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AGONOTES: A Robot Annotator for Argonaute Proteins

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Abstract

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 http://i.uestc.edu.cn/agonotes/. AGONOTES is a friendly tool for annotating Ago domains from a proteome or a series of protein sequences.

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Abbreviations

Ago:

Argonaute protein

AGONOTES:

Argonaute Notes

AaAgo:

Aquifex aeolicus argonaute

eAgo(s):

Eukaryotic argonaute protein(s)

ePIWIs:

ePIWI proteins

hAgo1:

Human argonaute 1

hAgo2:

Human argonaute 2

KpAgo:

Kluyveromyces polysporus argonaute

L1 domain:

Linker1 domain

L2 domain:

Linker2 domain

MID domain:

Middle domain

MpAgo:

Marinitoga piezophila argonaute

mAgo2:

Mouse argonaute 2

non-Ago(s):

Non-argonaute protein(s)

N domain:

N-terminal domain

NgAgo:

Natronobacterium gregoryi argonaute

pAgo(s):

Prokaryotic argonaute protein(s)

PAZ domain:

PIWI–Argonaute–Zwille domain

PIWI domain:

P element–induced wimpy testis domain

PfAgo:

Pyrococcus furiosus argonaute

pPIWIs:

pPIWI proteins

RsAgo:

Rhodobacter sphaeroides argonaute

SpAgo1:

Schizosaccharomyces pombe argonaute 1

TtAgo:

Thermus thermophilus argonaute

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Acknowledgements

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].

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Author notes

  1. Lixu Jiang and Min Yu contributed equally to this work.

Authors and Affiliations

  1. Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 637111, China

    Lixu Jiang, Min Yu, Yuwei Zhou, Zhongjie Tang, Ning Li, Juanjuan Kang, Bifang He & Jian Huang

  2. School of Medicine, Guizhou University, Guiyang, China

    Bifang He

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  1. Lixu Jiang
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Jiang, L., Yu, M., Zhou, Y. et al. AGONOTES: A Robot Annotator for Argonaute Proteins. Interdiscip Sci Comput Life Sci 12, 109–116 (2020). https://doi.org/10.1007/s12539-019-00349-4

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