Structure of the O-specific polysaccharide from a marine bacterium Echinicola pacifica КММ 6172Т containing 2,3-diacetamido-2,3-dideoxy-D-glucuronic acid

Tomshich, Svetlana V.; Kokoulin, Maxim S.; Kalinovsky, A. I.; Nedashkovskaya, Olga I.; Komandrova, Nadezhda A.

doi:10.1016/j.carres.2016.03.003

Cited by 5 publications

(6 citation statements)

References 10 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The nature of the extracted material was established by SDS-PAGE after silver-nitrate gel staining [17]. The gel showed, for both strains, a ladder-like pattern typical of an O-chain-containing LPS (i.e., an S-LPS) (Figure S1a), which was in agreement with our previous analysis [14,15]. The extracted LPS underwent extensive steps of purification comprising enzymatic treatment, dialysis, ultracentrifugation, and size-exclusion chromatography.…”

Section: Isolation and Fatty Acid Compositional Analysis Of The Lps F...supporting

confidence: 89%

“…Elykov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences. Both strains were cultivated for 48 h at ambient temperature on a medium composed of (/L): 5.0 g Bacto peptone (Difco, Franklin Lakes, NJ, USA), 2 g Bacto yeast extract (Difco), 0.2 g KH 2 PO 4 , 1.0, g glucose, and 0.05 g MgSO 4 in 50% (v/v) distilled water and 50% (v/v) natural seawater [14,15].…”

Section: Bacteria Isolation and Growthmentioning

confidence: 99%

“…The genus Echinicola accommodates only a few species that have been isolated from diverse marine sources and that are typically distinct from each other by several phenotypic features [13]. Here we report on two strains of this genus, E. pacifica KMM 6172 T isolated from the sea urchin Strongylocentrotus intermedius (Sea of Japan) [14], and E. vietnamensis KMM 6221 T isolated from seawater collected in a mussel farm located in a lagoon of Nha Trang Bay (South China Sea) [15]. Notably, we have previously shown that both bacteria express an S-LPS with unusual O-chain structures built up of a pentasaccharide repeating unit containing D-galactose, L-rhamnose, 2-acetoamido-2-deoxy-D-glucose, and 2,3-diacetamido-2,3-dideoxy-D-glucuronic acid for E. pacifica KMM 6172 T [14], and a tetrasaccharide composed of 2-acetamido-2-deoxy-D-glucuronic acid, 2-acetamido-2deoxy-D-galactose, D-glucuronic acid, and 3,6-dideoxy-L-xylo-hexose for E. vietnamensis KMM 6221 T [15].…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

The Unusual Lipid A Structure and Immunoinhibitory Activity of LPS from Marine Bacteria Echinicola pacifica KMM 6172T and Echinicola vietnamensis KMM 6221T

et al. 2021

Self Cite

View full text Add to dashboard Cite

Gram-negative bacteria experiencing marine habitats are constantly exposed to stressful conditions dictating their survival and proliferation. In response to these selective pressures, marine microorganisms adapt their membrane system to ensure protection and dynamicity in order to face the highly mutable sea environments. As an integral part of the Gram-negative outer membrane, structural modifications are commonly observed in the lipopolysaccharide (LPS) molecule; these mainly involve its glycolipid portion, i.e., the lipid A, mostly with regard to fatty acid content, to counterbalance the alterations caused by chemical and physical agents. As a consequence, unusual structural chemical features are frequently encountered in the lipid A of marine bacteria. By a combination of data attained from chemical, MALDI-TOF mass spectrometry (MS), and MS/MS analyses, here, we describe the structural characterization of the lipid A isolated from two marine bacteria of the Echinicola genus, i.e., E. pacifica KMM 6172T and E. vietnamensis KMM 6221T. This study showed for both strains a complex blend of mono-phosphorylated tri- and tetra-acylated lipid A species carrying an additional sugar moiety, a d-galacturonic acid, on the glucosamine backbone. The unusual chemical structures are reflected in a molecule that only scantly activates the immune response upon its binding to the LPS innate immunity receptor, the TLR4-MD-2 complex. Strikingly, both LPS potently inhibited the toxic effects of proinflammatory Salmonella LPS on human TLR4/MD-2.

show abstract

Section: Isolation and Fatty Acid Compositional Analysis Of The Lps F...supporting

confidence: 89%

Section: Bacteria Isolation and Growthmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

The Unusual Lipid A Structure and Immunoinhibitory Activity of LPS from Marine Bacteria Echinicola pacifica KMM 6172T and Echinicola vietnamensis KMM 6221T

et al. 2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…KMM 634 and Echinicola pacifica KMM 6172 T and on Acinetobacter baumannii strain ATCC 17961. [8][9][10] These types of dideoxysugars are typically synthesized via pathways initiating with nucleotide diphosphate-linked sugars.…”

Section: Introductionmentioning

confidence: 99%

Investigation of the enzymes required for the biosynthesis of 2,3‐diacetamido‐2,3‐dideoxy‐d‐glucuronic acid in Psychrobacter cryohalolentisK5^T

et al. 2022

View full text Add to dashboard Cite

Psychrobacter cryohalolentis K5 T is a Gram-negative bacterium first isolated from Siberian permafrost in 2006. It has a complex O-antigen containing L-rhamnose, D-galactose, two diacetamido-sugars, and one triacetamido-sugar. The biosynthetic pathway for one of the diacetamido-sugars, namely 2,3-diacetamido-2,3-dideoxy-D-glucuronic acid, is presently unknown. Utilizing the published genome sequence of P. cryohalolentis K5 T , we hypothesized that the genes designated Pcryo_0613, Pcryo_0614, Pcryo_0616, and Pcryo_0615 encode for a uridine dinucleotide (UDP)-N-acetyl-D-glucosamine 6-dehydrogenase, an nicotinamide adenine dinucleotide (oxidized) (NAD + )-dependent dehydrogenase, a pyridoxal 5 0 -phosphate (PLP)-dependent aminotransferase, and an N-acetyltransferase, respectively, activities of which would be required for the biosynthesis of this unusual carbohydrate. Here we present the cloning, overexpression, and purification of these hypothetical proteins. Kinetic data on the enzymes encoded by Pcryo_0613, Pcryo_0614, and Pcryo_0615 confirmed their postulated biochemical activities. In addition, the high-resolution X-ray structures of both the internal and external aldimine forms of the aminotransferase were determined to 1.25 and 1.0 Å, respectively. Finally, the three-dimensional architecture of the N-acetyltransferase in complex with its substrate and coenzyme A was solved to 1.8 Å resolution. Strikingly, the N-acetyltransferase was shown to adopt a new motif for UDP-sugar binding. The data presented herein provide additional insight into sugar biosynthesis in Gram-negative bacteria.Abbreviations: CoA, coenzyme A; HEPES, N-2-hydroxyethylpiperazie-N 0 -2-ethanesulfonic acid; HEPPS, N-2-hydroxyethylpiperazine-N 0 -3-propanesulfonic acid; HPLC, high-performance liquid chromatography; MES, 2-(N-morpholino)ethanesulfonic acid; NAD + , nicotinamide adenine dinucleotide (oxidized); NADH, nicotinamide adenine dinucleotide (reduced); NDP, nucleotide diphosphate; Ni-NTA, nickel-nitrilotriacetic acid; PLP, pyridoxal 5 0 -phosphate; rTEV, recombinant tobacco etch virus; Tris, tris-(hydroxymethyl)aminomethane; UDP, uridine dinucleotide; UDP-GlcNAc, uridine diphosphate N-acetylglucosamine.

show abstract

“…And a xylanase gene ( xynT ) from Echinicila rosea JL3085 T was cloned and recombinantly expressed in Escherichia coli BL21 23 . The O-specific polysaccharides are isolated from the lipopolysaccharide of Echinicola vietnamensis KMM 6221 T and Echinicola pacifica KMM 6172 T that reveals the polysaccharide is built up of branched tetrasaccharide repeating units 24 , 25 . Therefore, it is suggested that Echinicola strains play an important role in the carbon cycle in the marine environment.…”

Section: Introductionmentioning

confidence: 99%

Comparative genome characterization of Echinicola marina sp. nov., isolated from deep-sea sediment provide insight into carotenoid biosynthetic gene cluster evolution

Chen

et al. 2021

Sci Rep

View full text Add to dashboard Cite

Echinicola, carotenoid-pigmented bacteria, are isolated from various hypersaline environments. Carotenoid accumulation in response to salt stress can stabilize the cell membrane in order to survive. A pink-colored strain SCS 3–6 was isolated from the deep-sea sediment of the South China Sea. Growth was found to occur at 10–45 °C. The strain could tolerate 10% (w/v) NaCl concentration and grow at pH 5–9. The complete genome of SCS 3–6 comprises 5053 putative genes with a total 5,693,670 bp and an average G + C content of 40.11 mol%. The 16S rRNA gene sequence analysis indicated that strain SCS 3–6 was affiliated with the genus Echinicola, with the closely strains were Echinicola arenosa CAU 1574T (98.29%)and Echinicola shivajiensis AK12T (97.98%). For Echinicola species with available genome sequences, pairwise comparisons for average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) revealed ANIb values from 70.77 to 74.71%, ANIm values from 82.72 to 88.88%, and DDH values from 18.00 to 23.40%. To identify their genomic features, we compared their genomes with those of other Echinicola species. Phylogenetic analysis showed that strain SCS 3–6 formed a monophyletic clade. Genomic analysis revealed that strain SCS 3–6 possessed a complete synthetic pathway of carotenoid and speculated that the production was astaxanthin. Based on phenotypic and genotypic analyses in this study, strain SCS 3–6 is considered to represent a novel species of the genus Echinicola for which the name Echinicola marina sp. nov. is proposed. The type strain is SCS 3-6T (= GDMCC 1.2220T = JCM 34403T).

show abstract

Structure of the O-specific polysaccharide from a marine bacterium Echinicola pacifica КММ 6172Т containing 2,3-diacetamido-2,3-dideoxy-D-glucuronic acid

Cited by 5 publications

References 10 publications

The Unusual Lipid A Structure and Immunoinhibitory Activity of LPS from Marine Bacteria Echinicola pacifica KMM 6172T and Echinicola vietnamensis KMM 6221T

The Unusual Lipid A Structure and Immunoinhibitory Activity of LPS from Marine Bacteria Echinicola pacifica KMM 6172T and Echinicola vietnamensis KMM 6221T

Investigation of the enzymes required for the biosynthesis of 2,3‐diacetamido‐2,3‐dideoxy‐d‐glucuronic acid in Psychrobacter cryohalolentisK5^T

Comparative genome characterization of Echinicola marina sp. nov., isolated from deep-sea sediment provide insight into carotenoid biosynthetic gene cluster evolution

Contact Info

Product

Resources

About

Structure of the O-specific polysaccharide from a marine bacterium Echinicola pacifica КММ 6172Т containing 2,3-diacetamido-2,3-dideoxy-D-glucuronic acid

Cited by 5 publications

References 10 publications

The Unusual Lipid A Structure and Immunoinhibitory Activity of LPS from Marine Bacteria Echinicola pacifica KMM 6172T and Echinicola vietnamensis KMM 6221T

The Unusual Lipid A Structure and Immunoinhibitory Activity of LPS from Marine Bacteria Echinicola pacifica KMM 6172T and Echinicola vietnamensis KMM 6221T

Investigation of the enzymes required for the biosynthesis of 2,3‐diacetamido‐2,3‐dideoxy‐d‐glucuronic acid in Psychrobacter cryohalolentisK5T

Comparative genome characterization of Echinicola marina sp. nov., isolated from deep-sea sediment provide insight into carotenoid biosynthetic gene cluster evolution

Contact Info

Product

Resources

About

Investigation of the enzymes required for the biosynthesis of 2,3‐diacetamido‐2,3‐dideoxy‐d‐glucuronic acid in Psychrobacter cryohalolentisK5^T