Characterization of polar membrane lipids of the extremely halophilic bacterium Salinibacter ruber and possible role of cardiolipin

Metabolites from halophilic bacterial isolates Bacillus VITPS16 are cytotoxic against HeLa cells

The present study was aimed at evaluating the cytotoxic potential of selected halophilic bacterial metabolites. The use of the metabolomics approach in identifying the unexplored bioactive metabolites from halophilic bacterial isolate reduces time and complex experiments. In our study, we used UV/Visible spectroscopy, LC-MS/MS, and NMR to identify the metabolites present in the methanolic extract of the halophilic bacterium Bacillus VITPS16. MTT assay revealed that metabolite fractions (S1-79.61% and S2-85.74%) possess cytotoxic activity. Colonogenic assay confirmed the cytotoxic potential of the fractions and apoptosis assays showed that 83.37% of the cells undergo apoptosis at 10 mg/mL concentration (MF-S2). The DNA binding studies revealed the metabolite fraction interacts with DNA resulting in cytotoxicity. The study states that MF- S2 induced an antiproliferative effect that led to apoptosis through DNA binding as one of the possible pathways. The toxicity analysis using zebrafish indicated that the metabolite fractions are non-toxic even at 10 mg/mL concentration. Fraction MF-S2 is found to contain phosphoethanolamines, glycerophospholipids, sphingolipids, apocarotenoid, enigmol and its analogue, ankaflavin and flavonoid type of metabolites, which have been previously reported to have anti-cancer activity.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02724-9.

A systematic review of the interaction and effects generated by antimicrobial metallic substituents in bone tissue engineering

Changes brought about by metal ions and metal nanoparticles within bacterial cells and the damage caused to the cellular membrane upon contact with negatively charged surface components.

Carbon isotopic composition of lipid biomarkers from an endoevaporitic gypsum crust microbial mat reveals cycling of mineralized organic carbon

Microbial mats that inhabit gypsum deposits in ponds at Guerrero Negro, Baja California Sur, Mexico, developed distinct pigmented horizons that provided an opportunity to examine the fixation and flow of carbon through a trophic structure and, in conjunction with previous phylogenetic analyses, to assess the diagenetic fates of molecular δ¹³ C biosignatures. The δ¹³ C values of individual biomarker lipids, total carbon, and total organic carbon (TOC) were determined for each of the following horizons: tan-orange (TO) at the surface, green (G), purple (P), and olive-black (OB) at the bottom. δ¹³ C of individual fatty acids from intact polar lipids (IPFA) in TO were similar to δ¹³ C of dissolved inorganic carbon (DIC) in the overlying water column, indicating limited discrimination by cyanobacteria during CO₂ fixation. δ¹³ C_TOC of the underlying G was 3‰ greater than that of TO. The most δ¹³ C-depleted acetogenic lipids in the upper horizons were the cyanobacterial biomarkers C₁₇ n-alkanes and polyunsaturated fatty acids. Bishomohopanol was 4 to 7‰ enriched, relative to alkanes and intact polar fatty acids (IPFA), respectively. Acyclic C₂₀ isoprenoids were depleted by 14‰ relative to bishomohopanol. Significantly, ∆[δ¹³ C_TOC  - δ¹³ C_∑IPFA ] increased from 6.9‰ in TO to 14.7‰ in OB. This major trend might indicate that ¹³ C-enriched residual organic matter accumulated at depth. The permanently anoxic P horizon was dominated by anoxygenic phototrophs and sulfate-reducing bacteria. P hosted an active sulfur-dependent microbial community. IPFA and bishomohopanol were ¹³ C-depleted relative to upper crust by 7 and 4‰, respectively, and C₂₀ isoprenoids were somewhat ¹³ C-enriched. Synthesis of alkanes in P was evidenced only by ¹³ C-depleted n-octadecane and 8-methylhexadecane. In OB, the marked increase of total inorganic carbon δ¹³ C (δ¹³ C_TIC ) of >6‰ perhaps indicated terminal mineralization. This δ¹³ C_TIC increase is consistent with degradation of the osmolyte glycine betaine by methylotrophic methanogens and loss of ¹³ C-depleted methane from the mat.

A genome-scale metabolic network reconstruction of extremely halophilic bacterium Salinibacter ruber

A genome-scale metabolic network reconstruction of Salinibacter ruber DSM13855 is presented here. To our knowledge, this is the first metabolic model of an organism in the phylum Rhodothermaeota. This model, which will be called iMB631, was reconstructed based on genomic and biochemical data available on the strain Salinibacter ruber DSM13855. This network consists of 1459 reactions, 1363 metabolites and 631 genes. Model evaluation was performed based on existing biochemical data in the literature and also by performing laboratory experiments. For growth on different carbon sources, we show that iMB631 is able to correctly predict the growth in 91% of cases where growth has been observed experimentally and 83% of conditions in which S. ruber did not grow. The F-score was 93%, demonstrating a generally acceptable performance of the model. Based on the predicted flux distributions, we found that under certain autotrophic condition, a reductive tricarboxylic acid cycle (rTCA) has fluxes in all necessary reactions to support autotrophic growth. To include special metabolites of the bacterium, salinixanthin biosynthesis pathway was modeled based on the pathway proposed recently. For years, main glucose consumption pathway has been under debates in S. ruber. Using flux balance analysis, iMB631 predicts pentose phosphate pathway, rather than glycolysis, as the active glucose consumption method in the S. ruber.

Gemcitabine diphosphate choline is a major metabolite linked to the Kennedy pathway in pancreatic cancer models in vivo

BACKGROUND

The modest benefits of gemcitabine (dFdC) therapy in patients with pancreatic ductal adenocarcinoma (PDAC) are well documented, with drug delivery and metabolic lability cited as important contributing factors. We have used a mouse model of PDAC: KRAS(G12D); p53(R172H); pdx-Cre (KPC) that recapitulates the human disease to study dFdC intra-tumoural metabolism.

METHODS

LC-MS/MS and NMR were used to measure drug and physiological analytes. Cytotoxicity was assessed by the Sulphorhodamine B assay.

RESULTS

In KPC tumour tissue, we identified a new, Kennedy pathway-linked dFdC metabolite (gemcitabine diphosphate choline (GdPC)) present at equimolar amounts to its precursor, the accepted active metabolite gemcitabine triphosphate (dFdCTP). Utilising additional subcutaneous PDAC tumour models, we demonstrated an inverse correlation between GdPC/dFdCTP ratios and cytidine triphosphate (CTP). In tumour homogenates in vitro, CTP inhibited GdPC formation from dFdCTP, indicating competition between CTP and dFdCTP for CTP:phosphocholine cytidylyltransferase (CCT). As the structure of GdPC precludes entry into cells, potential cytotoxicity was assessed by stimulating CCT activity using linoleate in KPC cells in vitro, leading to increased GdPC concentration and synergistic growth inhibition after dFdC addition.

CONCLUSIONS

GdPC is an important element of the intra-tumoural dFdC metabolic pathway in vivo.

Molecular and lipid biomarker analysis of a gypsum-hosted endoevaporitic microbial community

Modern evaporitic microbial ecosystems are important analogs for understanding the record of earliest life on Earth. Although mineral-depositing shallow-marine environments were prevalent during the Precambrian, few such environments are now available today for study. We investigated the molecular and lipid biomarker composition of an endoevaporitic gypsarenite microbial mat community in Guerrero Negro, Mexico. The 16S ribosomal RNA gene-based phylogenetic analyses of this mat corroborate prior observations indicating that characteristic layered microbial communities colonize gypsum deposits world-wide despite considerable textural and morphological variability. Membrane fatty acid analysis of the surface tan/orange and lower green mat crust layers indicated cell densities of 1.6 × 10(9) and 4.2 × 10(9)  cells cm(-3) , respectively. Several biomarker fatty acids, ∆7,10-hexadecadienoic, iso-heptadecenoic, 10-methylhexadecanoic, and a ∆12-methyloctadecenoic, correlated well with distributions of Euhalothece, Stenotrophomonas, Desulfohalobium, and Rhodobacterales, respectively, revealed by the phylogenetic analyses. Chlorophyll (Chl) a and cyanobacterial phylotypes were present at all depths in the mat. Bacteriochlorophyl (Bchl) a and Bchl c were first detected in the oxic-anoxic transition zone and increased with depth. A series of monomethylalkanes (MMA), 8-methylhexadecane, 8-methylheptadecane, and 9-methyloctadecane were present in the surface crust but increased in abundance in the lower anoxic layers. The MMA structures are similar to those identified previously in cultures of the marine Chloroflexus-like organism 'Candidatus Chlorothrix halophila' gen. nov., sp. nov., and may represent the Bchl c community. Novel 3-methylhopanoids were identified in cultures of marine purple non-sulfur bacteria and serve as a probable biomarker for this group in the lower anoxic purple and olive-black layers. Together microbial culture and environmental analyses support novel sources for lipid biomarkers in gypsum crust mats.

Salinibacter: an extremely halophilic bacterium with archaeal properties

The existence of large number of a member of the Bacteroidetes in NaCl-saturated brines in saltern crystallizer ponds was first documented in 1999 based on fluorescence in situ hybridization studies. Isolation of the organism and its description as Salinibacter ruber followed soon. It is a rod-shaped, red-orange pigmented, extreme halophile that grows optimally at 20-30% salt. The genus is distributed worldwide in hypersaline environments. Today, the genus Salinibacter includes three species, and a somewhat less halophilic relative, Salisaeta longa, has also been documented. Although belonging to the Bacteria, Salinibacter shares many features with the Archaea of the family Halobacteriaceae that live in the same habitat. Both groups use KCl for osmotic adjustment of their cytoplasm, both mainly possess salt-requiring enzymes with a large excess of acidic amino acids, and both contain different retinal pigments: light-driven proton pumps, chloride pumps, and light sensors. Salinibacter produces an unusual carotenoid, salinixanthin that forms a light antenna and transfers energy to the retinal group of xanthorhodopsin, a light-driven proton pump. Other unusual features of Salinibacter and Salisaeta include the presence of novel sulfonolipids (halocapnine derivatives). Salinibacter has become an excellent model for metagenomic, biogeographic, ecological, and evolutionary studies.

Isolation of Squarebop I bacteriorhodopsin from biomass of coastal salterns

Squarebop I bacteriorhodopsin is a light-activated proton pump present in the membranes of the archeon Haloquadratum walsbyi, a square-shaped organism representing 50-60% of microbial population in the crystallizer ponds of the coastal salterns. Here we describe: (1) the operating mode of a bioreactor designed to concentrate the saltern biomass through a microfiltration process based on polyethersulfone hollow fibers; (2) the isolation of Squarebop I bacteriorhodopsin from solubilized biomass by means of a single chromatographic step; (3) tightly bound lipids to the isolated and purified protein as revealed by MALDI-TOF/MS analysis; (4) the photoactivity of Squarebop I bacteriorhodopsin isolated from environmental samples by flash spectroscopy. Yield of the isolation process is 150 μg of Squarebop I bacteriorhodopsin from 1l of 25-fold concentrated biomass. The possibility of using the concentrated biomass of salterns, as renewable resource for the isolation of functional bacteriorhodopsin and possibly other valuable bioproducts, is briefly discussed.

Snapshot of virus evolution in hypersaline environments from the characterization of a membrane-containing Salisaeta icosahedral phage 1

The multitude of archaea and bacteria inhabiting extreme environments has only become evident during the last decades. As viruses apply a significant evolutionary force to their hosts, there is an inherent value in learning about viruses infecting these extremophiles. In this study, we have focused on one such unique virus-host pair isolated from a hypersaline environment: an icosahedral, membrane-containing double-stranded DNA virus--Salisaeta icosahedral phage 1 (SSIP-1) and its halophilic host bacterium Salisaeta sp. SP9-1 closely related to Salisaeta longa. The architectural principles, virion composition, and the proposed functions associated with some of the ORFs of the virus are surprisingly similar to those found in viruses belonging to the PRD1-adenovirus lineage. The virion structure, determined by electron cryomicroscopy, reveals that the bulk of the outer protein capsid is composed of upright standing pseudohexameric capsomers organized on a T = 49 icosahedral lattice. Our results give a comprehensive description of a halophilic virus-host system and shed light on the relatedness of viruses based on their virion architecture.

The acylhalocapnines of halophilic bacteria: structural details of unusual sulfonate sphingoids

Sulfonate sphingoids or sulfonolipids are bioactive unusual compounds found in members of the Bacteroidetes family. The present report describes the structures of sulfonolipids of halophilic bacteria, sharing structural similarity with compounds of fungal origin inhibiting the serine palmitoyl transferase and with capnines, known as antagonists of von Willebrandt factor. Two sulfonolipids (SL1 and SL2) were isolated from the lipid extract of the halophile Salisaeta longa and analyzed by ESI-MS/MS. SL1 and SL2 structures have in common the long chain aminosulfonate 2-carboxy-2-amino-3,4-hydroxy-17 methyloctadec-5-ene-1-sulfonic for which the common name of halocapnine is suggested. The hydroxyl group on carbon 3 of aminosulfonate moiety is acylated: iso C15 and iso hydroxy C15 chains are present in SL1 and SL2, respectively. The levels of the two different sulfonolipids in the bacterium were found to be modulated by the proportion of sodium and magnesium ions in the environment.