Variation of Structure and Cellular Functions of Type IA Topoisomerases across the Tree of Life

Abstract

Topoisomerases regulate the topological state of cellular genomes to prevent impediments to vital cellular processes, including replication and transcription from suboptimal supercoiling of double-stranded DNA, and to untangle topological barriers generated as replication or recombination intermediates. The subfamily of type IA topoisomerases are the only topoisomerases that can alter the interlinking of both DNA and RNA. In this article, we provide a review of the mechanisms by which four highly conserved N-terminal protein domains fold into a toroidal structure, enabling cleavage and religation of a single strand of DNA or RNA. We also explore how these conserved domains can be combined with numerous non-conserved protein sequences located in the C-terminal domains to form a diverse range of type IA topoisomerases in Archaea, Bacteria, and Eukarya. There is at least one type IA topoisomerase present in nearly every free-living organism. The variation in C-terminal domain sequences and interacting partners such as helicases enable type IA topoisomerases to conduct important cellular functions that require the passage of nucleic acids through the break of a single-strand DNA or RNA that is held by the conserved N-terminal toroidal domains. In addition, this review will exam a range of human genetic disorders that have been linked to the malfunction of type IA topoisomerase.

Keywords: genetic diseases; genome topology; genomic instability; supercoiling; topoisomerase; type IA.

Figure 1

The Assembly and Features of N-terminal Domains. The four N-terminal domains D1–D4 are colored in cyan, red, pink, and green, respectively. The connections between domains are marked with arrowed dash lines. The figure is prepared based on the Mycobacterium tuberculosis Topo I (MtbTopo I) structure (PDB code: 5UJ1). For display purposes, the individually displayed domains are not drawn to the same scale.

Figure 2

The binding of the G-segment and conformational change in the presence/absence of Mg²⁺ ions. (A) An example of G-segment binding with N-terminal domains of MtbTopoI. The catalytic residue Y342 is drawn in stick format to indicate its position. The G-segment ssDNA is colored in orange. (B) The front and side views of the conformational changes of D4 upon G-segment binding. The ribbon diagram of D4 in grey represents the structure before G-segment binding (PDB code: 5UJ1). The structure in green represents the structure after binding (PDB code: 6CQI). The nucleotide positions of the G-segment DNA at the active site are marked on the left panel. A β-hairpin motif formed by β1 and β2 strands and the turn between them is used to indicate conformational change. (C) The catalytic sites in the absence or presence of Mg²⁺ ion (PDB codes: 6CQI and 6CQ2) are shown in the left and right panels, respectively. The green sphere labeled as W in the right panel represents a water molecule coordinated by the Mg²⁺ ion. Hydrogen bonds are drawn using dashed lines. (D) The conformational change induced by the presence of Mg²⁺ ions. The structure in grey represents a G-segment bound structure in the absence of Mg²⁺ ions (PDB code: 6CQI). The structure in colors represents the G-segment binding structure in the presence of Mg²⁺ ion (PDB code: 6CQ2). The two structures were aligned based on the α1 helix of the D4 domain.

Figure 3

The structures and DNA-binding properties of two Types of C-terminal domains, Topo_C_ZnRpt and Topo_C_Rpt. (A) The structure of a typical Topo_C_ZnRpt domain, represented by E. coli Topo I (EcTopoI) D7 domain. The Zn knuckle forming cysteines (in magenta), the hydrophobic core residues (in yellow), and the key DNA binding residues (in blue or grey) are drawn in stick format and labeled. On the right side of the figure is an electrostatic potential surface representation of the D7 domain. The figure shows a blue groove (with negative electrostatic potential) for potential DNA binding. (B) The structure of a typical Topo_C_Rpt domain, represented by M. smegmatis Topo I (MsmTopoI) D6 domain. The residues corresponding to the Zn knuckle-forming residues in the Topo_C_ZnRpt domain (Figure 3A) are drawn in stick format (in magenta) and labeled for comparison. The capping residue at the N-terminus of the α1 helix is also drawn in magenta to highlight its position. The hydrophobic core residues and the key DNA binding residues are displayed in yellow and blue or grey sticks, respectively. The break in the β3_β4 loop demonstrates the structural flexibility of the loop. On the right side of the figure is an electrostatic potential surface representation of the MsmTopoI D6 domain, which shows a similar blue groove for potential DNA binding as that of the EcTopoI D7 domain shown in Figure 3A above. The MsmTopoI D7 domain, which is not drawn in this figure, has similar DNA-binding features. (C) The interaction between EcTopoI D7 and ssDNA. The left side figure is an overview of ssDNA binding within the blue DNA-binding groove of EcTopoI D7. The right-side figure shows the molecular details of the interaction. (D) The simultaneous interaction of two MsmTopoI C-terminal domains, D6 and D7, with ssDNA. The left side figure is an overview of ssDNA binding within the extended DNA-binding groove formed by MsmTopoI D6 and D7 domains. The right side figure shows the molecular details of the interaction.