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Structural basis for C. elegans pairing center DNA binding specificity by the ZIM/HIM-8 family proteins

Author

Listed:
  • Meili Li

    (University of Science and Technology of China)

  • Chengming Zhu

    (University of Science and Technology of China)

  • Zheng Xu

    (Sichuan University)

  • Mingjing Xu

    (University of Science and Technology of China)

  • Yan Kuang

    (University of Science and Technology of China)

  • Xinhao Hou

    (University of Science and Technology of China)

  • Xinya Huang

    (University of Science and Technology of China)

  • Mengqi Lv

    (University of Science and Technology of China)

  • Yongrui Liu

    (University of Science and Technology of China)

  • Yong Zhang

    (University of Science and Technology of China)

  • Ziyan Xu

    (University of Science and Technology of China)

  • Xu Han

    (University of Science and Technology of China)

  • Suman Wang

    (University of Science and Technology of China)

  • Yunyu Shi

    (University of Science and Technology of China)

  • Shouhong Guang

    (University of Science and Technology of China)

  • Fudong Li

    (University of Science and Technology of China)

Abstract

Pairing center (PC) on each chromosome of Caenorhabditis elegans is crucial for homolog pairing and initiating synapsis. Within each PC, clusters of 11/12 bp DNA motif recruit one of four paralogous meiosis-specific proteins: ZIM-1, ZIM-2, ZIM-3, or HIM-8. However, the mechanistic basis underlying the specificity of ZIM/HIM-8-PC DNA interaction remains elusive. Here, we describe crystal structures of HIM-8, ZIM-1 and ZIM-2 DNA binding domains (ZF1, ZF2 and CTD) in complex with their cognate PC DNA motifs, respectively. These structures demonstrated the ZF1-2-CTD folds as an integrated structural unit crucial for its DNA binding specificity. Base-specific DNA-contacting residues are exclusively distributed on ZF1-2 and highly conserved. Furthermore, the CTD potentially contributes to the conformational diversity of ZF1-2, imparting binding specificity to distinct PC DNA motifs. These findings shed light on the mechanism governing PC DNA motif recognition by ZIM/HIM-8 proteins, suggesting a co-evolution relationship between PC DNA motifs and ZF1-2-CTD in shaping the specific recognition.

Suggested Citation

  • Meili Li & Chengming Zhu & Zheng Xu & Mingjing Xu & Yan Kuang & Xinhao Hou & Xinya Huang & Mengqi Lv & Yongrui Liu & Yong Zhang & Ziyan Xu & Xu Han & Suman Wang & Yunyu Shi & Shouhong Guang & Fudong L, 2024. "Structural basis for C. elegans pairing center DNA binding specificity by the ZIM/HIM-8 family proteins," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-54548-9
    DOI: 10.1038/s41467-024-54548-9
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    References listed on IDEAS

    as
    1. Yan Wang & Yanyan Chen & Juan Chen & Lijun Wang & Leitong Nie & Juanjuan Long & Haishuang Chang & Jian Wu & Chenhui Huang & Ming Lei, 2019. "The meiotic TERB1-TERB2-MAJIN complex tethers telomeres to the nuclear envelope," Nature Communications, Nature, vol. 10(1), pages 1-19, December.
    2. Xinhao Hou & Mingjing Xu & Chengming Zhu & Jianing Gao & Meili Li & Xiangyang Chen & Cheng Sun & Björn Nashan & Jianye Zang & Ying Zhou & Shouhong Guang & Xuezhu Feng, 2023. "Systematic characterization of chromodomain proteins reveals an H3K9me1/2 reader regulating aging in C. elegans," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    3. Josh Abramson & Jonas Adler & Jack Dunger & Richard Evans & Tim Green & Alexander Pritzel & Olaf Ronneberger & Lindsay Willmore & Andrew J. Ballard & Joshua Bambrick & Sebastian W. Bodenstein & David , 2024. "Accurate structure prediction of biomolecular interactions with AlphaFold 3," Nature, Nature, vol. 630(8016), pages 493-500, June.
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