Biology subjects

Kim Kim, J.

Publications and source records attributed to Kim Kim, J..

4 recordsLinked to original sources

bioRxiv2025

Proteasome activator Blm10 maintains cellular proteostatic balance and gamete quality in budding yeast

The proteasome is responsible for regulated protein degradation in eukaryotic cells. Its best characterized substrates are ubiquitinated proteins that are targeted to the 26S proteasome complex, consisting of a 19S regulatory particle (RP) capping the barrel-shaped 20S core peptidase (CP). The CP can interact with other caps, including Blm10/PA200, a nearly 250 kDa protein whose biological function is not well understood. Blm10 is upregulated during gametogenesis in budding yeast, suggestive of a natural stage-specific modulation of proteasome composition. Here, we investigate the function of Blm10 during yeast gametogenesis, identifying it as a weak activator of the proteasome that can displace the 19S RP from the CP. Due to this competition for the CP, overexpression of Blm10 can lead to attenuation of ubiquitin-dependent degradation and proteostatic defects. Cells lacking Blm10 also display markers of proteostatic stress, including Hsp104 foci and heat sensitivity, suggesting that Blm10 safeguards normal proteostatic balance. We find that Blm10 is important for producing fit gametes and ensuring full rejuvenation of aged cells following gametogenesis. Furthermore, we observe direct association of aggregate-prone proteins and protein-folding factors with immunoprecipitated Blm10-proteasomes. Finally, we discovered that 14-3-3 proteins Bmh1/2 are novel cofactors of Blm-10 bound proteasomes and describe how Blm10 controls CP gate configuration. Overall, our data suggest a role for Blm10-proteasomes in maintaining gamete proteostasis through fine-tuning of proteasome activity and prevention of protein aggregation.

molecular biology↗

bioRxiv2023

Poly-basic peptides and polymers as new drug candidate against Plasmodium falciparum

Plasmodium falciparum, the malaria-causing parasite, is a leading cause of infection-induced deaths worldwide. The preferred treatment approach is artemisinin-combination therapy, which couples fast-acting artemisinin derivatives with longer-acting drugs like lumefantrine, mefloquine, and amodiaquine. However, the urgency for new treatments has risen due to the parasites growing resistance to existing therapies. Our study shows that a common characteristic of the P. falciparum proteome - stretches of poly-lysine residues such as those found in proteins related to adhesion and pathogenicity - can serve as an effective peptide treatment for infected erythrocytes. A single dose of these poly-basic peptides can successfully diminish parasitemia in human erythrocytes in vitro with minimal toxicity. The effectiveness of the treatment correlates with the length of the poly-lysine peptide, with 30 lysine peptides supporting the eradication of erythrocytic parasites within 72 hours. PEG-ylation of the poly-lysine peptides or utilizing poly-lysine dendrimers and polymers further increases parasite clearance efficiency and bolsters the stability of these potential new therapeutics. Lastly, our affinity pull-downs and mass-spectrometry identify P. falciparums outer membrane proteins as likely targets for polybasic peptide medications. Since poly-lysine dendrimers are already FDA-approved for drug delivery, their adaptation as antimalarial drugs presents a promising new therapeutic strategy. One-Sentence SummaryOur study demonstrates that poly-lysine peptides, particularly those modified through PEG-ylation or in the form of poly-lysine dendrimers, can effectively reduce Plasmodium falciparum, the causative agent of malaria, in human erythrocytes in vitro, with potential for use as a promising new antimalarial therapy.

microbiology↗

bioRxiv2022

Use of a ubiquitous gene-editing tool in budding yeast causes off-target repression of neighboring gene protein synthesis

Precision genome-editing approaches have long been available in budding yeast, enabling introduction of gene deletions, epitope tag fusions, and promoter swaps through a selection-based strategy. Such approaches allow loci to be modified without disruption of coding or regulatory sequences of neighboring genes. Use of this approach to delete DBP1 however, led to silencing of expression and the resultant loss of function for the neighboring gene MRP51. We found that insertion of a resistance cassette to delete DBP1, drove a 5 extended alternative transcript for MRP51 which dampened Mrp51 protein synthesis. Misregulation of MRP51 occurred through an integrated transcriptional and translational repressive long undecoded transcript isoform (LUTI)-based mechanism that was recently shown to naturally regulate gene expression in yeast and other organisms. Cassette-induced MRP51 repression drove all mutant phenotypes we detected in cells deleted for DBP1. Selection cassette-mediated aberrant transcription events are not specific to this locus or a unique cassette but can be prevented by insertion of transcription insulators flanking the cassette. Our study suggests the existence of confounding off-target mutant phenotypes resulting from misregulated neighboring loci following genome edits in yeast. Furthermore, features of LUTI-based regulation are broadly conserved to eukaryotic organisms which indicates the potential that similar misregulation could be unnoticed in other edited organisms as well.

genetics↗

bioRxiv2019

Aurora B-dependent Ndc80 Degradation Regulates Kinetochore Composition in Meiosis

The kinetochore complex is a conserved machinery that connects chromosomes to spindle microtubules. During meiosis, the kinetochore is restructured to accommodate a specialized chromosome segregation pattern. In budding yeast, meiotic kinetochore remodeling is mediated by the temporal changes in the abundance of a single subunit called Ndc80. We have previously described the regulatory events that control the timely synthesis of Ndc80. Here, we report that Ndc80 turnover is also tightly regulated in meiosis: Ndc80 degradation is active in meiotic prophase, but not in metaphase I. Ndc80 degradation depends on the ubiquitin ligase APCAma1 and is mediated by the proteasome. Importantly, Aurora B-dependent Ndc80 phosphorylation, a mark that has been previously implicated in correcting erroneous microtubule-kinetochore attachments, is essential for Ndc80 degradation in a microtubule-independent manner. The N-terminus of Ndc80, including a 27-residue sequence and Aurora B phosphorylation sites, is both necessary and sufficient for kinetochore protein degradation. Finally, defects in Ndc80 turnover predispose meiotic cells to chromosome mis-segregation. Our study elucidates the mechanism by which meiotic cells modulate their kinetochore composition through regulated Ndc80 degradation, and demonstrates that Aurora B-dependent regulation of kinetochores extends beyond altering microtubule attachments.

genetics↗