Histone variants in archaea and the evolution of combinatorial chromatin complexity

Nucleosomes in eukaryotes act as platforms for the dynamic integration of epigenetic information. Posttranslational 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 modeling with phylogenetic analysis to shed light on archaeal histone paralogs, their evolutionary history, and capacity to generate 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. Using molecular dynamics simulations, we go on to identify unique paralogs in M. stadtmanae and Methanobrevibacter smithii that are characterized by unstable interfaces between dimers. 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.

The hydrogen threshold of obligately methyl-reducing methanogens

ABSTRACT Methanogenesis is the final step in the anaerobic degradation of organic matter. The most important substrates of methanogens are hydrogen plus carbon dioxide and acetate, but also the use of methanol, methylated amines, and aromatic methoxy groups appears to be more widespread than originally thought. Except for most members of the family Methanosarcinaceae, all methylotrophic methanogens require external hydrogen as reductant and therefore compete with hydrogenotrophic methanogens for this common substrate. Since methanogenesis from carbon dioxide consumes four molecules of hydrogen per molecule of methane, whereas methanogenesis from methanol requires only one, methyl-reducing methanogens should have an energetic advantage over hydrogenotrophic methanogens at low hydrogen partial pressures. However, experimental data on their hydrogen threshold is scarce and suffers from relatively high detection limits. Here, we show that the methyl-reducing methanogens Methanosphaera stadtmanae (Methanobacteriales), Methanimicrococcus blatticola (Methanosarcinales), and Methanomassiliicoccus luminyensis (Methanomassiliicoccales) consume hydrogen to partial pressures < 0.1 Pa, which is almost one order of magnitude lower than the thresholds for M. stadtmanae and M. blatticola reported in the only previous study on this topic. We conclude that methylotrophic methanogens should outcompete hydrogenotrophic methanogens for hydrogen and that their activity is limited by the availability of methyl groups.

Histone variants in archaea and the evolution of combinatorial chromatin complexity

ABSTRACTNucleosomes 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.

New Mode of Energy Metabolism in the Seventh Order of Methanogens as Revealed by Comparative Genome Analysis of “Candidatus Methanoplasma termitum”

ABSTRACTThe recently discovered seventh order of methanogens, theMethanomassiliicoccales(previously referred to as “Methanoplasmatales”), so far consists exclusively of obligately hydrogen-dependent methylotrophs. We sequenced the complete genome of “CandidatusMethanoplasma termitum” from a highly enriched culture obtained from the intestinal tract of termites and compared it with the previously published genomes of three other strains from the human gut, including the first isolate of the order. Like all other strains, “Ca. Methanoplasma termitum” lacks the entire pathway for CO2reduction to methyl coenzyme M and produces methane by hydrogen-dependent reduction of methanol or methylamines, which is consistent with additional physiological data. However, the shared absence of cytochromes and an energy-converting hydrogenase for the reoxidation of the ferredoxin produced by the soluble heterodisulfide reductase indicates thatMethanomassiliicoccalesemploy a new mode of energy metabolism, which differs from that proposed for the obligately methylotrophicMethanosphaera stadtmanae. Instead, all strains possess a novel complex that is related to the F420:methanophenazine oxidoreductase (Fpo) ofMethanosarcinalesbut lacks an F420-oxidizing module, resembling the apparently ferredoxin-dependent Fpo-like homolog inMethanosaeta thermophila. Since allMethanomassiliicoccalesalso lack the subunit E of the membrane-bound heterodisulfide reductase (HdrDE), we propose that the Fpo-like complex interacts directly with subunit D, forming an energy-converting ferredoxin:heterodisulfide oxidoreductase. The dual function of heterodisulfide inMethanomassiliicoccales, which serves both in electron bifurcation and as terminal acceptor in a membrane-associated redox process, may be a unique characteristic of the novel order.

Επίδραση των αιθέριων ελαίων της ρίγανης στα ζυμωτικά φαινόμενα και στην γαλακτοπαραγωγή αιγών

Η παρούσα εργασία είχε ως στόχο να εξετάσει αν ο χρόνος αποθήκευσης της ρίγανης (Origanum vulgare subsp. hirtum) μετά τη συγκομιδή της, η άλεση και η ανάμειξη αυτής στο μείγμα συμπυκνωμένων ζωοτροφών μειώνει την περιεκτικότητά της σε αιθέριο έλαιο. Οι μετρήσεις αυτές έδειξαν ότι στα αποξηραμένα φυτά ρίγανης παραμένει τουλάχιστον το 94 % των αιθερίων ελαίων που περιέχουν έξι μήνες μετά τη συγκομιδή και το 95,1 % μετά την άλεση και ανάμειξη αυτών στο μείγμα συμπυκνωμένων ζωοτροφών τέσσερις εβδομάδες μετά την ανάμειξη. Στην συνέχεια μελετήθηκε η επίδραση της ρίγανης στα ζυμωτικά φαινόμενα των προστομάχων και στην γαλακτοπαραγωγή αιγών. Στο 1ο πείραμα χρησιμοποιήθηκαν οκτώ αίγες φυλής Alpine οι οποίες χωρίστηκαν σε δύο ισοδύναμες ομάδες. Οι δύο ομάδες κατανάλωναν το ίδιο σιτηρέσιο με μόνη διαφορά ότι στο σιτηρέσιο της ομάδας της επέμβασης είχαν προστεθεί 20 g ξηράς δρόγης ρίγανης που περιείχαν 1g αιθέριου ελαίου. Από τις αίγες λαμβάνονταν δείγματα υγρού μεγάλης κοιλίας κάθε 15 ημέρες για χρονικό διάστημα 69 ημερών. Στα δείγματα αυτά προσδιορίστηκαν: το pH, η συγκέντρωση της αμμωνίας και των πτητικών λιπαρών οξέων, οι μικροβιακοί πληθυσμοί και ένας αριθμός πεπτικών ενζύμων (πρωτεάση, α-αμυλάση, κυταρινάση, ξυλανάση, λιπάση). Τα αποτελέσματα έδειξαν ότι αυξήθηκε (P<0,05) η συγκέντρωση της αμμωνίας στην ομάδα της διατροφικής επέμβασης καθ’όλη την πειραματική περίοδο. Εκ των μικροβιακών ενζύμων, παρατηρήθηκε αύξηση της πρωτεάσης (P<0,001), ενώ εκ των μικροβιακών πληθυσμών παρατηρήθηκε μείωση των μεθανοβακτηρίων (P<0,05) και του Methanosphaera stadtmanae (P<0,05). Στο 2ο πείραμα χρησιμοποιήθηκαν δώδεκα αίγες φυλής Alpine οι οποίες χωρίστηκαν σε δύο ισοδύναμες ομάδες. Ο διατροφικός χειρισμός ήταν ίδιος με το πρώτο πείραμα. Από τις αίγες λαμβάνονταν δείγματα γάλακτος και αίματος για χρονικό διάστημα 30 ημερών. Στα δείγματα αυτά προσδιορίστηκαν: η χημική σύσταση του γάλακτος, ορισμένα αντιοξειδωτικά ένζυμα (δεσμουτάση του υπεροξειδίου, καταλάση, τρανσφεράση γλουταθειόνης, οξειδάση γλουταθειόνης, ρεδουκτάση γλουταθειόνης, λακτοϋπεροξειδάση), η ολική αντιοξειδωτική ικανότητα και η συγκέντρωση των λιπαρών οξέων του γάλακτος. Τα αποτελέσματα έδειξαν αύξηση της ολικής αντιοξειδωτικής ικανότητας (P<0,001), της υπεροξειδάσης (P<0,001) και της ρεδουκτάσης της γλουταθειόνης (P<0,001).