AGONOTES: A Robot Annotator for Argonaute Proteins

  • Lixu Jiang
  • Min Yu
  • Yuwei Zhou
  • Zhongjie Tang
  • Ning Li
  • Juanjuan Kang
  • Bifang He
  • Jian HuangEmail author
Original research article


The argonaute protein (Ago) exists in almost all organisms. In eukaryotes, it functions as a regulatory system for gene expression. In prokaryotes, it is a type of defense system against foreign invasive genomes. The Ago system has been engineered for gene silencing and genome editing and plays an important role in biological studies. With an increasing number of genomes and proteomes of various microbes becoming available, computational tools for identifying and annotating argonaute proteins are urgently needed. We introduce AGONOTES (Argonaute Notes). It is a web service especially designed for identifying and annotating Ago. AGONOTES uses the BLASTP similarity search algorithm to categorize all submitted proteins into three groups: prokaryotic argonaute protein (pAgo), eukaryotic argonaute protein (eAgo), and non-argonaute protein (non-Ago). Argonaute proteins can then be aligned to the corresponding standard set of Ago sequences using the multiple sequence alignment program MUSCLE. All functional domains of Ago can further be curated from the alignment results and visualized easily through Bio::Graphic modules in the BioPerl bundle. Compared with existing tools such as CD-Search and available databases such as UniProt and AGONOTES showed a much better performance on domain annotations, which is fundamental in studying the new Ago. AGONOTES can be freely accessed at AGONOTES is a friendly tool for annotating Ago domains from a proteome or a series of protein sequences.


Argonaute protein Gene silencing Genome editing Similarity search Protein recognition Domain annotation 



Argonaute protein


Argonaute Notes


Aquifex aeolicus argonaute


Eukaryotic argonaute protein(s)


ePIWI proteins


Human argonaute 1


Human argonaute 2


Kluyveromyces polysporus argonaute

L1 domain

Linker1 domain

L2 domain

Linker2 domain

MID domain

Middle domain


Marinitoga piezophila argonaute


Mouse argonaute 2


Non-argonaute protein(s)

N domain

N-terminal domain


Natronobacterium gregoryi argonaute


Prokaryotic argonaute protein(s)

PAZ domain

PIWI–Argonaute–Zwille domain

PIWI domain

P element–induced wimpy testis domain


Pyrococcus furiosus argonaute


pPIWI proteins


Rhodobacter sphaeroides argonaute


Schizosaccharomyces pombe argonaute 1


Thermus thermophilus argonaute



The authors are grateful to the anonymous reviewers for their valuable suggestions and comments, which have led to the improvement of this paper. In addition, thanks to Hui Yang for valuable discussions and suggestions. This work was supported by the National Natural Science Foundation of China [Grant no. 61571095] and the China Postdoctoral Science Foundation Grant [Grant no. 2019M653369].

Compliance with Ethical Standards

Conflict of Interest

The authors declare no conflict of interest, financial or otherwise.

Human and Animal Rights

No animals/humans were used for studies that are the basis of this research.


  1. 1.
    Bohmert K, Camus I, Bellini C, Bouchez D, Caboche M, Benning C (1998) AGO1 defines a novel locus of Arabidopsis controlling leaf development. EMBO J 17(1):170–180. CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Makarova KS, Wolf YI, van der Oost J, Koonin EV (2009) Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements. Biol Direct 4:29. CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Sheng G, Zhao H, Wang J, Rao Y, Tian W, Swarts DC, van der Oost J, Patel DJ, Wang Y (2014) Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage. Proc Natl Acad Sci USA 111(2):652–657. CrossRefPubMedGoogle Scholar
  4. 4.
    Kaya E, Doxzen KW, Knoll KR, Wilson RC, Strutt SC, Kranzusch PJ, Doudna JA (2016) A bacterial Argonaute with noncanonical guide RNA specificity. Proc Natl Acad Sci USA 113(15):4057–4062. CrossRefPubMedGoogle Scholar
  5. 5.
    Parker JS, Roe SM, Barford D (2004) Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity. EMBO J 23(24):4727–4737. CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Song JJ, Smith SK, Hannon GJ, Joshua-Tor L (2004) Crystal structure of Argonaute and its implications for RISC slicer activity. Science 305(5689):1434–1437. CrossRefPubMedGoogle Scholar
  7. 7.
    Swarts DC, Makarova K, Wang Y, Nakanishi K, Ketting RF, Koonin EV, Patel DJ, van der Oost J (2014) The evolutionary journey of Argonaute proteins. Nat Struct Mol Biol 21(9):743–753. CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Olovnikov I, Chan K, Sachidanandam R, Newman DK, Aravin AA (2013) Bacterial argonaute samples the transcriptome to identify foreign DNA. Mol Cell 51(5):594–605. CrossRefPubMedGoogle Scholar
  9. 9.
    Swarts DC, Jore MM, Westra ER, Zhu Y, Janssen JH, Snijders AP, Wang Y, Patel DJ, Berenguer J, Brouns SJJ, van der Oost J (2014) DNA-guided DNA interference by a prokaryotic Argonaute. Nature 507(7491):258–261. CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Gao F, Shen XZ, Jiang F, Wu Y, Han C (2016) DNA-guided genome editing using the Natronobacterium gregoryi Argonaute. Nat Biotechnol 34(7):768–773. CrossRefPubMedGoogle Scholar
  11. 11.
    Lee SH, Turchiano G, Ata H, Nowsheen S, Romito M, Lou Z, Ryu SM, Ekker SC, Cathomen T, Kim JS (2016) Failure to detect DNA-guided genome editing using Natronobacterium gregoryi Argonaute. Nat Biotechnol 35(1):17–18. CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Burgess S, Cheng L, Gu F, Huang J, Huang Z, Lin S, Li J, Li W, Qin W, Sun Y, Songyang Z, Wei W, Wu Q, Wang H, Wang X, Xiong JW, Xi J, Yang H, Zhou B, Zhang B (2016) Questions about NgAgo. Protein Cell 7(12):913–915. CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Qi J, Dong Z, Shi Y, Wang X, Qin Y, Wang Y, Liu D (2016) NgAgo-based fabp11a gene knockdown causes eye developmental defects in zebrafish. Cell Res 26(12):1349–1352. CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Nguyen Q, Iritani A, Ohkita S, Vu BV, Yokoya K, Matsubara A, Ikeda KI, Suzuki N, Nakayashiki H (2018) A fungal Argonaute interferes with RNA interference. Nucleic Acids Res 46(5):2495–2508. CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Chai G, Yu M, Jiang L, Duan Y, Huang J (2017) HMMCAS: a web tool for the identification and domain annotations of Cas proteins. IEEE/ACM Trans Comput Biol Bioinf. CrossRefGoogle Scholar
  16. 16.
    Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014) Pfam: the protein families database. Nucleic acids research 42(Database issue):D222–D230. CrossRefPubMedGoogle Scholar
  17. 17.
    Chen W, Lv H, Nie F, Lin H (2019) i6 mA-Pred: Identifying DNA N6-methyladenine sites in the rice genome. Bioinformatics. CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Dao FY, Lv H, Wang F, Feng CQ, Ding H, Chen W, Lin H (2018) Identify origin of replication in Saccharomyces cerevisiae using two-step feature selection technique. Bioinformatics. CrossRefGoogle Scholar
  19. 19.
    He B, Chai G, Duan Y, Yan Z, Qiu L, Zhang H, Liu Z, He Q, Han K, Ru B, Guo FB, Ding H, Lin H, Wang X, Rao N, Zhou P, Huang J (2016) BDB: biopanning data bank. Nucleic Acids Res 44(D1):D1127–1132. CrossRefPubMedGoogle Scholar
  20. 20.
    He B, Jiang L, Duan Y, Chai G, Fang Y, Kang J, Yu M, Li N, Tang Z, Yao P, Wu P, Derda R, Huang J (2018) Biopanning data bank 2018: hugging next generation phage display. Database J Biolog Databases Curation. CrossRefGoogle Scholar
  21. 21.
    He B, Kang J, Ru B, Ding H, Zhou P, Huang J (2016) SABinder: a web service for predicting streptavidin-binding peptides. Biomed Res Int 2016:9175143. CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Huang J, Ru B, Zhu P, Nie F, Yang J, Wang X, Dai P, Lin H, Guo FB, Rao N (2012) MimoDB 2.0: a mimotope database and beyond. Nucleic acids research 40(Database issue):D271–D277. CrossRefPubMedGoogle Scholar
  23. 23.
    Kang J, Fang Y, Yao P, Li N, Tang Q, Huang J (2019) NeuroPP: a tool for the prediction of neuropeptide precursors based on optimal sequence composition. Interdiscip Sci 11(1):108–114. CrossRefPubMedGoogle Scholar
  24. 24.
    Li N, Kang J, Jiang L, He B, Lin H, Huang J (2017) PSBinder: a web service for predicting polystyrene surface-binding peptides. Biomed Res Int 2017:5761517. CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    Ru B, tHoen PA, Nie F, Lin H, Guo FB, Huang J (2014) PhD7Faster: predicting clones propagating faster from the Ph.D.-7 phage display peptide library. J Bioinform Comput Biol 12(1):1450005. CrossRefPubMedGoogle Scholar
  26. 26.
    Tang Q, Nie F, Kang J, Ding H, Zhou P, Huang J (2015) NIEluter: predicting peptides eluted from HLA class I molecules. J Immunol Methods 422:22–27. CrossRefPubMedGoogle Scholar
  27. 27.
    Xu ZC, Feng PM, Yang H, Qiu WR, Chen W, Lin H (2019) iRNAD: a computational tool for identifying D modification sites in RNA sequence. Bioinformatics. CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Zhang Y, Liu T, Chen L, Yang J, Yin J, Zhang Y, Yun Z, Xu H, Ning L, Guo F, Jiang Y, Lin H, Wang D, Huang Y, Huang J (2019) RIscoper: a tool for RNA–RNA interaction extraction from the literature. Bioinformatics. CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    UniProt C (2015) UniProt: a hub for protein information. Nucleic acids research 43(Database issue):D204–D212. CrossRefGoogle Scholar
  30. 30.
    Schultz J, Milpetz F, Bork P, Ponting CP (1998) SMART, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci USA 95(11):5857–5864CrossRefGoogle Scholar
  31. 31.
    Marchler-Bauer A, Bo Y, Han L, He J, Lanczycki CJ, Lu S, Chitsaz F, Derbyshire MK, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Lu F, Marchler GH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, Geer LY, Bryant SH (2017) CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res 45(D1):D200–D203. CrossRefPubMedGoogle Scholar
  32. 32.
    Servant F, Bru C, Carrere S, Courcelle E, Gouzy J, Peyruc D, Kahn D (2002) ProDom: automated clustering of homologous domains. Brief Bioinform 3(3):246–251. CrossRefPubMedGoogle Scholar
  33. 33.
    Swarts DC, Hegge JW, Hinojo I, Shiimori M, Ellis MA, Dumrongkulraksa J, Terns RM, Terns MP, van der Oost J (2015) Argonaute of the archaeon Pyrococcus furiosus is a DNA-guided nuclease that targets cognate DNA. Nucleic Acids Res 43(10):5120–5129. CrossRefPubMedPubMedCentralGoogle Scholar
  34. 34.
    Miyoshi T, Ito K, Murakami R, Uchiumi T (2016) Structural basis for the recognition of guide RNA and target DNA heteroduplex by Argonaute. Nat Commun 7:11846. CrossRefPubMedPubMedCentralGoogle Scholar
  35. 35.
    Yuan YR, Pei Y, Ma JB, Kuryavyi V, Zhadina M, Meister G, Chen HY, Dauter Z, Tuschl T, Patel DJ (2005) Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage. Mol Cell 19(3):405–419. CrossRefPubMedPubMedCentralGoogle Scholar
  36. 36.
    Schirle NT, Sheu-Gruttadauria J, MacRae IJ (2014) Structural basis for microRNA targeting. Science 346(6209):608–613. CrossRefPubMedPubMedCentralGoogle Scholar
  37. 37.
    Faehnle CR, Elkayam E, Haase AD, Hannon GJ, Joshua-Tor L (2013) The making of a slicer: activation of human Argonaute-1. Cell Rep 3(6):1901–1909. CrossRefPubMedPubMedCentralGoogle Scholar
  38. 38.
    Jee D, Yang JS, Park SM, Farmer DT, Wen J, Chou T, Chow A, McManus MT, Kharas MG, Lai EC (2018) Dual strategies for Argonaute2-Mediated biogenesis of erythroid miRNAs underlie conserved requirements for slicing in mammals. Mol Cell 69(2):265–278. CrossRefPubMedPubMedCentralGoogle Scholar
  39. 39.
    Nakanishi K, Weinberg DE, Bartel DP, Patel DJ (2012) Structure of yeast Argonaute with guide RNA. Nature 486(7403):368–374. CrossRefPubMedPubMedCentralGoogle Scholar
  40. 40.
    Wang Y, Geer LY, Chappey C, Kans JA, Bryant SH (2000) Cn3D: sequence and structure views for Entrez. Trends Biochem Sci 25(6):300–302CrossRefGoogle Scholar
  41. 41.
    Mount DW (2007) Using the basic local alignment search tool (BLAST). CSH protocols. CrossRefPubMedGoogle Scholar
  42. 42.
    Lemoine F, Correia D, Lefort V, Doppelt-Azeroual O, Mareuil F, Cohen-Boulakia S, Gascuel O (2019) new generation phylogenetic services for non-specialists. Nucleic Acids Res 47(W1):W260–W265. CrossRefPubMedPubMedCentralGoogle Scholar
  43. 43.
    Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M, Claverie JM, Gascuel O (2008) robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 36(Web Server issue):W465–W469. CrossRefPubMedPubMedCentralGoogle Scholar
  44. 44.
    Wu Z, Tan S, Xu L, Gao L, Zhu H, Ma C, Liang X (2017) NgAgo-gDNA system efficiently suppresses hepatitis B virus replication through accelerating decay of pregenomic RNA. Antiviral Res 145:20–23. CrossRefPubMedGoogle Scholar
  45. 45.
    Wei Q, Liao J, Yu X, Wang EJ, Wang C, Luu HH, Haydon RC, Lee MJ, He TC (2016) An NgAgo tool for genome editing: did CRISPR/Cas9 just find a competitor? Genes Dis 3(3):169–170. CrossRefPubMedPubMedCentralGoogle Scholar
  46. 46.
    Khin NC, Lowe JL, Jensen LM, Burgio G (2017) No evidence for genome editing in mouse zygotes and HEK293T human cell line using the DNA-guided Natronobacterium gregoryi Argonaute (NgAgo). PLoS One 12(6):e0178768. CrossRefPubMedPubMedCentralGoogle Scholar
  47. 47.
    Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792–1797. CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© International Association of Scientists in the Interdisciplinary Areas 2019

Authors and Affiliations

  1. 1.Center for Informational Biology, School of Life Science and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
  2. 2.School of MedicineGuizhou UniversityGuiyangChina

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