Importin α2 association with chromatin: Direct DNA binding via a novel DNA binding domain

Abstract

<jats:title>Abstract</jats:title><jats:p>The nuclear transport of proteins is important for facilitating appropriate nuclear functions. The proteins of the importin α family play key roles in nuclear transport as transport receptors for a huge number of nuclear proteins. Additionally, these proteins are also reported to possess other functions, including chromatin association and gene regulation. However, these non-transport functions of importin α are not yet fully understood, especially its molecular interaction with the chromatin and its consequences. Here, we report novel molecular characteristics of importin α involving the binding to multiple regions of chromatin. We newly identified a DNA binding domain-the Nucleic Acid Associating Trolley pole domain (NAAT domain) in the N terminal region of importin α within the conventional importin β binding (IBB) domain which is necessary for the nuclear transport of cargo proteins. We propose a “stroll and locate” model to explain how importin α associates with double-stranded DNA. This is the first study to delineate interaction between importin α with the chromatin via the NAAT domain, indicating the bifunctionality of the importin α N terminal region for the nuclear transport and the chromatin association.</jats:p>

Biochemical propensity mapping for structural and functional anatomy of importin α IBB domain

“…Differences in binding propensities such as those revealed here are also be found in other IBB domain binding molecules, such as DNA (Jibiki et al, 2021) and Rbbp4 (Tsujii et al, 2015). Moreover, as importin α plays an important role in multiple cellular events (Oka & Yoneda, 2018), there may exist additional unknown binding partners.…”

“…For example, K42 is retained by all consensus sequences and is highly conserved among species (Data S4). This residue is thought to be involved in binding to DNA (Jibiki et al, 2021) and Rbbp4 (Tsujii et al, 2015) and may be important for such functions. In addition, the biochemical/physicochemical propensity of small bulkiness was conserved at position 21, though the residue differed among family members (Figures S16 and S17).…”

“…Cargo release is achieved by RanGTP binding to importin β that mediates the dissociation of importin β from the complex (Floer et al, 1997; Gilchrist et al, 2002; Vetter et al, 1999), and by Nup50 or CAS binding to importin α (Gilchrist et al, 2002; Sun et al, 2013). Moreover, very recently we reported that importin α‐DNA binding can occur (with or without cargo), and part of the IBB acts as a subdomain named NAAT domain (Nuclear Acid Associating Trolley pole domain; Jibiki et al, 2021). Finally, importin α is exported out of the nucleus through the export function of CAS and is recycled (Matsuura & Stewart, 2004).…”

Loss of the importin Kpna2 causes infertility in male mice by disrupting the translocation of testis-specific transcription factors

“…When KPNA2 is only present in the cytoplasm, it can anchor proteins in the cytoplasm; however, when present in both nucleus and cytoplasm, it could be working as a nucleocytoplasmic transporter or as a regulator of gene expression in association with chromatin. 40 The fact that in Kpna2 -KO mice the number of produced spermatozoa is not affected indicates that KPNA2 is not essential until the protein is present in the nucleus at pachytene spermatocyte and spermatid stages, suggesting that at these stages its function may not be compensated by other importin αs. In agreement with this, we found that most DEGs occurred in spermatocytes and spermatids.…”

“…Besides a nuclear import role, KPNA2 may also act in the nucleus of late spermatocytes and spermatids by associating with chromatin via its direct DNA-binding ability, promoting gene expression. This feature, which has been examined in embryonic stem cells, 40 should be further explored to determine whether KPNA2 binds to DNA in spermatogenic cells. Whether through the regulation of transcription factors transported to the nucleus or through the control of expression due to its direct association with chromatin, KPNA2 was observed here to exert a specific control of the expression of gene clusters present in certain chromosomes.…”