Biology subjects

Umezawa, K.

Publications and source records attributed to Umezawa, K..

13 recordsLinked to original sources

bioRxiv2025

Isolation of Crenothrix bacteria reveals the distinct ecophysiologies of filamentous methanotrophs and adaptations to redox stress

At the dawn of modern microbiology, Cohn observed abundant filamentous bacteria in drinking water wells that he named Crenothrix polyspora. Subsequent research has revealed the methanotrophic metabolism of Crenothrix bacteria and their disproportionately high activity in stratified lakes compared to unicellular strains, yet laboratory cultivation has proven elusive, leaving the ecophysiology of Crenothrix bacteria largely unknown. Here we report the isolation of two methanotroph strains of the "lacustrine Crenothrix" clade from an iron-rich wetland and reveal their highly unique cell biologies and potential ecological roles. Using physiological approaches, we demonstrate that the strains perform a microaerobic methane metabolism while growing distinct filaments having wide and directionally oriented connective structures. The strains further have broad genomic repertoires for addressing redox stress that we show are uniquely associated with lacustrine Crenothrix compared to related methanotrophs based on genome data. Aligning with laboratory observations, we identify lacustrine Crenothrix bacteria along potential redox gradients in the wetland at iron-rich snow sites, and we further detect such bacteria in diverse global ecosystems based on public metagenome searches. Together, our data strongly point to an ecophysiology of lacustrine Crenothrix bacteria that is tightly linked to redox stress, and we propose these bacteria may uniquely store or share metabolic intermediates via their filamentous lifestyle to thrive under such conditions. Our results provide a fresh view of the diversity, evolution, and ecology of aerobic methanotrophs, connecting over 150 years of microbiology research opening vast new opportunities to probe bacterial adaptations that drive global methane cycling under redox stress.

microbiology↗

bioRxiv2025

Engineering a Covalent Linkage into a Dimeric De Novo Enzyme Reveals a Novel Life-Sustaining Mechanism

Designing novel proteins that share no homology with natural sequences, but which nonetheless provide life sustaining functions, is an important goal for synthetic biology. Towards this goal, we previously reported Syn-F4, the first de novo enzyme capable of catalyzing a life-sustaining reaction, both in vitro and in vivo. Syn-F4 catalyzes hydrolysis of the siderophore, ferric enterobactin, thereby releasing iron and enabling growth in iron-limited media of an otherwise inviable {Delta}fes strain of Escherichia coli. Although Syn-F4 provides a direct enzymatic replacement of the natural ferric enterobactin esterase encoded by Fes, it has a dramatically different structure and enzymatic mechanism than the natural Fes enzyme. The novel Syn-F4 enzyme forms a 4-helix bundle, comprising a homodimer of two -helical hairpins. Here we describe the engineering of a covalent peptide linkage into the homodimer to generate a single chain 4-helix bundle. As expected, the resulting linked protein (Syn-F4-Link) also rescued {Delta}fes cells in iron-limited media. Moreover, X-ray crystallography revealed a 3D structure similar to the parental homodimer. Surprisingly, however, the linked protein was not enzymatically active. Instead, Syn-F4-Link rescues {Delta}fes cells by upregulating biosynthesis of the enterobactin siderophore thereby enabling assimilation of sufficient iron to sustain cell growth. These findings demonstrate that two very similar de novo proteins can sustain cell growth using dramatically different biological mechanisms.

synthetic biology↗

bioRxiv2025

Temperature vaulting: A method for screening selective, slow- and tight-binding inhibitors targeting kinases in their non-native state

A polypeptide folds into its protein tertiary structure in the native state through a folding intermediate in the non-native state. The transition between these states is thermodynamically driven. A folding intermediate of dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) autophosphorylates intramolecularly, whereas DYRK1A in the native state no longer catalyzes this reaction. The alteration in substrate specificity suggests a conformational transition of DYRK1A during its folding process. Consistent with this hypothesis, we identified FINDY (1), which inhibits the intramolecular autophosphorylation but not the intermolecular phosphorylation, suggesting that the folding intermediate possesses an alternative inhibitor-binding site. Meanwhile, it remains an issue that the methods for approaching the alternative binding site require an intricate assay tailored to the individual target. Here we show a method, designated as "temperature vaulting," for screening the non-native-state-targeted inhibitors of DYRK1A. Transient heating of recombinant DYRK1A protein drove the reversible transition between the native state and the non-native state targeted by FINDY (1). At physiological temperature, FINDY (1) slowly bound to the DYRK1A protein. These results indicate that transient heating accelerates the slow-binding process by assisting the protein to overcome the high-energy barrier leading to the target non-native state. The energy barrier also slowed down the dissociation process, resulting in tight binding between DYRK1A and FINDY (1). Furthermore, this study suggests that the dissociation rate underlies the inhibition selectivity of FINDY (1) between DYRK1A and its family kinase DYRK1B. This method enables the identification of slow- and tight-binding inhibitors that have been missed in conventional assays. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/632643v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@be5661org.highwire.dtl.DTLVardef@1925beorg.highwire.dtl.DTLVardef@fceb5borg.highwire.dtl.DTLVardef@bfbf91_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSA temperature vaulting method facilitated the screening of a slow- and tight-binding inhibitor targeting DYRK1A in the non-native state. A structure-activity relationship study of FINDY (1) demonstrated that a slight alteration in chemical structure impacts the inhibition kinetics. A molecular dynamics simulation of DYRK1A revealed binding-ready conformations for FINDY (1). The dissociation rate may underlie the inhibition selectivity of FINDY (1) between DYRK1A and DYRK1B in cellular systems.

biophysics↗

bioRxiv2024

Osteogenic CpG oligodeoxynucleotide, iSN40, inhibits osteoclastogenesis in a TLR9-dependent manner

A CpG oligodeoxynucleotide (CpG-ODN), iSN40 (5-GGA ACG ATC CTC AAG CTT-3), was originally identified to promote osteoblast differentiation independent of Toll-like receptor 9 (TLR9). While CpG-ODNs are generally known to be recognized by TLR9 and inhibit osteoclasto-genesis. This study investigated the anti-osteoclastogenic effect of iSN40. The murine mono-cyte/macrophage cell line RAW264.7 was treated with receptor activator of nuclear factor-{kappa}B ligand (RANKL) to induce osteoclast differentiation, and the effects of iSN40 on osteoclast formation were quantified by tartrate-resistant acid phosphatase (TRAP) staining and real-time RT-PCR. iSN40 completely inhibited RANKL-induced differentiation into TRAP+ multinucleated osteoclasts by suppressing osteoclastogenic genes (Nfatc1, Ctsk, and Dcstamp) and inducing anti-/non-osteoclasto-genic genes (Irf8, Adgre1, and Il1b). Treatment with a TLR9 inhibitor, E6446, or mutation in the CpG motif of iSN40 abolished intracellular uptake and the anti-osteoclastogenic effect of iSN40. These results demonstrate that iSN40 is internalized subcellularly, recognized by TLR9 via its CpG motif, modulates RANKL-dependent osteoclastogenic gene expression, and ultimately inhibits osteoclast formation. Computational simulation of the iSN40 structure also suggested the importance of the superficial CpG motif for iSN40 function. Finally, iSN40 was confirmed to inhibit osteoclastogenesis of RAW264.7 cells cocultured with the murine osteoblast cell line MC3T3-E1, which is a model of bone remodeling. This study demonstrates that iSN40, which exerts both pro-osteogenic and anti-osteoclastogenic effects, may be a promising nucleic acid drug for osteoporosis.

cell biology↗

bioRxiv2024

Antimicrobial activity of the BAM complex-targeting peptides against multidrug-resistant gram-negative bacteria

Multidrug-resistant (MDR) Gram-negative bacteria represent a notable public health threat, necessitating the urgent development of new antimicrobial agents. The {beta}-barrel assembly machinery (BAM) complex, crucial for the biogenesis of outer membrane proteins in Gram-negative bacteria, emerges as a promising target for drug development. The BAM complex comprises five proteins (BamA-E), and its functionality might be disrupted by peptides targeting the BamA and BamB interface. We synthesized the peptide LTLR, located in the BamB interaction region with BamA in Pseudomonas aeruginosa, and assessed its anti-P. aeruginosa activity. This peptide demonstrated potential in enhancing antibiotic efficacy against P. aeruginosa. Conversely, LRTL, a scrambled version of LTLR, lacked activity, underscoring the importance of specific target site binding for the peptides adjuvant effect. Subsequently, we tested the hypothesis that peptide dimerization enhances its effectiveness. A dimeric peptide, composed of two LTLR sequences, was tested and found to possess bactericidal activity against P. aeruginosa, an outcome not observed with the monomeric form. Importantly, this dimeric peptide also showed bactericidal activity against MDR P. aeruginosa strains. In summary, our findings offer a foundation for developing novel antimicrobial agents against MDR Gram-negative bacteria. IMPORTANCEThis work demonstrates that (1) the {beta}-barrel assembly machinery (BAM) complex-targeting peptides can exhibit antimicrobial activity and that (2) the dimeric forms of these peptides exhibit bactericidal activity against multidrug-resistant (MDR) strains of P. aeruginosa and A. baumannii.

microbiology↗

bioRxiv2024

Development of the 12-base short dimeric myogenetic oligodeoxynucleotide that induces myogenic differentiation

A myogenetic oligodeoxynucleotide (myoDN), iSN04 (5-AGA TTA GGG TGA GGG TGA-3), is a single-stranded 18-base telomeric DNA that serves as an anti-nucleolin aptamer and induces myogenic differentiation, which is expected to be a nucleic acid drug for the prevention of disease-associated muscle wasting. To improve the drug efficacy and synthesis cost of myoDN, shortening the sequence while maintaining its structure-based function is a major challenge. Here, we report the novel 12-base non-telomeric myoDN, iMyo01 (5-TTG GGT GGG GAA-3), which has comparable myogenic activity to iSN04. iMyo01 as well as iSN04 promoted myotube formation of primary-cultured human myoblasts with upregulation of myogenic gene expression. Both iMyo01 and iSN04 interacted with nucleolin, but iMyo01 did not bind to berberine, the isoquinoline alkaloid that stabilizes iSN04. Nuclear magnetic resonance revealed that iMyo01 forms a G-quadruplex structure despite its short sequence. Native polyacrylamide gel electrophoresis and computational molecular dynamics simulation indicated that iMyo01 forms a homodimer to generate a G-quadru-plex. These results provide new insights into the aptamer truncation technology that preserves aptamer conformation and bioactivity for the development of efficient nucleic acid drugs. Key ContributionThis study reports the structure-based shortening of a myogenetic oligodeox-ynucleotide, iSN04, as an anti-nucleolin aptamer that induces myogenesis. The shortening technology of aptamers while maintaining their conformation and activity improves their potency of drug function and synthesis cost.

cell biology↗

bioRxiv2023

Myogenetic oligodeoxynucleotide induces myocardial differentiation of murine pluripotent stem cells

An 18-base myogenetic oligodeoxynucleotide (myoDN), iSN04, acts an anti-nucleolin aptamer and induces myogenic differentiation of skeletal muscle myoblasts. This study investigated the effect of iSN04 on murine embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). In the undifferentiated state, iSN04 inhibited the proliferation of ESCs and iPSCs but did not affect the expression of pluripotent markers. In the differentiating condition, iSN04 treatment of ESCs/iPSCs from day 5 onward dramatically induced the differentiation into Nkx2-5+ beating cardiomyocytes with upregulation of Gata4, Isl1, and Nkx2-5, whereas iSN04 treatment from earlier stages completely inhibited cardiomyogenesis. RNA sequencing revealed that iSN04 treatment from day 5 onward contributes to the generation of cardiac progenitors by modulating the Wnt signaling pathway. Immunostaining showed that iSN04 suppressed the cytoplasmic translocation of nucleolin and restricted it to the nucleoli. These results demonstrate that nucleolin inhibition by iSN04 facilitates the terminal differentiation of cardiac mesoderm into cardiomyocytes, but interferes with the differentiation of early mesoderm into the cardiac lineage. This is the first report on the generation of cardiomyocytes from pluripotent stem cells using a DNA aptamer. Since iSN04 did not induce hypertrophic responses in primary-cultured cardiomyocytes, iSN04 would be useful and safe for the regenerative therapy of heart failure using stem cell-derived cardiomyocytes.

cell biology↗

bioRxiv2023

Genistein enhances NAD+ biosynthesis by binding to Prohibitin 1 and upregulating nicotinamide phosphoribosyltransferase in adipocytes

Decreased NAD+ levels in adipocytes cause adipose-tissue dysfunction, leading to systemic glucose and lipid metabolism failure. Therefore, developing small molecules and nutraceuticals that can increase NAD+ levels in adipocytes is necessary. Genistein, a nutraceutical derived from soybeans, has various physiological activities and improves glucose and lipid metabolism. In this study, we aimed to unravel the effects of genistein on the intracellular NAD+ levels in adipocytes and the underlying molecular mechanisms. We showed that genistein enhanced NAD+ biosynthesis by increasing the expression of nicotinamide phosphoribosyltransferase (NAMPT), the rate-limiting enzyme in NAD+ biosynthesis. A pull-down assay using genistein-immobilized beads identified prohibitin 1 (PHB1) as a target protein of genistein. The knockdown of PHB1 suppressed the genistein-induced increase in NAMPT expression and NAD+ levels in adipocytes. Genistein-bound PHB1 contributed to the stabilization of the transcription factor CCAAT/enhancer-binding protein {beta} through activation of extracellular signal-regulated kinase, resulting in increased NAMPT expression at the transcriptional level. Genistein induced dephosphorylation of peroxisome proliferator-activated receptor at serine 273 and increased the insulin-sensitizing adipokine, adiponectin, in adipocytes, whereas the knockdown of NAMPT and PHB1 abolished these genistein-mediated effects. Our results proved the potential efficacy of nutraceuticals in promoting NAD+ levels and restoring metabolic function in adipocytes. Furthermore, we identified PHB1, localized to the plasma membrane, as a candidate target protein for increased expression of NAMPT in adipocytes. Overall, these findings will assist in developing NAD+ boosting strategies to alleviate the metabolic dysfunctions in adipose tissues. Significance StatementIncreasing NAD+ levels is an important preventive strategy for maintaining metabolic function. Here, we showed that genistein, a nutraceutical, which increases NAD+ levels in adipocytes, increased NAD+ biosynthesis by upregulating nicotinamide phosphoribosyltransferase (NAMPT), a rate-limiting enzyme in the NAD+ biosynthesis pathway. Our findings also showed that genistein increased NAMPT expression by binding to prohibitin 1 in the plasma membrane. Genistein-induced increase in NAD+ levels promoted adiponectin expression, an insulin-sensitizing adipokine, in adipocytes. This study provides evidence that nutraceuticals, such as genistein, are effective in enhancing NAD+ biosynthesis in adipocytes and that PHB1 is a candidate target protein for increased expression of NAMPT to maintain metabolic functions in adipose tissues.

biochemistry↗

bioRxiv2022

Identification of a novel osteogenetic oligodeoxynucleotide (osteoDN) that promotes osteoblast differentiation in a TLR9-independent manner

Recent studies have revealed that oligodeoxynucleotides (ODNs) designed from genome sequences have the potential to regulate cell fate. Currently, ODNs that conduct cell differentiation are nanomolecular drug candidates for regenerative medicine. Herein, we demonstrate that iSN40, an 18-base ODN derived from the Lacticaseibacillus rhamnosus GG genome, promoted the differentiation and calcification of osteoblasts that play a central role during bone formation. In the murine osteoblast cell line MC3T3-E1, iSN40 enhanced alkaline phosphatase activity at the early stage of differentiation and facilitated calcium deposition at the late stage by inducing the expression of osteogenic genes such as Msx2, osterix, collagen type 1, osteopontin, and osteocalcin. Intriguingly, the CpG motif within iSN40 was not required for its osteogenetic activity, indicating that iSN40 functions in a TLR9-independent manner. These data suggest that iSN40, serving as an osteogenetic ODN (osteoDN), as a drug seed that target osteoblasts for bone regeneration.

cell biology↗

bioRxiv2021

Bodily ownership of an independent supernumerary limb: An exploratory study

Can our brain perceive a sense of ownership towards an independent supernumerary limb; one that can be moved independently of any other limb and provides its own independent movement feedback? Following the rubberhand illusion experiment, a plethora of studies has shown that the human representation of self is very plastic. But previous studies have almost exclusively investigated ownership towards substitute artificial limbs, which are controlled by the movements of a real limb and/or limbs from which non-visual sensory feedback is provided on an existing limb. Here, to investigate whether the human brain can own an independent artificial limb, we first developed a novel independent robotic sixth finger. We allowed participants to train using the finger and examined whether it induced changes in the body representation using behavioral as well as cognitive measures. Our results suggest that unlike a substituted artificial limb (like in the rubber hand experiment), it is more difficult for humans to perceive a sense of ownership towards an independent limb. However, ownership does seem possible, as we observed clear tendencies of changes in the body representation that correlated with the cognitive reports of the sense of ownership. Our results provide the first evidence to show that an independent supernumerary limb can be embodied by the human brain.

neuroscience↗

bioRxiv2020

Myogenetic oligodeoxynucleotide (myoDN) complexed with berberine promotes differentiation of chicken skeletal muscle myoblasts

Skeletal muscle myoblasts are myogenic precursors that develop into myofibers during muscle formation. Improvement of myoblast differentiation is important for advancing meat production by domestic animals. We recently identified novel oligodeoxynucleotides (ODNs) termed myogenetic ODNs (myoDNs) that promote the differentiation of mammalian myoblasts. An isoquinoline alkaloid, berberine, forms a complex with one of the myoDNs, iSN04, and enhances its activities. This study investigated the effects of myoDNs on chicken myoblasts to elucidate their species-specific actions. Seven myoDNs (iSN01-iSN07) were found to facilitate the differentiation of chicken myoblasts into myosin heavy chain (MHC)-positive myocytes. The iSN04-berberine complex exhibited a higher myogenetic activity than iSN04 alone, which was shown to enhance the differentiation of myoblasts into myocytes, myotube formation, and myogenic gene expression (MyoD, myogenin, MHC, and myomaker). These data indicate that myoDNs promoting chicken myoblast differentiation may be used as potential feed additives in broiler diets.

cell biology↗

bioRxiv2020

Rapid profiling of drug-resistant bacteria using DNA-binding dyes and a nanopore-based DNA sequencer

Spread of drug-resistant bacteria is a serious problem worldwide. We thus designed a new sequence-based protocol that can quickly identify bacterial compositions of clinical samples and their drug-resistance profiles simultaneously. Here we utilized propidium monoazide (PMA) that prohibits DNA amplifications from dead bacteria, and subjected the original and antibiotics-treated samples to 16S rRNA metagenome sequencing. We tested our protocol on bacterial mixtures, and observed that sequencing reads derived from drug-resistant bacteria were significantly increased compared with those from drug-sensitive bacteria when samples were treated by antibiotics. Our protocol is scalable and will be useful for quickly profiling drug-resistant bacteria.

microbiology↗

bioRxiv2020

Identification of the myogenetic oligodeoxynucleotides (myoDNs) that promote differentiation of skeletal muscle myoblasts by targeting nucleolin

Herein we report that the 18-base telomeric oligodeoxynucleotides (ODNs) designed from the Lactobacillus rhamnosus GG genome promote differentiation of skeletal muscle myoblasts which are myogenic precursor cells. We termed these myogenetic ODNs (myoDNs). The activity of one of the myoDNs, iSN04, was independent of Toll-like receptors, but dependent on its conformational state. Molecular simulation and iSN04 mutants revealed stacking of the 13-15th guanines as a core structure for iSN04. The alkaloid berberine bound to the guanine stack and enhanced iSN04 activity, probably by stabilizing and optimizing iSN04 conformation. We further identified nucleolin as an iSN04-binding protein. Results showed that iSN04 antagonizes nucleolin, increases the levels of p53 protein translationally suppressed by nucleolin, and eventually induces myotube formation by modulating the expression of genes involved in myogenic differentiation and cell cycle arrest. This study shows that bacterial-derived myoDNs serve as aptamers and are potential nucleic acid drugs directly targeting myoblasts.

cell biology↗