New aminopeptidase from “microbial dark matter” archaeon

Michalska, K.; Steen, Andrew D.; Chhor, G.; Endres, M.; Webber, Austen T.; Bird, John; Lloyd, Karen G.; Joachimiak, A.

doi:10.1096/fj.15-272906

Cited by 18 publications

(15 citation statements)

References 41 publications

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“…The organoheterotrophic physiology of Bathyarchaeota was further supported through analyses of bathyarchaeotal genomes by single-cell genome and metagenome analyses, and genes encoding enzymes for the degradation, transport, and utilization of detrital proteins, aromatic compounds, and plant-derived carbohydrates were identified (2,11,14). Peptidase activity in the sediments was measured, and the gene of an extracellular peptidase from Bathyarchaeota was expressed in vitro and characterized, supporting the inferred capacity of Bathyarchaeota to degrade proteins (11,15). Meanwhile, stable-isotope probing experiments indicated that members of two subgroups assimilated several organic substrates, including acetate, glycine, urea, lipids, and complex mixtures of organic growth substrates, while showing no significant incorporation of carbon from proteins (16).…”

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confidence: 80%

Growth of sedimentaryBathyarchaeotaon lignin as an energy source

Liang

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

196

181

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Members of the archaeal phylum are among the most abundant microorganisms on Earth. Although versatile metabolic capabilities such as acetogenesis, methanogenesis, and fermentation have been suggested for bathyarchaeotal members, no direct confirmation of these metabolic functions has been achieved through growth of in the laboratory. Here we demonstrate, on the basis of gene-copy numbers and probing of archaeal lipids, the growth of subgroup Bathy-8 in enrichments of estuarine sediments with the biopolymer lignin. Other organic substrates (casein, oleic acid, cellulose, and phenol) did not significantly stimulate growth of Meanwhile, putative bathyarchaeotal tetraether lipids incorporated C fromC-bicarbonate only when added in concert with lignin. Our results are consistent with organoautotrophic growth of a bathyarchaeotal group with lignin as an energy source and bicarbonate as a carbon source and shed light into the cycling of one of Earth's most abundant biopolymers in anoxic marine sediment.

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confidence: 80%

Growth of sedimentaryBathyarchaeotaon lignin as an energy source

Liang

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

196

181

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“…Recent studies from marine and terrestrial subsurface environments has identified a variety of extracellular enzymes adapted to degrade detrital sedimentary organic matter (Michalska et al, 2015;Steen et al, 2019). Interestingly, the Salmeal sample (CGB7) contained a high fraction of unique unassigned Archaea (OTU8) as well as high abundance of uncultivated Acetothermia (OTU6).…”

Section: Discussionmentioning

confidence: 99%

“…Metagenome-assembled genomes have further revealed that diverse, heterotrophic microorganisms, with unknown physiologies, control the carbon flow in marine and hydrothermal deep-sea sediments via organic matter decomposition (Lloyd et al, 2013;Dombrowski et al, 2017). Hence, such microorganisms represent a great resource for finding new enzymes for biomedical, biotechnological, and industrial applications (Michalska et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Tailoring Hydrothermal Vent Biodiversity Toward Improved Biodiscovery Using a Novel in situ Enrichment Strategy

et al. 2020

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Deep-sea hydrothermal vents are amongst the most extreme environments on Earth and represent interesting targets for marine bioprospecting and biodiscovery. The microbial communities in hydrothermal vents are often dominated by chemolithoautotrophs utilizing simple chemical compounds, though the full extent of their heterotrophic abilities is still being explored. In the bioprocessing industry, where degradation of complex organic materials often is a major challenge, new microbial solutions are heavily needed. To meet these needs, we have developed novel in situ incubators and tested if deployment of recalcitrant materials from fish farming and wood-pulping industries introduced changes in the microbial community structure in hot marine hydrothermal sediments. The incubation chambers were deployed in sediments at the Bruse vent site located within the Jan Mayen vent field for 1 year, after which the microbial populations in the chambers were profiled by 16S rRNA Ion Torrent amplicon sequencing. A total of 921 operational taxonomic units (OTUs) were assigned into 74 different phyla where differences in community structure were observed depending on the incubated material, chamber depth below the sea floor and/or temperature. A high fraction of putative heterotrophic microbial lineages related to cultivated members within the Thermotogales were observed. However, considerable fractions of previously uncultivated and novel Thermotogales and Bacteroidetes were also identified. Moreover, several novel lineages (e.g., members within the DPANN superphylum, unidentified archaeal lineages, unclassified Thermoplasmatales and Candidatus division BRC-1 bacterium) of as-yet uncultivated thermophilic archaea and bacteria were identified. Overall, our data illustrate that amendment of hydrothermal vent communities by in situ incubation of biomass induces shifts in community structure toward increased fractions of heterotrophic microorganisms. The technologies utilized here could aid in subsequent metagenomics-based enzyme discovery for diverse industries.

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“…Tryptophan synthase has become a prototype system to study the peculiarities of allostery and substrate channeling (Hilario et al, 2016;Niks et al, 2013;Rhee et al, 1996;Rowlett et al, 1998;Spyrakis et al, 2006). TrpA is also one of the model proteins that have been used to investigate protein-folding mechanisms (Wu & Matthews, 2002;Bilsel et al, 1999;Yang et al, 2007;Vadrevu et al, 2008;Wu et al, 2007;Michalska et al, 2015). The sparsity of biochemical/structural investigations of other orthologs possibly stems from challenges in obtaining high-quality TrpAB samples and also from interest being focused on very detailed mechanistic aspects rather than on species-specific variations.…”

Section: Figurementioning

confidence: 99%

Conservation of the structure and function of bacterial tryptophan synthases

Michalska

Gale

Joachimiak

et al. 2019

Int Union Crystallogr J

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Tryptophan biosynthesis is one of the most characterized processes in bacteria, in which the enzymes from Salmonella typhimurium and Escherichia coli serve as model systems. Tryptophan synthase (TrpAB) catalyzes the final two steps of tryptophan biosynthesis in plants, fungi and bacteria. This pyridoxal 5′-phosphate (PLP)-dependent enzyme consists of two protein chains, α (TrpA) and β (TrpB), functioning as a linear αββα heterotetrameric complex containing two TrpAB units. The reaction has a complicated, multistep mechanism resulting in the β-replacement of the hydroxyl group of L-serine with an indole moiety. Recent studies have shown that functional TrpAB is required for the survival of pathogenic bacteria in macrophages and for evading host defense. Therefore, TrpAB is a promising target for drug discovery, as its orthologs include enzymes from the important human pathogens Streptococcus pneumoniae, Legionella pneumophila and Francisella tularensis, the causative agents of pneumonia, legionnaires' disease and tularemia, respectively. However, specific biochemical and structural properties of the TrpABs from these organisms have not been investigated. To fill the important phylogenetic gaps in the understanding of TrpABs and to uncover unique features of TrpAB orthologs to spearhead future drug-discovery efforts, the TrpABs from L. pneumophila, F. tularensis and S. pneumoniae have been characterized. In addition to kinetic properties and inhibitor-sensitivity data, structural information gathered using X-ray crystallography is presented. The enzymes show remarkable structural conservation, but at the same time display local differences in both their catalytic and allosteric sites that may be responsible for the observed differences in catalysis and inhibitor binding. This functional dissimilarity may be exploited in the design of species-specific enzyme inhibitors.

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New aminopeptidase from “microbial dark matter” archaeon

Cited by 18 publications

References 41 publications

Growth of sedimentaryBathyarchaeotaon lignin as an energy source

Growth of sedimentaryBathyarchaeotaon lignin as an energy source

Tailoring Hydrothermal Vent Biodiversity Toward Improved Biodiscovery Using a Novel in situ Enrichment Strategy

Conservation of the structure and function of bacterial tryptophan synthases

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