Biology subjects

Kokontis, C.

Publications and source records attributed to Kokontis, C..

3 recordsLinked to original sources

bioRxiv2026

A tripartite mechanism licenses RNA polymerase import into the phage nucleus

Nucleus-forming jumbo phages import a phage-encoded non-virion RNA polymerase (nvRNAP) into a proteinaceous nucleus, but how it is selected for import is unknown. Here, we identify an import pathway that couples nvRNAP subunit interactions with phage-encoded import factors. Maximal nvRNAP import requires a novel factor Imp7 (gp166) and the essential import factor Imp1. Imp7 is essential at environmental temperatures (20 C), where impaired nvRNAP import causes a profound loss of middle and late transcription and blocks phage DNA replication. Import of individual nvRNAP subunits also depends on other subunits, consistent with import licensing at the level of an assembled complex. In the absence of middle transcription and DNA replication, the phage nucleus surprisingly still assembles and segregates from the cytoplasm, demonstrating that nvRNAP nuclear localization and activity are not a critical checkpoint for nucleus assembly. Together, these findings define a specialized pathway for nuclear import of the multi-subunit RNAP and reveal that nuclear compartment assembly precedes the transcriptional and replicative programs required for its maturation.

microbiology↗

bioRxiv2024

Conserved jumbo phage factors required for protein import into a phage nucleus

Bacteriophages use diverse mechanisms to evade anti-phage defenses systems. {Phi}KZ-like jumbo phages assemble a proteinaceous nucleus-like compartment that excludes antagonistic host nucleases, while internalizing DNA replication and transcription machinery1,2,3,4. The phage factors required for protein import and the mechanisms of selectivity remain unknown, however. Here, we uncover an import system composed of proteins highly conserved across nucleus-forming phages, together with additional cargo-specific contributors. Using a genetic selection that forces the phage to decrease or abolish import of specific proteins, we determine that the import of five different phage nuclear-localized proteins (Nlp) all require distinct interfaces of the same factor, Imp1 (gp69). Imp1 forms discrete puncta in the phage nuclear periphery likely in complex with a direct interactor Imp6 (gp67), a conserved protein encoded nearby. The import of some proteins, including a host topoisomerase (TopA), additionally require Imp3 (gp59), a factor required for proper Imp1 function. Three additional phage proteins (Imp2, Imp4, Imp5) are also required for the import of two queried nuclear cargos, perhaps acting as specific adaptors. We therefore propose a core import system including Imp1, Imp3, and Imp6 with the highly selective Imp1 protein licensing transport through a protein lattice.

microbiology↗

bioRxiv2022

The {varphi}PA3 Phage Nucleus is Enclosed by a Self-Assembling, 2D Crystalline Lattice

A growing number of jumbo bacteriophages, with genomes exceeding 200 kb, have been found to establish a Phage Nucleus--a micron-scale, proteinaceous structure encompassing the replicating phage DNA. Bacteriophage and host proteins associated with replication and transcription are concentrated inside the Phage Nucleus while nucleotide synthesis, translation, and numerous other host and exogenous proteins are effectively excluded, including CRISPR-Cas and restriction endonuclease host defense systems. Here, we show that fragments of the Phage Nucleus isolated from {phi}PA3 infected Pseudomonas aeruginosa cells form a square lattice and demonstrate that the recombinantly purified primary Phage Nuclear Enclosure (PhuN) protein spontaneously assembles into sheets also constructed from a square lattice which we resolve to 3.8 [A] by cryo-EM. Our structure reveals that the flexible termini and large loops mediate adaptable inter-tetramer contacts that drive shell assembly into a C2-symmetric lattice. While the interfaces between subunits are mostly well packed, two of the interfaces are open, forming clear channels that likely have important functional implications for the transport of proteins, mRNA, and small molecules.

biochemistry↗