| 1. |
Shogo Ozaki, Chuyuan Lu, Ryusei Yoshida, Yasutaka Wakasugi, Shohei Sato, Tsutomu Katayama, A common mechanism and architecture of the dynamic nucleoprotein complex formed at the origin DNA of eubacterial chromosome replication, 第46回日本分子生物学会年会, 2023.12, Initiation of chromosome replication requires dynamic nucleoprotein complexes to establish replication forks. In Escherichia coli, the origin, oriC, comprises an AT-rich DNA unwinding element (DUE) and asymmetric DnaA box sequences guiding the DnaA initiator to form a highly ordered complex. This initiation complex promotes DUE unwinding and concomitantly binds the resultant single-stranded DUE in a sequence-specific manner, stabilizing the unwound state and facilitating assembly of the replisome components. While DnaA homologs are ubiquitous in eubacteria, the origin sequences differ significantly in respect with the number, direction, and spatial arrangement of DnaA boxes and DUE sequences, limiting our understanding of the general principles governing the process of DUE unwinding. Here, we investigate molecular mechanisms of a prototypic DnaA-oriC complex in the evolutionarily ancient hyperthermophile Thermotoga maritima. We reveal that the DnaA protein from this bacterium retains the ability to form an initiation complex on the cognate oriC, irrespective of DnaA box directions. This flexibility in DnaA assembly is likely driven by substantial swiveling of the DnaA box-binding domain relative to the DnaA AAA+ domain supporting DnaA-DnaA interaction. The resultant DnaA-oriC complexes bind to the three direct repeats of the trinucleotide TAG within single-stranded DUE, stabilizing DUE unwinding (Lu et al. JBC 2023). These findings provide insights into the conservation of fundamental mechanisms for DUE unwinding and single-stranded DUE binding by DnaA proteins across eubacteria, supporting the tunable nature of origin sequences in constructing the initiation complex.
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| 2. |
Shogo Ozaki,Chuyuan Lu, Ryusei Yoshida, Yasutaka Wakasugi, Tsutomu Katayama, A common insight into mechanisms of duplex unwinding at the origin DNA during eubacterial chromosome replication , 第96回日本生化学会大会ワークショップ「染色体DNA複製開始複合体と開始制御メカニズムの新たな展望」, 2023.11. |
| 3. |
Shogo Ozaki, The mechanism of chromosome replication in the alpha-proteobacterium Caulobacter crescentus., Research seminar, 2023.06. |
| 4. |
Shogo Ozaki, Dengyu Wang, Yasutaka Wakasugi, Naoto Itani, and Tsutomu Katayama, Analysis on the loading mechanism of the bacterial replicative DnaB helicase in the alpha-proteobacterium Caulobacter crescentus., NIG International Symposium 2022, 2022.10. |
| 5. |
Shogo Ozaki,Tsutomu Katayama, Analysis of the chromosomal replication mechanism in the eubacterium Caulobacter crescentus, 日本分子生物学会第44回大会, 2021.12. |
| 6. |
Shogo Ozaki、Yasutaka Wakasugi、Urs Jenal, Tsutomu Katayama, A novel divisome-associated protein spatially couples the Z-ring with the chromosomal replication terminus in Caulobacter crescentus, CAULOCONFERENCE 2020, 2020.04. |
| 7. |
尾崎 省吾, 若杉泰敬, 片山 勉, Identification and characterization of a novel DNA binding protein that colocalizes the chromosome replication terminus with cell division apparatus in Caulobacter crescentus, 第４２回日本分子生物学会年会, 2019.12, The bacterial chromosomes are spatially and timely organized to execute chromoso
me replication and segregation in a manner coupled to cell division. In the gram
-negative, alphaproteobacterium Caulobacter crescentus, subcellular posit
ioning of the individual chromosomal loci alters dynamically during chromosome r
eplication. In a pre-replication stage, the origin of chromosome replication is
sequestered to one pole of the cell while the terminus region is localized at th
e other cell pole. Upon initiation of chromosome replication, one of the newly-r
eplicated origin DNAs is driven toward the other cell pole to establish bipolar
localization of the origin DNAs. Concomitantly, the terminus region is recruited
to the midcell position where the bacterial tubulin homolog FtsZ colocalizes to
form cytokinetic Z-rings. Although this colocalization likely coordinates cell
division with dynamic chromosome architecture, the molecular basis for a physica
l link between the Z-rings and the terminus region remains unknown. In this stud
y, we identify the terminus-interactive DNA binding protein ZapT and show that i
t directly binds to a component associated with the Z-rings. Moreover, the za
pT gene is crucial to maintain normal cell division control in C. crescentus
. Together, we propose that ZapT acts as a molecular bridge that physically link
s the terminus region to the Z-rings, thereby ensuring precise processes in chro
mosome segregation and cell division. Because ZapT orthologs are conserved among
diverse proteobacterial species, our findings may represent a general mechanism
to coordinate cell division with chromosome organization in time and space.. |
| 8. |
片山勉, 三善賢弥, 林千尋, 吉田竜星, 杉山諒, 酒井隆至, 崎山友香里, 加生和寿, 川上広宣, 尾崎省吾, 永田麻梨子, Dynamic mechanisms of higher-order complexes for replication initiation and regulation of the E. coli genome, 第9２回日本生化学会大会, 2019.09. |
| 9. |
Hayashi C., Sakiyama Y., Nishimura M,. Akama Y., Ozaki S., and Katayama T., Role for the DnaA AAA+ domain N-terminus in interaction with DnaB helicase for replication initiation, The 11th 3R(Replication, Repair, Recombination)+3C(Chromosome, Chromatin, Cell cycle Symposium, 2018.11. |
| 10. |
Miyoshi K., Kasho K., Fujimitsu K., Ozaki S., and Katayama T., The scheduled replication initiation is regulated by timely IHF binding to specific chromosomal loci for activation and inactivation of the initiator DnaA in Escherichia coli, The 11th 3R(Replication, Repair, Recombination)+3C(Chromosome, Chromatin, Cell cycle Symposium, 2018.11. |
| 11. |
Katayama T., Sakiyama Y., Noguchi Y., Kasho K., Kawakami H., and Ozaki S., Central dynamics of DnaA-oriC complexes in DNA unwinding for initiation of chromosomal replication in E. coli: ssDUE-recruitment mechanism, The 11th 3R(Replication, Repair, Recombination)+3C(Chromosome, Chromatin, Cell cycle Symposium, 2018.11. |
| 12. |
Katayama T., Sakiyama Y., Noguchi Y., Kawakami H., and Ozaki S. , Central dynamics of DnaA oligomers in the initiation complex for chromosomal replication in Escherichia coli , EMBO Workshop "DNA replication, chromosome segregation and fate decisions" , 2018.09. |
| 13. |
Shogo Ozaki, Lori Christian, Urs Jenal, The second messenger signaling drives chromosome replication in the asymmetrically dividing bacterium Caulobacter crescentus, 第５６回日本生物物理学会年会, 2018.09. |
| 14. |
Analysis on the minimal functional structure of the DnaA complex for the regulation of duplex DNA unwinding. |
| 15. |
Mechanism of the inter-DnaA interactions for the ATP-DnaA-dependent activation of initiation complex. |
| 16. |
Analysis on the subcellular localization of DnaA associating protein, DiaA for stimulation of initiation complex formation in E. coli. |
| 17. |
Analysis on role for clamp binding of RisA in the chromosome partition in E. coli. |
| 18. |
Biochemical analysis for mutants of DnaC, a DNA helicase loader of replication initiation in E.coli. |
| 19. |
Analysis on the minimal functional elements of the replication origin in duplex DNA unwinding by DnaA. |
