Functional characterization of prokaryotic dark matter: the road so far and what lies ahead

•There is a large amount of uncharacterized gene products of prokaryotic origin.•Evidence suggests that these elements might provide novel biotechnological solutions.•This review outlines the challenges and potential of these prokaryotic gene products. [Display omitted] Eight-hundred thousand to one...

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Bibliographic Details
Published in:	Current research in microbial sciences Vol. 3; p. 100159
Main Authors:	Escudeiro, Pedro, Henry, Christopher S., Dias, Ricardo P.M.
Format:	Journal Article
Language:	English
Published:	Netherlands Elsevier B.V 01-01-2022 Elsevier
Subjects:	BASIC BIOLOGICAL SCIENCES Biotechnological Potential Functional Genomics Metagenomics Microbial Dark Matter Review Functional Genomics Biotechnological Potential Metagenomics Microbial Dark Matter
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Summary:	•There is a large amount of uncharacterized gene products of prokaryotic origin.•Evidence suggests that these elements might provide novel biotechnological solutions.•This review outlines the challenges and potential of these prokaryotic gene products. [Display omitted] Eight-hundred thousand to one trillion prokaryotic species may inhabit our planet. Yet, fewer than two-hundred thousand prokaryotic species have been described. This uncharted fraction of microbial diversity, and its undisclosed coding potential, is known as the “microbial dark matter” (MDM). Next-generation sequencing has allowed to collect a massive amount of genome sequence data, leading to unprecedented advances in the field of genomics. Still, harnessing new functional information from the genomes of uncultured prokaryotes is often limited by standard classification methods. These methods often rely on sequence similarity searches against reference genomes from cultured species. This hinders the discovery of unique genetic elements that are missing from the cultivated realm. It also contributes to the accumulation of prokaryotic gene products of unknown function among public sequence data repositories, highlighting the need for new approaches for sequencing data analysis and classification. Increasing evidence indicates that these proteins of unknown function might be a treasure trove of biotechnological potential. Here, we outline the challenges, opportunities, and the potential hidden within the functional dark matter (FDM) of prokaryotes. We also discuss the pitfalls surrounding molecular and computational approaches currently used to probe these uncharted waters, and discuss future opportunities for research and applications.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 ObjectType-Review-3 content type line 23 AC02-06CH11357 Foundation for Science and Technology of Portugal USDOE Office of Science (SC), Biological and Environmental Research (BER)
ISSN:	2666-5174 2666-5174
DOI:	10.1016/j.crmicr.2022.100159