MjCyc: Rediscovering the pathway-genome landscape of the first sequenced archaeon, Methanocaldococcus (Methanococcus) jannaschii
Summary: The genome of Methanocaldococcus (Methanococcus) jannaschii DSM 2661 was the first Archaeal genome to be sequenced in 1996. Subsequent sequence-based annotation cycles led to its first metabolic reconstruction in 2005. Leveraging new experimental results and function assignments, we have no...
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| Language: | English |
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Elsevier
2025-01-01
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| Series: | iScience |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004224027731 |
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| author | I. Baltsavia G. Stamoulos K. Tziavaras C. Bouas I. Katikaridou A. Dermaris A. Kothari I. Iliopoulos R. Caspi P.D. Karp N.C. Kyrpides C.A. Ouzounis |
| author_facet | I. Baltsavia G. Stamoulos K. Tziavaras C. Bouas I. Katikaridou A. Dermaris A. Kothari I. Iliopoulos R. Caspi P.D. Karp N.C. Kyrpides C.A. Ouzounis |
| author_sort | I. Baltsavia |
| collection | DOAJ |
| description | Summary: The genome of Methanocaldococcus (Methanococcus) jannaschii DSM 2661 was the first Archaeal genome to be sequenced in 1996. Subsequent sequence-based annotation cycles led to its first metabolic reconstruction in 2005. Leveraging new experimental results and function assignments, we have now re-annotated M. jannaschii, creating an updated resource with novel information and testable predictions in a pathway-genome database available at BioCyc.org. This reannotation effort has resulted in 652 function assignments with enzyme roles, accounting for a third of the total protein-coding entries for this genome. The updated resource includes 883 reactions, 540 enzymes, and 142 individual pathways. Despite notable progress in computational genomics, more than a third of the genome remains functionally uncharacterized. The publicly available MjCyc pathway-genome database holds great potential for the wider community to conduct research on the biology of methanogenic Archaea. |
| format | Article |
| id | doaj-art-e06708ef8c344954b73a64e3a0f896bd |
| institution | Kabale University |
| issn | 2589-0042 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj-art-e06708ef8c344954b73a64e3a0f896bd2024-12-29T04:47:51ZengElsevieriScience2589-00422025-01-01281111546MjCyc: Rediscovering the pathway-genome landscape of the first sequenced archaeon, Methanocaldococcus (Methanococcus) jannaschiiI. Baltsavia0G. Stamoulos1K. Tziavaras2C. Bouas3I. Katikaridou4A. Dermaris5A. Kothari6I. Iliopoulos7R. Caspi8P.D. Karp9N.C. Kyrpides10C.A. Ouzounis11Computational Biology Group, School of Medicine, University of Crete, Heraklion, Greece; Biological Computation & Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, GreeceBiological Computation & Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece; Biological Computation & Computational Biology Group, Artificial Intelligence & Information Analysis Lab, School of Informatics, Aristotle University of Thessalonica, Thessalonica, GreeceBiological Computation & Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece; Biological Computation & Computational Biology Group, Artificial Intelligence & Information Analysis Lab, School of Informatics, Aristotle University of Thessalonica, Thessalonica, GreeceBiological Computation & Computational Biology Group, Artificial Intelligence & Information Analysis Lab, School of Informatics, Aristotle University of Thessalonica, Thessalonica, GreeceBiological Computation & Computational Biology Group, Artificial Intelligence & Information Analysis Lab, School of Informatics, Aristotle University of Thessalonica, Thessalonica, GreeceBiological Computation & Computational Biology Group, Artificial Intelligence & Information Analysis Lab, School of Informatics, Aristotle University of Thessalonica, Thessalonica, GreeceBioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, USAComputational Biology Group, School of Medicine, University of Crete, Heraklion, GreeceBioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, USABioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA, USA; Corresponding authorDoE Joint Genome Institute, Berkeley, CA, USA; Environmental Genomics & Systems Biology Division, Lawrence Berkeley National Lab, Berkeley, CA, USABiological Computation & Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece; Biological Computation & Computational Biology Group, Artificial Intelligence & Information Analysis Lab, School of Informatics, Aristotle University of Thessalonica, Thessalonica, Greece; DoE Joint Genome Institute, Berkeley, CA, USA; Corresponding authorSummary: The genome of Methanocaldococcus (Methanococcus) jannaschii DSM 2661 was the first Archaeal genome to be sequenced in 1996. Subsequent sequence-based annotation cycles led to its first metabolic reconstruction in 2005. Leveraging new experimental results and function assignments, we have now re-annotated M. jannaschii, creating an updated resource with novel information and testable predictions in a pathway-genome database available at BioCyc.org. This reannotation effort has resulted in 652 function assignments with enzyme roles, accounting for a third of the total protein-coding entries for this genome. The updated resource includes 883 reactions, 540 enzymes, and 142 individual pathways. Despite notable progress in computational genomics, more than a third of the genome remains functionally uncharacterized. The publicly available MjCyc pathway-genome database holds great potential for the wider community to conduct research on the biology of methanogenic Archaea.http://www.sciencedirect.com/science/article/pii/S2589004224027731Gene networkBiological classificationGenomic analysis |
| spellingShingle | I. Baltsavia G. Stamoulos K. Tziavaras C. Bouas I. Katikaridou A. Dermaris A. Kothari I. Iliopoulos R. Caspi P.D. Karp N.C. Kyrpides C.A. Ouzounis MjCyc: Rediscovering the pathway-genome landscape of the first sequenced archaeon, Methanocaldococcus (Methanococcus) jannaschii iScience Gene network Biological classification Genomic analysis |
| title | MjCyc: Rediscovering the pathway-genome landscape of the first sequenced archaeon, Methanocaldococcus (Methanococcus) jannaschii |
| title_full | MjCyc: Rediscovering the pathway-genome landscape of the first sequenced archaeon, Methanocaldococcus (Methanococcus) jannaschii |
| title_fullStr | MjCyc: Rediscovering the pathway-genome landscape of the first sequenced archaeon, Methanocaldococcus (Methanococcus) jannaschii |
| title_full_unstemmed | MjCyc: Rediscovering the pathway-genome landscape of the first sequenced archaeon, Methanocaldococcus (Methanococcus) jannaschii |
| title_short | MjCyc: Rediscovering the pathway-genome landscape of the first sequenced archaeon, Methanocaldococcus (Methanococcus) jannaschii |
| title_sort | mjcyc rediscovering the pathway genome landscape of the first sequenced archaeon methanocaldococcus methanococcus jannaschii |
| topic | Gene network Biological classification Genomic analysis |
| url | http://www.sciencedirect.com/science/article/pii/S2589004224027731 |
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