TY - JOUR

T1 - The Y-ome Conundrum

T2 - Insights into Uncharacterized Genes and Approaches for Functional Annotation

AU - Sajid, Salvia

AU - Mashkoor, Maliha

AU - Jørgensen, Mikkel Girke

AU - Christensen, Lars Porskjær

AU - Hansen, Paul Robert

AU - Franzyk, Henrik

AU - Mirza, Osman

AU - Prabhala, Bala Krishna

N1 - Funding Information: The Higher Education Commission, Pakistan, is greatly acknowledged for funding overseas Ph.D. scholarship for SS. Publisher Copyright: © 2023, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.

PY - 2023

Y1 - 2023

N2 - The ever-increasing availability of genome sequencing data has revealed a substantial number of uncharacterized genes without known functions across various organisms. The first comprehensive genome sequencing of E. coli K12 revealed that more than 50% of its open reading frames corresponded to transcripts with no known functions. The group of protein-coding genes without a functional description and/or a recognized pathway, beginning with the letter “Y”, is classified as the “y-ome”. Several efforts have been made to elucidate the functions of these genes and to recognize their role in biological processes. This review provides a brief update on various strategies employed when studying the y-ome, such as high-throughput experimental approaches, comparative omics, metabolic engineering, gene expression analysis, and data integration techniques. Additionally, we highlight recent advancements in functional annotation methods, including the use of machine learning, network analysis, and functional genomics approaches. Novel approaches are required to produce more precise functional annotations across the genome to reduce the number of genes with unknown functions. Graphical abstract: [Figure not available: see fulltext.].

AB - The ever-increasing availability of genome sequencing data has revealed a substantial number of uncharacterized genes without known functions across various organisms. The first comprehensive genome sequencing of E. coli K12 revealed that more than 50% of its open reading frames corresponded to transcripts with no known functions. The group of protein-coding genes without a functional description and/or a recognized pathway, beginning with the letter “Y”, is classified as the “y-ome”. Several efforts have been made to elucidate the functions of these genes and to recognize their role in biological processes. This review provides a brief update on various strategies employed when studying the y-ome, such as high-throughput experimental approaches, comparative omics, metabolic engineering, gene expression analysis, and data integration techniques. Additionally, we highlight recent advancements in functional annotation methods, including the use of machine learning, network analysis, and functional genomics approaches. Novel approaches are required to produce more precise functional annotations across the genome to reduce the number of genes with unknown functions. Graphical abstract: [Figure not available: see fulltext.].

KW - Comparative omics

KW - E. coli

KW - Functional annotation

KW - Metabolic engineering

KW - Transportome deorphanization

KW - Uncharacterized genes

KW - Y-ome

U2 - 10.1007/s11010-023-04827-8

DO - 10.1007/s11010-023-04827-8

M3 - Review

C2 - 37610616

AN - SCOPUS:85168583091

JO - Molecular and Cellular Biochemistry

JF - Molecular and Cellular Biochemistry

SN - 0300-8177

ER -