviruses from all three subfamilies (alpha, beta and gamma). We discovered novel long non-coding RNAs, as well as splice and length isoforms of mRNAs. Moreover, our analysis uncovered an intricate network of transcriptional overlaps within the examined genomic regions. We demonstrated that herpesviruses display distinct patterns of transcriptional overlaps in the vicinity of or at the Oris. Our findings suggest the existence of a ‘super regulatory center’ in the genome of alphaherpesviruses that governs the initiation of both DNA replication and global transcription through multilayered interactions among the molecular machineries. LA - English DB - MTMT ER - TY - JOUR AU - Szuhaj, Márk AU - Kakuk, Balázs AU - Wirth, Roland AU - Rákhely, Gábor AU - Kovács, Kornél Lajos AU - Bagi, Zoltán TI - Regulation of the methanogenesis pathways by hydrogen at transcriptomic level in time JF - APPLIED MICROBIOLOGY AND BIOTECHNOLOGY J2 - APPL MICROBIOL BIOT VL - 107 PY - 2023 IS - 20 SP - 6315 EP - 6324 PG - 10 SN - 0175-7598 DO - 10.1007/s00253-023-12700-3 UR - https://m2.mtmt.hu/api/publication/34130955 ID - 34130955 N1 - Funding Agency and Grant Number: Hungarian National Research, Development and Innovation Fund [20203.1.2-ZFR-KVG-202000009]; Hungarian NRDIF [PD 132145, K143198, FK123902, 20192.1.13-TET_IN-202000016]; University of Szeged Funding text: Open access funding provided by University of Szeged. This study has been supported in part by the Hungarian National Research, Development and Innovation Fund project 2020-3.1.2-ZFR-KVG-2020-00009. RW, ZB, and KLK received support from the Hungarian NRDIF fund projects, PD 132145, K143198, FK123902, and 2019-2.1.13-TET_IN-2020-00016. AB - The biomethane formation from 4 H-2 + CO2 by pure cultures of two methanogens, Methanocaldococcus fervens and Methanobacterium thermophilum, has been studied. The goal of the study was to understand the regulation of the enzymatic steps associated with biomethane biosynthesis by H-2, using metagenomic, pan-genomic, and transcriptomic approaches. Methanogenesis in the autotrophic methanogen M. fervens could be easily "switched off" and "switched on" by H-2/CO2 within about an hour. In contrast, the heterotrophic methanogen M. thermophilum was practically insensitive to the addition of the H-2/CO2 trigger although this methanogen also converted H-2/CO2 to CH4. From practical points of view, the regulatory function of H-2/CO2 suggests that in the power-to-gas (P2G) renewable excess electricity conversion and storage systems, the composition of the biomethane-generating methanogenic community is essential for sustainable operation. In addition to managing the specific hydrogenotrophic methanogenesis biochemistry, H-2/CO2 affected several, apparently unrelated, metabolic pathways. The redox-regulated overall biochemistry and symbiotic relationships in the methanogenic communities should be explored in order to make the P2G technology more efficient. LA - English DB - MTMT ER - TY - JOUR AU - Tombácz, Dóra AU - Torma, Gábor AU - Gulyás, Gábor AU - Fülöp, Ádám AU - Dörmő, Ákos AU - Prazsák, István AU - Csabai, Zsolt AU - Mizik, Máté Levente AU - Hornyák, Ákos AU - Zádori, Zoltán AU - Kakuk, Balázs AU - Boldogkői, Zsolt TI - Hybrid sequencing discloses unique aspects of the transcriptomic architecture in equid alphaherpesvirus 1 JF - HELIYON J2 - HELIYON VL - 9 PY - 2023 IS - 7 PG - 16 SN - 2405-8440 DO - 10.1016/j.heliyon.2023.e17716 UR - https://m2.mtmt.hu/api/publication/34043441 ID - 34043441 LA - English DB - MTMT ER - TY - JOUR AU - Kakuk, Balázs AU - Dörmő, Ákos AU - Csabai, Zsolt AU - Kemenesi, Gábor AU - Holoubek, Jiří AU - Růžek, Daniel AU - Prazsák, István AU - Dani, Virág Éva AU - Dénes, Béla AU - Torma, Gábor AU - Jakab, Ferenc AU - Tóth, Gábor Endre AU - Földes, Fanni Vivien AU - Zana, Brigitta AU - Lanszki, Zsófia AU - Harangozó, Ákos AU - Fülöp, Ádám AU - Gulyás, Gábor AU - Mizik, Máté Levente AU - Kiss, András Attila AU - Tombácz, Dóra AU - Boldogkői, Zsolt TI - In-depth Temporal Transcriptome Profiling of Monkeypox and Host Cells using Nanopore Sequencing JF - SCIENTIFIC DATA J2 - SCI DATA VL - 10 PY - 2023 IS - 1 PG - 12 SN - 2052-4463 DO - 10.1038/s41597-023-02149-4 UR - https://m2.mtmt.hu/api/publication/33809377 ID - 33809377 AB - The recent human Monkeypox outbreak underlined the importance of studying basic biology of orthopoxviruses. However, the transcriptome of its causative agent has not been investigated before neither with short-, nor with long-read sequencing approaches. This Oxford Nanopore long-read RNA-Sequencing dataset fills this gap. It will enable the in-depth characterization of the transcriptomic architecture of the monkeypox virus, and may even make possible to annotate novel host transcripts. Moreover, our direct cDNA and native RNA sequencing reads will allow the estimation of gene expression changes of both the virus and the host cells during the infection. Overall, our study will lead to a deeper understanding of the alterations caused by the viral infection on a transcriptome level. LA - English DB - MTMT ER - TY - JOUR AU - Szűts, Viktória AU - Kelemen-Valkony, Ildikó AU - Ötvös, Ferenc AU - Repas, Zoltan AU - Kovács, András Sándor AU - Tóth, László AU - Kiss, András Attila AU - Lőrincz, Ádám AU - Szabó, P. Balázs AU - Gajdán, Krisztina AU - Kertai, Zoltán AU - Houshmand, Nazanin AU - Szutcs, Marcella AU - Obistioui, Diana AU - Velciov, Ariana B. AU - Halasy, Katalin AU - Deim, Zoltán AU - Deák, Dalma AU - Gál, József AU - Csanádi, József AU - Racskóné Domonkos, Ildikó TI - Life style and structure differences between species of freshwater fish JF - MEDICINA INTERNACIA REVUO J2 - MED INT REV VL - 30 PY - 2022 IS - 119 SP - 98 EP - 106 PG - 9 SN - 0465-5435 UR - https://m2.mtmt.hu/api/publication/33713093 ID - 33713093 LA - English DB - MTMT ER -