Genome-wide primary transcriptome analysis of H2-producing archaeon Thermococcus onnurineus NA1

Cho, Suhyung; Kim, Min‐Sik; Jeong, Yu‐Jin; Lee, Bo-Rahm; Lee, Jung-Hyun; Kang, Sung Gyun; Cho, Byung-Kwan

doi:10.1038/srep43044

Cited by 24 publications

(21 citation statements)

References 64 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Data visualization was performed using IGV v2.4.6 [90] and Gaggle Genome Browser [26]. Additionally to Halobacterium salinarum , this genome-wide dataset analysis was performed for: Haloferax volcanii DS2 (PRJNA324298) [8], Methanocaldococcus jannaschii DSM 2661 (PRJNA342613) [91], Thermococcus kodakarensis KOD1 (PRJNA242777) [10] and Thermococcus onnurineus NA1 (PRJNA339284) [92] (Table S10).…”

Section: Methodsmentioning

confidence: 99%

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

et al. 2018

View full text Add to dashboard Cite

Prokaryotic genomes show a high level of information compaction often with different molecules transcribed from the same locus. Although antisense RNAs have been relatively well studied, RNAs in the same strand, internal RNAs (intraRNAs), are still poorly understood. The question of how common is the translation of overlapping reading frames remains open. We address this question in the model archaeon Halobacterium salinarum. In the present work we used differential RNA-seq (dRNA-seq) in H. salinarum NRC-1 to locate intraRNA signals in subsets of internal transcription start sites (iTSS) and establish the open reading frames associated to them (intraORFs). Using C-terminally flagged proteins, we experimentally observed isoforms accurately predicted by intraRNA translation for kef1, acs3 and orc4 genes. We also recovered from the literature and mass spectrometry databases several instances of protein isoforms consistent with intraRNA translation such as the gas vesicle protein gene gvpC1. We found evidence for intraRNAs in horizontally transferred genes such as the chaperone dnaK and the aerobic respiration related cydA in both H. salinarum and Escherichia coli. Also, intraRNA translation evidence in H. salinarum, E. coli and yeast of a universal elongation factor (aEF-2, fusA and eEF-2) suggests that this is an ancient phenomenon present in all domains of life.

show abstract

Section: Methodsmentioning

confidence: 99%

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

et al. 2018

View full text Add to dashboard Cite

show abstract

“…The TSSs identified were further classified into five different types according to their positions and direction relative to the cognate genes as described in the previous reports (Fig. 2C ) 29 , 33 , 35 . First, 1,257 primary TSSs (pTSS) were assigned, when the TSS is located within 300 nt upstream of the currently annotated genes, which corresponds to 44.1% of the total genes in the S. aureus genome (note that the monocistronic and operonic structure have not been considered).…”

Section: Resultsmentioning

confidence: 99%

Genome-scale analysis of Methicillin-resistant Staphylococcus aureus USA300 reveals a tradeoff between pathogenesis and drug resistance

Choe

Szubin

Dahesh

et al. 2018

Sci Rep

Self Cite

View full text Add to dashboard Cite

Staphylococcus aureus infection is a rising public health care threat. S. aureus is believed to have elaborate regulatory networks that orchestrate its virulence. Despite its importance, the systematic understanding of the transcriptional landscape of S. aureus is limited. Here, we describe the primary transcriptome landscape of an epidemic USA300 isolate of community-acquired methicillin-resistant S. aureus. We experimentally determined 1,861 transcription start sites with their principal promoter elements, including well-conserved -35 and -10 elements and weakly conserved -16 element and 5′ untranslated regions containing AG-rich Shine-Dalgarno sequence. In addition, we identified 225 genes whose transcription was initiated from multiple transcription start sites, suggesting potential regulatory functions at transcription level. Along with the transcription unit architecture derived by integrating the primary transcriptome analysis with operon prediction, the measurement of differential gene expression revealed the regulatory framework of the virulence regulator Agr, the SarA-family transcriptional regulators, and β-lactam resistance regulators. Interestingly, we observed a complex interplay between virulence regulation, β-lactam resistance, and metabolism, suggesting a possible tradeoff between pathogenesis and drug resistance in the USA300 strain. Our results provide platform resource for the location of transcription initiation and an in-depth understanding of transcriptional regulation of pathogenesis, virulence, and antibiotic resistance in S. aureus.

show abstract

“…onnurineus (GSE85760 (Cho et al 2017)) is plotted as base mean and normalised mRNA respectively, in Figure S4. For M. smithii, we used the median value of histone expression across replicates for strain MsmPS in low formate, high hydrogen (GSE25408, (Hansen et al 2011)).…”

Section: Histone Expression Levels For Different Speciesmentioning

confidence: 99%

Histone variants in archaea and the evolution of combinatorial chromatin complexity

Stevens

Swadling

Hocher

et al. 2020

Preprint

View full text Add to dashboard Cite

Nucleosomes in eukaryotes act as platforms for the dynamic integration of epigenetic information. Post-translational modifications are reversibly added or removed and core histones exchanged for paralogous variants, in concert with changing demands on transcription and genome accessibility. Histones are also common in archaea. Their role in genome regulation, however, and the capacity of individual paralogs to assemble into histone-DNA complexes with distinct properties remain poorly understood. Here, we combine structural modelling with phylogenetic analysis to shed light on archaeal histone paralogs, their evolutionary history and capacity to generate complex combinatorial chromatin states through hetero-oligomeric assembly. Focusing on the human commensal Methanosphaera stadtmanae as a model archaeal system, we show that the heteromeric complexes that can be assembled from its seven histone paralogs vary substantially in DNA binding affinity and tetramer stability, occupying a large but densely populated chromatin state space. Using molecular dynamics simulations, we go on to identify unique paralogs in M. stadtmanae and Methanobrevibacter smithii that are characterized by unstable dimer:dimer interfaces. We propose that these paralogs act as capstones that prevent stable tetramer formation and extension into longer oligomers characteristic of model archaeal histones. Importantly, we provide evidence from phylogeny and genome architecture that these capstones, as well as other paralogs in the Methanobacteriales, have been maintained for hundreds of millions of years following ancient duplication events. Taken together, our findings indicate that at least some archaeal histone paralogs have evolved to play distinct and conserved functional roles, reminiscent of eukaryotic histone variants. We conclude that combinatorially complex histone-based chromatin is not restricted to eukaryotes and likely predates their emergence.

show abstract

Genome-wide primary transcriptome analysis of H2-producing archaeon Thermococcus onnurineus NA1

Cited by 24 publications

References 64 publications

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

Genome-scale analysis of Methicillin-resistant Staphylococcus aureus USA300 reveals a tradeoff between pathogenesis and drug resistance

Histone variants in archaea and the evolution of combinatorial chromatin complexity

Contact Info

Product

Resources

About