Z-DNA and Z-RNA are functionally important left-handed structures of nucleic acids, which play a significant role in several molecular and biological processes including DNA replication, gene expression regulation and viral nucleic acid sensing. Most proteins that have been proven to interact with Z-DNA/Z-RNA contain the so-called Zα domain, which is structurally well conserved. To date, only eight proteins with Zα domain have been described within a few organisms (including human, mouse, Danio rerio, Trypanosoma brucei and some viruses). Therefore, this paper aimed to search for new Z-DNA/Z-RNA binding proteins in the complete PDB structures database and from the AlphaFold2 protein models. A structure-based similarity search found 14 proteins with highly similar Zα domain structure in experimentally-defined proteins and 185 proteins with a putative Zα domain using the AlphaFold2 models. Structure-based alignment and molecular docking confirmed high functional conservation of amino acids involved in Z-DNA/Z-RNA, suggesting that Z-DNA/Z-RNA recognition may play an important role in a variety of cellular processes.

• Klíčová slova
• Z-DNA, Z-RNA, Zα domain, bioinformatics, protein binding,
• MeSH
• DNA vazebné proteiny chemie   metabolismus   MeSH
• interakční proteinové domény a motivy * MeSH
• konformace nukleové kyseliny MeSH
• konformace proteinů MeSH
• molekulární modely * MeSH
• proteiny vázající RNA chemie   metabolismus   MeSH
• RNA chemie   metabolismus   MeSH
• sekvence aminokyselin MeSH
• simulace molekulární dynamiky MeSH
• simulace molekulového dockingu MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• vztahy mezi strukturou a aktivitou MeSH
• Z-DNA chemie   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• DNA vazebné proteiny MeSH
• proteiny vázající RNA MeSH
• RNA MeSH
• Z-DNA MeSH

Sex chromosomes are an ideal system to study processes connected with suppressed recombination. We found evidence of microsatellite expansion, on the relatively young Y chromosome of the dioecious plant sorrel (Rumex acetosa, XY1Y2 system), but no such expansion on the more ancient Y chromosomes of liverwort (Marchantia polymorpha) and human. The most expanding motifs were AC and AAC, which also showed periodicity of array length, indicating the importance of beginnings and ends of arrays. Our data indicate that abundance of microsatellites in genomes depends on the inherent expansion potential of specific motifs, which could be related to their stability and ability to adopt unusual DNA conformations. We also found that the abundance of microsatellites is higher in the neighborhood of transposable elements (TEs) suggesting that microsatellites are probably targets for TE insertions. This evidence suggests that microsatellite expansion is an early event shaping the Y chromosome where this process is not opposed by recombination, while accumulation of TEs and chromosome shrinkage predominate later.

• MeSH
• A-DNA genetika   MeSH
• chromozomy rostlin genetika   MeSH
• duplikace genu MeSH
• hybridizace in situ fluorescenční MeSH
• lidé MeSH
• lidský chromozom Y genetika   MeSH
• Marchantia genetika   MeSH
• metafáze genetika   MeSH
• mikrosatelitní repetice genetika   MeSH
• modely genetické MeSH
• molekulární evoluce * MeSH
• periodicita MeSH
• Rumex genetika   MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza DNA MeSH
• transpozibilní elementy DNA genetika   MeSH
• Z-DNA genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• A-DNA MeSH
• transpozibilní elementy DNA MeSH
• Z-DNA MeSH