Bacteria are extremely adept at overcoming the effects of antibiotics through a variety of mechanisms. As a result, researchers are constantly searching for antibiotics with new mechanisms of action. Culp and coworkers recently utilized a phylogeny-guided approach to mine the genomes of Actinomycetes species for glycopeptides with novel targets. Their efforts yielded the identification of complestatin and corbomycin as antibiotics with a different target than other glycopeptides.
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http://dx.doi.org/10.1016/j.tips.2020.03.002 | DOI Listing |
Brief Bioinform
September 2024
Department of Zoology, University of Rajasthan, Jawahar Lal Nehru Marg, Talvandi, Jaipur, Rajasthan 302004, India.
Sequences derived from organisms sharing common evolutionary origins exhibit similarity, while unique sequences, absent in related organisms, act as good diagnostic marker candidates. However, the approach focused on identifying dissimilar regions among closely-related organisms poses challenges as it requires complex multiple sequence alignments, making computation and parsing difficult. To address this, we have developed a biologically inspired universal NAUniSeq algorithm to find the unique sequences for microorganism diagnosis by traveling through the phylogeny of life.
View Article and Find Full Text PDFJ Agric Food Chem
November 2023
Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin 300457, China.
D-Allulose, a functional sweetener, can be synthesized from fructose using D-allulose 3-epimerase (DAEase). Nevertheless, a majority of the reported DAEases have inadequate stability under harsh industrial reaction conditions, which greatly limits their practical applications. In this study, big data mining combined with a computer-guided free energy calculation strategy was employed to discover a novel DAEase with excellent thermostability.
View Article and Find Full Text PDFmSystems
April 2023
Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA.
Viruses can alter the abundance, evolution, and metabolism of microorganisms in the ocean, playing a key role in water column biogeochemistry and global carbon cycles. Large efforts to measure the contribution of eukaryotic microorganisms (e.g.
View Article and Find Full Text PDFSci Adv
February 2023
School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
The isomerization of xylose to xylulose is considered the most promising approach to initiate xylose bioconversion. Here, phylogeny-guided big data mining, rational modification, and ancestral sequence reconstruction strategies were implemented to explore new active xylose isomerases (XIs) for . Significantly, 13 new active XIs for were mined or artificially created.
View Article and Find Full Text PDFFront Microbiol
November 2022
Engineering Research Center of Industrial Microbiology (Ministry of Education) and College of Life Sciences, Fujian Normal University, Fuzhou, China.
3-Decalinoyltetramic acids (DTAs) are a class of natural products with chemical diversity and potent bioactivities. In fungal species there is a general biosynthetic route to synthesize this type of compounds, which usually features a polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS) and a lipocalin-like Diels-Alderase (LLDAse). Using a synthetic biology approach, combining the bioinformatics analysis prediction and heterologous expression, we mined a PKS-NRPS and LLDAse encoding gene cluster from the plant pathogenic fungus and characterized the cluster to be responsible for the biosynthesis of novel DTAs, macrophasetins.
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