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1.
Sci Rep ; 14(1): 21864, 2024 09 19.
Artículo en Inglés | MEDLINE | ID: mdl-39300146

RESUMEN

The decrease in sperm count and infertility is a global issue that remains unresolved. By screening environmental bacterial isolates, we have found that a novel lactic acid bacterium, Lactiplantibacillus plantarum SNI3, increased testis size, testosterone levels, sperm count, sexual activity and fertility in mice that have consumed the bacteria for four weeks. The abundance of L. plantarum in the colon microbiome was positively associated with sperm count. Fecal microbiota transplantation (FMT) from L. plantarum SNI3-dosed mice improved testicular functions in microbiome-attenuated recipient animals. To identify mediators that confer pro-reproductive effects on the host, untargeted in situ mass spectrometry metabolomics was performed on testis samples of L. plantarum SNI3-treated and control mice. Enrichment pathway analysis revealed several perturbed metabolic pathways in the testis of treated mice. Within the testis, a dipeptide, glutamyl-glutamate (GluGlu) was the most upregulated metabolite following L. plantarum SNI3 administration. To validate the pro-reproductive feature of GluGlu, systemic and local injections of the dipeptide have been performed. γ-GluGlu increased sperm count but had no effect on testosterone. These findings highlight the role of γ-GluGlu in mediating spermatogenetic effects of L. plantarum on the male mouse host and -following relevant human clinical trials- may provide future tools for treating certain forms of male infertility.


Asunto(s)
Dipéptidos , Espermatogénesis , Testículo , Animales , Masculino , Ratones , Dipéptidos/metabolismo , Testículo/metabolismo , Testículo/microbiología , Recuento de Espermatozoides , Trasplante de Microbiota Fecal , Testosterona/metabolismo , Interacciones Microbiota-Huesped , Metabolómica/métodos , Microbioma Gastrointestinal , Fertilidad
2.
J Phys Chem Lett ; 15(37): 9543-9547, 2024 Sep 19.
Artículo en Inglés | MEDLINE | ID: mdl-39265045

RESUMEN

This study investigates the lasing effects in a Fabry-Perot cavity to discern the binding interactions of thioflavin T (ThT) with various peptides associated with Alzheimer's disease, including Aß(1-42), KLVFFA, and diphenylalanine (FF) in the condensed phase. Utilizing kinetic lasing measurements, the research explores ThT emission enhancements due to specific groove binding in ß-sheet structures and highlights additional contributions from weak surface interactions and solvent-solute interactions. Lasing spectroscopy reveals a lack of transition of the FF system from its native state to an amyloid-like structure, challenging traditional ThT assay interpretations. These findings show the potential of lasing spectroscopy in elucidating the molecular basis of amyloid fibril formation and the development of diagnostic tools for amyloidogenic diseases.


Asunto(s)
Enfermedad de Alzheimer , Péptidos beta-Amiloides , Benzotiazoles , Benzotiazoles/química , Péptidos beta-Amiloides/química , Péptidos beta-Amiloides/metabolismo , Enfermedad de Alzheimer/metabolismo , Conformación Proteica en Lámina beta , Fragmentos de Péptidos/química , Fragmentos de Péptidos/metabolismo , Humanos , Fenilalanina/química , Dipéptidos/química , Dipéptidos/metabolismo , Unión Proteica , Cinética
3.
Autophagy ; 20(10): 2164-2185, 2024 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-39316747

RESUMEN

The GGGGCC hexanucleotide repeat expansion (HRE) of the C9orf72 gene is the most frequent cause of amyotrophic lateral sclerosis (ALS), a devastative neurodegenerative disease characterized by motor neuron degeneration. C9orf72 HRE is associated with lowered levels of C9orf72 expression and its translation results in the production of dipeptide-repeats (DPRs). To recapitulate C9orf72-related ALS disease in vivo, we developed a zebrafish model where we expressed glycine-proline (GP) DPR in a c9orf72 knockdown context. We report that C9orf72 gain- and loss-of-function properties act synergistically to induce motor neuron degeneration and paralysis with poly(GP) accumulating preferentially within motor neurons along with Sqstm1/p62 aggregation indicating macroautophagy/autophagy deficits. Poly(GP) levels were shown to accumulate upon c9orf72 downregulation and were comparable to levels assessed in autopsy samples of patients carrying C9orf72 HRE. Chemical boosting of autophagy using rapamycin or apilimod, is able to rescue motor deficits. Proteomics analysis of zebrafish-purified motor neurons unravels mitochondria dysfunction confirmed through a comparative analysis of previously published C9orf72 iPSC-derived motor neurons. Consistently, 3D-reconstructions of motor neuron demonstrate that poly(GP) aggregates colocalize to mitochondria, thus inducing their elongation and swelling and the failure of their processing by mitophagy, with mitophagy activation through urolithin A preventing locomotor deficits. Finally, we report apoptotic-related increased amounts of cleaved Casp3 (caspase 3, apoptosis-related cysteine peptidase) and rescue of motor neuron degeneration by constitutive inhibition of Casp9 or treatment with decylubiquinone. Here we provide evidence of key pathogenic steps in C9ALS-FTD that can be targeted through pharmacological avenues, thus raising new therapeutic perspectives for ALS patients.


Asunto(s)
Esclerosis Amiotrófica Lateral , Apoptosis , Autofagia , Proteína C9orf72 , Dipéptidos , Mitofagia , Neuronas Motoras , Pez Cebra , Neuronas Motoras/metabolismo , Neuronas Motoras/patología , Animales , Proteína C9orf72/genética , Proteína C9orf72/metabolismo , Mitofagia/genética , Apoptosis/genética , Humanos , Autofagia/genética , Autofagia/fisiología , Esclerosis Amiotrófica Lateral/metabolismo , Esclerosis Amiotrófica Lateral/patología , Esclerosis Amiotrófica Lateral/genética , Dipéptidos/farmacología , Dipéptidos/metabolismo , Mutación con Pérdida de Función/genética , Mitocondrias/metabolismo , Modelos Animales de Enfermedad
4.
Metab Eng ; 85: 105-115, 2024 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-39047893

RESUMEN

Cysteine and cystine are essential amino acids present in mammalian cell cultures. While contributing to biomass synthesis, recombinant protein production, and antioxidant defense mechanisms, cysteine poses a major challenge in media formulations owing to its poor stability and oxidation to cystine, a cysteine dimer. Due to its poor solubility, cystine can cause precipitation of feed media, formation of undesired products, and consequently, reduce cysteine bioavailability. In this study, a highly soluble cysteine containing dipeptide dimer, Ala-Cys-Cys-Ala (ACCA), was evaluated as a suitable alternative to cysteine and cystine in CHO cell cultures. Replacing cysteine and cystine in basal medium with ACCA did not sustain cell growth. However, addition of ACCA at 4 mM and 8 mM to basal medium containing cysteine and cystine boosted cell growth up to 15% and 27% in CHO-GS and CHO-K1 batch cell cultures respectively and led to a proportionate increase in IgG titer. 13C-Metabolic flux analysis revealed that supplementation of ACCA reduced glycolytic fluxes by 20% leading to more efficient glucose metabolism in CHO-K1 cells. In fed-batch cultures, ACCA was able to replace cysteine and cystine in feed medium. Furthermore, supplementation of ACCA at high concentrations in basal medium eliminated the need for any cysteine equivalents in feed medium and increased cell densities and viabilities in fed-batch cultures without any significant impact on IgG charge variants. Taken together, this study demonstrates the potential of ACCA to improve CHO cell growth, productivity, and metabolism while also facilitating the formulation of cysteine- and cystine-free feed media. Such alternatives to cysteine and cystine will pave the way for enhanced biomanufacturing by increasing cell densities in culture and extending the storage of highly concentrated feed media as part of achieving intensified bioproduction processes.


Asunto(s)
Cricetulus , Cisteína , Cistina , Dipéptidos , Células CHO , Animales , Cisteína/metabolismo , Cistina/metabolismo , Dipéptidos/metabolismo , Medios de Cultivo/química , Proliferación Celular/efectos de los fármacos
5.
J Chem Phys ; 161(4)2024 Jul 28.
Artículo en Inglés | MEDLINE | ID: mdl-39051836

RESUMEN

The ability to accurately predict protein-protein interactions is critically important for understanding major cellular processes. However, current experimental and computational approaches for identifying them are technically very challenging and still have limited success. We propose a new computational method for predicting protein-protein interactions using only primary sequence information. It utilizes the concept of physicochemical similarity to determine which interactions will most likely occur. In our approach, the physicochemical features of proteins are extracted using bioinformatics tools for different organisms. Then they are utilized in a machine-learning method to identify successful protein-protein interactions via correlation analysis. It was found that the most important property that correlates most with the protein-protein interactions for all studied organisms is dipeptide amino acid composition (the frequency of specific amino acid pairs in a protein sequence). While current approaches often overlook the specificity of protein-protein interactions with different organisms, our method yields context-specific features that determine protein-protein interactions. The analysis is specifically applied to the bacterial two-component system that includes histidine kinase and transcriptional response regulators, as well as to the barnase-barstar complex, demonstrating the method's versatility across different biological systems. Our approach can be applied to predict protein-protein interactions in any biological system, providing an important tool for investigating complex biological processes' mechanisms.


Asunto(s)
Proteínas Bacterianas , Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Aprendizaje Automático , Ribonucleasas/metabolismo , Ribonucleasas/química , Biología Computacional , Unión Proteica , Mapeo de Interacción de Proteínas/métodos , Dipéptidos/química , Dipéptidos/metabolismo , Fenómenos Químicos
6.
Sci Rep ; 14(1): 17083, 2024 07 24.
Artículo en Inglés | MEDLINE | ID: mdl-39048621

RESUMEN

Recent renewed interest in the possibility of life in the acidic clouds of Venus has led to new studies on organic chemistry in concentrated sulfuric acid. We have previously found that the majority of amino acids are stable in the range of Venus' cloud sulfuric acid concentrations (81% and 98% w/w, the rest being water). The natural next question is whether dipeptides, as precursors to larger peptides and proteins, could be stable in this environment. We investigated the reactivity of the peptide bond using 20 homodipeptides and find that the majority of them undergo solvolysis within a few weeks, at both sulfuric acid concentrations. Notably, a few exceptions exist. HH and GG dipeptides are stable in 98% w/w sulfuric acid for at least 4 months, while II, LL, VV, PP, RR and KK resist hydrolysis in 81% w/w sulfuric acid for at least 5 weeks. Moreover, the breakdown process of the dipeptides studied in 98% w/w concentrated sulfuric acid is different from the standard acid-catalyzed hydrolysis that releases monomeric amino acids. Despite a few exceptions at a single concentration, no homodipeptides have demonstrated stability across both acid concentrations studied. This indicates that any hypothetical life on Venus would likely require a functional substitute for the peptide bond that can maintain stability throughout the range of sulfuric acid concentrations present.


Asunto(s)
Dipéptidos , Ácidos Sulfúricos , Dipéptidos/química , Dipéptidos/metabolismo , Ácidos Sulfúricos/química , Hidrólisis , Medio Ambiente Extraterrestre/química , Estabilidad Proteica
7.
Biochem Biophys Res Commun ; 729: 150361, 2024 Oct 15.
Artículo en Inglés | MEDLINE | ID: mdl-38972141

RESUMEN

Carnosine, anserine, and homocarnosine are histidine-containing dipeptides (HCDs) abundant in the skeletal muscle and nervous system in mammals. To date, studies have extensively demonstrated effects of carnosine and anserine, the predominant muscular HCDs, on muscular functions and exercise performance. However, homocarnosine, the predominant brain HCD, is underexplored. Moreover, roles of homocarnosine and its related HCDs in the brain and behaviors remain poorly understood. Here, we investigated potential roles of endogenous brain homocarnosine and its related HCDs in behaviors by using carnosine synthase-1-deficient (Carns1-/-) mice. We found that old Carns1-/- mice (female 12 months old) exhibited hyperactivity- and depression-like behaviors with higher plasma corticosterone levels on light-dark transition and forced swimming tests, but had no defects in spontaneous locomotor activity, repetitive behavior, olfactory functions, and learning and memory abilities, as compared with their age-matched wild-type (WT) mice. We confirmed that homocarnosine and its related HCDs were deficient across brain areas of Carns1-/- mice. Homocarnosine deficiency exhibited small effects on its constituent γ-aminobutyric acid (GABA) in the brain, in which GABA levels in hypothalamus and olfactory bulb were higher in Carns1-/- mice than in WT mice. In WT mice, homocarnosine and GABA were highly present in hypothalamus, thalamus, and olfactory bulb, and their brain levels did not decrease in old mice when compared with younger mice (3 months old). Our present findings provide new insights into roles of homocarnosine and its related HCDs in behaviors and neurological disorders.


Asunto(s)
Conducta Animal , Depresión , Dipéptidos , Animales , Femenino , Dipéptidos/metabolismo , Ratones , Depresión/metabolismo , Depresión/genética , Encéfalo/metabolismo , Carnosina/análogos & derivados , Carnosina/metabolismo , Ratones Endogámicos C57BL , Ratones Noqueados , Hipercinesia/metabolismo , Hipercinesia/genética , Envejecimiento/metabolismo , Histidina/análogos & derivados , Histidina/metabolismo , Histidina/deficiencia
8.
Food Funct ; 15(14): 7364-7374, 2024 Jul 15.
Artículo en Inglés | MEDLINE | ID: mdl-38912915

RESUMEN

Bioactive peptides derived from food are promising health-promoting ingredients that can be used in functional foods and nutraceutical formulations. In addition to the potency towards the selected therapeutic target, the bioavailability of bioactive peptides is a major factor regarding clinical efficacy. We have previously shown that a low molecular weight peptide fraction (LMWPF) from poultry by-product hydrolysates possesses angiotensin-1-converting enzyme (ACE-1) and dipeptidyl-peptidase 4 (DPP4) inhibitory activities. The present study aimed to investigate the bioavailability of the bioactive peptides in the LMWPF. Prior to the investigation of bioavailability, a dipeptide YA was identified from this fraction as a dual inhibitor of ACE-1 and DPP4. Gastrointestinal (GI) stability and intestinal absorption of the bioactive peptides (i.e., YA as well as two previously reported bioactive dipeptides (VL and IY)) in the LMWPF were evaluated using the INFOGEST static in vitro digestion model and intestinal Caco-2 cell monolayer, respectively. Analysis of peptides after in vitro digestion confirmed that the dipeptides were resistant to the simulated GI conditions. After 4 hours of incubation, the concentration of the peptide from the apical side of the Caco-2 cell monolayer showed a significant decrease. However, the corresponding absorbed peptides were not detected on the basolateral side, suggesting that the peptides were not transported across the intestinal monolayer but rather taken up or metabolized by the Caco2 cells. Furthermore, when analyzing the gene expression of the Caco-2 cells upon peptide stimulation, a down-regulation of peptide transporters, the transcription factor CDX2, and the tight junction protein-1 (TJP1) was observed, suggesting the specific effects of the peptides on the Caco-2 cells. The study demonstrated that bioactive dipeptides found in the LMWPF were stable through in vitro GI digestion; however, the overall bioavailability may be hindered by inadequate uptake across the intestinal barrier.


Asunto(s)
Inhibidores de la Enzima Convertidora de Angiotensina , Dipeptidil Peptidasa 4 , Inhibidores de la Dipeptidil-Peptidasa IV , Absorción Intestinal , Hidrolisados de Proteína , Animales , Humanos , Inhibidores de la Enzima Convertidora de Angiotensina/química , Inhibidores de la Enzima Convertidora de Angiotensina/metabolismo , Inhibidores de la Enzima Convertidora de Angiotensina/farmacocinética , Inhibidores de la Enzima Convertidora de Angiotensina/farmacología , Disponibilidad Biológica , Células CACO-2 , Digestión , Dipéptidos/química , Dipéptidos/metabolismo , Dipéptidos/farmacocinética , Dipéptidos/farmacología , Dipeptidil Peptidasa 4/metabolismo , Inhibidores de la Dipeptidil-Peptidasa IV/química , Inhibidores de la Dipeptidil-Peptidasa IV/metabolismo , Inhibidores de la Dipeptidil-Peptidasa IV/farmacocinética , Inhibidores de la Dipeptidil-Peptidasa IV/farmacología , Tracto Gastrointestinal/metabolismo , Absorción Intestinal/efectos de los fármacos , Péptidos/química , Péptidos/metabolismo , Péptidos/farmacocinética , Péptidos/farmacología , Peptidil-Dipeptidasa A/metabolismo , Aves de Corral , Hidrolisados de Proteína/química , Hidrolisados de Proteína/farmacología
9.
Nat Cell Biol ; 26(7): 1047-1061, 2024 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-38839979

RESUMEN

The lysosomal degradation of macromolecules produces diverse small metabolites exported by specific transporters for reuse in biosynthetic pathways. Here we deorphanized the major facilitator superfamily domain containing 1 (MFSD1) protein, which forms a tight complex with the glycosylated lysosomal membrane protein (GLMP) in the lysosomal membrane. Untargeted metabolomics analysis of MFSD1-deficient mouse lysosomes revealed an increase in cationic dipeptides. Purified MFSD1 selectively bound diverse dipeptides, while electrophysiological, isotope tracer and fluorescence-based studies in Xenopus oocytes and proteoliposomes showed that MFSD1-GLMP acts as a uniporter for cationic, neutral and anionic dipeptides. Cryoelectron microscopy structure of the dipeptide-bound MFSD1-GLMP complex in outward-open conformation characterized the heterodimer interface and, in combination with molecular dynamics simulations, provided a structural basis for its selectivity towards diverse dipeptides. Together, our data identify MFSD1 as a general lysosomal dipeptide uniporter, providing an alternative route to recycle lysosomal proteolysis products when lysosomal amino acid exporters are overloaded.


Asunto(s)
Dipéptidos , Lisosomas , Lisosomas/metabolismo , Animales , Dipéptidos/metabolismo , Oocitos/metabolismo , Microscopía por Crioelectrón , Ratones , Xenopus laevis , Humanos , Ratones Noqueados , Simulación de Dinámica Molecular , Simportadores/metabolismo , Simportadores/genética , Simportadores/química , Femenino , Canales de Potencial de Receptor Transitorio
10.
Nat Commun ; 15(1): 4386, 2024 May 23.
Artículo en Inglés | MEDLINE | ID: mdl-38782953

RESUMEN

Sialin, a member of the solute carrier 17 (SLC17) transporter family, is unique in its ability to transport not only sialic acid using a pH-driven mechanism, but also transport mono and diacidic neurotransmitters, such as glutamate and N-acetylaspartylglutamate (NAAG), into synaptic vesicles via a membrane potential-driven mechanism. While most transporters utilize one of these mechanisms, the structural basis of how Sialin transports substrates using both remains unclear. Here, we present the cryogenic electron-microscopy structures of human Sialin: apo cytosol-open, apo lumen-open, NAAG-bound, and inhibitor-bound. Our structures show that a positively charged cytosol-open vestibule accommodates either NAAG or the Sialin inhibitor Fmoc-Leu-OH, while its luminal cavity potentially binds sialic acid. Moreover, functional analyses along with molecular dynamics simulations identify key residues in binding sialic acid and NAAG. Thus, our findings uncover the essential conformational states in NAAG and sialic acid transport, demonstrating a working model of SLC17 transporters.


Asunto(s)
Microscopía por Crioelectrón , Simulación de Dinámica Molecular , Humanos , Ácido N-Acetilneuramínico/metabolismo , Ácido N-Acetilneuramínico/química , Lisosomas/metabolismo , Células HEK293 , Conformación Proteica , Transportadores de Anión Orgánico/metabolismo , Transportadores de Anión Orgánico/química , Transportadores de Anión Orgánico/antagonistas & inhibidores , Dipéptidos/química , Dipéptidos/metabolismo , Dipéptidos/farmacología , Simportadores
11.
J Med Chem ; 67(10): 8247-8260, 2024 May 23.
Artículo en Inglés | MEDLINE | ID: mdl-38716576

RESUMEN

Prostate-specific membrane antigen (PSMA)-targeted radio ligand therapeutics (RLTs), such as [177Lu]Lu-PSMA-617 (Pluvicto), have been shown to accumulate in salivary glands and kidneys, potentially leading to undesired side effects. As unwanted accumulation in normal organs may derive from the cross-reactivity of PSMA ligands to glutamate carboxypeptidase III (GCPIII), it may be convenient to block this interaction with GCPIII-selective ligands. Parallel screening of a DNA-encoded chemical library (DEL) against GCPIII and PSMA allowed the identification of GCPIII binders. Structure-activity relationship (SAR) studies resulted in the identification of nanomolar GCPIII ligands with up to 1000-fold selectivity over PSMA. We studied the ability of GCPIII ligands to counteract the binding of [177Lu]Lu-PSMA-617 to human salivary glands by autoradiography and could demonstrate a partial radioprotection.


Asunto(s)
Dipéptidos , Compuestos Heterocíclicos con 1 Anillo , Lutecio , Humanos , Antígenos de Superficie , Autorradiografía , Dipéptidos/química , Dipéptidos/metabolismo , Glutamato Carboxipeptidasa II , Compuestos Heterocíclicos con 1 Anillo/química , Compuestos Heterocíclicos con 1 Anillo/metabolismo , Ligandos , Lutecio/química , Lutecio/metabolismo , Antígeno Prostático Específico , Radioisótopos/química , Radioisótopos/metabolismo , Radiofármacos/química , Radiofármacos/metabolismo , Radiofármacos/farmacocinética , Glándulas Salivales/metabolismo , Relación Estructura-Actividad , Distribución Tisular
12.
Phys Chem Chem Phys ; 26(22): 15968-15977, 2024 Jun 06.
Artículo en Inglés | MEDLINE | ID: mdl-38775038

RESUMEN

Relaxation times of nuclear spins often serve as a valuable source of information on the dynamics of various biochemical processes. Measuring relaxation as a function of the external magnetic field turned out to be extremely useful for the studies of weak ligand-protein interactions. We demonstrate that observing the relaxation of the long-lived spin order instead of longitudinal magnetization extends the capability of this approach. We studied the field-dependent relaxation of the longitudinal magnetization and the singlet order (SO) of methylene protons in alanine-glycine dipeptide and citrate in the presence of human serum albumin (HSA). As a result, SO relaxation proved to be more sensitive to ligand-protein interaction, providing higher relaxation contrast for various HSA concentrations. To assess the parameters of the binding process in more details, we utilized a simple analytical relaxation model to fit the experimental field dependences for both SO and T1 relaxation. We also tested the validity of our approach in the experiments with trimethylsilylpropanoic acid (TSP) used as a competitor in ligand binding with HSA.


Asunto(s)
Unión Proteica , Albúmina Sérica Humana , Ligandos , Humanos , Albúmina Sérica Humana/química , Albúmina Sérica Humana/metabolismo , Dipéptidos/química , Dipéptidos/metabolismo , Ácido Cítrico/química
13.
Appl Microbiol Biotechnol ; 108(1): 326, 2024 May 08.
Artículo en Inglés | MEDLINE | ID: mdl-38717487

RESUMEN

Aspartyl dipeptidase (dipeptidase E) can hydrolyze Asp-X dipeptides (where X is any amino acid), and the enzyme plays a key role in the degradation of peptides as nutrient sources. Dipeptidase E remains uncharacterized in Streptomyces. Orf2 from Streptomyces sp. 139 is located in the exopolysaccharide biosynthesis gene cluster, which may be a novel dipeptidase E with "S134-H170-D198" catalytic triad by sequence and structure comparison. Herein, recombinant Orf2 was expressed in E. coli and characterized dipeptidase E activity using the Asp-ρNA substrate. The optimal pH and temperature for Orf2 are 7.5 and 40 ℃; Vmax and Km of Orf2 are 0.0787 mM·min-1 and 1.709 mM, respectively. Orf2 exhibits significant degradation activities to Asp-Gly-Gly, Asp-Leu, Asp-His, and isoAsp-Leu and minimal activities to Asp-Pro and Asp-Ala. Orf2 contains a Ser-His-Asp catalytic triad characterized by point mutation. In addition, the Asp147 residue of Orf2 is also proven to be critical for the enzyme's activity through molecular docking and point mutation. Transcriptome analysis reveals the upregulation of genes associated with ribosomes, amino acid biosynthesis, and aminoacyl-tRNA biosynthesis in the orf2 mutant strain. Compared with the orf2 mutant strain and WT, the yield of crude polysaccharide does not change significantly. However, crude polysaccharides from the orf2 mutant strain exhibit a wider range of molecular weight distribution. The results indicate that the Orf2 links nutrient stress to secondary metabolism as a novel dipeptidase E. KEY POINTS: • A novel dipeptidase E with a Ser-His-Asp catalytic triad was characterized from Streptomyces sp. 139. • Orf2 was involved in peptide metabolism both in vitro and in vivo. • Orf2 linked nutrient stress to mycelia formation and secondary metabolism in Streptomyces.


Asunto(s)
Dipeptidasas , Streptomyces , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Proteínas Bacterianas/química , Dipeptidasas/metabolismo , Dipeptidasas/genética , Dipeptidasas/química , Dipéptidos/metabolismo , Concentración de Iones de Hidrógeno , Cinética , Simulación del Acoplamiento Molecular , Familia de Multigenes , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Proteínas Recombinantes/química , Streptomyces/genética , Streptomyces/enzimología , Especificidad por Sustrato , Temperatura
14.
Gut Microbes ; 16(1): 2356275, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38797999

RESUMEN

Multidrug-resistant microorganisms have become a major public health concern around the world. The gut microbiome is a gold mine for bioactive compounds that protect the human body from pathogens. We used a multi-omics approach that integrated whole-genome sequencing (WGS) of 74 commensal gut microbiome isolates with metabolome analysis to discover their metabolic interaction with Salmonella and other antibiotic-resistant pathogens. We evaluated differences in the functional potential of these selected isolates based on WGS annotation profiles. Furthermore, the top altered metabolites in co-culture supernatants of selected commensal gut microbiome isolates were identified including a series of dipeptides and examined for their ability to prevent the growth of various antibiotic-resistant bacteria. Our results provide compelling evidence that the gut microbiome produces metabolites, including the compound class of dipeptides that can potentially be applied for anti-infection medication, especially against antibiotic-resistant pathogens. Our established pipeline for the discovery and validation of bioactive metabolites from the gut microbiome as novel candidates for multidrug-resistant infections represents a new avenue for the discovery of antimicrobial lead structures.


Asunto(s)
Antibacterianos , Bacterias , Microbioma Gastrointestinal , Microbioma Gastrointestinal/efectos de los fármacos , Humanos , Bacterias/clasificación , Bacterias/metabolismo , Bacterias/aislamiento & purificación , Bacterias/genética , Bacterias/efectos de los fármacos , Antibacterianos/farmacología , Antibacterianos/metabolismo , Simbiosis , Metaboloma , Secuenciación Completa del Genoma , Farmacorresistencia Bacteriana Múltiple , Salmonella/efectos de los fármacos , Salmonella/metabolismo , Salmonella/genética , Dipéptidos/metabolismo , Dipéptidos/farmacología
15.
Nat Commun ; 15(1): 3574, 2024 Apr 27.
Artículo en Inglés | MEDLINE | ID: mdl-38678027

RESUMEN

Modified cyclic dipeptides represent a widespread class of secondary metabolites with diverse pharmacological activities, including antibacterial, antifungal, and antitumor. Here, we report the structural characterization of the Streptomyces noursei enzyme AlbAB, a cyclodipeptide oxidase (CDO) carrying out α,ß-dehydrogenations during the biosynthesis of the antibiotic albonoursin. We show that AlbAB is a megadalton heterooligomeric enzyme filament containing covalently bound flavin mononucleotide cofactors. We highlight that AlbAB filaments consist of alternating dimers of AlbA and AlbB and that enzyme activity is crucially dependent on filament formation. We show that AlbA-AlbB interactions are highly conserved suggesting that other CDO-like enzymes are likely enzyme filaments. As CDOs have been employed in the structural diversification of cyclic dipeptides, our results will be useful for future applications of CDOs in biocatalysis and chemoenzymatic synthesis.


Asunto(s)
Streptomyces , Streptomyces/enzimología , Streptomyces/genética , Proteínas Bacterianas/metabolismo , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Dipéptidos/química , Dipéptidos/metabolismo , Oxidorreductasas/metabolismo , Oxidorreductasas/química , Mononucleótido de Flavina/metabolismo , Mononucleótido de Flavina/química , Péptidos Cíclicos/química , Péptidos Cíclicos/metabolismo , Cristalografía por Rayos X , Modelos Moleculares , Antibacterianos/química , Antibacterianos/farmacología , Antibacterianos/metabolismo , Antibacterianos/biosíntesis
16.
Chembiochem ; 25(11): e202300854, 2024 Jun 03.
Artículo en Inglés | MEDLINE | ID: mdl-38613434

RESUMEN

The utilization of the glycated amino acids formyline and pyrraline as well as their peptide-bound derivatives by 14 Saccharomyces yeasts, including 6 beer yeasts (bottom and top fermenting), one wine yeast, 6 strains isolated from natural habitats and one laboratory reference yeast strain (wild type) was investigated. All yeasts were able to metabolize glycated amino acids via the Ehrlich pathway to the corresponding Ehrlich metabolites. While formyline and small amounts of pyrraline entered the yeast cells via passive diffusion, the amounts of dipeptide-bound MRPs, especially the dipeptides glycated at the C-terminus, decreased much faster, indicating an uptake into the yeast cells. Furthermore, the glycation-mediated hydrophobization in general leads to an faster degradation rate compared to the native lysine dipeptides. While the utilization of free formyline is yeast-specific, the amounts of (glycated) dipeptides decreased faster in the presence of brewer's yeasts, which also showed a higher formation rate of Ehrlich metabolites compared to naturally isolated strains. Due to rapid uptake of alanyl dipeptides, it can be assumed that the Ehrlich enzyme system of naturally isolated yeasts is overloaded and the intracellularly released MRP is primarily excreted from the cell. This indicates adaptation of technologically used yeasts to (glycated) dipeptides as a nitrogen source.


Asunto(s)
Dipéptidos , Norleucina , Dipéptidos/metabolismo , Dipéptidos/química , Norleucina/metabolismo , Norleucina/análogos & derivados , Norleucina/química , Saccharomyces/metabolismo , Saccharomyces cerevisiae/metabolismo , Glicosilación , Pirroles
17.
Nucleic Acids Res ; 52(12): 7171-7187, 2024 Jul 08.
Artículo en Inglés | MEDLINE | ID: mdl-38647082

RESUMEN

Decay of mRNAs can be triggered by ribosome slowdown at stretches of rare codons or positively charged amino acids. However, the full diversity of sequences that trigger co-translational mRNA decay is poorly understood. To comprehensively identify sequence motifs that trigger mRNA decay, we use a massively parallel reporter assay to measure the effect of all possible combinations of codon pairs on mRNA levels in S. cerevisiae. In addition to known mRNA-destabilizing sequences, we identify several dipeptide repeats whose translation reduces mRNA levels. These include combinations of positively charged and bulky residues, as well as proline-glycine and proline-aspartate dipeptide repeats. Genetic deletion of the ribosome collision sensor Hel2 rescues the mRNA effects of these motifs, suggesting that they trigger ribosome slowdown and activate the ribosome-associated quality control (RQC) pathway. Deep mutational scanning of an mRNA-destabilizing dipeptide repeat reveals a complex interplay between the charge, bulkiness, and location of amino acid residues in conferring mRNA instability. Finally, we show that the mRNA effects of codon pairs are predictive of the effects of endogenous sequences. Our work highlights the complexity of sequence motifs driving co-translational mRNA decay in eukaryotes, and presents a high throughput approach to dissect their requirements at the codon level.


Asunto(s)
Estabilidad del ARN , ARN Mensajero , Ribosomas , Saccharomyces cerevisiae , Ribosomas/metabolismo , Ribosomas/genética , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , ARN Mensajero/genética , ARN Mensajero/metabolismo , Estabilidad del ARN/genética , Codón/genética , Biosíntesis de Proteínas , Motivos de Nucleótidos , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Dipéptidos/genética , Dipéptidos/metabolismo
18.
Adv Sci (Weinh) ; 11(24): e2306671, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38639383

RESUMEN

Cancer metastasis is the leading cause of mortality in patients with hepatocellular carcinoma (HCC). To meet the rapid malignant growth and transformation, tumor cells dramatically increase the consumption of nutrients, such as amino acids. Peptide transporter 1 (PEPT1), a key transporter for small peptides, has been found to be an effective and energy-saving intracellular source of amino acids that are required for the growth of tumor cells. Here, the role of PEPT1 in HCC metastasis and its underlying mechanisms is explored. PEPT1 is upregulated in HCC cells and tissues, and high PEPT1 expression is associated with poor prognosis in patients with HCC. PEPT1 overexpression dramatically promoted HCC cell migration, invasion, and lung metastasis, whereas its knockdown abolished these effects both in vitro and in vivo. Mechanistic analysis revealed that high PEPT1 expression increased cellular dipeptides in HCC cells that are responsible for activating the MAP4K4/G3BP2 signaling pathway, ultimately facilitating the phosphorylation of G3BP2 at Thr227 and enhancing HCC metastasis. Taken together, these findings suggest that PEPT1 acts as an oncogene in promoting HCC metastasis through dipeptide-induced MAP4K4/G3BP2 signaling and that the PEPT1/MAP4K4/G3BP2 axis can serve as a promising therapeutic target for metastatic HCC.


Asunto(s)
Carcinoma Hepatocelular , Dipéptidos , Neoplasias Hepáticas , Transportador de Péptidos 1 , Transducción de Señal , Animales , Humanos , Masculino , Ratones , Proteínas Adaptadoras Transductoras de Señales/metabolismo , Proteínas Adaptadoras Transductoras de Señales/genética , Carcinoma Hepatocelular/metabolismo , Carcinoma Hepatocelular/genética , Carcinoma Hepatocelular/patología , Línea Celular Tumoral , Movimiento Celular , Dipéptidos/metabolismo , Dipéptidos/farmacología , Modelos Animales de Enfermedad , Neoplasias Hepáticas/metabolismo , Neoplasias Hepáticas/genética , Neoplasias Hepáticas/patología , Ratones Desnudos , Metástasis de la Neoplasia , Transportador de Péptidos 1/metabolismo , Transportador de Péptidos 1/genética , Proteínas de Unión al ARN/metabolismo , Proteínas de Unión al ARN/genética
19.
Ann Nucl Med ; 38(7): 574-583, 2024 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-38676906

RESUMEN

OBJECTIVE: The marked success of prostate-specific membrane antigen (PSMA)-targeting radioligands with albumin binder (ALB) is attributed to the improvement of blood retention and tumor accumulation. [111In]In-PNT-DA1, our PSMA-targeting radioligand with ALB, also achieved improved tumor accumulation due to its prolonged blood retention. Although the advantage of ALBs is related to their reversible binding to albumin, the relationship between albumin-binding and tumor accumulation of PSMA-targeting radioligands remains unclear because of the lack of information about radioligands with stronger albumin-binding than ALBs. In this study, we designed and synthesized [111In]In-PNT-DM-HSA, a new radioligand that consists of a PSMA-targeting radioligand covalently bound to albumin. The pharmacokinetics of [111In]In-PNT-DM-HSA was compared with those of [111In]In-PNT-DA1 and [111In]In-PSMA-617, a non-ALB-conjugated radioligand, to evaluate the relationship between albumin-binding and tumor accumulation. METHOD: The [111In]In-PNT-DM-HSA was prepared by incubation of [111In]In-PNT-DM, a PSMA-targeting radioligand including a maleimide group, and human serum albumin (HSA). The ability of [111In]In-PNT-DM-HSA was evaluated by in vitro assays. A biodistribution study using LNCaP tumor-bearing mice was conducted to compare the pharmacokinetics of [111In]In-PNT-DM-HSA, [111In]In-PNT-DA1, and [111In]In-PSMA-617. RESULTS: The [111In]In-PNT-DM-HSA was obtained at a favorable radiochemical yield and high radiochemical purity. In vitro assays revealed that [111In]In-PNT-DM-HSA had fundamental characteristics as a PSMA-targeting radioligand interacting with albumin covalently. In a biodistribution study, [111In]In-PNT-DM-HSA and [111In]In-PNT-DA1 showed higher blood retention than [111In]In-PSMA-617. On the other hand, the tumor accumulation of [111In]In-PNT-DA1 was much higher than [111In]In-PNT-DM-HSA and [111In]In-PSMA-617. CONCLUSIONS: These results indicate that the moderate reversible binding of ALB with albumin, not covalent binding, may play a critical role in enhancing the tumor accumulation of PSMA-targeting radioligands.


Asunto(s)
Antígenos de Superficie , Glutamato Carboxipeptidasa II , Animales , Ratones , Glutamato Carboxipeptidasa II/metabolismo , Antígenos de Superficie/metabolismo , Humanos , Masculino , Ligandos , Línea Celular Tumoral , Distribución Tisular , Unión Proteica , Albúminas/metabolismo , Neoplasias de la Próstata/metabolismo , Neoplasias de la Próstata/diagnóstico por imagen , Albúmina Sérica/metabolismo , Albúmina Sérica/química , Dipéptidos/farmacocinética , Dipéptidos/química , Dipéptidos/metabolismo , Radioisótopos de Indio
20.
Proc Natl Acad Sci U S A ; 121(17): e2307814121, 2024 Apr 23.
Artículo en Inglés | MEDLINE | ID: mdl-38621131

RESUMEN

Efforts to genetically reverse C9orf72 pathology have been hampered by our incomplete understanding of the regulation of this complex locus. We generated five different genomic excisions at the C9orf72 locus in a patient-derived induced pluripotent stem cell (iPSC) line and a non-diseased wild-type (WT) line (11 total isogenic lines), and examined gene expression and pathological hallmarks of C9 frontotemporal dementia/amyotrophic lateral sclerosis in motor neurons differentiated from these lines. Comparing the excisions in these isogenic series removed the confounding effects of different genomic backgrounds and allowed us to probe the effects of specific genomic changes. A coding single nucleotide polymorphism in the patient cell line allowed us to distinguish transcripts from the normal vs. mutant allele. Using digital droplet PCR (ddPCR), we determined that transcription from the mutant allele is upregulated at least 10-fold, and that sense transcription is independently regulated from each allele. Surprisingly, excision of the WT allele increased pathologic dipeptide repeat poly-GP expression from the mutant allele. Importantly, a single allele was sufficient to supply a normal amount of protein, suggesting that the C9orf72 gene is haplo-sufficient in induced motor neurons. Excision of the mutant repeat expansion reverted all pathology (RNA abnormalities, dipeptide repeat production, and TDP-43 pathology) and improved electrophysiological function, whereas silencing sense expression did not eliminate all dipeptide repeat proteins, presumably because of the antisense expression. These data increase our understanding of C9orf72 gene regulation and inform gene therapy approaches, including antisense oligonucleotides (ASOs) and CRISPR gene editing.


Asunto(s)
Esclerosis Amiotrófica Lateral , Demencia Frontotemporal , Humanos , Proteína C9orf72/genética , Proteína C9orf72/metabolismo , Alelos , Esclerosis Amiotrófica Lateral/metabolismo , Demencia Frontotemporal/metabolismo , Neuronas Motoras/metabolismo , Mutación , Expansión de las Repeticiones de ADN/genética , Dipéptidos/metabolismo
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