CoChat
Sign Up
Cited by 22

The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.

Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Gene Prediction Errors

Nagy, Alinda, Szláma, György, Szarka, Eszter, Trexler, Mária, Bányai, László, Patthy, László·2011·Genes
DOI 10.3390/genes2030449PMC PMC3927609
Open this paper in CoChat — free account

Abstract

In view of the fact that appearance of novel protein domain architectures (DA) is closely associated with biological innovations, there is a growing interest in the genome-scale reconstruction of the evolutionary history of the domain architectures of multidomain proteins. In such analyses, however, it is usually ignored that a significant proportion of Metazoan sequences analyzed is mispredicted and that this may seriously affect the validity of the conclusions. To estimate the contribution of errors in gene prediction to differences in DA of predicted proteins, we have used the high quality manually curated UniProtKB/Swiss-Prot database as a reference. For genome-scale analysis of domain architectures of predicted proteins we focused on RefSeq, EnsEMBL and NCBI’s GNOMON predicted sequences of Metazoan species with completely sequenced genomes. Comparison of the DA of UniProtKB/Swiss-Prot sequences of worm, fly, zebrafish, frog, chick, mouse, rat and orangutan with those of human Swiss-Prot entries have identified relatively few cases where orthologs had different DA, although the percentage with different DA increased with evolutionary distance. In contrast with this, comparison of the DA of human, orangutan, rat, mouse, chicken, frog, zebrafish, worm and fly RefSeq, EnsEMBL and NCBI’s GNOMON predicted protein sequences with those of the corresponding/orthologous human Swiss-Prot entries identified a significantly higher proportion of domain architecture differences than in the case of the comparison of Swiss-Prot entries. Analysis of RefSeq, EnsEMBL and NCBI’s GNOMON predicted protein sequences with DAs different from those of their Swiss-Prot orthologs confirmed that the higher rate of domain architecture differences is due to errors in gene prediction, the majority of which could be corrected with our FixPred protocol. We have also demonstrated that contamination of databases with incomplete, abnormal or mispredicted sequences introduces a bias in DA differences in as much as it increases the proportion of terminal over internal DA differences. Here we have shown that in the case of RefSeq, EnsEMBL and NCBI’s GNOMON predicted protein sequences of Metazoan species, the contribution of gene prediction errors to domain architecture differences of orthologs is comparable to or greater than those due to true gene rearrangements. We have also demonstrated that domain architecture comparison may serve as a useful tool for the quality control of gene predictions and may thus guide the correction of sequence errors. Our findings caution that earlier genome-scale studies based on comparison of predicted (frequently mispredicted) protein sequences may have led to some erroneous conclusions about the evolution of novel domain architectures of multidomain proteins. A reassessment of the DA evolution of orthologous and paralogous proteins is presented in an accompanying paper [1].

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.3390/genes2030449

Cites

3 of 3 references verified0 citation errors · 0 not checkable

Statistics

Figures

Figure 1 Correction of the sequence of complement component C7 of Gallus gallus with the FixPred protocol. The DA of GNOMON-predicted sequence of complement component C7 from Gallus gallus (XP_424774) was found to differ from those of its mammalian and fish orthologs (CO7_HUMAN, CO7_PIG, B5X0R1_SALSA): whereas the latter contain TSP_1, Ldl_recept_a, MACPF, TSP_1, Sushi and Sushi domains the ortholog of Gallus gallus lacks the domains downstream of the MACPF domain. The sequence “XP_424774_CORRECTED” was predicted by the use of alternative gene models and is supported by ESTs. The sequence predicted by FixPred was experimentally verified by cloning the full-length cDNA; the cDNA sequence was deposited in GenBank (accession cDNA: HQ878377; accession protein: ADY17228). (a) Comparison of the DAs of XP_424774 and XP_424774_CORRECTED with that of CO7_HUMAN; (b) Alignment of the sequences of XP_424774 and XP_424774_CORRECTED with those P_416936, XP_416936_CORRECTED with those of CO7_HUMAN, CO7_PIG and B5X0R1_SALSA.
Figure 1 Correction of the sequence of complement component C7 of Gallus gallus with the FixPred protocol. The DA of GNOMON-predicted sequence of complement component C7 from Gallus gallus (XP_424774) was found to differ from those of its mammalian and fish orthologs (CO7_HUMAN, CO7_PIG, B5X0R1_SALSA): whereas the latter contain TSP_1, Ldl_recept_a, MACPF, TSP_1, Sushi and Sushi domains the ortholog of Gallus gallus lacks the domains downstream of the MACPF domain. The sequence “XP_424774_CORRECTED” was predicted by the use of alternative gene models and is supported by ESTs. The sequence predicted by FixPred was experimentally verified by cloning the full-length cDNA; the cDNA sequence was deposited in GenBank (accession cDNA: HQ878377; accession protein: ADY17228). (a) Comparison of the DAs of XP_424774 and XP_424774_CORRECTED with that of CO7_HUMAN; (b) Alignment of the sequences of XP_424774 and XP_424774_CORRECTED with those P_416936, XP_416936_CORRECTED with those of CO7_HUMAN, CO7_PIG and B5X0R1_SALSA.CC BY · PubMed Central
Figure 2 Correction of the sequence of cathepsin H of Gallus gallus with the FixPred protocol. The DA of GNOMON-predicted sequence of cathepsin H from Gallus gallus (xp_001232765) was found to differ from those of its mammalian orthologs (CATH_HUMAN, CATH_MOUSE, CATH_PIG, CATH_RAT: whereas the DA of the latter contains an Inhibitor_I29 and a Peptidase_C1 domain, the chicken protein lacks the Inhibitor_I29 domain. The sequence “xp_001232765_corrected” was predicted by the use of ESTs bm427347, bi066433, am064052, bu425005 and bi064908. The sequence predicted by FixPred was experimentally verified by cloning the full-length cDNA; the cDNA sequence was deposited in GenBank (accession cDNA: JF514547; accession protein: AEC13302). (a) Comparison of the DAs of XP_001232765 and XP_001232765_CORRECTED with that of CATH_HUMAN; (b) Alignment of the sequences of XP_001232765 and XP_001232765 _CORRECTED with those of CATH_HUMAN, CATH_MOUSE, CATH_PIG, CATH_RAT.
Figure 2 Correction of the sequence of cathepsin H of Gallus gallus with the FixPred protocol. The DA of GNOMON-predicted sequence of cathepsin H from Gallus gallus (xp_001232765) was found to differ from those of its mammalian orthologs (CATH_HUMAN, CATH_MOUSE, CATH_PIG, CATH_RAT: whereas the DA of the latter contains an Inhibitor_I29 and a Peptidase_C1 domain, the chicken protein lacks the Inhibitor_I29 domain. The sequence “xp_001232765_corrected” was predicted by the use of ESTs bm427347, bi066433, am064052, bu425005 and bi064908. The sequence predicted by FixPred was experimentally verified by cloning the full-length cDNA; the cDNA sequence was deposited in GenBank (accession cDNA: JF514547; accession protein: AEC13302). (a) Comparison of the DAs of XP_001232765 and XP_001232765_CORRECTED with that of CATH_HUMAN; (b) Alignment of the sequences of XP_001232765 and XP_001232765 _CORRECTED with those of CATH_HUMAN, CATH_MOUSE, CATH_PIG, CATH_RAT.CC BY · PubMed Central

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Show all 3 references

Research works printed but not linked: 60

  1. Nagy, A., and Patthy, L. (2011). Reassessing Domain Architecture Evolution of Metazoan Proteins: Contribution of Different Evolutionary Mechanisms. Genes, submitted for publication. · DOI
  2. Tordai, 2005, Modules, multidomain proteins and organismic complexity, FEBS J., 272, 5064, 10.1111/j.1742-4658.2005.04917.x · DOI
  3. Nagy, 2008, Identification and correction of abnormal, incomplete and mispredicted proteins in public databases, BMC Bioinf., 9, 353, 10.1186/1471-2105-9-353 · DOI
  4. Weiner, 2006, Domain deletions and substitutions in the modular protein evolution, FEBS J., 273, 2037, 10.1111/j.1742-4658.2006.05220.x · DOI
  5. Harrow, 2009, Identifying protein-coding genes in genomic sequences, Genome Biol., 10, 201, 10.1186/gb-2009-10-1-201 · DOI
  6. Bernal, 2007, Global discriminative learning for higher-accuracy computational gene prediction, PLoS Comput. Biol., 3, e54, 10.1371/journal.pcbi.0030054 · DOI
  7. Finn, 2010, The Pfam protein families database, Nucleic Acids Res., 38, D211, 10.1093/nar/gkp985 · DOI · Paper page
  8. Fong, 2008, Protein subfamily assignment using the conserved domain database, BMC Res. Notes, 1, 114, 10.1186/1756-0500-1-114 · DOI
  9. Homepage of Conserved Domains Database. Available online: http://www.ncbi.nlm.nih.gov/sites/entrez?db=cdd (accessed on 04 May 2011).
  10. Greene, 2007, The CATH domain structure database: New protocols and classification levels give a more comprehensive resource for exploring evolution, Nucleic Acids Res., 35, D291, 10.1093/nar/gkl959 · DOI
  11. Andreeva, 2008, Data growth and its impact on the SCOP database: New developments, Nucleic Acids Res., 36, D419, 10.1093/nar/gkm993 · DOI
  12. Wang, 2006, Global phylogeny determined by the combination of protein domains in proteomes, Mol. Biol. Evol., 23, 2444, 10.1093/molbev/msl117 · DOI
  13. Gough, 2005, Convergent evolution of domain architectures (is rare), Bioinformatics, 21, 1464, 10.1093/bioinformatics/bti204 · DOI
  14. Lin, 2006, An initial strategy for comparing proteins at the domain architecture level, Bioinformatics, 22, 2081, 10.1093/bioinformatics/btl366 · DOI
  15. Lee, 2008, DAhunter: a web-based server that identifies homologous proteins by comparing domain architecture, Nucleic Acids Res., 36, W60, 10.1093/nar/gkn172 · DOI
  16. Kawashima, 2007, Comparative pair-wise domain-combinations for screening the clade specific domain-architectures in metazoan genomes, Genome Inform., 19, 50
  17. Przytycka, 2006, Graph theoretical insights into evolution of multidomain proteins, Comput. Biol., 13, 351, 10.1089/cmb.2006.13.351 · DOI
  18. Kawashima, 2009, Domain shuffling and the evolution of vertebrates, Genome Res., 19, 1393, 10.1101/gr.087072.108 · DOI
  19. Basu, 2008, Evolution of protein domain promiscuity in eukaryotes, Genome Res., 18, 449, 10.1101/gr.6943508 · DOI
  20. Forslund, 2008, Domain tree-based analysis of protein architecture evolution, Mol. Biol. Evol., 25, 254, 10.1093/molbev/msm254 · DOI
  21. Zhang, 2010, Domain architecture evolution of pattern-recognition receptors, Immunogenetics, 62, 263, 10.1007/s00251-010-0428-1 · DOI
  22. Ekman, 2007, Quantification of the elevated rate of domain rearrangements in metazoa, J. Mol. Biol., 372, 1337, 10.1016/j.jmb.2007.06.022 · DOI
  23. Koonin, 2000, The impact of comparative genomics on our understanding of evolution, Cell, 101, 573, 10.1016/S0092-8674(00)80867-3 · DOI
  24. Ponting, 2002, The natural history of protein domains, Annu. Rev. Biophys. Biomol. Struct., 31, 45, 10.1146/annurev.biophys.31.082901.134314 · DOI
  25. Patthy, 1985, Evolution of the proteases of blood coagulation and fibrinolysis by assembly from modules, Cell, 41, 657, 10.1016/S0092-8674(85)80046-5 · DOI
  26. Li, 2003, OrthoMCL: Identification of ortholog groups for eukaryotic genomes, Genome Res., 13, 2178, 10.1101/gr.1224503 · DOI · Paper page
  27. Chen, 2007, Assessing performance of orthology detection strategies applied to eukaryotic genomes, PLoS One, 2, e383, 10.1371/journal.pone.0000383 · DOI
  28. Buljan, 2009, The evolution of protein domain families, Biochem. Soc. Trans., 37, 751, 10.1042/BST0370751 · DOI
  29. Buljan, 2010, Quantifying the mechanisms of domain gain in animal proteins, Genome Biol., 11, R74, 10.1186/gb-2010-11-7-r74 · DOI · Paper page
  30. Fong, 2007, Modeling the evolution of protein domain architectures using maximum parsimony, J. Mol. Biol., 366, 307, 10.1016/j.jmb.2006.11.017 · DOI
  31. Moore, 2008, Arrangements in the modular evolution of proteins, Trends Biochem. Sci., 33, 444, 10.1016/j.tibs.2008.05.008 · DOI
  32. Nagy, A., Banyai, L., and Patthy, L. (2011). Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Errors Caused by Confusing Paralogs and Epaktologs. Genes, submitted for publication. · DOI
  33. Yu, 2005, Nested genes in the human genome, Genomics, 86, 414, 10.1016/j.ygeno.2005.06.008 · DOI
  34. Assis, 2008, Nested genes and increasing organizational complexity of metazoan genomes, Trends Genet., 24, 475, 10.1016/j.tig.2008.08.003 · DOI
  35. Kumar, 2009, An overview of nested genes in eukaryotic genomes, Eukaryotic Cell, 8, 1321, 10.1128/EC.00143-09 · DOI
  36. Kaplan, 1999, A novel developmentally regulated gene in lung mesenchyme: homology to a tumor-derived trypsin inhibitor, Am. J. Physiol., 276, L1027
  37. Trexler, 2000, The LCCL module, Eur. J. Biochem., 267, 5751, 10.1046/j.1432-1327.2000.01641.x · DOI
  38. Hedges, 2006, TimeTree: A public knowledge-base of divergence times among organisms, Bioinformatics, 22, 2971, 10.1093/bioinformatics/btl505 · DOI · Paper page
  39. Neumann, 2001, An alternative amino-terminus expressed in the central nervous system converts agrin to a type II transmembrane protein, Mol. Cell. Neurosci., 17, 208, 10.1006/mcne.2000.0932 · DOI
  40. Ip, 2000, Cloning and characterization of muscle-specific kinase in chicken, Mol. Cell. Neurosci., 16, 661, 10.1006/mcne.2000.0892 · DOI
  41. Xu, 2005, Genetic evidence of a strong functional constraint of neurotrypsin during primate evolution, Cytogenet Genome Res., 108, 303, 10.1159/000081523 · DOI
  42. UniProt Consortium (2010). The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res., 38, D142–D148. · DOI
  43. Homepage of RefSeq database. Available online: http://www.ncbi.nlm.nih.gov/RefSeq/ (accessed on 04 May 2011).
  44. Hubbard, 2009, Ensembl 2009, Nucleic Acids Res., 37, D690, 10.1093/nar/gkn828 · DOI
  45. Sayers, 2010, Database resources of the National Center for Biotechnology Information, Nucleic Acids Res., 38, D5, 10.1093/nar/gkp967 · DOI
  46. Homepage of the National Center for Biotechnology Information. Available online: http://www.ncbi.nlm.nih.gov/ (accessed on 04 May 2011).
  47. Homepage of Gnomon, the NCBI eukaryotic gene prediction tool. Available online: http://www.ncbi.nlm.nih.gov/genome/guide/gnomon.shtml (accessed on 04 May 2011).
  48. Anderson, 2009, CDD: Specific functional annotation with the conserved domain database, Nucleic Acids Res., 37, D205, 10.1093/nar/gkn845 · DOI
  49. Letunic, 2009, SMART 6: Recent updates and new developments, Nucleic Acids Res., 37, D229, 10.1093/nar/gkn808 · DOI
  50. Stanke, 2005, AUGUSTUS: A web server for gene prediction in eukaryotes that allows user-defined constraints, Nucleic Acids Res., 33, W465, 10.1093/nar/gki458 · DOI
  51. Birney, 2004, GeneWise and Genomewise, Genome Res., 14, 988, 10.1101/gr.1865504 · DOI · Paper page
  52. Yeh, 2001, Computational inference of homologous gene structures in the human genome, Genome Res., 11, 803, 10.1101/gr.175701 · DOI
  53. Salamov, 2000, Ab initio gene finding in Drosophila genomic DNA, Genome Res., 10, 516, 10.1101/gr.10.4.516 · DOI
  54. Li, 2003, OrthoMCL: Identification of ortholog groups for eukaryotic genomes, Genome Res., 13, 2178, 10.1101/gr.1224503 · DOI · Paper page
  55. Chen, 2007, Assessing performance of orthology detection strategies applied to eukaryotic genomes, PLoS One, 2, e383, 10.1371/journal.pone.0000383 · DOI
  56. Wu, 2006, Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: A test case in the euasterid plant clade, Genetics, 174, 1407, 10.1534/genetics.106.062455 · DOI
  57. Vallender, 2009, Bioinformatic approaches to identifying orthologs and assessing evolutionary relationships, Methods, 49, 50, 10.1016/j.ymeth.2009.05.010 · DOI
  58. Clamp, 2007, Distinguishing protein-coding and noncoding genes in the human genome, Proc. Natl. Acad. Sci. USA, 104, 19428, 10.1073/pnas.0709013104 · DOI · Paper page
  59. Berglund, 2008, In Paranoid 6: Eukaryotic ortholog clusters with inparalogs, Nucleic Acids Res., 36, D263, 10.1093/nar/gkm1020 · DOI
  60. Heinicke, 2007, The Princeton Protein Orthology Database (P-POD): A comparative genomics analysis tool for biologists, PLoS One, 2, e766, 10.1371/journal.pone.0000766 · DOI

Cited by

Sorted by citations

Metadata

Authors
Nagy, A., Szláma, G., Szarka, E., Trexler, M., Bányai, L., & Patthy, L.
Affiliations
Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H-1113 Budapest, Hungary
Venue
Genes
Publisher
MDPI AG
Published
2011-07-13
Volume
2
Issue
3
Pages
449-501
ISSN
2073-4425
DOI
10.3390/genes2030449
PMC
PMC3927609
Cited by
22
References
3
Language
en
Update notices
correction (2011-07-13)
Licence
creativecommons.org/licenses/by/3.0/ (vor)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review