Balázs Kakuk - Academia.edu (original) (raw)

Papers by Balázs Kakuk

bioRxiv (Cold Spring Harbor Laboratory), May 1, 2024

Environmental Microbiome, 2024

Applied Microbiology and Biotechnology

The biomethane formation from 4 H2 + CO2 by pure cultures of two methanogens, Methanocaldococcus ... more The biomethane formation from 4 H2 + 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 H2, using metagenomic, pan-genomic, and transcriptomic approaches. Methanogenesis in the autotrophic methanogen M. fervens could be easily “switched off” and “switched on” by H2/CO2 within about an hour. In contrast, the heterotrophic methanogen M. thermophilum was practically insensitive to the addition of the H2/CO2 trigger although this methanogen also converted H2/CO2 to CH4. From practical points of view, the regulatory function of H2/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 methano...

Scientific Data, May 9, 2023

mentioned DGE, DTE, DTU and biological pathway analyses. Taken together, the almost 1.5 million v... more mentioned DGE, DTE, DTU and biological pathway analyses. Taken together, the almost 1.5 million viral and almost 13 million host reads enable the in-depth and temporal characterization of the Monkeypox transcriptome and the effect of the viral infection on the host gene expression.

Kaposi's sarcoma-associated herpesvirus (KSHV) is a large, oncogenic DNA virus belonging to t... more Kaposi's sarcoma-associated herpesvirus (KSHV) is a large, oncogenic DNA virus belonging to the gammaherpesvirus subfamily. KSHV has been extensively studied with various high-throughput RNA-sequencing approaches to map the transcription start and end sites, the splice junctions, and the translation initiation sites. Despite these efforts, the comprehensive annotation of the viral transcriptome remains incomplete. In the present study, we generated a long-read sequencing dataset of the lytic and latent KSHV transcriptome using native RNA and direct cDNA sequencing methods. This was supplemented with CAGE sequencing based on a short-read platform. We also utilized datasets from previous publications for our analysis. As a result of this combined approach, we have identified a number of novel viral transcripts and RNA isoforms and have either corroborated or improved the annotation of previously identified viral RNA molecules, thereby notably enhancing our comprehension of the tra...

Research Square (Research Square), Apr 2, 2021

Background. The detailed molecular machinery of the complex microbiological cell factory of bioga... more Background. The detailed molecular machinery of the complex microbiological cell factory of biogas/biomethane production is not fully understood. One of the main puzzling process control elements is the formation, consumption and regulatory role of hydrogen (H 2). Reduction of carbon dioxide (CO 2) by H 2 is rate limiting factor in methanogenesis, but the community intends to keep H 2 concentration low in order to maintain the redox balance of the overall system. H 2 metabolism in methanogens becomes increasingly important in the Power-toGas renewable energy conversion and storage technologies.

Az emberiség Földünknek és a bioszférának egyre nagyobb és egyre inkább visszafordíthatatlan káro... more Az emberiség Földünknek és a bioszférának egyre nagyobb és egyre inkább visszafordíthatatlan károkat okozott. Ennek egyik oka a folyamatosan növekedő energiaigényünk, hiszen kielégítésére leginkább fosszilis energiahordozókat égetünk el, azonban ezáltal üvegházhatású gázok és különböző károsanyagok szabadulnak fel, jutnak környezetünkbe. A megújuló energiák használata részben megoldást nyújthat, ám szükség van ezen technológiák továbbfejlesztésére, hogy versenyezni tudjanak a fosszilis energiákkal. A biomassza az egyik legnagyobb mértékben hozzáférhető energiaforrás, melyből számos energiahordozó állítható elő. Az egyik legszélesebb körben felhasználható ezek közül a biogáz, amely a biomassza levegőmentes bomlása (anaerob fermentáció) során keletkező, metánt és szén-dioxidot tartalmazó gázelegy. A biogáz előállítása rendkívül sokféle alapanyagból, vagyis szubsztrátból lehetséges, mint pl. szennyvíziszap, mezőgazdasági és élelmiszeripari melléktermékek, sertés- vagy marhatrágya, ille...

ABSTRACTIn the last couple of years, the rapid advances and decreasing costs of sequencing techno... more ABSTRACTIn the last couple of years, the rapid advances and decreasing costs of sequencing technologies have revolutionized transcriptomic research. Long-read sequencing (LRS) techniques are able to detect full-length RNA molecules in a single run without the need for additional assembly steps. LRS studies have revealed an unexpected transcriptomic complexity in a variety of organisms, including viruses. A number of transcripts with proven or putative regulatory role, mapping close to or overlapping the replication origins (Oris) and the nearby transcription activator genes, have been described in herpesviruses. In this study, we applied both newly generated and previously published LRS and short-read sequencing datasets to discover additional Ori-proximal transcripts in nine herpesviruses belonging to all of the three subfamilies (alpha, beta and gamma). We identified novel long non-coding RNAs (lncRNAs), as well as splice and length isoforms of mRNAs and lncRNAs. Furthermore, our ...

The recent Monkeypox outbreak showed the importance of studying the basic biology of orthopoxviru... more The recent Monkeypox outbreak showed the importance of studying the 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. Our direct cDNA and native RNA sequencing data enable the in-depth characterization of the transcriptomic architecture and dynamics of the gene expressions of monkeypox virus; and also the deeper understanding of the changes it causes in the host cells on a transcriptome level.

GigaScience, Oct 17, 2022

Background: Recent studies have disclosed the genome, transcriptome, and epigenetic compositions ... more Background: Recent studies have disclosed the genome, transcriptome, and epigenetic compositions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the effect of viral infection on gene expression of the host cells. It has been demonstrated that, besides the major canonical transcripts, the viral genome also codes for noncanonical RNA molecules. While the structural characterizations have revealed a detailed transcriptomic architecture of the virus, the kinetic studies provided poor and often misleading results on the dynamics of both the viral and host transcripts due to the low temporal resolution of the infection event and the low virus/cell ratio (multiplicity of infection [MOI] = 0.1) applied for the infection. It has never been tested whether the alteration in the host gene expressions is caused by aging of the cells or by the viral infection. Findings: In this study, we used Oxford Nanopore's direct cDNA and direct RNA sequencing methods for the generation of a highcoverage, high temporal resolution transcriptomic dataset of SARS-CoV-2 and of the primate host cells, using a high infection titer (MOI = 5). Sixteen sampling time points ranging from 1 to 96 hours with a varying time resolution and 3 biological replicates were used in the experiment. In addition, for each infected sample, corresponding noninfected samples were employed. The raw reads were mapped to the viral and to the host reference genomes, resulting in 49,661,499 mapped reads (54,62 Gbs). The genome of the viral isolate was also sequenced and phylogenetically classified. Conclusions: This dataset can serve as a valuable resource for profiling the SARS-CoV-2 transcriptome dynamics, the virus-host interactions, and the RNA base modifications. Comparison of expression profiles of the host gene in the virally infected and in noninfected cells at different time points allows making a distinction between the effect of the aging of cells in culture and the viral infection. These data can provide useful information for potential novel gene annotations and can also be used for studying the currently available bioinformatics pipelines.

In this study, a structural profiling of equid alphaherpesvirus 1 (EHV-1) transcriptome was carri... more In this study, a structural profiling of equid alphaherpesvirus 1 (EHV-1) transcriptome was carried out using next-generation (Illumina) and third-generation (Oxford Nanopore Technologies) sequencing platforms. We annotated the canonical mRNA molecules and their isoforms, including transcript start and end site isoforms, and splice variants. Additionally, a number of putative 5′-truncated mRNAs containing shorter in-frame ORFs were detected. We also demonstrated that EHV-1 produces a high number of non-coding transcripts, including antisense and intergenic RNAs. One of the most remarkable features of the EHV-1 is the generation of abundant fusion transcripts some of which encoding chimeric polypeptides. We observed a higher number of splicing and transcriptional overlaps than in related viruses. Additionally, we found that many upstream genes of tandem gene clusters have their own transcript end sites (TESs) besides the co-terminal TESs, which is rare in other alphaherpesviruses. We...

Additional file 4: Figure S4. KEGG heatmap.

Additional file 6: Table S2. Genes and qPCR primers used in this study.

bioRxiv (Cold Spring Harbor Laboratory), May 1, 2024

Environmental Microbiome, 2024

Applied Microbiology and Biotechnology

The biomethane formation from 4 H2 + CO2 by pure cultures of two methanogens, Methanocaldococcus ... more The biomethane formation from 4 H2 + 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 H2, using metagenomic, pan-genomic, and transcriptomic approaches. Methanogenesis in the autotrophic methanogen M. fervens could be easily “switched off” and “switched on” by H2/CO2 within about an hour. In contrast, the heterotrophic methanogen M. thermophilum was practically insensitive to the addition of the H2/CO2 trigger although this methanogen also converted H2/CO2 to CH4. From practical points of view, the regulatory function of H2/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 methano...

Scientific Data, May 9, 2023

mentioned DGE, DTE, DTU and biological pathway analyses. Taken together, the almost 1.5 million v... more mentioned DGE, DTE, DTU and biological pathway analyses. Taken together, the almost 1.5 million viral and almost 13 million host reads enable the in-depth and temporal characterization of the Monkeypox transcriptome and the effect of the viral infection on the host gene expression.

Kaposi's sarcoma-associated herpesvirus (KSHV) is a large, oncogenic DNA virus belonging to t... more Kaposi's sarcoma-associated herpesvirus (KSHV) is a large, oncogenic DNA virus belonging to the gammaherpesvirus subfamily. KSHV has been extensively studied with various high-throughput RNA-sequencing approaches to map the transcription start and end sites, the splice junctions, and the translation initiation sites. Despite these efforts, the comprehensive annotation of the viral transcriptome remains incomplete. In the present study, we generated a long-read sequencing dataset of the lytic and latent KSHV transcriptome using native RNA and direct cDNA sequencing methods. This was supplemented with CAGE sequencing based on a short-read platform. We also utilized datasets from previous publications for our analysis. As a result of this combined approach, we have identified a number of novel viral transcripts and RNA isoforms and have either corroborated or improved the annotation of previously identified viral RNA molecules, thereby notably enhancing our comprehension of the tra...

Research Square (Research Square), Apr 2, 2021

Background. The detailed molecular machinery of the complex microbiological cell factory of bioga... more Background. The detailed molecular machinery of the complex microbiological cell factory of biogas/biomethane production is not fully understood. One of the main puzzling process control elements is the formation, consumption and regulatory role of hydrogen (H 2). Reduction of carbon dioxide (CO 2) by H 2 is rate limiting factor in methanogenesis, but the community intends to keep H 2 concentration low in order to maintain the redox balance of the overall system. H 2 metabolism in methanogens becomes increasingly important in the Power-toGas renewable energy conversion and storage technologies.

Az emberiség Földünknek és a bioszférának egyre nagyobb és egyre inkább visszafordíthatatlan káro... more Az emberiség Földünknek és a bioszférának egyre nagyobb és egyre inkább visszafordíthatatlan károkat okozott. Ennek egyik oka a folyamatosan növekedő energiaigényünk, hiszen kielégítésére leginkább fosszilis energiahordozókat égetünk el, azonban ezáltal üvegházhatású gázok és különböző károsanyagok szabadulnak fel, jutnak környezetünkbe. A megújuló energiák használata részben megoldást nyújthat, ám szükség van ezen technológiák továbbfejlesztésére, hogy versenyezni tudjanak a fosszilis energiákkal. A biomassza az egyik legnagyobb mértékben hozzáférhető energiaforrás, melyből számos energiahordozó állítható elő. Az egyik legszélesebb körben felhasználható ezek közül a biogáz, amely a biomassza levegőmentes bomlása (anaerob fermentáció) során keletkező, metánt és szén-dioxidot tartalmazó gázelegy. A biogáz előállítása rendkívül sokféle alapanyagból, vagyis szubsztrátból lehetséges, mint pl. szennyvíziszap, mezőgazdasági és élelmiszeripari melléktermékek, sertés- vagy marhatrágya, ille...

ABSTRACTIn the last couple of years, the rapid advances and decreasing costs of sequencing techno... more ABSTRACTIn the last couple of years, the rapid advances and decreasing costs of sequencing technologies have revolutionized transcriptomic research. Long-read sequencing (LRS) techniques are able to detect full-length RNA molecules in a single run without the need for additional assembly steps. LRS studies have revealed an unexpected transcriptomic complexity in a variety of organisms, including viruses. A number of transcripts with proven or putative regulatory role, mapping close to or overlapping the replication origins (Oris) and the nearby transcription activator genes, have been described in herpesviruses. In this study, we applied both newly generated and previously published LRS and short-read sequencing datasets to discover additional Ori-proximal transcripts in nine herpesviruses belonging to all of the three subfamilies (alpha, beta and gamma). We identified novel long non-coding RNAs (lncRNAs), as well as splice and length isoforms of mRNAs and lncRNAs. Furthermore, our ...

The recent Monkeypox outbreak showed the importance of studying the basic biology of orthopoxviru... more The recent Monkeypox outbreak showed the importance of studying the 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. Our direct cDNA and native RNA sequencing data enable the in-depth characterization of the transcriptomic architecture and dynamics of the gene expressions of monkeypox virus; and also the deeper understanding of the changes it causes in the host cells on a transcriptome level.

GigaScience, Oct 17, 2022

Background: Recent studies have disclosed the genome, transcriptome, and epigenetic compositions ... more Background: Recent studies have disclosed the genome, transcriptome, and epigenetic compositions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the effect of viral infection on gene expression of the host cells. It has been demonstrated that, besides the major canonical transcripts, the viral genome also codes for noncanonical RNA molecules. While the structural characterizations have revealed a detailed transcriptomic architecture of the virus, the kinetic studies provided poor and often misleading results on the dynamics of both the viral and host transcripts due to the low temporal resolution of the infection event and the low virus/cell ratio (multiplicity of infection [MOI] = 0.1) applied for the infection. It has never been tested whether the alteration in the host gene expressions is caused by aging of the cells or by the viral infection. Findings: In this study, we used Oxford Nanopore's direct cDNA and direct RNA sequencing methods for the generation of a highcoverage, high temporal resolution transcriptomic dataset of SARS-CoV-2 and of the primate host cells, using a high infection titer (MOI = 5). Sixteen sampling time points ranging from 1 to 96 hours with a varying time resolution and 3 biological replicates were used in the experiment. In addition, for each infected sample, corresponding noninfected samples were employed. The raw reads were mapped to the viral and to the host reference genomes, resulting in 49,661,499 mapped reads (54,62 Gbs). The genome of the viral isolate was also sequenced and phylogenetically classified. Conclusions: This dataset can serve as a valuable resource for profiling the SARS-CoV-2 transcriptome dynamics, the virus-host interactions, and the RNA base modifications. Comparison of expression profiles of the host gene in the virally infected and in noninfected cells at different time points allows making a distinction between the effect of the aging of cells in culture and the viral infection. These data can provide useful information for potential novel gene annotations and can also be used for studying the currently available bioinformatics pipelines.

In this study, a structural profiling of equid alphaherpesvirus 1 (EHV-1) transcriptome was carri... more In this study, a structural profiling of equid alphaherpesvirus 1 (EHV-1) transcriptome was carried out using next-generation (Illumina) and third-generation (Oxford Nanopore Technologies) sequencing platforms. We annotated the canonical mRNA molecules and their isoforms, including transcript start and end site isoforms, and splice variants. Additionally, a number of putative 5′-truncated mRNAs containing shorter in-frame ORFs were detected. We also demonstrated that EHV-1 produces a high number of non-coding transcripts, including antisense and intergenic RNAs. One of the most remarkable features of the EHV-1 is the generation of abundant fusion transcripts some of which encoding chimeric polypeptides. We observed a higher number of splicing and transcriptional overlaps than in related viruses. Additionally, we found that many upstream genes of tandem gene clusters have their own transcript end sites (TESs) besides the co-terminal TESs, which is rare in other alphaherpesviruses. We...

Additional file 4: Figure S4. KEGG heatmap.

Additional file 6: Table S2. Genes and qPCR primers used in this study.