Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis

Other than the Methanobacteriales and Methanomassiliicoccales, the characteristics of archaea that inhabit the animal microbiome are largely unknown. Methanimicrococcus blatticola, a member of the Methanosarcinales, currently reunites two unique features within this order: it is a colonizer of the animal digestive tract and can only reduce methyl compounds with H2 for methanogenesis, a increasingly recognized metabolism in the archaea and whose origin remains debated. To understand the origin of these characteristics, we have carried out a large-scale comparative genomic analysis. We infer the loss of more than a thousand genes in M. blatticola, by far the largest genome reduction across all Methanosarcinales. These include numerous elements for sensing the environment and adapting to more stable gut conditions, as well as a significant remodeling of the cell surface components likely involved in host and gut microbiota interactions. Several of these modifications parallel those previously observed in phylogenetically distant archaea and bacteria from the animal microbiome, suggesting large-scale convergent mechanisms of adaptation to the gut. Strikingly, M. blatticola has lost almost all genes coding for the H4MPT methyl branch of the Wood–Ljungdahl pathway (to the exception of mer), a phenomenon never reported before in any member of Class I or Class II methanogens. The loss of this pathway illustrates one of the evolutionary processes that may have led to the emergence of methyl-reducing hydrogenotrophic methanogens, possibly linked to the colonization of organic-rich environments (including the animal gut) where both methyl compounds and hydrogen are abundant.

Structure and mechanism of a dehydratase/decarboxylase enzyme couple involved in polyketide β-methyl branch incorporation

Complex polyketides of bacterial origin are biosynthesised by giant assembly-line like megaenzymes of the type 1 modular polyketide synthase (PKS) class. The trans-AT family of modular PKSs, whose biosynthetic frameworks diverge significantly from those of the archetypal cis-AT type systems represent a new paradigm in natural product enzymology. One of the most distinctive enzymatic features common to trans-AT PKSs is their ability to introduce methyl groups at positions β to the thiol ester in the growing polyketide chain. This activity is achieved through the action of a five protein HCS cassette, comprising a ketosynthase, a 3-hydroxy-3-methylglutaryl-CoA synthase, a dehydratase, a decarboxylase and a dedicated acyl carrier protein. Here we report a molecular level description, achieved using a combination of X-ray crystallography, in vitro enzyme assays and site-directed mutagenesis, of the bacillaene synthase dehydratase/decarboxylase enzyme couple PksH/PksI, responsible for the final two steps in β-methyl branch installation in this trans-AT PKS. Our work provides detailed mechanistic insight into this biosynthetic peculiarity and establishes a molecular framework for HCS cassette enzyme exploitation and manipulation, which has future potential value in guiding efforts in the targeted synthesis of functionally optimised ‘non-natural’ natural products.

Genomic expansion of archaeal lineages resolved from deep Costa Rica sediments

Numerous archaeal lineages are known to inhabit marine subsurface sediments, although their distributions, metabolic capacities and interspecies interactions are still not well understood. Abundant and diverse archaea were recently reported in Costa Rica (CR) margin subseafloor sediments recovered during IODP Expedition 334. Here, we recover metagenome-assembled genomes (MAGs) of archaea from the CR-margin and compare them to their relatives from shallower settings. We describe 31 MAGs of 6 different archaeal lineages (Lokiarchaeota, Thorarchaeota, Heimdallarchaeota, Bathyarcheota, Thermoplasmatales and Hadesarchaea) and thoroughly analyze representative MAGs from the phyla Lokiarchaeota and Bathyarchaeota. Our analysis suggests the potential capabilities of Lokiarchaeota members to anaerobically degrade aliphatic and aromatic hydrocarbons. We show it is genetically possible and energetically feasible for Lokiarchaeota to degrade benzoate if they associate with organisms using nitrate, nitrite and sulfite as electron acceptors, which suggests a possibility of syntrophic relationships between Lokiarchaeota and nitrite and sulfite reducers. The novel Bathyarchaeota lineage possesses an incomplete methanogenesis pathway lacking the methyl co-enzyme M reductase complex and encodes a non-canonical acetogenic pathway potentially coupling methylotrophy to acetogenesis via the methyl branch of Wood-Ljundahl pathway. These novel metabolic characteristics suggest the potential of this Bathyarchaeota lineage to be a transition between methanogenic and acetogenic Bathyarchaeota lineages. This work substantially expands our knowledge about the metabolic function repertoire of marine benthic archaea.

Modification of Montmorillonite with Diamine Surfactants

Sodium montmorillonite (Na-MMT) was modified with various type of diamine surfactants. The modification imparts hydrophobic characters of MMT, thus enhancing its compatibility and dispersibility in polymer matrix. In this research, pristine MMT was modified with three types of diamine surfactants, namely, 1,3 diaminopropane (DAP), 1,8 diamino octane (DAO) and 1,5 diamino-2-Methyl pentane (DAMP). These diamines have different molecular structures where DAP has a short linear structure, DAO has eight carbons while DAMP has a methyl branch on its backbone. The modification was carried via cationic exchange process. X-ray diffraction (XRD) analysis showed the enhancement of d-spacing of MMT galleries and the formation of intercalated structure with the incorporation of diamines. Overall, type of diamines did not give significant effect on the d-spacing values with DAMP-MMT exhibited a slightly higher d-spacing at 13. 36 Å. The presence of methyl branch on the DAMP backbone was thought provide more spacing for the diamine to intercalate through the MMT gallery. Meanwhile, the detection of –NH bending amine group at 1470 cm-1 on the Fourier infrared (FTIR) spectra, corresponding to the free surfactant tail, had confirmed the successfulness of cationic exchange reaction between the diamines and MMT surface.

Self-assembly of long chain fatty acids: effect of a methyl branch

The morphology and molecular conformation of monolayers of straight chain and methyl-branched fatty acids have been investigated by VSFS and AFM, revealing domains in the latter case, due to inverse micellar packing constraints.

Isomerization of alkyl branched alkynoic acids

Acetylenic acids are isomerized by alkali metal amides of 1,3-diaminopropane to 3,5-dienoic acids. An acid with a methyl branch at C-3 separating the carboxyl from the triple bond is rearranged to a mixture of the terminal alkynoic acid and two isomeric 3,5-dienoic acids. The corresponding 4-methyl compound affords the terminal alkynoic acid, one 3,5-dienoic acid, and two cyclized products, cis- and trans-3-methyl-5-(octylidene)-1-cyclopentanecarboxylic acids. Propargylic acids branched at C-5 and C-6 are rearranged to the appropriately substituted 3,5-dienoic acids in moderate yield.