Biology subjects

Kim, J. G.

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

3 recordsLinked to original sources

bioRxiv2025

Implementing N-terminomics and machine learning to probe in vivo Nt-arginylation

N-terminal arginylation (Nt-arginylation) serves as a protein degradation signal in both the ubiquitin-proteasome system and the autophagy-lysosomal pathway. However, the scarcity of arginylated proteins in cells and limitations in current identification methods have hindered progress in this field. In this study, we developed a novel integrated approach that combines N-terminomics (N-terminomic enrichment, LC-MS/MS, and tandem database search) with advanced machine learning-based filtering strategies to successfully identify in vivo Nt-arginylation with unprecedented sensitivity and specificity. By utilizing Arg-starting peptides from missed cleavage products as physicochemical proxies for ATE1-mediated Nt-arginylation, we trained a transfer learning-based model to predict MS2 spectra and retention times of candidate peptides. Additionally, near-isobaric modifications were filtered by statistically analyzing mass error deviations in MS2 fragment ions. Using this approach, we identified 134 Nt-arginylation sites in thapsigargin-treated HeLa cells, revealing a significant increase of Nt-arginylome under unfolded protein response (UPR) stress. Arginylated proteins originate from various organelles, including ER, nucleus and mitochondria. Notably, arginylation frequently occurred at sites processed by caspases or where signal peptides had been cleaved. Several proteins identified in our arginylome study were validated for their interaction with the R-catcher, an Nt-Arginylation bait derived from the p62 ZZ domain. Temporal profiling of N-terminal arginylation sites post-stress induction via targeted proteomics revealed a sequential response pattern. The UPR signal transducer ATF4 exhibited the most rapid increase, followed by N-terminal arginylation of caspase-3 substrates, and subsequently by arginylation at signal peptide cleavage sites among endoplasmic reticulum proteins. Our novel machine learning-based filtering methodologies enable the discovery of rare post-translational modifications by implementing specialized filtering strategies tailored to the unique physicochemical properties of terminal modifications, with potential applications in biomarker discovery, drug target identification, and elucidation of disease-specific protein regulation mechanism.

systems biology↗

bioRxiv2022

The salivary and nasopharyngeal microbiomes are associated with SARS-CoV-2 infection and disease severity

Oral and upper respiratory microbiota play important roles in modulating host immune responses to viral infection. As emerging evidence suggests the host microbiome may be involved in the pathophysiology of COVID-19, we aimed to investigate associations between the oral and nasopharyngeal microbiome and COVID-19 severity. We collected saliva (n = 78) and nasopharyngeal swab (n = 66) samples from a COVID-19 cohort and characterized the microbiomes using 16S ribosomal RNA gene sequencing. We also examined associations between the salivary and nasopharyngeal microbiome and age, COVID-19 symptoms, and blood cytokines. SARS-CoV-2 infection status, but not COVID-19 severity, was associated with community-level differences in the oral and nasopharyngeal microbiomes. Salivary and nasopharyngeal microbiome alpha diversity negatively correlated with age and were associated with fever and diarrhea. Several bacterial genera were differentially abundant by COVID-19 severity, including oral Bifidobacterium, Lactobacillus, and Solobacterium, all of which were depleted in patients with severe COVID-19. Nasopharyngeal Paracoccus was depleted while nasopharyngeal Proteus, Cupravidus, and Lactobacillus were increased in patients with severe COVID-19. Further analysis revealed that the abundance of oral Bifidobacterium was negatively associated with plasma concentrations of known COVID-19 biomarkers interleukin 17F (IL-17F) and monocyte chemoattractant protein-1 (MCP-1). In conclusion, our results suggest COVID-19 disease severity is associated with the relative abundance of certain bacterial taxa.

microbiology↗

bioRxiv2019

Functions of ventral visual cortex after bilateral hippocampal loss

Repeated stimuli elicit attenuated responses in visual cortex relative to novel stimuli. This adaptation phenomenon can be considered a form of rapid learning and a signature of perceptual memory. Adaptation occurs not only when a stimulus is repeated immediately, but also when there is a lag in terms of time and other intervening stimuli before the repetition. But how does the visual system keep track of which stimuli are repeated, especially after long delays and many intervening stimuli? We hypothesized that the hippocampus supports long-lag adaptation, given that it learns from single experiences, maintains information over delays, and sends feedback to visual cortex. We tested this hypothesis with fMRI in an amnesic patient, LSJ, who has encephalitic damage to the medial temporal lobe resulting in complete bilateral hippocampal loss. We measured adaptation at varying time lags between repetitions in functionally localized visual areas that were intact in LSJ. We observed that these areas track information over a few minutes even when the hippocampus is unavailable. Indeed, LSJ and controls were identical when attention was directed away from the repeating stimuli: adaptation occurred for lags up to three minutes, but not six minutes. However, when attention was directed toward stimuli, controls now showed an adaptation effect at six minutes but LSJ did not. These findings suggest that visual cortex can support one-shot perceptual memories lasting for several minutes but that the hippocampus is necessary for adaptation in visual cortex after longer delays when stimuli are task-relevant.

neuroscience↗