scholarly journals A roadmap for metagenomic enzyme discovery

2021 ◽  
Author(s):  
Serina L. Robinson ◽  
Jörn Piel ◽  
Shinichi Sunagawa
Keyword(s):  
Biosynthetic Enzymes ◽  
Functional Metagenomics ◽  
Enzyme Discovery ◽  
Experimental Strategies

Shotgun metagenomic approaches to uncover new enzymes are underdeveloped relative to PCR- or activity-based functional metagenomics. Here we review computational and experimental strategies to discover biosynthetic enzymes from metagenomes.

scholarly journals Novel Soil-Derived Beta-Lactam, Chloramphenicol, Fosfomycin and Trimethoprim Resistance Genes Revealed by Functional Metagenomics

Antibiotics ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 378
Author(s):  
Inka Marie Willms ◽  
Maja Grote ◽  
Melissa Kocatürk ◽  
Lukas Singhoff ◽  
Alina Andrea Kraft ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Reference Database ◽  
Functional Metagenomics ◽  
Beta Lactam ◽  
Public Attention ◽  
Soil Ecosystems ◽  
High Level ◽  
Antibiotic Efflux

Antibiotic resistance genes (ARGs) in soil are considered to represent one of the largest environmental resistomes on our planet. As these genes can potentially be disseminated among microorganisms via horizontal gene transfer (HGT) and in some cases are acquired by clinical pathogens, knowledge about their diversity, mobility and encoded resistance spectra gained increasing public attention. This knowledge offers opportunities with respect to improved risk prediction and development of strategies to tackle antibiotic resistance, and might help to direct the design of novel antibiotics, before further resistances reach hospital settings or the animal sector. Here, metagenomic libraries, which comprise genes of cultivated microorganisms, but, importantly, also those carried by the uncultured microbial majority, were screened for novel ARGs from forest and grassland soils. We detected three new beta-lactam, a so far unknown chloramphenicol, a novel fosfomycin, as well as three previously undiscovered trimethoprim resistance genes. These ARGs were derived from phylogenetically diverse soil bacteria and predicted to encode antibiotic inactivation, antibiotic efflux, or alternative variants of target enzymes. Moreover, deduced gene products show a minimum identity of ~21% to reference database entries and confer high-level resistance. This highlights the vast potential of functional metagenomics for the discovery of novel ARGs from soil ecosystems.

scholarly journals Ancient origin of fucosylated xyloglucan in charophycean green algae

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Maria Dalgaard Mikkelsen ◽  
Jesper Harholt ◽  
Bjørge Westereng ◽  
David Domozych ◽  
Stephen C. Fry ◽  
...  
Keyword(s):  
Green Algae ◽  
Structural Component ◽  
Cell Walls ◽  
Uronic Acid ◽  
Structural Elucidation ◽  
Land Plants ◽  
Evolutionary Significance ◽  
Biosynthetic Enzymes ◽  
Major Structural Component ◽  
Mesotaenium Caldariorum

AbstractThe charophycean green algae (CGA or basal streptophytes) are of particular evolutionary significance because their ancestors gave rise to land plants. One outstanding feature of these algae is that their cell walls exhibit remarkable similarities to those of land plants. Xyloglucan (XyG) is a major structural component of the cell walls of most land plants and was originally thought to be absent in CGA. This study presents evidence that XyG evolved in the CGA. This is based on a) the identification of orthologs of the genetic machinery to produce XyG, b) the identification of XyG in a range of CGA and, c) the structural elucidation of XyG, including uronic acid-containing XyG, in selected CGA. Most notably, XyG fucosylation, a feature considered as a late evolutionary elaboration of the basic XyG structure and orthologs to the corresponding biosynthetic enzymes are shown to be present in Mesotaenium caldariorum.

Experimental strategies on enhancing toxic gases uptake of metal–organic frameworks

2021 ◽  
Vol 430 ◽  
pp. 213738
Author(s):  
Ehsan Binaeian ◽  
El-Sayed M. El-Sayed ◽  
Mojtaba Khanpour Matikolaei ◽  
Daqiang Yuan
Keyword(s):  
Metal Organic Frameworks ◽  
Toxic Gases ◽  
Metal Organic ◽  
Experimental Strategies

scholarly journals Role of metagenomics in prospecting novel endoglucanases, accentuating functional metagenomics approach in second-generation biofuel production: a review

2021 ◽  
Author(s):  
Ninian Prem Prashanth Pabbathi ◽  
Aditya Velidandi ◽  
Tanvi Tavarna ◽  
Shreyash Gupta ◽  
Ram Sarvesh Raj ◽  
...  
Keyword(s):  
Second Generation ◽  
Biofuel Production ◽  
Functional Metagenomics ◽  
Generation Biofuel
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