Functional and transcriptomic investigation of laccase activity in the presence of PCB29 identifies two novel enzymes and the multicopper oxidase repertoire of a marine-derived fungus

Nikolaivits, Efstratios; Siaperas, Romanos; Agrafiotis, Andreas; Ouazzani, Jamal; Magoulas, Antoniοs; Gioti, Αnastasia

doi:10.1016/j.scitotenv.2021.145818

Cited by 19 publications

(13 citation statements)

References 86 publications

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“…Following genome assembly of Cladosporium sp . TM-S3 [ 61 ], transcriptome assembly and a phylogenetic analysis revealed the full diversity of the symbiont’s multicopper oxidases, enzymes commonly involved in oxidative degradation [ 62 ]. Among these, 2 laccase-like proteins shown to remove up to 71% of the polychlorinated biphenyl compound are now being expressed to optimize their use as novel biocatalysts.…”

Section: Scientific Impact Storiesmentioning

confidence: 99%

0s and 1s in marine molecular research: a regional HPC perspective

et al. 2021

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High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade’s experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility’s future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned.

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Section: Scientific Impact Storiesmentioning

confidence: 99%

0s and 1s in marine molecular research: a regional HPC perspective

et al. 2021

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“…The remaining enzymes are categorized as Auxiliary Activities (AAs) in the CAZy database and comprise carbohydrate oxidases, redox enzymes involved in diverse functions such as lignin degradation and metabolism of lignin-derived compounds [ 40 ]. AA members (in total 18) were assigned to AA1 and AA4 families; the former are multicopper oxidases that use diphenols and related substances as donors and oxygen as acceptors [ 41 ], while the latter are potential vanillyl-alcohol oxidases [ 42 ].…”

Section: Resultsmentioning

confidence: 99%

A Comparative Analysis of Weizmannia coagulans Genomes Unravels the Genetic Potential for Biotechnological Applications

Aulitto

Martínez-Álvarez

Fiorentino

et al. 2022

IJMS

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The production of biochemicals requires the use of microbial strains with efficient substrate conversion and excellent environmental robustness, such as Weizmannia coagulans species. So far, the genomes of 47 strains have been sequenced. Herein, we report a comparative genomic analysis of nine strains on the full repertoire of Carbohydrate-Active enZymes (CAZymes), secretion systems, and resistance mechanisms to environmental challenges. Moreover, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) immune system along with CRISPR-associated (Cas) genes, was also analyzed. Overall, this study expands our understanding of the strain’s genomic diversity of W. coagulans to fully exploit its potential in biotechnological applications.

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“…Several methods have been tried to remove pollutants from the environment, such as incineration, landfilling and dredging, or a combination of these (Nikolaivits et al, 2021). However, these conventional methods are expensive, time-consuming and can release toxic compounds or produce secondary pollutants.…”

Section: Biodegradationmentioning

confidence: 99%

Marine-derived fungi as biocatalysts

Virués-Segovia

Muñoz-Mira²,

Durán-Patrón³

et al. 2023

Front. Microbiol.

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Marine microorganisms account for over 90% of ocean biomass and their diversity is believed to be the result of their ability to adapt to extreme conditions of the marine environment. Biotransformations are used to produce a wide range of high-added value materials, and marine-derived fungi have proven to be a source of new enzymes, even for activities not previously discovered. This review focuses on biotransformations by fungi from marine environments, including bioremediation, from the standpoint of the chemical structure of the substrate, and covers up to September 2022.

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Functional and transcriptomic investigation of laccase activity in the presence of PCB29 identifies two novel enzymes and the multicopper oxidase repertoire of a marine-derived fungus

Cited by 19 publications

References 86 publications

0s and 1s in marine molecular research: a regional HPC perspective

0s and 1s in marine molecular research: a regional HPC perspective

A Comparative Analysis of Weizmannia coagulans Genomes Unravels the Genetic Potential for Biotechnological Applications

Marine-derived fungi as biocatalysts

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