Biology subjects

Nobu, M. K.

Publications and source records attributed to Nobu, M. K..

11 recordsLinked to original sources

bioRxiv2026

Emergence of histone-based chromatin complexity in Asgard archaea

The emergence of the eukaryotes coincided with the diversification of histone proteins and their post-translational modifications by enzymes that constitute the core of eukaryotic chromatin. Yet the evolutionary origins of this regulatory machinery are unknown. Here, we show that the key molecular components of histone-based chromatin regulation are present in the Asgard archaea, the closest prokaryotic relatives of eukaryotes. Asgard histones are abundant and have extended N-terminal tails rich in lysine residues that can be post-translationally modified, all of which are features shared with eukaryotic histones. In line with these findings, we identify enzymes from Asgard archaea that deposit or remove lysine acetylation on histone tails in vitro. Moreover, Asgard sirtuin deacetylases (SIR2 proteins) restore chromatin silencing in yeast, demonstrating the functional compatibility of Asgard enzymes with eukaryotic histone substrates. Our findings establish that the foundations of histone-based chromatin predate eukaryogenesis and place Asgard archaea as an evolutionary intermediate in the emergence of eukaryotic chromatin.

evolutionary biology↗

bioRxiv2026

A representative of a ubiquitous bacterial lineage parasitically feeds on host RNA

Cellular metabolism is widely understood as an integrated network of redox reactions, energy conservation, and biosynthetic pathways. Here we show that across diverse prokaryotic lineages, loss of redox-associated functions is coupled with loss of nucleotide biosynthesis, raising a fundamental question of how such metabolically reduced organisms sustain cell growth. One of the most widespread and diverse lineages of prokaryotes--Minisyncoccota or Patescibacteriota--constitutes the majority of lineages exhibiting this pattern. To investigate how such organisms persist, we cultivated and characterized a representative of this lineage from a deep aquifer. The organism attaches to and penetrates growing bacterial host cells, and directly uptakes host RNA, concomitant with its depletion in the host. The metabolically reduced parasite cleaves host-derived RNA to directly supply cellular energy currencies and precursors for RNA/DNA synthesis, NTPs, without invoking canonical metabolic pathways. Codon usage in the parasite is complementary to that of its host, potentially minimizing translation of host-derived mRNA. Comparative genomics and phylogenetics indicate that these features are widespread and likely ancestral across the lineage. Exploitation of host RNA as a metabolic resource reveals a previously unrecognized metabolic strategy that demonstrates cellular metabolism can be sustained through direct utilization of informational macromolecules and thereby taps into an omnipresent energy reservoir, potentially supporting the environmental ubiquity of the metabolically reduced lineage.

microbiology↗

bioRxiv2025

Eukaryotes' closest relatives are internally simple syntrophic archaea

Eukaryotes are theorized to have originated from an archaeal phylum Promethearchaeota (formerly Asgard archaea)1,2. The first cultured representatives revealed valuable insight3,4 but are distantly related to the first eukaryotic common ancestor (FECA), leaving many unknowns regarding this archaeons biology. Here, we report isolation of two strains belonging to the order proposed as FECAs closest relative, Hodarchaeales,5 as members of a pure co- and tri-culture with methanogenic partners. Both are obligately anaerobic, syntrophic, peptide-degrading, and mesophilic archaea that have simple internal cell structure and produce protrusions and vesicles, like Promethearchaeales3,4. All strains demonstrate behavior focused on cell construction rather than division, unlike typical prokaryotes6. Strain HC1 possesses genes associated with aerobic lifestyles but lacks complete pathways for aerobic respiration and co-cultures cannot grow under (micro)aerobic conditions, suggesting the genes support oxygen detoxification rather than respiration. Reflecting this, HC1 can survive and grow under microaerobic conditions only when aerobic organisms are present. Phylogenetic analyses indicate FECA may have possessed these genes and thus some aerotolerance. Physiological, genomic, and phylogenetic observations indicate FECA was a simple-celled anaerobic syntrophic peptide-degrading archaeon with a non-growth-centric lifestyle and potential adaptations towards an oxygenated planet--the archaea-eukaryote transition was steep in both cell structure and aerobiosis.

microbiology↗

bioRxiv2023

Microscopic and metatranscriptomic analyses revealed unique cross-domain symbiosis between Candidatus Patescibacteria/candidate phyla radiation (CPR) and methanogenic archaea in anaerobic ecosystems

To verify the parasitic lifestyle of Candidatus Patescibacteria in the enrichment cultures derived from a methanogenic bioreactor, we applied multifaceted approaches combining cultivation, microscopy, metatranscriptomic, and protein structure prediction analyses. Cultivation experiments with the addition of exogenous methanogenic archaea with acetate, amino acids, and nucleoside monophosphates and 16S rRNA gene sequencing confirmed the increase in the relative abundance of Ca. Patescibacteria and methanogens. The predominant Ca. Patescibacteria were Ca. Yanofskybacteria and 32-520 lineages (to which belongs to class Ca. Paceibacteria) and positive linear relationships (r2 [≥] 0.70) between the relative abundance of Ca. Yanofskybacteria and Methanothrix, suggesting that the tendency of the growth rate is similar to that of the host. By fluorescence in situ hybridization (FISH) observations, the FISH signals of Methanothrix and Methanospirillum cells with Ca. Yanofskybacteria and with 32-520 lineages, respectively, were significantly lower than those of the methanogens without Ca. Patescibacteria, suggesting their parasitic interaction. The TEM and SEM observations also support parasitism in that the cell walls and plugs of these methanogens associated with submicron cells were often deformed. In particular, some Methanothrix-like filamentous cells were dented where the submicron cells were attached. Metatranscriptomic and protein structure prediction analyses identified highly expressed secreted genes from the genomes of Ca. Yanofskybacteria and 32-520, and these genes contain adhesion-related domains to the host cells. Considering the results through the combination of microscopic observations, gene expression, and computational protein modeling, we propose that the interactions between Ca. Yanofskybacteria and 32-520 belonging to class Ca. Paceibacteria and methanogenic archaea are parasitism.

microbiology↗

bioRxiv2022

Symbiosis between Patescibacteria and Archaea discovered in wastewater-treating bioreactors

Each prokaryotic domain, Bacteria and Archaea, contains a large and diverse group of organisms characterized with ultrasmall cell size and symbiotic lifestyles - Patescibacteria (also known as Candidate Phyla Radiation/CPR) and DPANN archaea. Cultivation-based approaches have revealed that Patesibacteria and DPANN symbiotically interact with bacterial and archaeal partners/hosts respectively, but cross-domain symbiosis/parasitism has never been observed. Here, we discovered physical interaction between ultramicrobacterial Patescibacteria and methanogenic archaea using cultures from anaerobic wastewater treatment sludge. In the cultures, we observed physical attachment of ultramicrobial cells to cells resembling Methanothrix and Methanospirillum using transmission electron microscopy and successfully detected physical association of Ca. Yanofskybacteria and Methanothrix using fluorescence in situ hybridization (FISH) (other ultramicrosized bacterial cells, presumably Patescibacteria, were also observed to attach on Methanospirillum). This was further confirmed to be a symbiosis rather than simple aggregation based on the observation that most ultramicrobacterial cells attached to Methanothrix were Ca. Yanofskybacteria and positive correlation (p < 0.05) between the relative abundance of Patescibacteria lineages and methanogenic archaea (e.g., Ca. Yanofskybacteria-Methanothrix and uncultured clade 32-520-Methanospirillum). The results shed light on a novel cross-domain symbiosis and inspire potential strategies for culturing CPR/DPANN.

microbiology↗

bioRxiv2021

Chasing the metabolism of novel syntrophic acetate-oxidizing bacteria in thermophilic methanogenic chemostats

BackgroundAcetate is the major intermediate of anaerobic digestion of organic waste to CH4. In anaerobic methanogenic systems, acetate degradation is carried out by either acetoclastic methanogenesis or a syntrophic degradation by a syntrophy of acetate oxidizers and hydrogenotrophic methanogens. Due to challenges in isolation of syntrophic acetate-oxidizing bacteria (SAOB), the diversity and metabolism of SAOB, as well as the mechanisms of their interactions with methanogenic partners remain poorly understood. ResultsIn this study, we successfully enriched previously unknown SAOB by operating continuous thermophilic anaerobic chemostats fed with acetate, propionate, butyrate, or isovalerate as the sole carbon and energy source. They represent novel clades belonging to Clostridia, Thermoanaerobacteraceae, Anaerolineae, and Gemmatimonadetes. In these SAOB, acetate is degraded through reverse Wood-Ljungdahl pathway or an alternative pathway mediated by the glycine cleavage system, while the SAOB possessing the latter pathway dominated the bacterial community. Moreover, H2 is the major product of the acetate degradation by these SAOB, which is mediated by [FeFe]-type electron-confurcating hydrogenases, formate dehydrogenases, and NADPH reoxidation complexes. We also identified the methanogen partner of these SAOB in acetate-fed chemostat, Methanosarcina thermophila, which highly expressed genes for CO2-reducing methanogenesis and hydrogenases to supportively consuming H2 at transcriptional level. Finally, our bioinformatical analyses further suggested that these previously unknown syntrophic lineages were prevalent and might play critical roles in thermophilic methanogenic reactors. ConclusionThis study expands our understanding on the phylogenetic diversity and in situ biological functions of uncultured syntrophic acetate degraders, and presents novel insights on how they interact with their methanogens partner. These knowledges strengthen our awareness on the important role of SAO in thermophilic methanogenesis and may be applied to manage microbial community to improve the performance and efficiency of anaerobic digestion.

microbiology↗

bioRxiv2021

Unique metabolic strategies in Hadean analogues reveal hints for primordial physiology

Primordial microorganisms are postulated to have emerged in H2-rich alkaline Hadean serpentinite-hosted environments with homoacetogenesis as a core metabolism. However, investigation of two modern serpentinization-active analogues of early Earth reveals that conventional H2-/CO2-dependent homoacetogenesis is thermodynamically unfavorable in situ due to picomolar CO2 levels. Through metagenomics and thermodynamics, we discover unique taxa capable of metabolism adapted to the habitat. This included a novel deep-branching phylum, "Ca. Lithoacetigenota", that exclusively inhabits Hadean analogues and harbors genes encoding alternative modes of H2-utilizing lithotrophy. Rather than CO2, these metabolisms utilize reduced carbon compounds detected in situ presumably serpentinization-derived: formate and glycine. The former employs a partial homoacetogenesis pathway and the latter a distinct pathway mediated by a rare selenoprotein - the glycine reductase. A survey of serpentinite-hosted system microbiomes shows that glycine reductases are diverse and nearly ubiquitous in Hadean analogues. "Ca. Lithoacetigenota" glycine reductases represent a basal lineage, suggesting that catabolic glycine reduction is an ancient bacterial innovation for gaining energy from geogenic H2 even under serpentinization-associated hyperalkaline, CO2-poor conditions. This draws remarkable parallels with ancestral archaeal H2-driven methyl-reducing methanogenesis recently proposed. Unique non-CO2-reducing metabolic strategies presented here may provide a new view into metabolisms that supported primordial life and the diversification of LUCA towards Archaea and Bacteria.

microbiology↗

bioRxiv2019

Membrane-bounded nucleoid discovered in a cultivated bacterium of the candidate phylum ‘Atribacteria’

A key feature that differentiates prokaryotes from eukaryotes is the absence of an intracellular membrane surrounding the chromosomal DNA. Here, we report isolation of an anaerobic bacterium that possesses an additional intracytoplasmic membrane surrounding a nucleoid, affiliates with the yet-to-be-cultivated ubiquitous phylum Ca. Atribacteria, and possesses unique genomic features likely associated with organization of complex cellular structure. Exploration of the uncharted microorganism overturned the prevailing dogma of prokaryotic cell structure.

microbiology↗

bioRxiv2019

Isolation of an archaeon at the prokaryote-eukaryote interface

The origin of eukaryotes remains enigmatic. Current data suggests that eukaryotes may have risen from an archaeal lineage known as \"Asgard archaea\". Despite the eukaryote-like genomic features found in these archaea, the evolutionary transition from archaea to eukaryotes remains unclear due to the lack of cultured representatives and corresponding physiological insight. Here we report the decade-long isolation of a Lokiarchaeota-related Asgard archaeon from deep marine sediment. The archaeon, \"Candidatus Prometheoarchaeum syntrophicum strain MK-D1\", is an anaerobic, extremely slow-growing, small cocci ([~]550 nm), that degrades amino acids through syntrophy. Although eukaryote-like intracellular complexities have been proposed for Asgard archaea, the isolate has no visible organella-like structure. Ca. P. syntrophicum instead displays morphological complexity - unique long, and often, branching protrusions. Based on cultivation and genomics, we propose an \"Entangle-Engulf-Enslave (E3) model\" for eukaryogenesis through archaea-alphaproteobacteria symbiosis mediated by the physical complexities and metabolic dependency of the hosting archaeon.

microbiology↗

bioRxiv2019

A hydrogen dependent geochemical analogue of primordial carbon and energy metabolism

Hydrogen gas, H2, is generated in alkaline hydrothermal vents from reactions of iron containing minerals with water during a geological process called serpentinization. It has been a source of electrons and energy since there was liquid water on the early Earth, and it fuelled early anaerobic ecosystems in the Earths crust1-3. H2 is the electron donor for the most ancient route of biological CO2 fixation, the acetyl-CoA (or Wood-Ljungdahl) pathway, which unlike any other autotrophic pathway simultaneously supplies three key requirements for life: reduced carbon in the form of acetyl groups, electrons in the form of reduced ferredoxin, and ion gradients for energy conservation in the form of ATP4,5. The pathway is linear, not cyclic, it releases energy rather than requiring energy input, its enzymes are replete with primordial metal cofactors6,7, it traces to the last universal common ancestor8 and abiotic, geochemical organic syntheses resembling segments of the pathway occur in hydrothermal vents today9,10. Laboratory simulations of the acetyl-CoA pathways reactions include the nonenzymatic synthesis of thioesters from CO and methylsulfide11, the synthesis of acetate12 and pyruvate13 from CO2 using native iron or external electrochemical potentials14 as the electron source. However, a full abiotic analogue of the acetyl-CoA pathway from H2 and CO2 as it occurs in life has not been reported to date. Here we show that three hydrothermal minerals -- awaruite (Ni3Fe), magnetite (Fe3O4) and greigite (Fe3S4) -- catalyse the fixation of CO2 with H2 at 100 {degrees}C under alkaline aqueous conditions. The product spectrum includes formate (100 mM), acetate (100 M), pyruvate (10 M), methanol (100 M), and methane. With these simple catalysts, the overall exergonic reaction of the acetyl-CoA pathway is facile, shedding light on both the geochemical origin of microbial metabolism and on the nature of abiotic formate and methane synthesis in modern hydrothermal vents.

evolutionary biology↗

bioRxiv2019

Elucidating syntrophic butyrate-degrading populations in anaerobic digesters using stable isotope-informed genome-resolved metagenomics

Linking the genomic content of uncultivated microbes to their metabolic functions remains a critical challenge in microbial ecology. Resolving this challenge has implications for improving our management of key microbial interactions in biotechnologies such as anaerobic digestion, which relies on slow-growing syntrophic and methanogenic communities to produce renewable methane from organic waste. In this study, we combined DNA stable isotope probing (SIP) with genome-centric metagenomics to recover the genomes of populations enriched in 13C after feeding 13C-labeled butyrate. Differential abundance analysis on recovered genomic bins across the SIP metagenomes identified two metagenome-assembled genomes (MAGs) that were significantly enriched in the heavy 13C DNA. Phylogenomic analysis assigned one MAG to the genus Syntrophomonas, and the other MAG to the genus Methanothrix. Metabolic reconstruction of the annotated genomes showed that the Syntrophomonas genome encoded all the enzymes for beta-oxidizing butyrate, as well as several mechanisms for interspecies electron transfer via electron transfer flavoproteins, hydrogenases, and formate dehydrogenases. The Syntrophomonas genome shared low average nucleotide identity (< 95%) with any cultured representative species, indicating it is a novel species that plays a significant role in syntrophic butyrate degradation within anaerobic digesters. The Methanothrix genome contained the complete pathway for aceticlastic methanogenesis, indicating that it was enriched in 13C from syntrophic acetate transfer. This study demonstrates the potential of stable-isotope-informed genome-resolved metagenomics to elucidate the nature of metabolic cooperation in slow-growing uncultured microbial populations, such as syntrophic bacteria and methanogens, that are important to waste treatment as well as global carbon cycling. ImportancePredicting the metabolic potential and ecophysiology of mixed microbial communities remains a major challenge, especially for slow-growing anaerobes that are difficult to isolate. Unraveling the in-situ metabolic activities of uncultured species could enable a more descriptive framework to model substrate transformations by microbiomes, which has broad implications for advancing the fields of biotechnology, global biogeochemistry, and human health. Here, we investigated the in-situ function of mixed microbiomes by combining DNA-stable isotope probing with metagenomics to identify the genomes of active syntrophic populations converting butyrate, a C4 fatty acid, into methane within anaerobic digesters. This approach thus moves beyond the mere presence of metabolic genes to resolve who is doing what by obtaining confirmatory assimilation of labeled substrate into the DNA signature. Our findings provide a framework to further link the genomic identities of uncultured microbes with their ecological function within microbiomes driving many important biotechnological and global processes.

microbiology↗