scholarly journals Integrated Omics Strategy Reveals Cyclic Lipopeptides Empedopeptins from Massilia sp. YMA4 and Their Biosynthetic Pathway

Marine Drugs ◽  
2021 ◽  
Vol 19 (4) ◽  
pp. 209
Author(s):  
Shang-Tse Ho ◽  
Ying-Ning Ho ◽  
Chih Lin ◽  
Wei-Chen Hsu ◽  
Han-Jung Lee ◽  
...  
Keyword(s):  
Amino Acid ◽  
Antibiotic Activity ◽  
Bioactive Metabolites ◽  
Null Mutant ◽  
Bacterial Strains ◽  
Isolation And Purification ◽  
Cyclic Lipopeptides ◽  
A Genome ◽  
Mutant Strains ◽  
Integrated Omics

Empedopeptins—eight amino acid cyclic lipopeptides—are calcium-dependent antibiotics that act against Gram-positive bacteria such as Staphylococcus aureus by inhibiting cell wall biosynthesis. However, to date, the biosynthetic mechanism of the empedopeptins has not been well identified. Through comparative genomics and metabolomics analysis, we identified empedopeptin and its new analogs from a marine bacterium, Massilia sp. YMA4. We then unveiled the empedopeptin biosynthetic gene cluster. The core nonribosomal peptide gene null-mutant strains (ΔempC, ΔempD, and ΔempE) could not produce empedopeptin, while dioxygenase gene null-mutant strains (ΔempA and ΔempB) produced several unique empedopeptin analogs. However, the antibiotic activity of ΔempA and ΔempB was significantly reduced compared with the wild-type, demonstrating that the hydroxylated amino acid residues of empedopeptin and its analogs are important to their antibiotic activity. Furthermore, we found seven bacterial strains that could produce empedopeptin-like cyclic lipopeptides using a genome mining approach. In summary, this study demonstrated that an integrated omics strategy can facilitate the discovery of potential bioactive metabolites from microbial sources without further isolation and purification.

10 THE ROLE OF DIETARY L-SERINE IN THE REGULATION OF INTESTINAL MUCUS BARRIER DURING INFLAMMATION

2020 ◽  
Vol 26 (Supplement_1) ◽  
pp. S42-S42
Author(s):  
Kohei Sugihara ◽  
Nobuhiko Kamada
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Gut Microbiota ◽  
Control Diet ◽  
Bacterial Strains ◽  
Germ Free ◽  
Intestinal Mucus ◽  
Gnotobiotic Mice ◽  
Mucus Barrier

Abstract Background Recent accumulating evidence suggests that amino acids have crucial roles in the maintenance of intestinal homeostasis. In inflammatory bowel disease (IBD), amino acid metabolism is changed in both host and the gut microbiota. Among amino acids, L-serine plays a central role in several metabolic processes that are essential for the growth and survival of both mammalian and bacterial cells. However, the role of L-serine in intestinal homeostasis and IBD remains incompletely understood. In this study, we investigated the effect of dietary L-serine on intestinal inflammation in a murine model of colitis. Methods Specific pathogen-free (SPF) mice were fed either a control diet (amino acid-based diet) or an L-serine-deficient diet (SDD). Colitis was induced by the treatment of dextran sodium sulfate (DSS). The gut microbiome was analyzed by 16S rRNA sequencing. We also evaluate the effect of dietary L-serine in germ-free mice and gnotobiotic mice that were colonized by a consortium of non-mucolytic bacterial strains or the consortium plus mucolytic bacterial strains. Results We found that the SDD exacerbated experimental colitis in SPF mice. However, the severity of colitis in SDD-fed mice was comparable to control diet-fed mice in germ-free condition, suggesting that the gut microbiota is required for exacerbation of colitis caused by the restriction of dietary L-serine. The gut microbiome analysis revealed that dietary L-serine restriction fosters the blooms of a mucus-degrading bacterium Akkermansia muciniphila and adherent-invasive Escherichia coli in the inflamed gut. Consistent with the expansion of mucolytic bacteria, SDD-fed mice showed a loss of the intestinal mucus layer. Dysfunction of the mucus barrier resulted in increased intestinal permeability, thereby leading to bacterial translocation to the intestinal mucosa, which subsequently increased the severity of colitis. The increased intestinal permeability and subsequent bacterial translocation were observed in SDD-fed gnotobiotic mice that colonized by mucolytic bacteria. In contrast, dietary L-serine restriction did not alter intestinal barrier integrity in gnotobiotic mice that colonized only by non-mucolytic bacteria. Conclusion Our results suggest that dietary L-serine regulates the integrity of the intestinal mucus barrier during inflammation by limiting the expansion of mucus degrading bacteria.

scholarly journals Novel Amino Acid Derivatives of Quinolines as Potential Antibacterial and Fluorophore Agents

2020 ◽  
Vol 88 (4) ◽  
pp. 57
Author(s):  
Oussama Moussaoui ◽  
Rajendra Bhadane ◽  
Riham Sghyar ◽  
El Mestafa El Hadrami ◽  
Soukaina El Amrani ◽  
...  
Keyword(s):  
Amino Acid ◽  
Methyl Esters ◽  
Amino Acid Derivatives ◽  
Bacterial Strains ◽  
Fluorescent Properties ◽  
Topoisomerase Iv ◽  
Microdilution Method ◽  
Hydrolysis Of ◽  
Derivatives Of

A new series of amino acid derivatives of quinolines was synthesized through the hydrolysis of amino acid methyl esters of quinoline carboxamides with alkali hydroxide. The compounds were purified on silica gel by column chromatography and further characterized by TLC, NMR and ESI-TOF mass spectrometry. All compounds were screened for in vitro antimicrobial activity against different bacterial strains using the microdilution method. Most of the synthesized amino acid-quinolines show more potent or equipotent inhibitory action against the tested bacteria than their correspond esters. In addition, many of them exhibit fluorescent properties and could possibly be utilized as fluorophores. Molecular docking and simulation studies of the compounds at putative bacterial target enzymes suggest that the antimicrobial potency of these synthesized analogues could be due to enzyme inhibition via their favorable binding at the fluoroquinolone binding site at the GyrA subunit of DNA gyrase and/or the ParC subunit of topoisomerase-IV.

scholarly journals Identification and Characterization of the First Virulent Phages, Including a Novel Jumbo Virus, Infecting Ochrobactrum spp.

2020 ◽  
Vol 21 (6) ◽  
pp. 2096
Author(s):  
Przemyslaw Decewicz ◽  
Piotr Golec ◽  
Mateusz Szymczak ◽  
Monika Radlinska ◽  
Lukasz Dziewit
Keyword(s):  
Dna Methyltransferase ◽  
Wastewater Treatment Plants ◽  
Biogas Production ◽  
Genome Mining ◽  
Sewage Sample ◽  
Bacterial Strains ◽  
Regulatory Circuits ◽  
A Genome ◽  
Insightful Analysis

The Ochrobactrum genus consists of an extensive repertoire of biotechnologically valuable bacterial strains but also opportunistic pathogens. In our previous study, a novel strain, Ochrobactrum sp. POC9, which enhances biogas production in wastewater treatment plants (WWTPs) was identified and thoroughly characterized. Despite an insightful analysis of that bacterium, its susceptibility to bacteriophages present in WWTPs has not been evaluated. Using raw sewage sample from WWTP and applying the enrichment method, two virulent phages, vB_OspM_OC and vB_OspP_OH, which infect the POC9 strain, were isolated. These are the first virulent phages infecting Ochrobactrum spp. identified so far. Both phages were subjected to thorough functional and genomic analyses, which allowed classification of the vB_OspM_OC virus as a novel jumbo phage, with a genome size of over 227 kb. This phage encodes DNA methyltransferase, which mimics the specificity of cell cycle regulated CcrM methylase, a component of the epigenetic regulatory circuits in Alphaproteobacteria. In this study, an analysis of the overall diversity of Ochrobactrum-specific (pro)phages retrieved from databases and extracted in silico from bacterial genomes was also performed. Complex genome mining allowed us to build similarity networks to compare 281 Ochrobactrum-specific viruses. Analyses of the obtained networks revealed a high diversity of Ochrobactrum phages and their dissimilarity to the viruses infecting other bacteria.

scholarly journals Terminal deoxynucleotidyltransferase. Alignment of α- and β-subunits of the core enzyme along the primary translation product

1985 ◽  
Vol 227 (3) ◽  
pp. 1003-1007 ◽  
Author(s):  
C M Beach ◽  
S K Chan ◽  
T C Vanaman ◽  
M S Coleman
Keyword(s):  
Amino Acid ◽  
Nucleotide Sequence ◽  
Amino Acid Sequence ◽  
Beta Subunits ◽  
Isolation And Purification ◽  
C Terminus ◽  
Human Lymphoblast ◽  
Catalytically Active ◽  
Single Polypeptide ◽  
Dna Nucleotide Sequence

Terminal deoxynucleotidyltransferase exists in multiple Mr forms, all apparently generated from a single polypeptide of 62kDa. On isolation and purification, the smallest catalytically active protein of this enzyme consists of two subunits, alpha (12kDa) and beta (30kDa). Recently a complementary-DNA nucleotide sequence has been reported for a portion of the enzyme from human lymphoblast. We have pinpointed the locations of the alpha- and beta-subunits within the elucidated nucleotide sequence. From these data, the portions of the nucleotide sequence coding for the catalytically important area of the transferase can be estimated. Here the amino acid sequence of a number of tryptic peptides from calf alpha- and beta-subunits is presented. Because of the striking homology between the amino acid sequence of the calf enzyme and that predicted for human lymphoblast enzyme, it is possible for us to conclude that the alpha-subunit was generated from the C-terminus of the precursor protein and the beta-subunit was non-overlapping and proximal.

Isolation and Structural Characterization of Antioxidant Peptides from Degreased Apricot Seed Kernels

2018 ◽  
Vol 101 (5) ◽  
pp. 1661-1663 ◽  
Author(s):  
Haisheng Zhang ◽  
Jing Xue ◽  
Huanxia Zhao ◽  
Xinshuai Zhao ◽  
Huanhuan Xue ◽  
...  
Keyword(s):  
Amino Acid ◽  
Antioxidant Activities ◽  
Gel Filtration ◽  
Reversed Phase ◽  
Amino Acid Sequences ◽  
Seed Kernel ◽  
Antioxidant Peptides ◽  
Food Preservatives ◽  
Isolation And Purification ◽  
Rp Hplc

Abstract Background: The composition and sequence of amino acids have a prominent influence on the antioxidant activities of peptides. Objective: A series of isolation and purification experiments was conducted to explore the amino acid sequence of antioxidant peptides, which led to its antioxidation causes. Methods: The degreased apricot seed kernels were hydrolyzed by compound proteases of alkaline protease and flavor protease (3:2, u/u) to prepare apricot seed kernel hydrolysates (ASKH). ASKH were separated into ASKH-A and ASKH-B by dialysis bag. ASKH-B (MW < 3.5 kDa) was further separated into fractions by Sephadex G-25 and G-15 gel-filtration chromatography. Reversed-phase HPLC (RP-HPLC) was performed to separate fraction B4b into two antioxidant peptides (peptide B4b-4 and B4b-6). Results: The amino acid sequences were Val-Leu-Tyr-Ile-Trp and Ser-Val-Pro-Tyr-Glu, respectively. Conclusions: The results suggested that ASKH antioxidant peptides may have potential utility as healthy ingredients and as food preservatives due to their antioxidant activity. Highlights: Materials with regional characteristics were selected to explore, and hydrolysates were identified by RP-HPLC and matrix-assisted laser desorption ionization-time-of-flight-MS to obtain amino acid sequences.

scholarly journals The heparin–protein complex of ox liver capsule. Isolation and chemical characterization

1969 ◽  
Vol 112 (2) ◽  
pp. 167-172 ◽  
Author(s):  
A Serafini-Fracassini ◽  
J J Durward ◽  
L. Floreani
Keyword(s):  
Amino Acid ◽  
Column Chromatography ◽  
Catalytic Hydrogenation ◽  
Protein Complex ◽  
Amino Acid Analysis ◽  
Chemical Characterization ◽  
Isolation And Purification ◽  
Liver Capsule ◽  
Heparin Fractions ◽  
Good Agreement

1. A procedure for the isolation and purification of the heparin–protein complex from ox liver capsule, based on the solubility properties of mucopolysaccharide–cetylpyridinium complexes, is described. 2. The yield of the heparin–protein complex with this method averages 35mg./100g. of dry ox liver capsule. 3. The results of analyses on the polysaccharide show good agreement with values previously published for purified heparin fractions. 4. The amino acid analysis of the protein component shows several similarities to that of chondromucoprotein. 5. The results of β-carbonyl elimination, either with or without catalytic hydrogenation, and column chromatography after β-elimination, show that the polysaccharide is covalently bound to the protein.

ANTIMICROBIAL STUDIES OF NEWLY SYNTHESIZED 1H-BENZOTRIAZOLE-1-ACETYL-AMINO ACID METHYL ESTERS /PEPTIDE DERIVATIVES

INDIAN DRUGS ◽  
2013 ◽  
Vol 50 (12) ◽  
pp. 27-33
Author(s):  
K. Kaur ◽  
◽  
R Kaur ◽  
A. Kaur
Keyword(s):  
Amino Acid ◽  
1H Nmr Spectroscopy ◽  
Methyl Esters ◽  
Penicillium Expansum ◽  
Antimicrobial Compounds ◽  
Bacterial Strains ◽  
Antimicrobial Studies ◽  
Acid Methyl ◽  
Peptide Derivatives ◽  
Amino Acid Methyl Esters

Benzotriazole-1-acetic acid was coupled with amino acid methyl esters/ dipeptides/ tripeptides/tetrapeptides in the presence of DCC as a coupling agent and NMM as a base under continuous stirringfor 36 hrs. The reactions were monitored by TLC. The newly synthesized compounds were analyzedand the structures were confirmed by IR and 1H NMR spectroscopy. The synthesized compounds weretested against bacterial strains Bacillus subtilis, Staphylococcus aureus and Escherichia coli by usingciprofloxacin as standard in the concentration of 20?g/mL. All the compounds were also tested againstfungal strains Candida albicans, Aspergillus niger and Penicillium expansum by using fluconazole asstandard in the concentration of 10?g/mL. Compounds 1, 2, 3 and 4 were found to be more potent antimicrobial compounds.

Direction of chromosome rearrangements in Saccharomyces cerevisiae by use of his3 recombinational substrates

1988 ◽  
Vol 8 (10) ◽  
pp. 4370-4380
Author(s):  
M T Fasullo ◽  
R W Davis
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Chromosomal Dna ◽  
Yeast Saccharomyces Cerevisiae ◽  
Coding Sequences ◽  
Mutant Strains ◽  
Genetic Techniques ◽  
Orthogonal Field ◽  
His3 Gene ◽  
Tandem Duplications

We used the his3 recombinational substrates (his3 fragments) to direct large interchromosomal (translocations) and intrachromosomal (deletions and tandem duplications) rearrangements in the yeast Saccharomyces cerevisiae. In strains completely deleted for the wild-type HIS3 gene, his3 fragments, one containing a deletion of 5' amino acid coding sequences and the other containing a deletion of 3' amino acid coding sequences, were first placed at preselected sites by homologous recombination. His+ revertants that arose via spontaneous mitotic recombination between the two his3 fragments were selected. This strategy was used to direct rearrangements in both RAD52+ and rad52 mutant strains. Translocations occurred in the RAD52+ genetic background and were characterized by orthogonal field alternating gel electrophoresis of yeast chromosomal DNA and by standard genetic techniques. An unexpected translocation was also identified in which HIS3 sequences were amplified. Two types of tandem duplications of the GAL(7, 10, 1) locus were also directed, and one type was not observed in rad52 mutants. Recombination mechanisms are discussed to account for these differences.

Low pH reduces the activity of ceftolozane/tazobactam in human urine, but confirms current breakpoints for urinary tract infections

2019 ◽  
Vol 75 (3) ◽  
pp. 593-599 ◽  
Author(s):  
Alina Karoline Nussbaumer-Pröll ◽  
Sabine Eberl ◽  
Birgit Reiter ◽  
Thomas Stimpfl ◽  
Christoph Dorn ◽  
...  
Keyword(s):  
Urinary Tract ◽  
Urinary Tract Infections ◽  
Human Urine ◽  
Negative Impact ◽  
Low Ph ◽  
Antibiotic Activity ◽  
Clinical Isolates ◽  
Acidic Ph ◽  
Bacterial Strains ◽  
Tract Infections

Abstract Background Acidic pH has been shown to impact the antibiotic activity of non-β-lactams in urine. Objectives To investigate the in vitro activity of ceftolozane/tazobactam compared with meropenem at different pH settings in urine. Methods We determined the MICs for 30 clinical isolates of Escherichia coli, 25 clinical isolates of Klebsiella pneumoniae and 24 clinical isolates of Proteus mirabilis in pooled human urine and standard growth medium at pH 5 and 7. Time–kill curves were produced for one representative clinical isolate of tested bacterial strains in urine at pH 5, 6 and 7 for both antibiotics at concentrations above and below the MIC. HPLC analysis of the stability of ceftolozane/tazobactam and meropenem was performed at different pH values. Results The median MICs of both antibiotics were up to 8-fold higher at pH 5 than at pH 7. Bacterial growth of E. coli was not impacted by pH, while for K. pneumoniae and P. mirabilis low pH slightly reduced growth. Compared with pH 7, pH 5 resulted in a significant decrease in antibiotic activity with a delta of up to 3 log10 bacterial counts after 24 h. Impact of acidic pH was lowest for P. mirabilis; however, this strain metabolically increased the pH during experiments. Stability was not impacted by low pH. Conclusions Acidic pH had a significant negative impact on the activity of ceftolozane/tazobactam and meropenem in urine. Considering concentrations achieved in urine, our results confirm existing breakpoints and do not advocate increasing ceftolozane/tazobactam breakpoints for urinary tract infections.

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