bims-nucpor 2021-09-19 papers

Issue of 2021–09–19
five papers selected by
Sara Mingu, Johannes Gutenberg University

Angew Chem Int Ed Engl. 2021 Sep 16.

Construction of A High-flux Protein Transport Channel Inspired by the Nuclear Pore Complex.

Lei Yang, Ming Cheng, Jiaxin Quan, Siyun Zhang, Lu Liu, Robert P Johnson, Fan Zhang, Haibing Li.

Inspired by the nuclear pore complex (NPC), herein we have established a biomimetic high-flux protein delivery system via the selective introduction of pillar[5]arene-based host-guest system into one side of an artificial concave (hour-glass) shaped nanochannels. With a transport flux of 660 lysozymes per minute, the system provides efficient high-flux protein transport at a rate which is significantly higher than that of an unmodified nanochannel and conventional bilateral symmetrical modified nanochannels. In view of these promising results, the use of artificial nanochannels to improve protein transport not only provides a new potential chemical model for biological research and better understanding of protein transport behavior in the living systems, but also provides a high-flux protein transporter device, which may have applications in the design of protein drug release systems, protein separation systems and microfluidics in the near future.

Keywords: Host-Guest systems; Pillar[5]arene; biomimetic; high-flux; protein delivery

DOI: https://doi.org/10.1002/anie.202110273

EMBO J. 2021 Sep 15. e107839

Non-genetic and genetic rewiring underlie adaptation to hypomorphic alleles of an essential gene.

Altea Targa, Katherine E Larrimore, Cheng Kit Wong, Yu Lin Chong, Ronald Fung, Joseph Lee, Hyungwon Choi, Giulia Rancati.

Adaptive evolution to cellular stress is a process implicated in a wide range of biological and clinical phenomena. Two major routes of adaptation have been identified: non-genetic changes, which allow expression of different phenotypes in novel environments, and genetic variation achieved by selection of fitter phenotypes. While these processes are broadly accepted, their temporal and epistatic features in the context of cellular evolution and emerging drug resistance are contentious. In this manuscript, we generated hypomorphic alleles of the essential nuclear pore complex (NPC) gene NUP58. By dissecting early and long-term mechanisms of adaptation in independent clones, we observed that early physiological adaptation correlated with transcriptome rewiring and upregulation of genes known to interact with the NPC; long-term adaptation and fitness recovery instead occurred via focal amplification of NUP58 and restoration of mutant protein expression. These data support the concept that early phenotypic plasticity allows later acquisition of genetic adaptations to a specific impairment. We propose this approach as a genetic model to mimic targeted drug therapy in human cells and to dissect mechanisms of adaptation.

Keywords: CRISPR-Cas9; NPC; genetic adaptation; hypomorphic alleles; transcriptome rewiring

DOI: https://doi.org/10.15252/embj.2021107839

Genes Cells. 2021 Sep 14.

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

Kazuya Jibiki, Takashi S Kodama, Atsushi Suenaga, Yota Kawase, Noriko Shibazaki, Shin Nomoto, Seiya Nagasawa, Misaki Nagashima, Shieri Shimodan, Renan Kikuchi, Mina Okayasu, Ruka Takashita, Rashid Mehmood, Noriko Saitoh, Yoshihiro Yoneda, Ken-Ichi Akagi, Noriko Yasuhara.

The nuclear transport of proteins is important for facilitating appropriate nuclear functions. The importin α family proteins play key roles in nuclear transport as transport receptors for copious nuclear proteins. Additionally, these proteins possess other functions, including chromatin association and gene regulation. However, these non-transport functions of importin α are not yet fully understood, especially their molecular-level mechanisms and consequences for functioning with chromatin. Here, we report the novel molecular characteristics of importin α binding to diverse DNA sequences in chromatin. We newly identified and characterised 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 that is necessary for nuclear transport of cargo proteins. Furthermore, we found that the DNA binding of importin α synergistically coupled the recruitment of its cargo protein to DNA. This is the first study to delineate the interaction between importin α and chromatin DNA via the NAAT domain, indicating the bifunctionality of the importin α N-terminal region for nuclear transport and chromatin association.

Keywords: DNA-binding protein; chromatin; importin α; nuclear transport; nucleus; protein−DNA interaction; α-helix

DOI: https://doi.org/10.1111/gtc.12896

J Virol. 2021 Sep 15. JVI0095721

Cell culture evolution of a HSV-1/VZV UL34/ORF24 chimeric virus reveals novel functions for HSV genes in capsid nuclear egress.

Richard J Roller, Tineke Hassman, Alison Haugo-Crooks.

HSV and VZV are both members of the alphaherpesvirus subfamily, but are of different genera. Substitution of the HSV-1 UL34 coding sequence with that of its VZV homolog, ORF24, results in a virus that has defects in viral growth, spread, capsid egress, and nuclear lamina disruption very similar to those seen in a UL34-null virus despite normal interaction between ORF24 protein and HSV pUL31 and proper localization of the nuclear egress complex at the nuclear envelope. Minimal selection for growth in cell culture resulted in viruses that grew and spread much more efficiently that the parental chimeric virus. These viruses varied in their ability to support nuclear lamina disruption, normal nuclear egress complex localization and capsid de-envelopment. Single mutations that suppress the growth defect were mapped to the coding sequences of ORF24, ICP22 and ICP4 and one virus carried single mutations in each of the ICP22 and US3 coding sequences. The phenotypes of these viruses support a role for ICP22 in nuclear lamina disruption and a completely unexpected role for the major transcriptional regulator, ICP4, in capsid nuclear egress. Importance Interactions among virus proteins are critical for assembly and egress of virus particles, and such interactions are attractive targets for antiviral therapy. Identification of critical functional interactions can be slow and tedious. Capsid nuclear egress of herpesviruses is a critical event in the assembly and egress pathway and is mediated by two proteins that are conserved among herpesviruses, pUL31 and pUL34. Here we describe a cell culture evolution approach to identify other viral gene products that functionally interact with pUL34.

DOI: https://doi.org/10.1128/JVI.00957-21

Proteins. 2021 Sep 18.

Phosphorylation in the accessory domain of yeast histone chaperone protein 1 exposes the nuclear export signal sequence.

Sho Ashida, Rikuri Morita, Yasuteru Shigeta, Ryuhei Harada.

Histone chaperone proteins assist in the formation of the histone octamers, the scaffold proteins that facilitate the packing of DNA into nucleosomes in the cell nucleus. One such histone chaperone protein is yeast nucleosome assembly protein 1 (yNap1), the crystal structure of which has been determined and found to have a nuclear export signal (NES) sequence within its long α-helix. Experimental evidence obtained from mutagenesis studies of the budding yeast suggests that the NES is necessary for the transport of yNap1 from the cell nucleus to the cytosol. However, the NES sequence is masked by an accessory domain, the exact role of which has not yet been elucidated, especially in nucleocytoplasmic transport. To clarify the role of the accessory domain, we focused on its phosphorylation since proteomic experiments have identified multiple phosphorylation sites on yNap1. To study this phenomenon computationally, all-atom molecular dynamics simulations of the non-phosphorylated yNap1 (Nap1-nonP) and phosphorylated yNap1 (Nap1-P) systems were performed. Specifically, we addressed how the NES sequence is exposed to the protein surface by measuring its solvent-accessible surface area (SASA). It was found that the median of the SASA distribution of Nap1-P was greater than that of Nap1-nonP, indicating that phosphorylation in the accessory domain exposes the NES, resulting in its increased accessibility. In conclusion, yNap1 might modulate the accessibility of the NES by dislocating the accessory domain through its phosphorylation. This article is protected by copyright. All rights reserved.

Keywords: Histone chaperone; Molecular dynamics; Nuclear export signal/sequence; Phosphorylation

DOI: https://doi.org/10.1002/prot.26240