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Comprehensive evolutionary analysis and nomenclature of plant G3BPs

View ORCID ProfileAala A Abulfaraj, Hajime Ohyanagi, Kosuke Goto, View ORCID ProfileKatsuhiko Mineta, Takashi Gojobori, View ORCID ProfileHeribert Hirt, View ORCID ProfileNaganand Rayapuram  Correspondence email
Aala A Abulfaraj
1Biological Sciences Department, College of Science and Arts, King Abdulaziz University, Rabigh, Saudi Arabia
Roles: Formal analysis, Methodology, Writing—original draft, review, and editing
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  • ORCID record for Aala A Abulfaraj
Hajime Ohyanagi
2Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
3Joint Center for Researchers, Associates and Clinicians Data Center, National Center for Global Health and Medicine1-21-1, Tokyo, Japan
Roles: Formal analysis, Validation, Investigation, Visualization, Methodology, Writing—original draft, review, and editing
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Kosuke Goto
2Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
4Marine Open Innovation (MaOI) Institute Shimizu-Marine Building, Shizuoka, Japan
Roles: Formal analysis, Investigation, Methodology, Writing—original draft
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Katsuhiko Mineta
2Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
Roles: Formal analysis, Investigation, Methodology, Writing—original draft
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  • ORCID record for Katsuhiko Mineta
Takashi Gojobori
2Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
Roles: Supervision, Validation, Project administration, Writing—review and editing
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Heribert Hirt
5Center for Desert Agriculture (CDA), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
6Institute of Plant Sciences Paris-Saclay IPS2, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Sud, Université Evry, Université Paris-Saclay, Orsay, France
7Max Perutz Laboratories, University of Vienna, Vienna, Austria
Roles: Conceptualization, Supervision, Validation, Project administration, Writing—review and editing
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Naganand Rayapuram
5Center for Desert Agriculture (CDA), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
Roles: Conceptualization, Data curation, Formal analysis, Supervision, Methodology, Project administration, Writing—original draft, review, and editing
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  • ORCID record for Naganand Rayapuram
  • For correspondence: naganand.rayapuram@kaust.edu.sa
Published 26 May 2022. DOI: 10.26508/lsa.202101328
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    Figure S1. Phylogenetic tree of 922 G3BP proteins from 382 eukaryotic species (fungi, metazoans, and plants).

    Source data are available for this figure.

    Source Data for Figure S1[LSA-2021-01328_SdataFS1.zip]

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    Figure 1. Phylogenetic tree of 148 G3BP proteins from 39 eukaryotic species (fungi, metazoans, and plants).

    Source data are available for this figure.

    Source Data for Figure 1[LSA-2021-01328_SdataF1.zip]

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    Figure 2. Phylogenetic relationships in 21 G3BP protein sequences from five representative species in land plants (Arabidopsis thaliana, Oryza sativa, Amborella trichopoda, Physcomitrella patens, and Marchantia polymorpha).

    A phylogenetic tree of G3BP proteins. Their domain structures detected by searching against Pfam-A database with Hidden Markov Model (hmmscan) were shown on the right (threshold: E-value ≤ 1 × 10−4 and aligned region ≥ 50% against registered domain length). The positions of G3BP-A–specific amino acid differences detected in the NTF2 domains (AT5G43960, ERN15925, OS02T0131700-0, and OS04T0510500-01) are shown as reversed yellow triangles.

    Source data are available for this figure.

    Source Data for Figure 2[LSA-2021-01328_SdataF2.zip]

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    Figure 3. Aminoacid sequence alignment of the the NTF2 domain in G3BPs.

    (A) Alignment of NTF2 domain regions of 21 G3BP protein sequences from five representative species in land plants (Arabidopsis thaliana, Oryza sativa, Amborella trichopoda, Physcomitrella patens, and Marchantia polymorpha). The three G3BP-A–specific amino acid differences detected are shown in red rectangles. (B) Details for the G3BP-A–specific amino acid differences in the four protein sequences. For example, A14Y stands for the consensus A (Alanine) residue at 14th position changed to Y (Tyrosine) in G3BP-A.

  • Figure S2.
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    Figure S2. Full-length alignment with 21 G3BP protein sequences from five representative species in land plants (Arabidopsis thaliana, Oryza sativa, Amborella trichopoda, Physcomitrella patens, and Marchantia polymorpha).

    The three G3BP-A–specific amino acid differences detected in the NTF2 domain were shown in red rectangles.

  • Figure 4.
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    Figure 4. Change in the number of G3BP genes in plant evolutionary history.

    (A) A graphical representation of G3BP genes during plant evolution. The arrows indicate the common origin of eukaryotic G3BPs, the basal land plants, and basal angiosperms. The average number of G3BPs in each category is indicated in black. In parenthesis, the average number of G3BP-As is indicated in red, whereas that of G3BP-Bs is indicated in blue. (B) Table showing the number of G3BP othologs for selected species under different categories.

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    Figure S3. Ancestral state of the number of G3BP orthologs among 39 representative species.

    Colors show the number of orthologs. Left and right semicircles represent the minimum and the maximum numbers in the reconstruction.

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    Table 1.

    List of Arabidopsis G3BPs with novel nomenclature

    NameFamilyAGI numberFormer nameFunctionReference
    AtG3BP7AAt5G43960AtG3BP-like AtG3BP2Virus resistance induced upon virus infectionKrapp et al (2017), Abulfaraj et al (2018), and Reuper et al (2021a, 2021b)
    AtG3BP6BAt3G25150AtG3BP3Induced upon virus infectionAbulfaraj et al (2018) and Reuper et al (2021a, 2021b)
    AtG3BP5At3G07250Not yet characterizedAbulfaraj et al (2018)
    AtG3BP1At5G48650AtG3BP1 AtG3BP7Regulator of stomatal and apoplastic immunity induced upon virus infectionAbulfaraj et al (2018) and Reuper et al (2021a, 2021b)
    AtG3BP8At5G60980AtG3BP1Induced upon virus infectionAbulfaraj et al (2018) and Reuper et al (2021a, 2021b)
    AtG3BP2At1G13730AtG3BP5Not induced upon virus infectionAbulfaraj et al (2018) and Reuper et al (2021a, 2021b)
    AtG3BP4At2G03640AtG3BP6Induced upon virus infectionAbulfaraj et al (2018) and Reuper et al (2021a, 2021b)
    AtG3BP3At1G69250AtG3BP4Induced upon virus infectionAbulfaraj et al (2018) and Reuper et al (2021a, 2021b)

Supplementary Materials

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  • Table S1. Protein sequences of 39 representative species. [LSA-2021-01328_TableS1.docx]

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Phylogeny of plant G3BPs
Aala A Abulfaraj, Hajime Ohyanagi, Kosuke Goto, Katsuhiko Mineta, Takashi Gojobori, Heribert Hirt, Naganand Rayapuram
Life Science Alliance May 2022, 5 (9) e202101328; DOI: 10.26508/lsa.202101328

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Phylogeny of plant G3BPs
Aala A Abulfaraj, Hajime Ohyanagi, Kosuke Goto, Katsuhiko Mineta, Takashi Gojobori, Heribert Hirt, Naganand Rayapuram
Life Science Alliance May 2022, 5 (9) e202101328; DOI: 10.26508/lsa.202101328
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Volume 5, No. 9
September 2022
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