1
|
Sajid S, Mashkoor M, Jørgensen MG, Christensen LP, Hansen PR, Franzyk H, Mirza O, Prabhala BK. The Y-ome Conundrum: Insights into Uncharacterized Genes and Approaches for Functional Annotation. Mol Cell Biochem 2023:10.1007/s11010-023-04827-8. [PMID: 37610616 DOI: 10.1007/s11010-023-04827-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/09/2023] [Indexed: 08/24/2023]
Abstract
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.
Collapse
Affiliation(s)
- Salvia Sajid
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen Ø, Denmark
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Maliha Mashkoor
- Department of Surgery, Center for Surgical Sciences, Zealand University Hospital, Lykkebækvej 1, 4600, Køge, Denmark
| | - Mikkel Girke Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Lars Porskjær Christensen
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Paul Robert Hansen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen Ø, Denmark
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen Ø, Denmark
| | - Osman Mirza
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen Ø, Denmark
| | - Bala Krishna Prabhala
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.
| |
Collapse
|
2
|
Tantoso E, Eisenhaber B, Sinha S, Jensen LJ, Eisenhaber F. Did the early full genome sequencing of yeast boost gene function discovery? Biol Direct 2023; 18:46. [PMID: 37574542 PMCID: PMC10424406 DOI: 10.1186/s13062-023-00403-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 08/01/2023] [Indexed: 08/15/2023] Open
Abstract
BACKGROUND Although the genome of Saccharomyces cerevisiae (S. cerevisiae) was the first one of a eukaryote organism that was fully sequenced (in 1996), a complete understanding of the potential of encoded biomolecular mechanisms has not yet been achieved. Here, we wish to quantify how far the goal of a full list of S. cerevisiae gene functions still is. RESULTS The scientific literature about S. cerevisiae protein-coding genes has been mapped onto the yeast genome via the mentioning of names for genomic regions in scientific publications. The match was quantified with the ratio of a given gene name's occurrences to those of any gene names in the article. We find that ~ 230 elite genes with ≥ 75 full publication equivalents (FPEs, FPE = 1 is an idealized publication referring to just a single gene) command ~ 45% of all literature. At the same time, about two thirds of the genes (each with less than 10 FPEs) are described in just 12% of the literature (in average each such gene has just ~ 1.5% of the literature of an elite gene). About 600 genes have not been mentioned in any dedicated article. Compared with other groups of genes, the literature growth rates were highest for uncharacterized or understudied genes until late nineties of the twentieth century. Yet, these growth rates deteriorated and became negative thereafter. Thus, yeast function discovery for previously uncharacterized genes has returned to the level of ~ 1980. At the same time, literature for anyhow well-studied genes (with a threshold T10 (≥ 10 FPEs) and higher) remains steadily growing. CONCLUSIONS Did the early full genome sequencing of yeast boost gene function discovery? The data proves that the moment of publishing the full genome in reality coincides with the onset of decline of gene function discovery for previously uncharacterized genes. If the current status of literature about yeast molecular mechanisms can be extrapolated into the future, it will take about another ~ 50 years to complete the yeast gene function list. We found that a small group of scientific journals contributed extraordinarily to publishing early reports relevant to yeast gene function discoveries.
Collapse
Affiliation(s)
- Erwin Tantoso
- Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute (BII), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore.
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.
| | - Birgit Eisenhaber
- Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute (BII), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore.
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.
- LASA - Lausitz Advanced Scientific Applications gGmbH, Straße Der Einheit 2-24, 02943, Weißwasser, Federal Republic of Germany.
| | - Swati Sinha
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Frank Eisenhaber
- Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute (BII), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore.
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.
- LASA - Lausitz Advanced Scientific Applications gGmbH, Straße Der Einheit 2-24, 02943, Weißwasser, Federal Republic of Germany.
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.
| |
Collapse
|
3
|
Tantoso E, Eisenhaber B, Sinha S, Jensen LJ, Eisenhaber F. About the dark corners in the gene function space of Escherichia coli remaining without illumination by scientific literature. Biol Direct 2023; 18:7. [PMID: 36855185 PMCID: PMC9976479 DOI: 10.1186/s13062-023-00362-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 02/21/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Although Escherichia coli (E. coli) is the most studied prokaryote organism in the history of life sciences, many molecular mechanisms and gene functions encoded in its genome remain to be discovered. This work aims at quantifying the illumination of the E. coli gene function space by the scientific literature and how close we are towards the goal of a complete list of E. coli gene functions. RESULTS The scientific literature about E. coli protein-coding genes has been mapped onto the genome via the mentioning of names for genomic regions in scientific articles both for the case of the strain K-12 MG1655 as well as for the 95%-threshold softcore genome of 1324 E. coli strains with known complete genome. The article match was quantified with the ratio of a given gene name's occurrence to the mentioning of any gene names in the paper. The various genome regions have an extremely uneven literature coverage. A group of elite genes with ≥ 100 full publication equivalents (FPEs, FPE = 1 is an idealized publication devoted to just a single gene) attracts the lion share of the papers. For K-12, ~ 65% of the literature covers just 342 elite genes; for the softcore genome, ~ 68% of the FPEs is about only 342 elite gene families (GFs). We also find that most genes/GFs have at least one mentioning in a dedicated scientific article (with the exception of at least 137 protein-coding transcripts for K-12 and 26 GFs from the softcore genome). Whereas the literature growth rates were highest for uncharacterized or understudied genes until 2005-2010 compared with other groups of genes, they became negative thereafter. At the same time, literature for anyhow well-studied genes started to grow explosively with threshold T10 (≥ 10 FPEs). Typically, a body of ~ 20 actual articles generated over ~ 15 years of research effort was necessary to reach T10. Lineage-specific co-occurrence analysis of genes belonging to the accessory genome of E. coli together with genomic co-localization and sequence-analytic exploration hints previously completely uncharacterized genes yahV and yddL being associated with osmotic stress response/motility mechanisms. CONCLUSION If the numbers of scientific articles about uncharacterized and understudied genes remain at least at present levels, full gene function lists for the strain K-12 MG1655 and the E. coli softcore genome are in reach within the next 25-30 years. Once the literature body for a gene crosses 10 FPEs, most of the critical fundamental research risk appears overcome and steady incremental research becomes possible.
Collapse
Affiliation(s)
- Erwin Tantoso
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.,Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute (BII), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Birgit Eisenhaber
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.,Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute (BII), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Swati Sinha
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.,Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute (BII), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Frank Eisenhaber
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), 60 Biopolis Street, Singapore, 138672, Republic of Singapore. .,Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute (BII), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore. .,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.
| |
Collapse
|