scholarly journals Reclassification of SLC22 Transporters: Analysis of OAT, OCT, OCTN, and other Family Members Reveals 8 Functional Subgroups

2019 ◽  
Author(s):  
Darcy Engelhart ◽  
Jeffry C. Granados ◽  
Da Shi ◽  
Milton Saier ◽  
Michael Baker ◽  
...  
Keyword(s):  
Uric Acid ◽  
Sequence Similarity ◽  
Organic Anion ◽  
Signaling Molecules ◽  
In Vitro Assays ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
In Vivo Models ◽  
Protein Motifs

AbstractAmong transporters, the SLC22 family is emerging as a central hub of endogenous physiology. The family consists of organic anion transporters (OATs), organic cation transporters (OCTs) and zwitterion transporters (OCTNs). Despite being known as “drug” transporters, these multi-specific, oligo-specific, and relatively mono-specific transporters facilitate the movement of metabolites and key signaling molecules. An in-depth reanalysis supports a reassignment of these proteins into eight functional subgroups with four new subgroups arising from the previously defined OAT subclade. These OAT subgroups are: OATS1 (SLC22A6, SLC22A8, and SLC22A20), OATS2 (SLC22A7), OATS3 (SLC22A11, SLC22A12, and Slc22a22), and OATS4 (SLC22A9, SLC22A10, SLC22A24, and SLC22A25). We propose merging the OCTN (SLC22A4, SLC22A5, and Slc22a21) and OCT-related (SLC22A15 and SLC22A16) subclades into the OCTN/OCTN-related subgroup. Functional support for the eight subgroups comes from network analysis of data from GWAS, in vivo models, and in vitro assays. These data emphasize shared substrate specificity of SLC22 transporters for characteristic metabolites such as prostaglandins, uric acid, carnitine, creatinine, and estrone sulfate. Some important subgroup associations include: OATS1 with metabolites, signaling molecules, uremic toxins and odorants, OATS2 with cyclic nucleotides, OATS3 with uric acid, OATS4 with conjugated sex hormones, particularly etiocholanolone glucuronide, OCT with monoamine neurotransmitters, and OCTN/OCTN-related with ergothioneine and carnitine derivatives. The OAT-like and OAT-related subgroups remain understudied and therefore do not have assigned functionality. Relatedness within subgroups is supported by multiple sequence alignments, evolutionarily conserved protein motifs, genomic localization, and tissue expression. We also highlight low level sequence similarity of SLC22 members with other non-transport proteins. Our data suggest that the SLC22 family can work among itself, as well as with other transporters and enzymes, to optimize levels of numerous metabolites and signaling molecules, as proposed by the Remote Sensing and Signaling Theory.

scholarly journals Analysis of the diversity of the glycoside hydrolase family 130 in mammal gut microbiomes reveals a novel mannoside-phosphorylase function

2020 ◽  
Vol 6 (10) ◽  
Author(s):  
Ao Li ◽  
Elisabeth Laville ◽  
Laurence Tarquis ◽  
Vincent Lombard ◽  
David Ropartz ◽  
...  
Keyword(s):  
Glycoside Hydrolase ◽  
Sequence Similarity ◽  
Gut Bacteria ◽  
Glycoside Hydrolase Family ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Content Type ◽  
Multiple Sequence Alignments ◽  
Hydrolase Family

Mannoside phosphorylases are involved in the intracellular metabolization of mannooligosaccharides, and are also useful enzymes for the in vitro synthesis of oligosaccharides. They are found in glycoside hydrolase family GH130. Here we report on an analysis of 6308 GH130 sequences, including 4714 from the human, bovine, porcine and murine microbiomes. Using sequence similarity networks, we divided the diversity of sequences into 15 mostly isofunctional meta-nodes; of these, 9 contained no experimentally characterized member. By examining the multiple sequence alignments in each meta-node, we predicted the determinants of the phosphorolytic mechanism and linkage specificity. We thus hypothesized that eight uncharacterized meta-nodes would be phosphorylases. These sequences are characterized by the absence of signal peptides and of the catalytic base. Those sequences with the conserved E/K, E/R and Y/R pairs of residues involved in substrate binding would target β-1,2-, β-1,3- and β-1,4-linked mannosyl residues, respectively. These predictions were tested by characterizing members of three of the uncharacterized meta-nodes from gut bacteria. We discovered the first known β-1,4-mannosyl-glucuronic acid phosphorylase, which targets a motif of the Shigella lipopolysaccharide O-antigen. This work uncovers a reliable strategy for the discovery of novel mannoside-phosphorylases, reveals possible interactions between gut bacteria, and identifies a biotechnological tool for the synthesis of antigenic oligosaccharides.

scholarly journals Systems Biology Analysis Reveals Eight SLC22 Transporter Subgroups, Including OATs, OCTs, and OCTNs

2020 ◽  
Vol 21 (5) ◽  
pp. 1791 ◽  
Author(s):  
Darcy C. Engelhart ◽  
Jeffry C. Granados ◽  
Da Shi ◽  
Milton H. Saier Jr. ◽  
Michael E. Baker ◽  
...  
Keyword(s):  
Cyclic Nucleotides ◽  
Signaling Molecules ◽  
In Vitro Assays ◽  
Specific Substrate ◽  
In Vivo Models ◽  
Using Data ◽  
Carnitine Derivatives ◽  
Metabolite Network

The SLC22 family of OATs, OCTs, and OCTNs is emerging as a central hub of endogenous physiology. Despite often being referred to as “drug” transporters, they facilitate the movement of metabolites and key signaling molecules. An in-depth reanalysis supports a reassignment of these proteins into eight functional subgroups, with four new subgroups arising from the previously defined OAT subclade: OATS1 (SLC22A6, SLC22A8, and SLC22A20), OATS2 (SLC22A7), OATS3 (SLC22A11, SLC22A12, and Slc22a22), and OATS4 (SLC22A9, SLC22A10, SLC22A24, and SLC22A25). We propose merging the OCTN (SLC22A4, SLC22A5, and Slc22a21) and OCT-related (SLC22A15 and SLC22A16) subclades into the OCTN/OCTN-related subgroup. Using data from GWAS, in vivo models, and in vitro assays, we developed an SLC22 transporter-metabolite network and similar subgroup networks, which suggest how multiple SLC22 transporters with mono-, oligo-, and multi-specific substrate specificity interact to regulate metabolites. Subgroup associations include: OATS1 with signaling molecules, uremic toxins, and odorants, OATS2 with cyclic nucleotides, OATS3 with uric acid, OATS4 with conjugated sex hormones, particularly etiocholanolone glucuronide, OCT with neurotransmitters, and OCTN/OCTN-related with ergothioneine and carnitine derivatives. Our data suggest that the SLC22 family can work among itself, as well as with other ADME genes, to optimize levels of numerous metabolites and signaling molecules, involved in organ crosstalk and inter-organismal communication, as proposed by the remote sensing and signaling theory.

scholarly journals Hypouricemic and Anti-oxidant Effects of Chrysanthemum indicum L. and Cornus officinalis In Vitro and In Vivo Models

2021 ◽  
Author(s):  
Ok-kyung Kim ◽  
Jeong Moon Yun ◽  
Minhee Lee ◽  
Dakyung Kim ◽  
Jeongmin Lee
Keyword(s):  
Uric Acid ◽  
Organic Anion ◽  
Organic Anion Transporter ◽  
In Vivo Models ◽  
Expression Levels ◽  
Cornus Officinalis ◽  
Anion Transporter ◽  
Chrysanthemum Indicum

Abstract Background: Hyperuricemia, abnormally excess accumulation of uric acid, is caused by an imbalance between the production and excretion of uric acid and is a major cause of gout. We compared the effects of extracts from Chrysanthemum indicum L. (Ci) and Cornus officinalis Siebold & Zucc (Co) on hyperuricemia, both individually and in combination (FSU-CC), Methods: We used hypoxanthine-treated human liver cancer (HepG2) cells and primary mouse renal proximal tubule cells for in vitro model, and potassium oxonate-induced hyperuricemic mice for in vivo model.Results: We found that treatment of Ci, Co, and FSU-CC suppressed the activity of xanthine oxidase and mRNA expression of xanthine dehydrogenase, while inducing an increase in the expression levels of the organic anion transporter 1 and organic anion transporter 3 proteins and a decrease in the expression levels of glucose transporter 9 and urate transporter 1 proteins. Particularly, treatment and supplementation with FSU-CC showed stronger effects than those of supplementation with either Ci or Co alone. We observed that the excretion of creatinine and uric acid in the combination of Ci and Co was higher than that observed in their individual supplementations and was similar to that of the normal group.Conclusions: Therefore, our data suggest that a combination of Ci and Co may potentially be used for the development of effective natural anti-hyperuricemic functional foods.

scholarly journals Probiotic and Functional Properties of Limosilactobacillus reuteri INIA P572

Nutrients ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1860
Author(s):  
Patricia Diez-Echave ◽  
Izaskun Martín-Cabrejas ◽  
José Garrido-Mesa ◽  
Susana Langa ◽  
Teresa Vezza ◽  
...  
Keyword(s):  
In Vitro Assays ◽  
Immunomodulatory Activity ◽  
Probiotic Properties ◽  
Protective Effects ◽  
Mice Model ◽  
In Vivo Models ◽  
Food Borne ◽  
Gastrointestinal Conditions

Limosilactobacillus reuteri INIA P572 is a strain able to produce the antimicrobial compound reuterin in dairy products, exhibiting a protective effect against some food-borne pathogens. In this study, we investigated some probiotic properties of this strain such as resistance to gastrointestinal passage or to colonic conditions, reuterin production in a colonic environment, and immunomodulatory activity, using different in vitro and in vivo models. The results showed a high resistance of this strain to gastrointestinal conditions, as well as capacity to grow and produce reuterin in a human colonic model. Although the in vitro assays using the RAW 264.7 macrophage cell line did not demonstrate direct immunomodulatory properties, the in vivo assays using a Dextran Sulphate Sodium (DSS)-induced colitic mice model showed clear immunomodulatory and protective effects of this strain.

Curcumin: Natural Antimicrobial and Anti Inflammatory Agent

2021 ◽  
pp. 1-8
Author(s):  
Pehlivanović Belma ◽  
Čaklovica Kenan ◽  
Lagumdžija Dina ◽  
Omerović Naida ◽  
Žiga Smajić Nermina ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Protein Denaturation ◽  
Dose Range ◽  
In Vitro Assays ◽  
Natural Antimicrobial ◽  
In Vivo Models ◽  
Vitro Assay ◽  
Inflammatory Agent ◽  
Anti Inflammatory

The pursuance of novel antimicrobial and anti-inflammatory agents has been expanding due to a significant need for more efficient pharmacotherapy of various infections and chronic diseases. During the last decade, pharmacokinetics, pharmacodynamics and pharmacological properties of curcumin have been extensively studied. The aim of the present study was to evaluate the antibacterial activity of curcumin against both Gram-positive and Gram-negative bacteria as well as its antifungal activity by using in vitro agar well diffusion assay. Moreover, the anti-inflammatory activity of curcumin was determined with in vitro assay of inhibition of protein denaturation. Results demonstrated wide antimicrobial activity of curcumin upon all of the test bacteria and fungi. The strongest activity of curcumin was observed at a concentration of 0.50 mg/ml against S. aureus, L. monocytogenes, E. coli, P. aeruginosa and C. albicans, resulting in a maximum zone of inhibition of 14.7 mm, 14.3 mm, 13.7 mm, 10.7 mm and 10.7 mm, respectively. Findings suggested that the antimicrobial activity of curcuminis dependent upon the concentrations. Furthermore, results demonstrated high effectiveness of curcumin compared to standard acetylsalicylic acid in inhibiting heat-induced protein denaturation, which activity is also depended upon the concentrations. The present study emphasises the potential application of curcumin as a natural antimicrobial and anti-inflammatory agent. However, findings of this study are restricted to in vitro assays and consideration should be given to conducting a study involving wider dose range test substances as well as including further research on in vivo models.

scholarly journals Molecular and Symptom Analysis Reveal the Presence of New Phytoplasmas Associated with Sugarcane Grassy Shoot Disease in India

Plant Disease ◽  
2007 ◽  
Vol 91 (11) ◽  
pp. 1413-1418 ◽  
Author(s):  
Kanchan Nasare ◽  
Amit Yadav ◽  
Anil K. Singh ◽  
K. B. Shivasharanappa ◽  
Y. S. Nerkar ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sequence Similarity ◽  
Pcr Amplification ◽  
Saccharum Officinarum ◽  
23S Rrna ◽  
Rrna Gene ◽  
Sequence Alignments ◽  
High Sequence Similarity ◽  
Multiple Sequence ◽  
Very High

A total of 240 sugarcane (Saccharum officinarum) plants showing phenotypic symptoms of sugarcane grassy shoot (SCGS) disease were collected from three states of India, Maharashtra, Karnataka, and Uttar Pradesh. Phytoplasmas were detected in all symptomatic samples by the polymerase chain reaction (PCR) amplification of phytoplasma-specific 16S rRNA gene and 16S-23S rRNA spacer region (SR) sequences. No amplification was observed when DNA from asymptomatic plant samples was used as a template. Sixteen samples were selected on the basis of phenotypic symptoms and geographic location, and cloning and sequencing of the 16S rRNA and spacer regions were performed. Multiple sequence alignments of the 16S rRNA sequences revealed that they share very high sequence similarity with phytoplasmas of rice yellow dwarf, 16SrXI. However, the 16S-23S rRNA SR sequence analysis revealed that while the majority of phytoplasmas shared very high (>99%) sequence similarity with previously reported sugarcane phytoplasmas, two of them, namely BV2 (DQ380342) and VD7 (DQ380343), shared relatively low sequence similarity (79 and 84%, respectively). Therefore, these two phytoplasmas may be previously unreported ones that cause significant yield losses in sugarcane in India.

scholarly journals In vitro methods for the study of microbial biofilms

2011 ◽  
Vol 1 (1) ◽  
pp. 031-040 ◽  
Keyword(s):  
Ferrite Nanoparticles ◽  
In Vitro Assays ◽  
Confocal Laser ◽  
Microbial Biofilm ◽  
In Vivo Models ◽  
Microbial Biofilms ◽  
Human Pathology ◽  
Biofilm Development

The emergence of microbial biofilm related infections (bacterial and fungal) has a significant impact for the human pathology in the entire world. The understanding of microbial infections related to the biofilm development on tissues or indwelling devices was possible by using different qualitative and quantitative in vitro assays, in continuous and discontinuous systems, as well as in vivo models. A necessary step for obtaining more standardized, reliable and comparable results among different laboratories is the simplification of the available techniques used for investigating the biofilm formation and properties, including the biofilms susceptibility to antibiotics. The aim of the present study was to exemplify a series of available methods for the investigation of in vitro microbial biofilms developed on inert substrata, as well as coated with ferrite nanoparticles, using as experimental model a Sacharomyces cerevisiae strain. Microbial biofilm architecture was directly examined by two microscopy techniques (inverted microscopy and confocal laser microscopy scanning). The in vitro study of the influence of suspended ferrite nanoparticles on planktonic cells growth, adherence and consecutive biofilm development on inert substrata was performed by using a simple microtiter method.

scholarly journals Pyridoxal-5′-phosphate as an oxygenase cofactor: Discovery of a carboxamide-forming, α-amino acid monooxygenase-decarboxylase

2018 ◽  
Vol 115 (5) ◽  
pp. 974-979 ◽  
Author(s):  
Ying Huang ◽  
Xiaodong Liu ◽  
Zheng Cui ◽  
Daniel Wiegmann ◽  
Giuliana Niro ◽  
...  
Keyword(s):  
Amino Acid ◽  
Flavin Adenine Dinucleotide ◽  
Sequence Similarity ◽  
In Vitro Assays ◽  
Complete Conversion ◽  
Mechanistic Studies ◽  
Biochemical Characteristics ◽  
Biochemical Studies ◽  
Isomeric Product

Capuramycins are antimycobacterial antibiotics that consist of a modified nucleoside named uridine-5′-carboxamide (CarU). Previous biochemical studies have revealed that CarU is derived from UMP, which is first converted to uridine-5′-aldehyde in a reaction catalyzed by the dioxygenase CapA and subsequently to 5′-C-glycyluridine (GlyU), an unusual β–hydroxy-α-amino acid, in a reaction catalyzed by the pyridoxal-5′-phosphate (PLP)-dependent transaldolase CapH. The remaining steps that are necessary to furnish CarU include decarboxylation, O atom insertion, and oxidation. We demonstrate that Cap15, which has sequence similarity to proteins annotated as bacterial, PLP-dependent l-seryl-tRNA(Sec) selenium transferases, is the sole catalyst responsible for complete conversion of GlyU to CarU. Using a complementary panel of in vitro assays, Cap15 is shown to be dependent upon substrates O2 and (5′S,6′R)-GlyU, the latter of which was unexpected given that (5′S,6′S)-GlyU is the isomeric product of the transaldolase CapH. The two products of Cap15 are identified as the carboxamide-containing CarU and CO2. While known enzymes that catalyze this type of chemistry, namely α-amino acid 2-monooxygenase, utilize flavin adenine dinucleotide as the redox cofactor, Cap15 remarkably requires only PLP. Furthermore, Cap15 does not produce hydrogen peroxide and is shown to directly incorporate a single O atom from O2 into the product CarU and thus is an authentic PLP-dependent monooxygenase. In addition to these unusual discoveries, Cap15 activity is revealed to be dependent upon the inclusion of phosphate. The biochemical characteristics along with initiatory mechanistic studies of Cap15 are reported, which has allowed us to assign Cap15 as a PLP-dependent (5′S,6′R)-GlyU:O2 monooxygenase-decarboxylase.

scholarly journals Virulence of the emerging pathogen, Burkholderia pseudomallei, depends upon the O-linked oligosaccharyltransferase, PglL

2020 ◽  
Vol 15 (4) ◽  
pp. 241-257
Author(s):  
Samuel J Willcocks ◽  
Carmen Denman ◽  
Felipe Cia ◽  
Elizabeth McCarthy ◽  
Jon Cuccui ◽  
...  
Keyword(s):  
Burkholderia Pseudomallei ◽  
Galleria Mellonella ◽  
In Vitro Assays ◽  
In Vivo Models ◽  
Bacterial Fitness ◽  
Isogenic Mutants ◽  
Type Strains ◽  
Broad Role

Aim: We sought to characterize the contribution of the O-OTase, PglL, to virulence in two Burkholderia spp. by comparing isogenic mutants in Burkholderia pseudomallei with the related species, Burkholderia thailandensis. Materials & methods: We utilized an array of in vitro assays in addition to Galleria mellonella and murine in vivo models to assess virulence of the mutant and wild-type strains in each Burkholderia species. Results: We found that pglL contributes to biofilm and twitching motility in both species. PglL uniquely affected morphology; cell invasion; intracellular motility; plaque formation and intergenus competition in B. pseudomallei. This mutant was attenuated in the murine model, and extended survival in a vaccine-challenge experiment. Conclusion: Our data support a broad role for pglL in bacterial fitness and virulence, particularly in B. pseudomallei.

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