Phosphorus-31 nuclear magnetic resonance study of the effect of pentachlorophenol (PCP) on the physiologies of PCP-degrading microorganisms

Bile acid fitness determinants of a Bacteroides fragilis isolate from a human pouchitis patient

IMPORTANCE

The Gram-negative bacterium Bacteroides fragilis is a common member of the human gut microbiota that colonizes multiple host niches and can influence human physiology through a variety of mechanisms. Identification of genes that enable B. fragilis to grow across a range of host environments has been impeded in part by the relatively limited genetic tractability of this species. We have developed a high-throughput genetic resource for a B. fragilis strain isolated from a UC pouchitis patient. Bile acids limit microbial growth and are altered in abundance in UC pouches, where B. fragilis often blooms. Using this resource, we uncovered pathways and processes that impact B. fragilis fitness in bile and that may contribute to population expansions during bouts of gut inflammation.

Bile acid fitness determinants of a Bacteroides fragilis isolate from a human pouchitis patient

Bacteroides fragilis comprises 1-5% of the gut microbiota in healthy humans but can expand to >50% of the population in ulcerative colitis (UC) patients experiencing inflammation. The mechanisms underlying such microbial blooms are poorly understood, but the gut of UC patients has physicochemical features that differ from healthy patients and likely impact microbial physiology. For example, levels of the secondary bile acid deoxycholate (DC) are highly reduced in the ileoanal J-pouch of UC colectomy patients. We isolated a B. fragilis strain from a UC patient with pouch inflammation (i.e. pouchitis) and developed it as a genetic model system to identify genes and pathways that are regulated by DC and that impact B. fragilis fitness in DC and crude bile. Treatment of B. fragilis with a physiologically relevant concentration of DC reduced cell growth and remodeled transcription of one-quarter of the genome. DC strongly induced expression of chaperones and select transcriptional regulators and efflux systems and downregulated protein synthesis genes. Using a barcoded collection of ≈50,000 unique insertional mutants, we further defined B. fragilis genes that contribute to fitness in media containing DC or crude bile. Genes impacting cell envelope functions including cardiolipin synthesis, cell surface glycosylation, and systems implicated in sodium-dependent bioenergetics were major bile acid fitness factors. As expected, there was limited overlap between transcriptionally regulated genes and genes that impacted fitness in bile when disrupted. Our study provides a genome-scale view of a B. fragilis bile response and genetic determinants of its fitness in DC and crude bile.

Exploring the membrane toxicity of decabromodiphenyl ethane (DBDPE): Based on cell membranes and lipid membranes model

Decabromodiphenyl ethane (DBDPE) is widely used in industry as an alternative to the decabromodiphenyl ether (BDEs). The large-scale use of DBDPE could lead to rapid growth of the human accumulation level of DBDPE. However, the biophysics of accumulation of DBDPE in cell membranes, as one of determinants of DBDPE metabolism is not clear. In the present study, detailed observations of cell lactate dehydrogenase (LDH) and reactive oxygen species (ROS) levels measurements proved that the DBDPE exposure to cell could result in significant cell membrane damage by concentration-dependent manners. The fluorescence anisotropy analysis supported the evidence that high concentration DBDPE bound decreased membrane fluidity significantly. Besides it, a detailed molecular dynamic (MD) simulation was approached to investigate the effects of DBDPE on the DPPC (dipalmitoyl phosphatidylcholine) phospholipid bilayer, which was constructed as the model of cell membrane. The molecular dynamic simulation revealed that DBDPE molecules can easily enter the membrane from the aqueous phase. Under the concentration of a threshold, the DBDPE molecules tended to aggregate inside the DPPC bilayer and caused pore formation. The bound of high concentration of DBDPE could result in significant variations in DPPC bilayer with a less dense, more disorder and rougher layer. The knowledge about DBDPEs interactions with lipid membranes is fundamentally essential to understand the in vivo process of DBDPE and the physical basis for the toxicity of DBDPE in cell membranes.

Headgroup structure and fatty acid chain length of the acidic phospholipids modulate the interaction of membrane mimetic vesicles with the antimicrobial peptide protegrin-1

The interaction of protegrin-1 (PG-1), a small beta-sheet antimicrobial peptide with acidic phospholipid model membranes was investigated by differential scanning calorimetry. We found that PG-1 can distinguish between liposomes of the anionic phospholipids DPPG, DPPS and DPPA, eventhough the headgroups of these phospholipids all have the same net charge and they carry the same hydrocarbon chains. Specifically, PG-1 had only a minor effect on the thermotropic phase behavior of DPPA liposomes, while it interacted preferentially with the fluid phase of DPPS. Furthermore, PG-1 could induce a phase separation in DPPG liposomes resulting in the formation of peptide-rich domains even at low concentrations of the peptide. However, this peptide-rich domain was not evident when the fatty acyl chains were longer or shorter by two carbon atoms. In addition, PG-1 can also form peptide-rich domains in DPPS vesicles but only at high concentrations of the peptide. These results suggest that in addition to an overall negative charge, the structural features of the phospholipid headgroups, lipid packing and thus membrane fluidity will influence the interaction with PG-1, thereby modulating its biological activity.

Fluorescent methods to study DNA, RNA, proteins and cytoplasmic membrane polarization in the pentachlorophenol-mineralizing bacterium Sphingomonas sp. UG30 during nutrient starvation in water

The effect of sodium pentachlorophenolate (NaPCP) exposure on the nutrient-starved pentachlorophenol (PCP)-mineralizing bacterium Sphingomonas sp. UG30 was assessed using fluorescent methods to measure DNA, RNA, total cellular protein, and cytoplasmic membrane proteins. UG30 cells were inoculated into sterilized Speed River (Guelph, ON, Canada) water samples in the presence of 50, 100, and 250 ppm NaPCP. No marked changes were observed in the total cellular DNA, RNA or protein levels over 90 d, indicating the macromolecular composition of UG30 was not affected by both nutrient limitation and NaPCP. Total cell counts as determined by DAPI staining also did not change over 90 d. Over the same period, viable counts decreased with increasing concentrations of NaPCP. At 250 ppm NaPCP, viable cell counts decreased over 6 orders of magnitude after 1 hr exposure. Cell numbers partially recovered once NaPCP was degraded. The UG30 cytoplasmic membrane polarization ratio also decreased after NaPCP was depleted. The decreased polarization value at the end of the study period suggested the UG30 membrane was more fluid and that this increase in fluidity was due to nutrient starvation effects rather than exposure to NaPCP. These results indicated that UG30 is a robust organism that is able to degrade NaPCP even under adverse conditions and fluorescent methods are useful for determining macromolecular concentrations and cytoplasmic membrane polarization values.

Distribution of pentachlorophenol in phospholipid bilayers: a molecular dynamics study

Molecular dynamics computer simulations of pentachlorophenol (PCP) in palmitoyl-oleoyl-phosphatidylethanolamine and palmitoyl-oleoyl-phosphatidylcholine lipid bilayers were carried out to investigate the distribution of PCP and the effects of PCP on the phospholipid bilayer structure. Starting from two extreme starting structures, including PCP molecules outside the lipid bilayer, the PCP distribution converges in simulations of up to 50 ns. PCP preferentially occupies the region between the carbonyl groups and the double bonds in the acyl chains of the lipid molecules in the bilayer. In the presence of PCP, the lipid chain order increases somewhat in both chains, and the average tilt angle of the lipid chains decreases. The increase in the lipid chain order in the presence of PCP was more pronounced in the palmitoyl-oleoyl-phosphatidylcholine bilayer compared to the palmitoyl-oleoyl-phosphatidylethanolamine bilayer. The number of trans conformations of lipid chain dihedrals does not change significantly. PCP aligns parallel to the alkyl chains of the lipid to optimize the packing in the dense ordered chain region of the bilayer. The hydroxyl group of PCP forms hydrogen bonds with both water and lipid oxygen atoms in the water/lipid interface region.

Characterization of tetrachlorohydroquinone reductive dehalogenase from Sphingomonas sp. UG30

Tetrachlorohydroquinone reductive dehalogenase (PcpC) is the second of three enzymes that catalyze the initial degradation of pentachlorophenol in Sphingomonas sp. UG30 and several other bacterial strains. The UG30 PcpC shares a high degree (94%) of primary sequence identity with the well-studied PcpC from Sphingobium chlorophenolicum ATCC 39723. Significant differences, however, were observed between the two PcpC enzymes in some of their functional and kinetic properties. The temperature optimum of the UG30 PcpC is 10 degrees C higher and the pH optimum is approximately 2 units higher than the S. chlorophenolicum PcpC. In addition, the S. chlorophenolicum PcpC is subject to inhibition by the substrate tetrachlorohydroquinone (TCHQ), and this has necessitated the use of a mutant enzyme, which was not inhibited by TCHQ, for kinetic studies. In contrast, the UG30 PcpC was not inhibited by TCHQ and this may allow detailed kinetic and mechanistic studies using the wild-type enzyme.

Towards a structure-function analysis of bovine lactoferricin and related tryptophan- and arginine-containing peptides

The iron-binding protein lactoferrin is a multifunctional protein that has antibacterial, antifungal, antiviral, antitumour, anti-inflammatory, and immunoregulatory properties. All of these additional properties appear to be related to its highly basic N-terminal region. This part of the protein can be released in the stomach by pepsin cleavage at acid pH. The 25-residue antimicrobial peptide that is released is called lactoferricin. In this work, we review our knowledge about the structure of the peptide and attempt to relate this to its many functions. Microcalorimetry and fluorescence spectroscopy data regarding the interaction of the peptide with model membranes show that binding to net negatively charged bacterial and cancer cell membranes is preferred over neutral eukaryotic membranes. Binding of the peptide destabilizes the regular membrane bilayer structure. Residues that are of particular importance for the activity of lactoferricin are tryptophan and arginine. These two amino acids are also prevalent in "penetratins", which are regions of proteins or synthetic peptides that can spontaneously cross membranes and in short hexapeptide antimicrobial peptides derived through combinatorial chemistry. While the antimicrobial, antifungal, antitumour, and antiviral properties of lactoferricin can be related to the Trp/Arg-rich portion of the peptide, we suggest that the anti-inflammatory and immunomodulating properties are more related to a positively charged region of the molecule, which, like the alpha- and beta-defensins, may act as a chemokine. Few small peptides are involved in as wide a range of host defense functions as bovine and human lactoferricin.

Cardiolipin: a proton trap for oxidative phosphorylation

The role of specific lipid structures in biological membranes has been elusive. There are hundreds of them in nature. Why has nature made them? How do they aid in the functioning of membrane proteins? Genetics with its 'knock out' organisms declares that functions persist in the absence of any particular lipid. Nonetheless some lipids, such as cardiolipin (CL), are associated with particular functions in the cell. It may merely expand the variety of culture conditions (pH, temperature, etc.) under which the wild-type organism survives. This article explores a unique role of CL as a proton trap within membranes that conduct oxidative phosphorylation and therefore the synthesis of ATP. CL's pK(2) (above 8.0) provides a role for it as a headgroup proton trap for oxidative phosphorylation. It suggests why CL is found in membranes that pump protons. The high pK(2) also indicates that the headgroup has but one negative charge in the neutral pH range. Data on the binding of CL to all of the oxidative phosphorylation proteins suggest that the CL may aggregate the oxidative phosphorylation proteins into a patch while it restricts pumped protons within its headgroup domain - supplying protons to the ATP synthase with minimal changes in the bulk phase pH.