Biology subjects

Nagata, R.

Publications and source records attributed to Nagata, R..

7 recordsLinked to original sources

bioRxiv2025

Cellular fitness is determined by ribosomal protein S12-mediated release of a truncated Xrp1

Multicellular tissues require continuous optimization to maintain their structure and function by actively eliminating viable, yet unfit cells via a mechanism known as cell competition. During this process, unfit loser cells commonly upregulate the C/EBP family transcription factor Xrp1, which causes their elimination, indicating that intracellular Xrp1 levels determine cellular fitness. However, despite its central role, the mechanism by which Xrp1 is upregulated in unfit cells remains unknown. Here, we show that Xrp1 is upregulated through a previously unrecognized post-transcriptional regulatory mechanism mediated by the ribosomal protein S12 (RpS12). Surprisingly, Xrp1 mRNA is abundantly expressed even in wild-type cells, yet it is not translated. This is due to an upstream open reading frame (uORF) located in the 5UTR of the initial coding exon of Xrp1 mRNA, which inhibits the translation of the main Xrp1 ORF. Intriguingly, in unfit cells, RpS12 causes splicing-mediated skipping of this initial exon, leading to the use of an alternate start codon that generates a short isoform of Xrp1 protein, causing cell death. Notably, protein structural analysis reveals that RpS12 is highly homologous to that of a spliceosomal component SNU13, suggesting the role of RpS12 in directly regulating alternative splicing of Xrp1 mRNA. Our findings thus provide not only a mechanistic insights into how cellular fitness is determined but also how tissue optimization is achieved.

cell biology↗

bioRxiv2022

Analysis of genetic relatedness between gastric and oral H. pylori in patients with early gastric cancer using multilocus sequence typing

Although oral cavity is the second most colonized site after the stomach, the association between gastric and oral Helicobacter pylori remains unclear. This study aimed to compare the genetic relatedness between gastric and oral H. pylori in Japanese patients with early gastric cancer by multilocus sequence typing (MLST) analysis using seven housekeeping genes. Gastric biopsy specimens and oral samples, including saliva, supragingival dental biofilm, and superficial layers of the tongue, were collected from 21 patients positive for H. pylori by a fecal antigen test. The number of H. pylori allelic profiles of seven loci obtained from oral and gastric samples ranged from zero to seven since the yield of DNA was small even when the nested PCR was performed. The alleles of seven loci from both collection sites were determined from only one patient, and two out of seven alleles matched between oral and gastric samples. MLST analysis revealed that only one sample had a matching oral and gastric H. pylori genotype, suggesting that different genotypes of H. pylori inhabit the oral cavity and gastric mucosa. The phylogenetic analysis showed that oral H. pylori in two patients was markedly similar to gastric H. pylori, implying that the the origins of two strains may be the same, and the stomach and the oral cavity may be infected at the same time. In brief, although different genotypes of H. pylori exist in the oral cavity independently of H. pylori present in the stomach, there are rare cases in which the same H. pylori is present in the stomach and the oral cavity. It is necessary to establish a culture method for oral H. pylori for elucidating whether the oral cavity will act as the source of the gastric infection, as our analysis was based on a limited number of allele sequences. Author summaryHericobacter pylori is a clinically important pathogen that causes chronic gastritis and peptic ulcers, which are associated with gastric carcinoma. Oral H. pylori DNA has also been detected in a range of oral specimens, including saliva, supra- or sub-gingival biofilm, dentin caries, dental pulp, infected root canal, and coating of the tongue. Thus, researchers speculate that the main route of transmission of gastric H. pylori infections is via the oral cavity, however, there is inadequate evidence to support this suggestion. This study aimed to investigate if the oral and gastric H. pylori have the same origin using multilocus sequence typing. The results of this study provided some insight into the role of oral cavity as the source of H. pylori infections in stomach.

microbiology↗

bioRxiv2020

C9orf72- derived proline:arginine poly-dipeptides disturb cytoskeletal architecture

Amyotrophic lateral sclerosis (ALS) is an irreversible neurodegenerative disease caused by the degeneration of motor neurons, and cytoskeletal instability is considered to be involved in neurodegeneration. A hexanucleotide repeat expansion of the C9orf72, one of the most common causes of familial ALS, produces toxic proline:arginine (PR) poly-dipeptides. PR poly-dipeptides binds polymeric forms of low complexity sequences and intracellular puncta, thereby altering intermediate filaments (IFs). However, how PR poly-dipeptides affect the cytoskeleton, including IFs, microtubules and actin filaments, remains unknown. Here we performed a synthetic PR poly-dipeptide treatment on mammalian cells and investigated how it affects morphology of cytoskeleton and cell behaviors. We observed that PR poly-dipeptide treatment induce the degradation of vimentin bundles at perinucleus and dissociation of {beta}-tubulin network. PR poly-dipeptides also lead to alteration of actin filaments toward to cell contours and strength cortical actin filaments via activation of ERM (ezrin/radixin/moesin) proteins. In addition, we found that PR poly-dipeptides promote phosphorylation of paxillin and recruitment of vinculin on focal adhesions, which lead to maturation of focal adhesions. Finally, we evaluated the effects of PR poly-dipeptides on mechanical property and stress response. Interestingly, treatment of PR poly-dipeptides increased the elasticity of the cell surface, leading to maladaptive response to cyclic stretch. These results suggest that PR poly-dipeptides cause mechanically sensitive structural reorganization and disrupt the cytoskeleton architecture.

biochemistry↗

bioRxiv2019

Human URAT1/SLC22A12 gene promoter is regulated by 27-hydroxycholesterol through estrogen response elements

Elevated levels of uric acid, a metabolite of purine in humans, is related to various diseases, such as gout, atherosclerosis and renal dysfunction. The excretion and reabsorption of uric acid to/from urine is tightly regulated by uric acid transporters. The amino acid sequences of uric acid reabsorption transporters, URAT1/SLC22A12, OAT4/SLC22A11, and OAT10/SLC22A13, share closer phylogenic relationship, whereas the gene promoter sequences are distant phylogenic relationship. Through the single-cell RNA-sequencing analysis of an adult human kidney, we found that only a small number of cells express these transporters, despite their role in the regulation of serum uric acid levels. Transcriptional motif analysis on these transporter genes, revealed that the URAT1/SLC22A12 gene promoter displayed the most conserved estrogen response elements (EREs) among the three transporters. The endogenous selective estrogen receptor modulator (SERM) 27-hydroxycholesterol (27HC) had positive effects on the transcriptional activity of URAT1/SLC22A12. We also found that 27HC increased the protein and gene expression of URAT1/SLC22A12 in mouse kidneys and human kidney organoids, respectively. These results strongly suggest the role of 27HC for URAT1/SLC22A12 expression in renal proximal tubules and upregulation of serum uric acid levels and also show the relationship between cholesterol metabolism and serum uric acid regulation. Significance StatementThe elevated levels of serum uric acid cause various diseases, and the excretion/reabsorption of uric acid to/from urine is tightly regulated by the uric acid transporters. We found that despite the role in serum uric acid regulation, only a small number of cells express URAT1/SLC22A12. We also found that URAT1/SLC22A12 gene promoter region has effective estrogen response elements, and endogenous selective estrogen receptor (ER) modulator 27-hydroxycholesterol (27HC) increased URAT1/SLC22A12 expression in the mice kidneys and human kidney organoids. These suggest that 27HC increases URAT1/SLC22A12 expression and upregulate serum uric acid levels. Since 27HC connects cholesterol metabolism, our study indicates the important link between cholesterol metabolism and serum uric acid regulation, and also provides a novel therapeutic approach to hyperuricemia.

biochemistry↗

bioRxiv2019

Brainstem organoids from human pluripotent stem cells contain neural crest population

The brainstem controls heartbeat, blood pressure and respiration, which are life-sustaining functions, therefore, disorders of the brainstem can be lethal. Brain organoids derived from human pluripotent stem cells recapitulate the course of human brain development and are expected to be useful for medical research on central nervous system disorders. However, existing organoid models have limitations, hampering the elucidation of diseases affecting specific components of the brain. Here, we developed a method to generate human brainstem organoids (hBSOs), containing neural crest stem cells as well as midbrain/hindbrain progenitors, noradrenergic and cholinergic neurons, and dopaminergic neurons, demonstrated by specific electrophysiological signatures. Single-cell RNA sequence analysis, together with proteomics and electrophysiology, revealed that the cellular population in these organoids was similar to that of the human brainstem and neural crest, which raises the possibility of making use of hBSOs in grafting for transplantation, efficient drug screenings and modeling the neural crest diseases.

developmental biology↗

bioRxiv2019

Toxic PR poly-dipeptides encoded by the C9orf72 repeat expansion target Kapβ2 and dysregulate phase separation of low-complexity domains

Low-complexity (LC) domains of proteins are found in about one fifth of human proteome, and a group of LC-domains form labile cross-{beta} polymers and liquid-like droplets. Polymers and droplets formed from LC-domains are dynamically regulated by posttranslational modifications and molecular chaperones including nuclear transport receptors. Repeat expansion in the first intron of a gene designated C9orf72, which is the most prevalent form of familial amyotrophic lateral sclerosis (ALS), causes nucleocytoplasmic transport deficit, however, the detailed mechanism remains unsolved. Here we show that the proline:arginine (PR) poly-dipeptides encoded by the C9orf72 repeat expansion bound nuclear transport receptor Kap{beta}2 through its nuclear localization signal (NLS) recognition motif, and inhibited the ability of Kap{beta}2 to melt fused in sarcoma (FUS) droplets by competing interaction with FUS. The findings in this study offer mechanistic insights as to how the C9orf72 repeat expansion disables nucleocytoplasmic transport and causes neurodegenerative diseases.

molecular biology↗

bioRxiv2019

Mucin O-glycans facilitate symbiosynthesis to maintain gut immune homeostasis

The dysbiosis of gut microbiota has been implicated in the pathogenesis of inflammatory bowel diseases (IBDs); however, the underlying mechanisms have not yet been elucidated. Heavily glycosylated mucin not only establishes a first-line barrier against pathogens, but also serves as a niche for microbial growth. We hypothesized that dysbiosis may cause abnormal mucin utilization and microbial metabolic dysfunction. To test this hypothesis, we analyzed short-chain fatty acids (SCFAs) and mucin components in the stool samples of 40 healthy subjects, 49 ulcerative colitis (UC) patients, and 44 Crohns disease (CD) patients from Japan. The levels of n-butyrate were significantly lower in the stools of both the CD and UC patients than in those of the healthy subjects. Correlation analysis identified 7 bacterial species positively correlated with n-butyrate levels, among which the major n-butyrate producer, Faecalibacterium prausnitzii, was particularly underrepresented in CD patients, but not in UC patients. In UC patients, there were inverse correlations between mucin O-glycan levels and the production of SCFAs, such as n-butyrate, suggesting that mucin O-glycans act as an endogenous fermentation substrate for n-butyrate production. Indeed, mucin-fed rodents exhibited enhanced n-butyrate production, leading to the expansion of RORgt+Treg cells and IgA-producing cells in the colonic lamina propria. Importantly, the availability of mucin-associated O-glycans to the microbiota was significantly reduced in n-butyrate-deficient UC patients. Taken together, our findings highlight the biological significance of the symbiosynthesis pathway in the production of n-butyrate, which maintains gut immune homeostasis.

microbiology↗