Fig 2 - available from: Microbial Cell Factories
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Interkingdom alignment and in silico modeling of ClC family antiporters. a Amino acid alignments for external (left) and internal (right) gating domains in genes annotated with COG0038 (H + /Cl − antiporter ClcA) in L. reuteri, E. coli, mouse, and human (see Additional file 3: Table S3 for gene/genome identifiers). Antiporters and channels are grouped separately and sequence logos (top) denote the conservation of each residue in the antiporter class. Gating glutamate residues are marked (★). Residues are colored by side chain chemistry (aromatic-black, acidic-red, basic-blue, nonpolar-yellow, polar-green). b The ribbon model of ClcA is shown in red, overlapped with models for EriC (white) and EriC2 (blue). Gating glutamate residues are displayed as space-filling atomic surfaces. The external gate is displayed in green (ClcA E148, EriC E144, EriC2 E139), and the internal gate is highlighted in yellow (ClcA E203, EriC E199, EriC2 E193). Models were generated with SwissModel, and visualized with MOLMOL
Source publication
Background:
Histamine is a key mediator of the anti-inflammatory activity conferred by the probiotic organism Lactobacillus reuteri ATCC PTA 6475 in animal models of colitis and colorectal cancer. In L. reuteri, histamine synthesis and secretion requires L-histidine decarboxylase and a L-histidine/histamine exchanger. Chloride channel (ClC)-family...
Contexts in source publication
Context 1
... and external gating regions required for coupled proton/chloride antiport. By searching the functional annotations of the L. reuteri 6475 genome for the ClC proton/chloride antiporter (COG0038) we identified four potential genes of interest in L. reuteri, and compared them to their homologs from E. coli, human, and mouse. The alignments in Fig. 2a demonstrate that only two of these genes (EriC and EriC2) are true antiporters as evidenced by the presence of the gating glutamates in both the external and internal domains. Natively, these proteins function as homodimers, with each pore able to carry out independent proton/chloride exchange. Using an E. coli template (ClcA, PDB: ...
Context 2
... amino acid sequences of EriC and EriC2. For both proteins the overall sequence identity to the template for the modeled regions was 29% (data not shown). However, the sequence identity for the ± 10 amino acids around the internal and external glutamates was 52% and 43%, indicating greater reliability of the models for the two regions of interest (Fig. ...
Context 3
... repeated measures ANOVA analysis with Dunnett's multiple comparison test was used to determine statistical differences between strains. A pilot experiment (N = 6) was performed as above with wild type L. reuteri co-stained with pHrodo Red as described above and Hoechst 33342 DNA stain (10 μg/mL final concentration, Ex 353 nm/Em 483 nm) to ensure minimal loss of whole cell signal during the vacuum plate assay (Additional file 2: Figure S2). Representative images of stained wild type L. reuteri under native and standard curve conditions were taken on a Zeiss AxioImager Z1 microscope with a Hamamatsu Electron Multiplier CCD camera. ...
Citations
... 17,50 Studies have demonstrated that the alteration in chloride transporter activity can modulate histidine metabolism by altering intracellular pH and membrane potential in Lactobacillus sp. 51 Additionally, the chloride channel in E. coli has been shown to serve as an electrical shunt, preventing excessive hyperpolarization of the inner membrane and facilitating the amino acid transport. 17 These findings suggest that the attenuation of biofilm formation in the mutant I may be related to its effect on chloride transporter activity, which potentially modulates TA biosynthesis by altering intracellular pH and membrane potential. ...
Enterococcus faecalis (E. faecalis) is one of the major pathogenic bacteria responsible for surgical site infections. Biofilm infections are major hospital‐acquired infections. Previous studies suggested that ions could regulate biofilm formation in microbes. Volatile anesthetics, frequently administered in surgical setting, target ion channels. Here, we investigated the role of ion channels/transporters and volatile anesthetics in the biofilm formation by E. faecalis MMH594 strain and its ion transporter mutants. We found that a chloride transporter mutant significantly reduced biofilm formation compared to the parental strain. Downregulation of teichoic acid biosynthesis in the chloride transporter mutant impaired biofilm matrix formation and cellular adhesion, leading to mitigated biofilm formation. Among anesthetics, isoflurane exposure enhanced biofilm formation in vitro and in vivo. The upregulation of de novo purine biosynthesis pathway by isoflurane exposure potentially enhanced biofilm formation, an essential process for DNA, RNA, and ATP synthesis. We also demonstrated that isoflurane exposure to E. faecalis increased cyclic‐di‐AMP and extracellular DNA production, consistent with the increased purine biosynthesis. We further showed that isoflurane enhanced the enzymatic activity of phosphoribosyl pyrophosphate synthetase (PRPP‐S). With the hypothesis that isoflurane directly bound to PRPP‐S, we predicted isoflurane binding site on it using rigid docking. Our study provides a better understanding of the underlying mechanisms of E. faecalis biofilm formation and highlights the potential impact of an ion transporter and volatile anesthetic on this process. These findings may lead to the development of novel strategies for preventing E. faecalis biofilm formation and improving patient outcomes in clinical settings.
... Evolutionary history in comparison with environmental filtering leads to larger changes in ecological preferences of microorganisms (Thomas et al., 2016;Morrissey et al., 2019). Furthermore, microbial response traits to pH seem to be deeply phylogenetically conserved (Martiny et al., 2015), which is related to the critical effect of pH on bacterial diversity and community structure as well as cell membrane structure and ion transporters (Fierer and Jackson, 2006;Rousk et al., 2010;Hall et al., 2019;Yang et al., 2019). In this study, the abundant PHB displayed stronger phylogenetic signals revealing that abundant PHB may have higher phylogenetic niche conservatism in respect to their evolutionary history, i.e. microbial adaptability to ongoing environmental changes (Losos, 2008). ...
Phosphorus deficiency is a prevailing environmental phenomenon in natural environments and phosphate-solubilizing bacteria, e.g., phosphatase (phoD)-harboring bacteria, can enhance phosphorus availability. Yet, it remains largely unclear about ecological roles and diversity maintenance of rare and abundant phoD-harboring bacteria (PHB) in natural environments. We collected soils and sediments from wetlands on the Tibetan Plateau, and estimated community composition and diversity maintenance of rare and abundant PHB by using Illumina MiSeq sequencing and multiple statistical analyses (e.g., environmental breadth and phylogenetic signal). We found significant decays of community similarities against geographical distance at taxonomic and phylogenetic levels. Rare PHB presented higher α- and β-diversity as well as broader environmental breadths, whereas abundant taxa displayed stronger phylogenetic signals and weaker environmental constraint. Stochastic processes governed PHB community assembly in terms of rare and abundant taxa, and pH played decisive roles in shaping assembly, diversity, and composition of rare and abundant PHB communities. Consequently, community diversity of rare rather than abundant PHB showed significantly negative effect on alkaline phosphatase (ALP) activity, and environmental pH rather than ALP affected more on phosphorus availability. According to abundance and presence-absence analyses, our results emphasized distinct differences in distribution patterns and diversity maintenance mechanisms of rare and abundant PHB. Our findings could help to predict diversity loss of PHB in response to environmental changes, and might guide the environmental protection for wetlands on the Tibetan Plateau via changing environmental pH.
... Additionally, patients with UAP had higher abundance of Lactobacillaceae, which was significantly positively correlated with the serum histidine. This may be because Lactobacillaceae was involved in the metabolism and absorption of histidine [35,36]. Similarly, another clinical study also demonstrated that the CAD patients had increased Lactobacillales abundance [37]. ...
Background:
Unstable angina pectoris (UAP) is a type of Coronary artery disease (CAD) characterized by a series of angina symptoms. Insulin-like growth factor 1 (IGF-1) system may be related to CAD. However, the correlation between the IGF-1 system, metabolism, and gut microbiota has not been studied. In the present study, we investigated the alterations of serum IGF-1 system, metabolomics, and gut microbiota in patients with UAP.
Methods:
Serum and stool samples from healthy volunteers and UAP patients were collected. Serum metabolomics, PAPP-A, IGF-1, IGFBP-4, STC2, hs-CRP, TNF-α, and IL-6 were detected in serum samples by LC-MS, and commercial ELISA kits, respectively. Fecal short-chain fatty acids (SCFAs) were measured by gas chromatography. 16S rDNA was used to measure the changes of the gut microbiota. The correlation of the above indicators was analyzed.
Results:
There were 24 upregulated and 31 downregulated metabolites in the serum of UAP patients compared to those in the controls. Pathway analysis showed that these metabolites were enriched in pathways including linoleic acid metabolism, amino acid metabolism, starch metabolism, sucrose metabolism, and citrate cycle (TCA cycle), etc. Additionally, the UAP patients had lower fecal levels of 2-hydroxyisobutyric acid and succinic acid. 16S rDNA sequencing results showed that the relative abundances of Bacteroidetes, Synergistetes, Lactobacillaceae, Burkholderiaceae, Synergistaceae, and Subdoligranulum were significantly higher in the UAP patients than the healthy subjects. Moreover, the UAP patients had lower serum IGF-1, IGFBP-4, and STC2 and higher serum inflammatory cytokines (hs-CRP, TNF-α, and IL-6) levels than the healthy controls. Furthermore, there was a strong correlation between serum amino acids and IL-6, which played an important role in the development of UAP.
Conclusions:
These results indicated that the UAP patients had decreased serum IGF-1 level and imbalanced amino acids metabolism, which may be caused by the altered gut microbiota. It may provide a new therapeutic strategy for unstable angina pectoris.
... The filter plate was then loaded into a Synergy HT plate reader with incubation at 37°C. A citrate buffer series was used to examine intracellular pH due to the wide pH range and its successful application with other lactic acid bacteria [43]. Fluorescence (ex: 560 nm/em: 590 nm) was recorded every 5 min over a 50 min timeframe, first in a common buffer (pH 7.6, min 0-10), then in the test buffers at pH 3-8 (min . ...
Background
Bifidobacteria are commensal microbes of the mammalian gastrointestinal tract. In this study, we aimed to identify the intestinal colonization mechanisms and key metabolic pathways implemented by Bifidobacterium dentium .
Results
B. dentium displayed acid resistance, with high viability over a pH range from 4 to 7; findings that correlated to the expression of Na+/H+ antiporters within the B. dentium genome. B. dentium was found to adhere to human MUC2+ mucus and harbor mucin-binding proteins. Using microbial phenotyping microarrays and fully-defined media, we demonstrated that in the absence of glucose, B. dentium could metabolize a variety of nutrient sources. Many of these nutrient sources were plant-based, suggesting that B. dentium can consume dietary substances. In contrast to other bifidobacteria, B. dentium was largely unable to grow on compounds found in human mucus; a finding that was supported by its glycosyl hydrolase (GH) profile. Of the proteins identified in B. dentium by proteomic analysis, a large cohort of proteins were associated with diverse metabolic pathways, indicating metabolic plasticity which supports colonization of the dynamic gastrointestinal environment.
Conclusions
Taken together, we conclude that B. dentium is well adapted for commensalism in the gastrointestinal tract.
... The precursor of histamine is histidine, and hdc also promotes the formation of histamine. The types of hdc are pyridoxal 5′-phosphate-dependent enzyme and pyruvate-dependent enzyme according to the difference of coenzyme (Hall et al., 2019). Histidine decarboxylase was detected in three strains of M. caseolyticus in this study (Y ZC 2, Y ZC 3, and Y YXN 2), and the three strains could produce histamine. ...
Objectives
Accumulation of nitrite and biogenic amines (BAs) in fermented meat products is a matter of public health concern. The study aimed to screen nitrite-degrading and BA-degrading strains from sour porridges and sausages and bacon products in China.
Materials and Methods
After screening out 12 strains, the degradation of nitrite, the degradation of BAs, the activities of nitrite-reducing enzymes, and the detection of genes involved in the BAs were assessed by spectrophotometry method with hydrochloric acid naphthalene ethylenediamine, high-performance liquid chromatography, GENMED kit, and polymerase chain reaction, respectively.
Results
Pediococcus pentosaceus labelled M SZ1 2 and M GC 2, Lactobacillus plantarum labelled M SZ2 2, and Staphylococcus xylosus labelled Y CC 3 were selected. The activity of nitrite-reducing enzyme in M SZ2 2 was 2.663 units/mg. The degradation rate of total BAs of M SZ2 2 was 93.24%. The degradation rates of nitrite and BAs of M SZ1 2 were 86.49% and 37.87%, respectively. The activity of nitrite-reducing enzyme in M SZ1 2 was up to 1.962 units/mg. M GC 2 showed higher degradation rates of nitrite (89.19%) and Y CC 3 showed higher degradation rates of BAs (36.16%). The genes encoding the multicopper oxidases (suf I/D2EK17) were detected in the four strains, which also did not contain BAs (histidine decarboxylase (hdc), tyrosine decarboxylase (tdc), ornithine decarboxylase (odc), lysine decarboxylase (ldc)) formation encoding genes.
Conclusion
These four strains (M SZ1 2, M GC 2, M SZ2 2, and Y CC 3) are promising candidates to use as starter cultures for nitrite and BAs in fermented sausages.
Lactobacillus reuteri ( L. reuteri) , a type of Lactobacillus spp., is a gut symbiont that can colonize many mammals. Since it was first isolated in 1962, a multitude of research has been conducted to investigate its function and unique role in different diseases as an essential probiotic. Among these, the basic functions, beneficial effects, and underlying mechanisms of L. reuteri have been noticed and understood profoundly in intestinal diseases. The origins of L. reuteri strains are diverse, with humans, rats, and piglets being the most common. With numerous L. reuteri strains playing significant roles in different intestinal diseases, DSM 17938 is the most widely used in humans, especially in children. The mechanisms by which L. reuteri improves intestinal disorders include protecting the gut barrier, suppressing inflammation and the immune response, regulating the gut microbiota and its metabolism, and inhibiting oxidative stress. While a growing body of studies focused on L. reuteri , there are still many unknowns concerning its curative effects, clinical safety, and precise mechanisms. In this review, we initially interpreted the basic functions of L. reuteri and its related metabolites. Then, we comprehensively summarized its functions in different intestinal diseases, including inflammatory bowel disease, colorectal cancer, infection-associated bowel diseases, and pediatric intestinal disorders. We also highlighted some important molecules in relation to the underlying mechanisms. In conclusion, L. reuteri has the potential to exert a beneficial impact on intestinal diseases, which should be further explored to obtain better clinical application and therapeutic effects.
