Engineered Sphingomonas sp. KT-1 PahZ1 monomers efficiently degrade poly(aspartic acid)

Lamantia, Timothy; Jansch, Amanda L; Marsee, Justin D.; Weiland, Mitch H.; Miller, Justin M.

doi:10.1016/j.bpc.2021.106745

Cited by 3 publications

(8 citation statements)

References 27 publications

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“…In addition, the gut microbiota enriched in the BSM group were capable of anti-inflammation or using polysaccharides, such as Ruminiclostridium , Herbivorax , and Sphingomonas , and these had been reported to degrade polysaccharides such as lignocellulose, cellulose, and hemicellulose. 50–52 The abundances of Alistipes and Odoribacter in the BSM group were significantly increased compared with the Control and DSS groups, which has been reported to be involved in anti-inflammation within the gut. 53,54 Also, Lima et al found that Odoribacter played a role in protecting immune cells under UC conditions.…”

Section: Discussionmentioning

confidence: 96%

“…(B) The heatmap of the relative abundance of genera enriched in the DSS group and reported functions [42][43][44][45][46][47][48][49]53,[58][59][60][61][67][68][69][70]. (C) The heatmap of the relative abundance of genera enriched in the BSM group and reported functions 7,50,[53][54][55]60,[62][63][64][65][66]. * means significant difference compared to the control, p < 0.05; # means significant difference compared to DSS, p < 0.05.…”

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confidence: 99%

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A special polysaccharide hydrogel coated onBrasenia schreberi: preventive effects against ulcerative colitisviamodulation of gut microbiota

Wan

Liu

et al. 2023

Food Funct.

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Section: Discussionmentioning

confidence: 96%

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confidence: 99%

A special polysaccharide hydrogel coated onBrasenia schreberi: preventive effects against ulcerative colitisviamodulation of gut microbiota

Wan

Liu

et al. 2023

Food Funct.

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“…The start of the mature protein is underlined with the aspartate corresponding to residue 42 of the UniProt accession code: B6VQA9. All PahZ1 homologues were transformed, expressed, and purified using the same conditions as PahZ1 KT‑1 , as described previously. , …”

Section: Methodsmentioning

confidence: 99%

“…The reactions were started by the addition of tPAA and samples were incubated at 37 °C for 15 min. Reactions were stopped by incubating at 90 °C for 15 min which caused precipitation of the enzyme . Subsequently, samples were centrifuged at 17,000 g for 5 min and the supernatant was stored at −80 °C until later use, when 10 μL of each sample was injected onto a Biozen 3 μm dSEC-2, 200 Å, 300 × 7.8 mm LC column (Phenomenex, Torrance CA) attached to a Shimadzu GPC with a refractive index detector equilibrated in 50 mM HEPES (pH = 7.0).…”

Section: Methodsmentioning

confidence: 99%

“…Reactions were stopped by incubating at 90 °C for 15 min which caused precipitation of the enzyme. 33 Subsequently, samples were centrifuged at 17,000g for 5 min and the supernatant was stored at −80 °C until later use, when 10 μL of each sample was injected onto a Biozen 3 μm dSEC-2, 200 Å, 300 × 7.8 mm LC column (Phenomenex, Torrance CA) attached to a Shimadzu GPC with a refractive index detector equilibrated in 50 mM HEPES (pH = 7.0). Enzyme activity was determined by taking the ratio of the tPAA peak area (6.2−7.7 min) to the internal loading standard thyroglobulin peak area (5.0−6.2 min) and comparing these values to the respective ratio from PahZ1 without DNA which served as the 100% activity value.…”

Section: ■ Introductionmentioning

confidence: 99%

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Novel DNA-Binding Activity Exhibited by Poly(aspartic acid) Hydrolase-1 Inhibits Poly(aspartic acid) Hydrolase Activity

Couch,

Marsee,

Callaway

et al. 2024

Biochemistry

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Significant attention has been shifted toward the use and development of biodegradable polymeric materials to mitigate environmental accumulation and potential health impacts. One such material, poly(aspartic acid) (PAA), is a biodegradable alternative to superabsorbent poly(carboxylates), like poly(acrylate). Three enzymes are known to hydrolyze PAA: PahZ1 KT-1 and PahZ2 KT-1 from Sphingomonas sp. KT-1 and PahZ1 KP-2 from Pedobacter sp. KP-2. We previously reported the X-ray crystal structure for PahZ1 KT-1 , which revealed a homodimer complex with a strongly cationic surface spanning one side of each monomer. Here, we report the first characterization of any polymer hydrolase binding to DNA, where modeling data predict binding of the polyanionic DNA near the cationic substrate binding surface. Our data reveal that PahZ1 homologues from Sphingomonas sp. KT-1 and Pedobacter sp. KP-2 bind ssDNA and dsDNA with nanomolar binding affinities. PahZ1 KT-1 binds ssDNA and dsDNA with an apparent dissociation constant, K D,app = 81 ± 14 and 19 ± 1 nM, respectively, and these estimates are similar to the same behaviors exhibited by PahZ1 KP-2 . Gel permeation chromatography data reveal that dsDNA binding promotes inhibition of PahZ1-catalyzed PAA biodegradation for each homologue. We propose a working model wherein binding of PahZ1 to extracellular biofilm DNA aids in the localization of the hydrolase to the environment in which PAA would first be encountered, thereby providing a mechanism to degrade extracellular PAA and potentially harvest aspartic acid for nutritional uptake.

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Identification and complete genome sequence analysis of the pathogen causing mango bacterial dry rot

Liu,

He,

Xie

et al. 2024

Preprint

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Mango bacterial dry rot has become an increasingly serious issue in the mango-producing regions of Guangdong, China, leading to dry and necrotic leaves and branches. In order to identify the causal agent of this disease and determine its taxonomic status, the causative bacteria were isolated and characterized through pathogenicity tests, morphological observations, culture feature assessments, 16S rRNA gene sequence assays, and complete genome sequencing. The results revealed that the causal agent belongs to Sphingomonas sanguinis. The pathogenic bacterium, strain NY01, is gram-negative, forms a yellow lawn, has a rod-shaped structure with a cell size of approximately 0.7 to 1.4 µm, and possesses a single polar flagellum with slow motility. The 16S rRNA gene sequence of strain NY01 showed 99% sequence identity with Sphingomonas sanguinis. Strain NY01 has an optimal growth temperature of 28°C and can tolerate a salinity range of 0.1–3.0%. It is capable of utilizing glucose for energy under both aerobic and anaerobic conditions. The complete genome of strain NY01 consists of one chromosome (3,280,800 bp) and three plasmids (275,887 bp, 143,601 bp, and 37,326 bp), containing 3,593 predicted genes, 59 transfer RNA (tRNA) sequences, and 12 rRNA sequences. This study clarified the taxonomic status of the pathogenic bacteria, analyzed the biological characteristics of the pathogenic bacteria, and explored pathogenic factors. These findings can serve as a theoretical basis for understanding the occurrence and progression of the disease, as well as for implementing effective prevention and control measures.

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Engineered Sphingomonas sp. KT-1 PahZ1 monomers efficiently degrade poly(aspartic acid)

Cited by 3 publications

References 27 publications

A special polysaccharide hydrogel coated onBrasenia schreberi: preventive effects against ulcerative colitisviamodulation of gut microbiota

A special polysaccharide hydrogel coated onBrasenia schreberi: preventive effects against ulcerative colitisviamodulation of gut microbiota

Novel DNA-Binding Activity Exhibited by Poly(aspartic acid) Hydrolase-1 Inhibits Poly(aspartic acid) Hydrolase Activity

Identification and complete genome sequence analysis of the pathogen causing mango bacterial dry rot

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