Deep-sea hydrothermal vent bacteria related to human pathogenic Vibrio species

During Alvin and Nautile dives in 1999, samples were collected from water surrounding sulfide chimneys of a hydrothermal vent along the East Pacific Rise and four mesophilic bacteria were isolated, including a novel Vibrio species, Vibrio antiquarius. Genomic, functional, and phylogenetic analyses indicate an intriguing blend of genomic features related to adaptation and animal symbiotic association, and also revealed the presence of virulence genes commonly found in Vibrio species pathogenic for humans. The presence of these virulence genes in an ecologically distinct Vibrio species was surprising. It is concluded that pathogenicity genes serve a far more fundamental ecological role than solely causation of human disease.

Vibrio species are both ubiquitous and abundant in marine coastal waters, estuaries, ocean sediment, and aquaculture settings worldwide. We report here the isolation, characterization, and genome sequence of a novel Vibrio species, Vibrio antiquarius, isolated from a mesophilic bacterial community associated with hydrothermal vents located along the East Pacific Rise, near the southwest coast of Mexico. Genomic and phenotypic analysis revealed V. antiquarius is closely related to pathogenic Vibrio species, namely Vibrio alginolyticus, Vibrio parahaemolyticus, Vibrio harveyi, and Vibrio vulnificus, but sufficiently divergent to warrant a separate species status. The V. antiquarius genome encodes genes and operons with ecological functions relevant to the environment conditions of the deep sea and also harbors factors known to be involved in human disease caused by freshwater, coastal, and brackish water vibrios. The presence of virulence factors in this deep-sea Vibrio species suggests a far more fundamental role of these factors for their bacterial host. Comparative genomics revealed a variety of genomic events that may have provided an important driving force in V. antiquarius evolution, facilitating response to environmental conditions of the deep sea.                          

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Las levaduras pueden producir morfina y opiáceos

Biotechnology is about to make morphine production as simple as brewing beer. A paper published on 18 May in Nature Chemical Biology reports the creation of a yeast strain containing the first half of a biochemical pathway that turns simple sugars into morphine — mimicking the process by which poppies make opiates. Combined with other advances, researchers predict that it will be only a few years — or even months — before a single engineered yeast strain can complete the entire process.

Dueber and colleagues’ work does not reach that goal. But it demonstrates that, given the right genes and biochemical machinery, yeast can convert glucose into the intermediate compound (S)-reticuline — the first half of the poppy’s morphine-production pathway.

Benzylisoquinoline alkaloids (BIAs) are a diverse family of plant-specialized metabolites that include the pharmaceuticals codeine and morphine and their derivatives. Microbial synthesis of BIAs holds promise as an alternative to traditional crop-based manufacturing. Here we demonstrate the production of the key BIA intermediate (S)-reticuline from glucose in Saccharomyces cerevisiae. To aid in this effort, we developed an enzyme-coupled biosensor for the upstream intermediate L-3,4-dihydroxyphenylalanine (L-DOPA). Using this sensor, we identified an active tyrosine hydroxylase and improved its L-DOPA yields by 2.8-fold via PCR mutagenesis. Coexpression of DOPA decarboxylase enabled what is to our knowledge the first demonstration of dopamine production from glucose in yeast, with a 7.4-fold improvement in titer obtained for our best mutant enzyme. We extended this pathway to fully reconstitute the seven-enzyme pathway from L-tyrosine to (S)-reticuline. Future work to improve titers and connect these steps with downstream pathway branches, already demonstrated in S. cerevisiae, will enable low-cost production of many high-value BIAs.

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X-domain of peptide synthetases recruits oxygenases crucial for glycopeptide biosynthesis

Non-ribosomal peptide synthetase (NRPS) mega-enzyme complexes are modular assembly lines that are involved in the biosynthesis of numerous peptide metabolites independently of the ribosome¹. The multiple interactions between catalytic domains within the NRPS machinery are further complemented by additional interactions with external enzymes, particularly focused on the final peptide maturation process. An important class of NRPS metabolites that require extensive external modification of the NRPS-bound peptide are the glycopeptide antibiotics (GPAs), which include vancomycin and teicoplanin^{2, 3}. These clinically relevant peptide antibiotics undergo cytochrome P450-catalysed oxidative crosslinking of aromatic side chains to achieve their final, active conformation^{4, 5, 6, 7, 8, 9, 10, 11, 12}. However, the mechanism underlying the recruitment of the cytochrome P450 oxygenases to the NRPS-bound peptide was previously unknown. Here we show, through in vitro studies, that the X-domain^{13, 14}, a conserved domain of unknown function present in the final module of all GPA NRPS machineries, is responsible for the recruitment of oxygenases to the NRPS-bound peptide to perform the essential side-chain crosslinking. X-ray crystallography shows that the X-domain is structurally related to condensation domains, but that its amino acid substitutions render it catalytically inactive. We found that the X-domain recruits cytochrome P450 oxygenases to the NRPS and determined the interface by solving the structure of a P450–X-domain complex. Additionally, we demonstrated that the modification of peptide precursors by oxygenases in vitro—in particular the installation of the second crosslink in GPA biosynthesis—occurs only in the presence of the X-domain. Our results indicate that the presentation of peptidyl carrier protein (PCP)-bound substrates for oxidation in GPA biosynthesis requires the presence of the NRPS X-domain to ensure conversion of the precursor peptide into a mature aglycone, and that the carrier protein domain alone is not always sufficient to generate a competent substrate for external cytochrome P450 oxygenases.




Domain labels for NRPS proteins (Tcp9–12): A, adenylation (selected amino acids indicated above the module: Hpg, 4-hydroxyphenylglycine; Dpg, 3,5-dihydroxyphenylglycine); C, condensation; E, epimerization; T, thiolation/peptidyl carrier protein (PCP); TE, thioesterase; X, domain of unknown function. Essential P450-catalysed aglycone rigidification takes place through crosslinking of aromatic side chains (OxyA–C, OxyE). Each crosslinking reaction is performed by a specific Oxy protein, with the products of each Oxy protein indicated schematically; standard ring nomenclature is indicated on the teicoplanin aglycone in red lettering.

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Complex archaea that bridge the gap between prokaryotes and eukaryotes

The origin of the eukaryotic cell remains one of the most contentious puzzles in modern biology. Recent studies have provided support for the emergence of the eukaryotic host cell from within the archaeal domain of life, but the identity and nature of the putative archaeal ancestor remain a subject of debate. Here we describe the discovery of ‘Lokiarchaeota’, a novel candidate archaeal phylum, which forms a monophyletic group with eukaryotes in phylogenomic analyses, and whose genomes encode an expanded repertoire of eukaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities. 

Our results provide strong support for hypotheses in which the eukaryotic host evolved from a bona fide archaeon, and demonstrate that many components that underpin eukaryote-specific features were already present in that ancestor. This provided the host with a rich genomic ‘starter-kit’ to support the increase in the cellular and genomic complexity that is characteristic of eukaryotes.


a, Schematic overview of the metagenomics approach. BI, Bayesian inference; ML, maximum likelihood. b, Bayesian phylogeny of concatenated alignments comprising 36 conserved phylogenetic marker proteins using sophisticated models of protein evolution (Methods), showing eukaryotes branching within Lokiarchaeota. Numbers above and below branches refer to Bayesian posterior probability and maximum-likelihood bootstrap support values, respectively. Posterior probability values above 0.7 and bootstrap support values above 70 are shown. Scale indicates the number of substitutions per site. c, Phylogenetic breakdown of the Lokiarchaeum proteome, in comparison with proteomes of Korarchaeota, Aigarchaeota (Caldiarchaeum) and Miscellaneous Crenarchaeota Group (MCG) archaea. Category ‘Other’ contains proteins assigned to the root of cellular organisms, to viruses and to unclassified proteins.

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