Genomic Analysis of Sphingopyxis sp. USTB-05 for Biodegrading Cyanobacterial Hepatotoxins

Liu, Chao; Xu, Qianqian; Zhao, Zhenzhen; Zhang, Haiyang; Liu, Xiaolu; Chen, Yin; Liu, Yang; Yan, Hai

doi:10.3390/toxins14050333

Cited by 11 publications

(7 citation statements)

References 48 publications

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“…The culture solution of YC02 was prepared, and the bacterial precipitate was collected by the centrifugation of 10,000 rpm for 20 min at 4 °C, which was sent to Meiji Bio Co. (Shanghai, China) for sequencing the draft genome [ 39 ].…”

Section: Methodsmentioning

confidence: 99%

Biodegradation of Uric Acid by Bacillus paramycoides-YC02

et al. 2023

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High serum uric acid levels, known as hyperuricemia (HUA), are associated with an increased risk of developing gout, chronic kidney disease, cardiovascular disease, diabetes, and other metabolic syndromes. In this study, a promising bacterial strain capable of biodegrading uric acid (UA) was successfully isolated from Baijiu cellar mud using UA as the sole carbon and energy source. The bacterial strain was identified as Bacillus paramycoides-YC02 through 16S rDNA sequence analysis. Under optimal culture conditions at an initial pH of 7.0 and 38 °C, YC02 completely biodegraded an initial UA concentration of 500 mg/L within 48 h. Furthermore, cell-free extracts of YC02 were found to catalyze and remove UA. These results demonstrate the strong biodegradation ability of YC02 toward UA. To gain further insight into the mechanisms underlying UA biodegradation by YC02, the draft genome of YC02 was sequenced using Illumina HiSeq. Subsequent analysis revealed the presence of gene1779 and gene2008, which encode for riboflavin kinase, flavin mononucleotide adenylyl transferase, and flavin adenine dinucleotide (FAD)-dependent urate hydroxylase. This annotation was based on GO or the KEEG database. These enzymes play a crucial role in the metabolism pathway, converting vitamin B2 to FAD and subsequently converting UA to 5-hydroxyisourate (HIU) with the assistance of FAD. Notably, HIU undergoes a slow non-enzymatic breakdown into 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) and (S)-allantoin. The findings of this study provide valuable insights into the metabolism pathway of UA biodegradation by B. paramycoides-YC02 and offer a potential avenue for the development of bacterioactive drugs against HUA and gout.

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Section: Methodsmentioning

confidence: 99%

Biodegradation of Uric Acid by Bacillus paramycoides-YC02

et al. 2023

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“…Although mechanical removal of cyanobacterial biomass is often used in China as an emergency response (e.g., to prevent health risks associated with cyanobacteria toxins; Chen et al, 2017), the lack of cost‐effective techniques for its drying challenges subsequent re‐use (Chen et al, 2006; Chen et al, 2012). Water quality may benefit from the concurrent removal of polychlorinated biphenyls (PCBs) and microcystins (0.5 and 900 kg annually, respectively), but these substances complicate further treatment, and potential technologies are under development to address this (e.g., use of bacterial strains; Dexter et al, 2018; Liu et al, 2022). Soil‐based treatments are widely used but could pose environmental, ecological, and public health risks (e.g., microcystin leaching to groundwater, bioaccumulation in crops; Chen et al, 2012).…”

Section: Potential Sustainable Lake Restoration and Circular Economy:...mentioning

confidence: 99%

Sustainable lake restoration: From challenges to solutions

Tammeorg,

Chorus,

Spears

et al. 2023

WIREs Water

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Sustainable management of lakes requires us to overcome ecological, economic, and social challenges. These challenges can be addressed by focusing on achieving ecological improvement within a multifaceted, co‐beneficial context. In‐lake restoration measures may promote more rapid ecosystem responses than is feasible with catchment measures alone, even if multiple interventions are needed. In particular, we identify restoration methods that support the overarching societal target of a circular economy through the use of nutrients, sediments, or biomass that are removed from a lake, in agriculture, as food, or for biogas production. In this emerging field of sustainable restoration techniques, we show examples, discuss benefits and pitfalls, and flag areas for further research and development. Each lake should be assessed individually to ensure that restoration approaches will effectively address lake‐specific problems, do not harm the target lake or downstream ecosystems, are cost‐effective, promote delivery of valuable ecosystem services, minimize conflicts in public interests, and eliminate the necessity for repeated interventions. Achieving optimal, sustainable results from lake restoration relies on multidisciplinary research and close interactions between environmental, social, political, and economic sectors.This article is categorized under: Science of Water > Water Quality Water and Life > Stresses and Pressures on Ecosystems Water and Life > Conservation, Management, and Awareness

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“…The morphology of YY01 was observed with a microscope (CX41, Olympus, Tokyo, Japan). YY01 was inoculated into an MRS medium and incubated at 37 • C with a shaking speed of 200 rpm for 24 h. The culture solutions of YY01 were prepared, and bacterial precipitates were collected by the centrifugation of 10,000 rpm at 4 • C for 20 min and sent to Sangon Biotech (Shanghai, China) for sequencing the draft genome [29]. The bacterial genome was sequenced using de novo sequencing technology, and the genome sequence was assembled from scratch using bioinformatics.…”

Section: Identification and Draft Genome Sequencing Of Yy01mentioning

confidence: 99%

Biodegradation of Cholesterol by Enterococcus faecium YY01

Yang,

Ahmad,

Liu

et al. 2023

Microorganisms

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Cholesterol (CHOL) is one of the risk factors causing the blockage of the arterial wall, atherosclerosis, coronary heart disease, and other serious cardiovascular diseases. Here, a promising bacterial strain for biodegrading CHOL was successfully isolated from the gut of healthy individuals and identified as Enterococcus faecium YY01 with an analysis of the 16S rDNA sequence. An initial CHOL of 1.0 g/L was reduced to 0.5 g/L in 5 days, and glucose and beef extract were found to be optimal carbon and nitrogen sources for the rapid growth of YY01, respectively. To gain further insight into the mechanisms underlying CHOL biodegradation, the draft genome of YY01 was sequenced using Illumina HiSeq. Choloylglycine hydrolase, acyltransferase, and alkyl sulfatase was encoded by gene0586, gene1890, and gene2442, which play crucial roles in converting 3α, 7α, 12α-trihydroxy-5β-choranic acid to choline-CoA and then choline-CoA to bile acid. Notably, choloylglycine hydrolase was closely related to the biosynthesis of both primary and secondary bile acid. The findings of this study provide valuable insights into the metabolism pathway of CHOL biodegradation by YY01 and offer a potential avenue for the development of bacterioactive drugs against hypercholesterolemia.

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Genomic Analysis of Sphingopyxis sp. USTB-05 for Biodegrading Cyanobacterial Hepatotoxins

Cited by 11 publications

References 48 publications

Biodegradation of Uric Acid by Bacillus paramycoides-YC02

Biodegradation of Uric Acid by Bacillus paramycoides-YC02

Sustainable lake restoration: From challenges to solutions

Biodegradation of Cholesterol by Enterococcus faecium YY01

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