Visual Analysis of Protein–Protein Interaction Docking Models Using COZOID Tool

Jurčík, Adam; Furmanová, Katarína; Kozlíková, Barbora; Paleček, Jan

doi:10.1007/978-1-4939-9873-9_7

Cited by 4 publications

(2 citation statements)

References 21 publications

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“…The AlphaFold tools [ 72 , 73 ] were used to generate in silico fission yeast SMC5/6 subunits and complex models. Structural models were analysed as previously described [ 6 , 74 ]. Structures were visualized using PyMOL Molecular Graphics System.…”

Section: Methodsmentioning

confidence: 99%

The SAGA histone acetyltransferase module targets SMC5/6 to specific genes

Mahrik

Štefanovie

Marešová

et al. 2023

Epigenetics & Chromatin

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Background Structural Maintenance of Chromosomes (SMC) complexes are molecular machines driving chromatin organization at higher levels. In eukaryotes, three SMC complexes (cohesin, condensin and SMC5/6) play key roles in cohesion, condensation, replication, transcription and DNA repair. Their physical binding to DNA requires accessible chromatin. Results We performed a genetic screen in fission yeast to identify novel factors required for SMC5/6 binding to DNA. We identified 79 genes of which histone acetyltransferases (HATs) were the most represented. Genetic and phenotypic analyses suggested a particularly strong functional relationship between the SMC5/6 and SAGA complexes. Furthermore, several SMC5/6 subunits physically interacted with SAGA HAT module components Gcn5 and Ada2. As Gcn5-dependent acetylation facilitates the accessibility of chromatin to DNA-repair proteins, we first analysed the formation of DNA-damage-induced SMC5/6 foci in the Δgcn5 mutant. The SMC5/6 foci formed normally in Δgcn5, suggesting SAGA-independent SMC5/6 localization to DNA-damaged sites. Next, we used Nse4-FLAG chromatin-immunoprecipitation (ChIP-seq) analysis in unchallenged cells to assess SMC5/6 distribution. A significant portion of SMC5/6 accumulated within gene regions in wild-type cells, which was reduced in Δgcn5 and Δada2 mutants. The drop in SMC5/6 levels was also observed in gcn5-E191Q acetyltransferase-dead mutant. Conclusion Our data show genetic and physical interactions between SMC5/6 and SAGA complexes. The ChIP-seq analysis suggests that SAGA HAT module targets SMC5/6 to specific gene regions and facilitates their accessibility for SMC5/6 loading.

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Section: Methodsmentioning

confidence: 99%

The SAGA histone acetyltransferase module targets SMC5/6 to specific genes

Mahrik

Štefanovie

Marešová

et al. 2023

Epigenetics & Chromatin

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“…The AlphaFold/ColabFold tools (Mirdita et al., 2022; Varadi et al., 2022) were used to generate in silico moss PpSMC5/6 subunit and complex models. Structural models were analyzed as previously described (Byska et al., 2020). Structures were visualized by Pymol software (Schrodinger, Inc., New York, NY, USA).…”

Section: Methodsmentioning

confidence: 99%

Characterization of the conserved features of the NSE6 subunit of the Physcomitrium patens SMC5/6 complex

et al. 2023

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SUMMARYStructural maintenance of chromosomes (SMC) complexes are molecular machines ensuring chromatin organization at higher levels. They play direct roles in cohesion, condensation, replication, transcription, and DNA repair. Their cores are composed of long‐armed SMC, kleisin, and kleisin‐associated subunits. Additional factors, like NSE6 within SMC5/6, bind to SMC core complexes and regulate their activities. In the human HsNSE6/SLF2, we recently identified a new CANIN domain. Here we tracked down its sequence homology to lower plants, selected the bryophyte Physcomitrium patens, and analyzed PpNSE6 protein–protein interactions to explore its conservation in detail. We identified a previously unrecognized core sequence motif conserved from yeasts to humans within the NSE6 CANIN domain. This motif mediates the interaction between NSE6 and its NSE5 partner in yeasts and plants. In addition, the CANIN domain and its preceding PpNSE6 sequences bind both PpSMC5 and PpSMC6 arms. Interestingly, we mapped the PpNSE6‐binding site at the PpSMC5 arm right next to the PpNSE2‐binding surface. The position of NSE6 at SMC arms suggests its role in the regulation of SMC5/6 dynamics. Consistent with the regulatory role of NSE6 subunits, Ppnse6 mutant lines were viable and sensitive to the DNA‐damaging drug bleomycin and lost a large portion of rDNA copies. These moss mutants also exhibited reduced growth and developmental aberrations. Altogether, our data showed the conserved function of the NSE6 subunit and architecture of the SMC5/6 complex across species.

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