Conserved unique peptide patterns (CUPP) online platform 2.0: implementation of +1000 JGI fungal genomes

Barrett, Kristian; Hunt, Cameron J.; Lange, Lene; Grigoriev, Igor V.; Meyer, Anne S.

doi:10.1093/nar/gkad385

Title: Conserved unique peptide patterns (CUPP) online platform 2.0: implementation of +1000 JGI fungal genomes

Journal Article · 22 May 2023 · Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkad385 · OSTI ID:2234073

^[1]; Hunt, Cameron J. ^[2]; Lange, Lene ^[3];

^[4];

^[2]

Technical University of Denmark, Lyngby (Denmark); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). USDOE Joint BioEnergy Institute
Technical University of Denmark, Lyngby (Denmark)
BioEconomy, Valby (Denmark)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). USDOE Joint BioEnergy Institute; University of California, Berkeley, CA (United States)

Carbohydrate-processing enzymes, CAZymes, are classified into families based on sequence and three-dimensional fold. Because many CAZyme families contain members of diverse molecular function (different EC-numbers), sophisticated tools are required to further delineate these enzymes. Such delineation is provided by the peptide-based clustering method CUPP, Conserved Unique Peptide Patterns. CUPP operates synergistically with the CAZy family/subfamily categorizations to allow systematic exploration of CAZymes by defining small protein groups with shared sequence motifs. The updated CUPP library contains 21,930 of such motif groups including 3,842,628 proteins. The new implementation of the CUPP-webserver, https://cupp.info/, now includes all published fungal and algal genomes from the Joint Genome Institute (JGI), genome resources MycoCosm and PhycoCosm, dynamically subdivided into motif groups of CAZymes. This allows users to browse the JGI portals for specific predicted functions or specific protein families from genome sequences. Thus, a genome can be searched for proteins having specific characteristics. All JGI proteins have a hyperlink to a summary page which links to the predicted gene splicing including which regions have RNA support. The new CUPP implementation also includes an update of the annotation algorithm that uses only a fourth of the RAM while enabling multi-threading, providing an annotation speed below 1 ms/protein.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); Novo Nordisk Foundation

Grant/Contract Number:: AC02-05CH11231; NNF21OC0066330; NNF22OC0072911

OSTI ID:: 2234073

Journal Information:: Nucleic Acids Research, Vol. 51, Issue W1; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

References (25)

101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens Haridas, S.; Albert, R.; Binder, M. Studies in Mycology, Vol. 96 https://doi.org/10.1016/j.simyco.2020.01.003	journal	June 2020
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses Huerta-Cepas, Jaime; Szklarczyk, Damian; Heller, Davide Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1085	journal	November 2018
The carbohydrate-active enzymes database (CAZy) in 2013 Lombard, Vincent; Golaconda Ramulu, Hemalatha; Drula, Elodie Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1178	journal	November 2013
dbCAN2: a meta server for automated carbohydrate-active enzyme annotation Zhang, Han; Yohe, Tanner; Huang, Le Nucleic Acids Research, Vol. 46, Issue W1 https://doi.org/10.1093/nar/gky418	journal	May 2018
Database resources of the National Center for Biotechnology Information in 2023 Sayers, Eric W.; Bolton, Evan E.; Brister, J. Rodney Nucleic Acids Research, Vol. 51, Issue D1 https://doi.org/10.1093/nar/gkac1032	journal	November 2022
SignalP 6.0 predicts all five types of signal peptides using protein language models Teufel, Felix; Almagro Armenteros, José Juan; Johansen, Alexander Rosenberg Nature Biotechnology, Vol. 40, Issue 7 https://doi.org/10.1038/s41587-021-01156-3	journal	January 2022
UniProt: the Universal Protein Knowledgebase in 2023 Nucleic Acids Research, Vol. 51, Issue D1 https://doi.org/10.1093/nar/gkac1052	journal	November 2022
Gene family expansions and transcriptome signatures uncover fungal adaptations to wood decay Hage, Hayat; Miyauchi, Shingo; Virágh, Máté Environmental Microbiology https://doi.org/10.1111/1462-2920.15423	journal	February 2021
SACCHARIS: an automated pipeline to streamline discovery of carbohydrate active enzyme activities within polyspecific families and de novo sequence datasets Jones, Darryl R.; Thomas, Dallas; Alger, Nicholas Biotechnology for Biofuels, Vol. 11, Issue 1 https://doi.org/10.1186/s13068-018-1027-x	journal	February 2018
Discovery of novel secretome CAZymes from Penicillium sclerotigenum by bioinformatics and explorative proteomics analyses during sweet potato pectin digestion Barrett, Kristian; Zhao, Hai; Hao, Pengfei Frontiers in Bioengineering and Biotechnology, Vol. 10 https://doi.org/10.3389/fbioe.2022.950259	journal	September 2022
Conserved unique peptide patterns (CUPP) online platform: peptide-based functional annotation of carbohydrate active enzymes Barrett, Kristian; Hunt, Cameron J.; Lange, Lene Nucleic Acids Research, Vol. 48, Issue W1 https://doi.org/10.1093/nar/gkaa375	journal	May 2020
The carbohydrate-active enzyme database: functions and literature Drula, Elodie; Garron, Marie-Line; Dogan, Suzan Nucleic Acids Research, Vol. 50, Issue D1 https://doi.org/10.1093/nar/gkab1045	journal	November 2021
InterPro in 2022 Paysan-Lafosse, Typhaine; Blum, Matthias; Chuguransky, Sara Nucleic Acids Research, Vol. 51, Issue D1 https://doi.org/10.1093/nar/gkac993	journal	November 2022
PhycoCosm, a comparative algal genomics resource Grigoriev, Igor V.; Hayes, Richard D.; Calhoun, Sara Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa898	journal	October 2020
A classification of glycosyl hydrolases based on amino acid sequence similarities Henrissat, B. Biochemical Journal, Vol. 280, Issue 2 https://doi.org/10.1042/bj2800309	journal	December 1991
CD-HIT: accelerated for clustering the next-generation sequencing data Fu, Limin; Niu, Beifang; Zhu, Zhengwei Bioinformatics, Vol. 28, Issue 23 https://doi.org/10.1093/bioinformatics/bts565	journal	October 2012
Genomic characterization of three marine fungi, including Emericellopsis atlantica sp. nov. with signatures of a generalist lifestyle and marine biomass degradation Hagestad, Ole Christian; Hou, Lingwei; Andersen, Jeanette H. IMA Fungus, Vol. 12, Issue 1 https://doi.org/10.1186/s43008-021-00072-0	journal	August 2021
Peptide-based functional annotation of carbohydrate-active enzymes by conserved unique peptide patterns (CUPP) Barrett, Kristian; Lange, Lene Biotechnology for Biofuels, Vol. 12, Issue 1 https://doi.org/10.1186/s13068-019-1436-5	journal	April 2019
eggNOG 6.0: enabling comparative genomics across 12 535 organisms Hernández-Plaza, Ana; Szklarczyk, Damian; Botas, Jorge Nucleic Acids Research, Vol. 51, Issue D1 https://doi.org/10.1093/nar/gkac1022	journal	November 2022
Fast and sensitive protein alignment using DIAMOND Buchfink, Benjamin; Xie, Chao; Huson, Daniel H. Nature Methods, Vol. 12, Issue 1 https://doi.org/10.1038/nmeth.3176	journal	November 2014
Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions Mistry, Jaina; Finn, Robert D.; Eddy, Sean R. Nucleic Acids Research, Vol. 41, Issue 12 https://doi.org/10.1093/nar/gkt263	journal	April 2013
A parts list for fungal cellulosomes revealed by comparative genomics Haitjema, Charles H.; Gilmore, Sean P.; Henske, John K. Nature Microbiology, Vol. 2, Issue 8 https://doi.org/10.1038/nmicrobiol.2017.87	journal	May 2017
Widespread adenine N6-methylation of active genes in fungi Mondo, Stephen J.; Dannebaum, Richard O.; Kuo, Rita C. Nature Genetics, Vol. 49, Issue 6 https://doi.org/10.1038/ng.3859	journal	May 2017
MycoCosm portal: gearing up for 1000 fungal genomes Grigoriev, Igor V.; Nikitin, Roman; Haridas, Sajeet Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1183	journal	December 2013
Pfam: The protein families database in 2021 Mistry, Jaina; Chuguransky, Sara; Williams, Lowri Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa913	journal	October 2020