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1.
Nucleic Acids Res ; 51(15): 7900-7913, 2023 08 25.
Artículo en Inglés | MEDLINE | ID: mdl-37462073

RESUMEN

PHO84 is a budding yeast gene reported to be negatively regulated by its cognate antisense transcripts both in cis and in trans. In this study, we performed Transient-transcriptome sequencing (TT-seq) to investigate the correlation of sense/antisense pairs in a dbp2Δ strain and found over 700 sense/antisense pairs, including PHO84, to be positively correlated, contrasting the prevailing model. To define what mechanism regulates the PHO84 gene and how this regulation could have been originally attributed to repression by the antisense transcript, we conducted a series of molecular biology and genetics experiments. We now report that the 3' untranslated region (3'UTR) of PHO84 plays a repressive role in sense expression, an activity not linked to the antisense transcripts. Moreover, we provide results of a genetic screen for 3'UTR-dependent repression of PHO84 and show that the vast majority of identified factors are linked to negative regulation. Finally, we show that the PHO84 promoter and terminator form gene loops which correlate with transcriptional repression, and that the RNA-binding protein, Tho1, increases this looping and the 3'UTR-dependent repression. Our results negate the current model for antisense non-coding transcripts of PHO84 and suggest that many of these transcripts are byproducts of open chromatin.


Asunto(s)
ARN sin Sentido , Saccharomyces cerevisiae , Regiones no Traducidas 3'/genética , Cromatina , Genómica , ARN sin Sentido/genética , ARN sin Sentido/metabolismo , Saccharomyces cerevisiae/metabolismo , Regulación Fúngica de la Expresión Génica
2.
Arterioscler Thromb Vasc Biol ; 43(9): 1713-1718, 2023 09.
Artículo en Inglés | MEDLINE | ID: mdl-37409529

RESUMEN

BACKGROUND: Little is known whether electronic cigarettes (ECIG) increase vulnerability to future atherosclerotic cardiovascular disease. We determined, using an ex vivo mechanistic atherogenesis assay, whether proatherogenic changes including monocyte transendothelial migration and monocyte-derived foam cell formation are increased in people who use ECIGs. METHODS: In a cross-sectional single-center study using plasma and peripheral blood mononuclear cells from healthy participants who are nonsmokers or with exclusive use of ECIGs or tobacco cigarettes (TCIGs), autologous peripheral blood mononuclear cells with patient plasma and pooled peripheral blood mononuclear cells from healthy nonsmokers with patient plasma were utilized to dissect patient-specific ex vivo proatherogenic circulating factors present in plasma and cellular factors present in monocytes. Our main outcomes were monocyte transendothelial migration (% of blood monocyte cells that undergo transendothelial migration through a collagen gel) and monocyte-derived foam cell formation as determined by flow cytometry and the median fluorescence intensity of the lipid-staining fluorochrome BODIPY in monocytes of participants in the setting of an ex vivo model of atherogenesis. RESULTS: Study participants (N=60) had median age of 24.0 years (interquartile range [IQR], 22.0-25.0 years), and 31 were females. Monocyte transendothelial migration was increased in people who exclusively used TCIGs (n=18; median [IQR], 2.30 [ 1.29-2.82]; P<0.001) and in people who exclusively used ECIGs (n=21; median [IQR], 1.42 [ 0.96-1.91]; P<0.01) compared with nonsmoking controls (n=21; median [IQR], 1.05 [0.66-1.24]). Monocyte-derived foam cell formation was increased in people who exclusively used TCIGs (median [IQR], 2.01 [ 1.59-2.49]; P<0.001) and in people who exclusively used ECIGs (median [IQR], 1.54 [ 1.10-1.86]; P<0.001) compared with nonsmoker controls (median [IQR], 0.97 [0.86-1.22]). Both monocyte transendothelial migration and monocyte-derived foam cell formation were higher in TCIG smokers compared with ECIG users and in ECIG users who were former smokers versus ECIG users who were never smokers (P<0.05 for all comparisons). CONCLUSIONS: The finding of alterations in proatherogenic properties of blood monocytes and plasma in TCIG smokers compared with nonsmokers validates this assay as a strong ex vivo mechanistic tool with which to measure proatherogenic changes in people who use ECIGs. Similar yet significantly less severe alterations in proatherogenic properties of monocytes and plasma were detected in the blood from ECIG users. Future studies are necessary to determine whether these findings are attributable to a residual effect of prior smoking or are a direct effect of current ECIG use.


Asunto(s)
Aterosclerosis , Sistemas Electrónicos de Liberación de Nicotina , Vapeo , Adulto , Femenino , Humanos , Masculino , Adulto Joven , Aterosclerosis/etiología , Estudios Transversales , Leucocitos Mononucleares , Vapeo/efectos adversos
3.
Mol Cell ; 61(3): 393-404, 2016 Feb 04.
Artículo en Inglés | MEDLINE | ID: mdl-26833086

RESUMEN

Long non-coding (lnc)RNAs, once thought to merely represent noise from imprecise transcription initiation, have now emerged as major regulatory entities in all eukaryotes. In contrast to the rapidly expanding identification of individual lncRNAs, mechanistic characterization has lagged behind. Here we provide evidence that the GAL lncRNAs in the budding yeast S. cerevisiae promote transcriptional induction in trans by formation of lncRNA-DNA hybrids or R-loops. The evolutionarily conserved RNA helicase Dbp2 regulates formation of these R-loops as genomic deletion or nuclear depletion results in accumulation of these structures across the GAL cluster gene promoters and coding regions. Enhanced transcriptional induction is manifested by lncRNA-dependent displacement of the Cyc8 co-repressor and subsequent gene looping, suggesting that these lncRNAs promote induction by altering chromatin architecture. Moreover, the GAL lncRNAs confer a competitive fitness advantage to yeast cells because expression of these non-coding molecules correlates with faster adaptation in response to an environmental switch.


Asunto(s)
ADN de Hongos/metabolismo , Metabolismo Energético , ARN de Hongos/metabolismo , ARN Largo no Codificante/metabolismo , Saccharomyces cerevisiae/metabolismo , Transcripción Genética , Activación Transcripcional , Adaptación Fisiológica , Ensamble y Desensamble de Cromatina , ARN Helicasas DEAD-box/genética , ARN Helicasas DEAD-box/metabolismo , ADN de Hongos/química , ADN de Hongos/genética , Metabolismo Energético/genética , Galactosa/metabolismo , Regulación Fúngica de la Expresión Génica , Glucosa/metabolismo , Familia de Multigenes , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Conformación de Ácido Nucleico , ARN de Hongos/química , ARN de Hongos/genética , ARN Largo no Codificante/química , ARN Largo no Codificante/genética , Proteínas Represoras/genética , Proteínas Represoras/metabolismo , Ribonucleasa H/genética , Ribonucleasa H/metabolismo , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Factores de Tiempo
4.
J Bacteriol ; 205(12): e0032023, 2023 12 19.
Artículo en Inglés | MEDLINE | ID: mdl-37991380

RESUMEN

IMPORTANCE: Bacterial pathogens have vastly distinct sites that they inhabit during infection. This requires adaptation due to changes in nutrient availability and antimicrobial stress. The bacterial surface is a primary barrier, and here, we show that the bacterial pathogen Shigella flexneri increases its surface decorations when it transitions to an intracellular lifestyle. We also observed changes in bacterial and host cell fatty acid homeostasis. Specifically, intracellular S. flexneri increased the expression of their fatty acid degradation pathway, while the host cell lipid pool was significantly depleted. Importantly, bacterial proliferation could be inhibited by fatty acid supplementation of host cells, thereby providing novel insights into the possible link between human malnutrition and susceptibility to S. flexneri.


Asunto(s)
Proteínas Bacterianas , Shigella flexneri , Humanos , Proteínas Bacterianas/metabolismo , Shigella flexneri/metabolismo , Ácidos Grasos/metabolismo , Lípidos
5.
Mol Microbiol ; 118(4): 403-416, 2022 10.
Artículo en Inglés | MEDLINE | ID: mdl-36006410

RESUMEN

Enterobacterales have developed a specialized outer membrane polysaccharide (enterobacterial common antigen [ECA]). ECA biosynthesis begins on the cytoplasmic side of the inner membrane (IM) where glycosyltransferases sequentially add sugar moieties to form a complete repeat unit which is then translocated across the IM by WzxE before being polymerized into short linear chains by WzyE/WzzE. Research into WecG, the enzyme responsible for generating ECA lipid-II, has not progressed beyond Barr et al. (1988) who described WecG as a membrane protein. Here we revise our understanding of WecG and re-characterize it as a peripherally associated membrane protein. Through the use of Western immunoblotting we show that WecG in Shigella flexneri is maintained to the IM via its three C-terminal helices and further identify key residues in helix II which are critical for this interaction which has allowed us to identify WecG as a GT-E glycosyltransferase. We investigate the possibility of protein complexes and ultimately show that ECA lipid-I maintains WecG to the membrane which is crucial for its function. This research is the first since Barr et al. (1988) to investigate the biochemistry of WecG and reveals possible novel drug targets to inhibit WecG and thus ECA function and cell viability.


Asunto(s)
Enterobacteriaceae , Glicosiltransferasas , Enterobacteriaceae/metabolismo , Antígenos Bacterianos/metabolismo , Proteínas de la Membrana , Polisacáridos , Azúcares , Lípidos
7.
Cell ; 134(4): 624-33, 2008 Aug 22.
Artículo en Inglés | MEDLINE | ID: mdl-18724935

RESUMEN

Gene expression requires proper messenger RNA (mRNA) export and translation. However, the functional links between these consecutive steps have not been fully defined. Gle1 is an essential, conserved mRNA export factor whose export function is dependent on the small molecule inositol hexakisphosphate (IP(6)). Here, we show that both Gle1 and IP(6) are required for efficient translation termination in Saccharomyces cerevisiae and that Gle1 interacts with termination factors. In addition, Gle1 has a conserved physical association with the initiation factor eIF3, and gle1 mutants display genetic interactions with the eIF3 mutant nip1-1. Strikingly, gle1 mutants have defects in initiation, whereas strains lacking IP(6) do not. We propose that Gle1 functions together with IP(6) and the DEAD-box protein Dbp5 to regulate termination. However, Gle1 also independently mediates initiation. Thus, Gle1 is uniquely positioned to coordinate the mRNA export and translation mechanisms. These results directly impact models for perturbation of Gle1 function in pathophysiology.


Asunto(s)
Proteínas Portadoras/metabolismo , Ácido Fítico/metabolismo , Biosíntesis de Proteínas , ARN Mensajero/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/metabolismo , ARN Helicasas DEAD-box/metabolismo , Factor 3 de Iniciación Eucariótica/metabolismo , Proteínas de Complejo Poro Nuclear , Proteínas de Transporte Nucleocitoplasmático/metabolismo , Factores de Terminación de Péptidos/metabolismo , Isoformas de Proteínas/metabolismo , Saccharomyces cerevisiae/genética
8.
J Bacteriol ; 204(4): e0054621, 2022 04 19.
Artículo en Inglés | MEDLINE | ID: mdl-35293778

RESUMEN

Outer membrane (OM) polysaccharides allow bacteria to resist harsh environmental conditions and antimicrobial agents, traffic to and persist in pathogenic niches, and evade immune responses. Shigella flexneri has two OM polysaccharide populations, being enterobacterial common antigen (ECA) and lipopolysaccharide (LPS) O antigen (Oag); both are polymerized into chains by separate homologs of the Wzy-dependent pathway. The two polysaccharide pathways, along with peptidoglycan (PG) biosynthesis, compete for the universal biosynthetic membrane anchor, undecaprenyl phosphate (Und-P), as the finite pool of available Und-P is critical in all three cell wall biosynthetic pathways. Interactions between the two OM polysaccharide pathways have been proposed in the past where, through the use of mutants in both pathways, various perturbations have been observed. Here, we show for the first time that mutations in one of the two OM polysaccharide pathways can affect each other, dependent on where the mutation lies along the pathway, while the second pathway remains genetically intact. We then expand on this and show that the mutations also affect PG biosynthesis pathways and provide data which supports that the classical mutant phenotypes of cell wall mutants are due to a lack of available Und-P. Our work here provides another layer in understanding the complex intricacies of the cell wall biosynthetic pathways and demonstrates their interdependence on Und-P, the universal biosynthetic membrane anchor. IMPORTANCE Bacterial outer membrane polysaccharides play key roles in a range of bacterial activities from homeostasis to virulence. Two such OM polysaccharide populations are ECA and LPS Oag, which are synthesized by separate homologs of the Wzy-dependent pathway. Both ECA and LPS Oag biosynthesis join with PG biosynthesis to form the cell wall biosynthetic pathways, which all are interdependent on the availability of Und-P for proper function. Our data show the direct effects of cell wall pathway mutations affecting all related pathways when they themselves remain genetically unchanged. This work furthers our understanding of the complexities and interdependence of the three cell wall pathways.


Asunto(s)
Vías Biosintéticas , Antígenos O , Antígenos Bacterianos , Lipopolisacáridos , Antígenos O/genética , Shigella flexneri/genética
9.
J Bacteriol ; 204(9): e0022422, 2022 Sep 20.
Artículo en Inglés | MEDLINE | ID: mdl-35980183

RESUMEN

Shigella flexneri implements the Wzy-dependent pathway to biosynthesize the O antigen (Oag) component of its surface lipopolysaccharide. The inner membrane polymerase WzySF catalyzes the repeat addition of undecaprenol-diphosphate-linked Oag (Und-PP-RUs) to produce a polysaccharide, the length of which is tightly regulated by two competing copolymerase proteins, WzzSF (short-type Oag; 10 to 17 RUs) and WzzpHS-2 (very-long-type Oag; >90 RUs). The nature of the interaction between WzySF and WzzSF/WzzpHS-2 in Oag polymerization remains poorly characterized, with the majority of the literature characterizing the individual protein constituents of the Wzy-dependent pathway. Here, we report instead a major investigation into the specific binding interactions of WzySF with its copolymerase counterparts. For the first time, a region of WzySF that forms a unique binding site for WzzpHS-2 has been identified. Specifically, this work has elucidated key WzySF moieties at the N- and C-terminal domains (NTD and CTD) that form an intramolecular pocket modulating the WzzpHS-2 interaction. Novel copurification data highlight that disruption of residues within this NTD-CTD pocket impairs the interaction with WzzpHS-2 without affecting WzzSF binding, thereby specifically disrupting polymerization of longer polysaccharide chains. This study provides a novel understanding of the molecular interaction of WzySF with WzzSF/WzzpHS-2 in the Wzy-dependent pathway and, furthermore, detects the Wzy/Wzz/Und-PP-Oag complex for the first time. Beyond S. flexneri, this work may be extended to provide insight into the interactions between protein homologues expressed by related species, especially members of Enterobacteriaceae, that produce dual Oag chain length determinants. IMPORTANCE Shigella flexneri is a pathogen causing significant morbidity and mortality, predominantly devastating the pediatric age group in developing countries. A major virulence factor contributing to S. flexneri pathogenesis is its surface lipopolysaccharide, which is comprised of three domains: lipid A, core oligosaccharide, and O antigen (Oag). The Wzy-dependent pathway is the most common biosynthetic mechanism implemented for Oag biosynthesis by Gram-negative bacteria, including S. flexneri. The nature of the interaction between the polymerase, WzySF, and the polysaccharide copolymerases, WzzSF and WzzpHS-2, in Oag polymerization is poorly characterized. This study investigates the molecular interplay between WzySF and its copolymerases, deciphering key interactions in the Wzy-dependent pathway that may be extended beyond S. flexneri, providing insight into Oag biosynthesis in Gram-negative bacteria.


Asunto(s)
Antígenos O , Shigella flexneri , Proteínas Bacterianas/metabolismo , Niño , Difosfatos/metabolismo , Humanos , Lípido A/metabolismo , Lipopolisacáridos/metabolismo , Shigella flexneri/genética , Shigella flexneri/metabolismo , Factores de Virulencia/metabolismo
10.
Microbiology (Reading) ; 168(4)2022 04.
Artículo en Inglés | MEDLINE | ID: mdl-35470793

RESUMEN

Enterobacteriales have evolved a specialized outer membrane polysaccharide [Enterobacterial Common Antigen (ECA)] which allows them to persist in various environmental niches. Biosynthesis of ECA initiates on the cytoplasmic leaflet of the inner membrane (IM) where glycosyltransferases assemble ECA repeat units (RUs). Complete RUs are then translocated across the IM and assembled into polymers by ECA-specific homologues of the Wzy-dependent pathway. Consisting of the membrane proteins Wzx, Wzy and Wzz, the Wzy-dependent pathway is the most common polysaccharide biosynthetic pathway in Gram-negative bacteria where it is most notably involved in LPS O antigen (Oag) biosynthesis. As such, the majority of research directed towards these proteins has been orientated towards Oag biosynthetic homologues with little directed towards ECA homologues. Belonging to the Shape, Elongation, Division and Sporulation (SEDS) protein family, Wzy proteins are polymerases, and are characterized as possessing little or no peptide homology among homologues as well as being polytopic membrane proteins with functionally relevant residues within periplasmic loops, as defined by C-terminal reporter fusion topology mapping. Here, we present the first the first major study into the ECA polymerase WzyE. Multiple sequence alignments and topology mapping showed that WzyE is unlike WzyB proteins involved with Oag biosynthesis WzyE displays high peptide conservation across Enterobacteriales. In silico structures and reporter mapping allowed us to identify possible functionally conserved residues with WzyESF's periplasmic loops, which we showed were crucial for its function. This work provides novel insight into Wzy proteins and suggests that WzyE is an optimal model to investigate Wzy proteins and the Wzy-dependent pathway.


Asunto(s)
Proteínas Bacterianas , Shigella flexneri , Antígenos Bacterianos/metabolismo , Proteínas Bacterianas/metabolismo , Proteínas de la Membrana/metabolismo , Nucleotidiltransferasas/metabolismo , Antígenos O/química , Shigella flexneri/genética , Shigella flexneri/metabolismo
11.
J Urol ; 207(4): 823-831, 2022 04.
Artículo en Inglés | MEDLINE | ID: mdl-34854746

RESUMEN

PURPOSE: The underlying premise of prostate cancer active surveillance (AS) is that cancers likely to metastasize will be recognized and eliminated before cancer-related disease can ensue. Our study was designed to determine the prostate cancer upgrading rate when biopsy guided by magnetic resonance imaging (MRGBx) is used before entry and during AS. MATERIALS AND METHODS: The cohort included 519 men with low- or intermediate-risk prostate cancer who enrolled in prospective studies (NCT00949819 and NCT00102544) between February 2008 and February 2020. Subjects were preliminarily diagnosed with Gleason Grade Group (GG) 1 cancer; AS began when subsequent MRGBx confirmed GG1 or GG2. Participants underwent confirmatory MRGBx (targeted and systematic) followed by surveillance MRGBx approximately every 12 to 24 months. The primary outcome was tumor upgrading to ≥GG3. RESULTS: Upgrading to ≥GG3 was found in 92 men after a median followup of 4.8 years (IQR 3.1-6.5) after confirmatory MRGBx. Upgrade-free probability after 5 years was 0.85 (95% CI 0.81-0.88). Cancer detected in a magnetic resonance imaging lesion at confirmatory MRGBx increased risk of subsequent upgrading during AS (HR 2.8; 95% CI 1.3-6.0), as did presence of GG2 (HR 2.9; 95% CI 1.1-8.2) In men who upgraded ≥GG3 during AS, upgrading was detected by targeted cores only in 27%, systematic cores only in 25% and both in 47%. In 63 men undergoing prostatectomy, upgrading from MRGBx was found in only 5 (8%). CONCLUSIONS: When AS begins and follows with MRGBx (targeted and systematic), upgrading rate (≥GG3) is greater when tumor is initially present within a magnetic resonance imaging lesion or when pathology is GG2 than when these features are absent.


Asunto(s)
Biopsia Guiada por Imagen/métodos , Imagen por Resonancia Magnética , Neoplasias de la Próstata/diagnóstico por imagen , Neoplasias de la Próstata/patología , Espera Vigilante/métodos , Anciano , Estudios de Seguimiento , Humanos , Masculino , Persona de Mediana Edad , Clasificación del Tumor , Estudios Prospectivos , Prostatectomía , Neoplasias de la Próstata/cirugía , Factores de Riesgo
12.
Nicotine Tob Res ; 24(3): 413-415, 2022 02 14.
Artículo en Inglés | MEDLINE | ID: mdl-34410424

RESUMEN

INTRODUCTION: The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the virus responsible for the COVID-19 pandemic, gains entry into the host cell when its Spike protein is cleaved by host proteases TMPRSS2 and furin, thereby markedly increasing viral affinity for its receptor, angiotensin-converting enzyme-2 (ACE2). In rodent and diseased human lungs, tobacco cigarette (TCIG) smoke increases ACE2, but the effect of electronic cigarette vaping (ECIG) is unknown. It is unknown whether nicotine (in both TCIGs and ECIGs) or non-nicotine constituents unique to TCIG smoke increase expression of key proteins in COVID-19 pathogenesis. METHODS: Immune (CD45+) cells collected before the pandemic in otherwise healthy young people, including TCIG smokers (n = 9), ECIG vapers (n = 12), or nonsmokers (NS) (n = 12), were studied. Using flow cytometry, expression of key proteins in COVID-19 pathogenesis were compared among these groups. RESULTS: TCIG smokers and ECIG vapers had similar smoking or vaping burdens as indicated by similar plasma cotinine levels. TCIG smokers compared with NS had a significantly increased percentage of cells that were positive for ACE2 (10-fold, p < .001), TMPRSS2 (5-fold, p < .001), and ADAM17 (2.5-fold, p < .001). Additionally, the mean fluorescence intensity (MFI) consistently showed greater mean ACE2 (2.2-fold, p < .001), TMPRSS2 (1.5-fold, p < .001), furin (1.1-fold, p < .05), and ADAM17 (2-fold, p < .001) in TCIG smokers compared with NS. In ECIG vapers, furin MFI was increased (1.15-fold, p < .05) and TMPRSS2 MFI tended to be increased (1.1-fold, p = .077) compared with NS. CONCLUSIONS: The finding that key instigators of COVID-19 infection are lower in ECIG vapers compared with TCIG smokers is intriguing and warrants additional investigation to determine if switching to ECIGs is an effective harm reduction strategy. However, the trend toward increased proteases in ECIG vapers remains concerning. IMPLICATIONS: (1) This is the first human study to report a marked increase in proteins critical for COVID-19 infection, including ACE2, TMPRSS2, and ADAM17, in immune cells from healthy tobacco cigarette smokers without lung disease compared with e-cigarette vapers and nonsmokers. (2) These findings warrant additional investigation to determine whether switching to electronic cigarettes may be an effective harm reduction strategy in smokers addicted to nicotine who are unable or unwilling to quit. (3) The increase in proteases in electronic cigarette vapers remains concerning.


Asunto(s)
COVID-19 , Sistemas Electrónicos de Liberación de Nicotina , Productos de Tabaco , Vapeo , Adolescente , Humanos , No Fumadores , Pandemias , SARS-CoV-2 , Fumadores , Nicotiana
13.
Proc Natl Acad Sci U S A ; 116(41): 20453-20461, 2019 10 08.
Artículo en Inglés | MEDLINE | ID: mdl-31548374

RESUMEN

G-quadruplexes (G4) are noncanonical secondary structures formed in guanine-rich DNA and RNA sequences. MYC, one of the most critical oncogenes, forms a DNA G4 in its proximal promoter region (MycG4) that functions as a transcriptional silencer. However, MycG4 is highly stable in vitro and its regulatory role would require active unfolding. Here we report that DDX5, one of the founding members of the DEAD-box RNA helicase family, is extremely proficient at unfolding MycG4-DNA. Our results show that DDX5 is a highly active G4-resolvase that does not require a single-stranded overhang and that ATP hydrolysis is not directly coupled to G4-unfolding of DDX5. The chromatin binding sites of DDX5 are G-rich sequences. In cancer cells, DDX5 is enriched at the MYC promoter and activates MYC transcription. The DDX5 interaction with the MYC promoter and DDX5-mediated MYC activation is inhibited by G4-interactive small molecules. Our results uncover a function of DDX5 in resolving DNA and RNA G4s and suggest a molecular target to suppress MYC for cancer intervention.


Asunto(s)
ARN Helicasas DEAD-box/química , G-Cuádruplex , Ácidos Nucleicos/química , Proteínas Proto-Oncogénicas c-myc/química , Línea Celular , Cromatina , ARN Helicasas DEAD-box/genética , ARN Helicasas DEAD-box/metabolismo , Regulación de la Expresión Génica , Humanos , Desplegamiento Proteico , Proteínas Proto-Oncogénicas c-myc/genética
14.
J Bacteriol ; 203(22): e0041321, 2021 10 25.
Artículo en Inglés | MEDLINE | ID: mdl-34491798

RESUMEN

Shigella flexneri can synthesize polysaccharide chains having complex sugars and a regulated number of repeating units. S. flexneri lipopolysaccharide O antigen (Oag) is synthesized by the Wzy-dependent pathway, which is the most common pathway used in bacteria for polysaccharide synthesis. The inner membrane protein WzyB polymerizes the Oag repeat units into chains, while the polysaccharide copolymerases WzzB and WzzpHS2 determine the average number of repeat units or "the modal length," termed short type and very long type. Our data show for the first time a direct interaction between WzyB and WzzpHS2, with and without the use of the chemical cross-linker dithiobis (succinimidyl propionate) (DSP). Additionally, mutations generated via random and site-directed mutagenesis identify a region of WzyB that caused diminished function and significantly decreased very long Oag chain polymerization, and that affected the aforementioned interaction. These results provide insight into the mechanisms underlying the regulation of Oag biosynthesis. IMPORTANCE Complex polysaccharide chains are synthesized by bacteria, usually at a regulated number of repeating units, which has broad implications for bacterial pathogenesis. One example is the O antigen (Oag) component of lipopolysaccharide that is predominantly synthesized by the Wzy-dependent pathway. Our findings show for the first time a direct physical interaction between WzyB and WzzpHS2. Additionally, a set of Wzy mutant constructs were generated, revealing a proposed active site/switch region involved in the activity of WzyB and the physical interaction with WzzpHS2. Combined, these findings further understanding of the Wzy-dependent pathway. The identification of a novel interaction with the polysaccharide copolymerase WzzpHS2 and the region of WzyB that is involved in this aforementioned interaction and its impact on WzyB Oag synthesis activity have significant implication for the prevention/treatment of bacterial diseases and discovery of novel biotechnologies.


Asunto(s)
Proteínas Bacterianas/metabolismo , Regulación Bacteriana de la Expresión Génica/fisiología , Shigella flexneri/metabolismo , Proteínas Bacterianas/genética , ADN Bacteriano , Mutagénesis , Mutación , Plásmidos/genética , Plásmidos/metabolismo , Shigella flexneri/genética
15.
J Biol Chem ; 295(27): 8988-8998, 2020 07 03.
Artículo en Inglés | MEDLINE | ID: mdl-32376686

RESUMEN

DEAD-box helicase 5 (DDX5) is a founding member of the DEAD-box RNA helicase family, a group of enzymes that regulate ribonucleoprotein formation and function in every aspect of RNA metabolism, ranging from synthesis to decay. Our laboratory previously found that DDX5 is involved in energy homeostasis, a process that is altered in many cancers. Small cell lung cancer (SCLC) is an understudied cancer type for which effective treatments are currently unavailable. Using an array of methods, including short hairpin RNA-mediated gene silencing, RNA and ChIP sequencing analyses, and metabolite profiling, we show here that DDX5 is overexpressed in SCLC cell lines and that its down-regulation results in various metabolic and cellular alterations. Depletion of DDX5 resulted in reduced growth and mitochondrial dysfunction in the chemoresistant SCLC cell line H69AR. The latter was evidenced by down-regulation of genes involved in oxidative phosphorylation and by impaired oxygen consumption. Interestingly, DDX5 depletion specifically reduced intracellular succinate, a TCA cycle intermediate that serves as a direct electron donor to mitochondrial complex II. We propose that the oncogenic role of DDX5, at least in part, manifests as up-regulation of respiration supporting the energy demands of cancer cells.


Asunto(s)
ARN Helicasas DEAD-box/metabolismo , Mitocondrias/metabolismo , Carcinoma Pulmonar de Células Pequeñas/metabolismo , Línea Celular Tumoral , Citoplasma/metabolismo , ARN Helicasas DEAD-box/fisiología , Humanos , Mitocondrias/fisiología , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , ARN Helicasas/metabolismo , ARN Interferente Pequeño/metabolismo , Ribonucleoproteínas/metabolismo
16.
J Biol Chem ; 295(4): 905-913, 2020 01 24.
Artículo en Inglés | MEDLINE | ID: mdl-31843970

RESUMEN

An R-loop is a three-stranded nucleic acid structure that consists of a DNA:RNA hybrid and a displaced strand of DNA. R-loops occur frequently in genomes and have significant physiological importance. They play vital roles in regulating gene expression, DNA replication, and DNA and histone modifications. Several studies have uncovered that R-loops contribute to fundamental biological processes in various organisms. Paradoxically, although they do play essential positive functions required for important biological processes, they can also contribute to DNA damage and genome instability. Recent evidence suggests that R-loops are involved in a number of human diseases, including neurological disorders, cancer, and autoimmune diseases. This review focuses on the molecular basis for R-loop-mediated gene regulation and genomic instability and briefly discusses methods for identifying R-loops in vivo It also highlights recent studies indicating the role of R-loops in DNA double-strand break repair with an updated view of much-needed future goals in R-loop biology.


Asunto(s)
Estructuras R-Loop , Reparación del ADN , Técnicas Genéticas , Inestabilidad Genómica , Modelos Moleculares
17.
Biol Chem ; 402(5): 637-644, 2021 04 27.
Artículo en Inglés | MEDLINE | ID: mdl-33857360

RESUMEN

RNA helicases are enzymes that exist in all domains of life whose canonical functions include ATP-dependent remodeling of RNA structures and displacement of proteins from ribonucleoprotein complexes (RNPs). These enzymes play roles in virtually all processes of RNA metabolism, including pre-mRNA splicing, rRNA processing, nuclear mRNA export, translation and RNA decay. Here we review emerging noncanonical substrates of RNA helicases including RNA-DNA hybrids (R-loops) and RNA and DNA G-quadruplexes and discuss their biological significance.


Asunto(s)
ARN Helicasas DEAD-box , ARN Helicasas DEAD-box/genética , ARN Helicasas DEAD-box/metabolismo , Reparación del ADN , G-Cuádruplex , Humanos , Especificidad por Sustrato
18.
Medicina (Kaunas) ; 57(1)2021 Jan 07.
Artículo en Inglés | MEDLINE | ID: mdl-33430427

RESUMEN

Background and objectives: Limited evidence exists exploring perceptions of which aspects of a pain management program are perceived as valuable and impactful. The aim of this study was to explore patient beliefs about which aspects of a pain management program were valued and/or had perceived impact. Materials and Methods: One-on-one structured interviews were conducted with 11 adults three months after their completion of the Spark Pain Program at Westmead Hospital, Sydney, Australia. Concepts in the transcripts were inductively identified and explored, utilizing thematic analysis to better understand their relevance to the study aim. Results: Four themes emerged: (1) "The program overall was positive, but…"; (2) "I valued my improved knowledge and understanding of pain, but…"; (3) "I valued the stretching/relaxation/pacing/activity monitoring"; and (4) "I valued being part of a supportive and understanding group". Participants reported that they liked being treated as an individual within the group. A lack of perceived personal relevance of key messages was identified in some participants; it appears that patients in pain programs must determine that changes in knowledge, beliefs, and attitudes are personally relevant in order for the changes to have a significant impact on them. Conclusions: This study provides new insights into aspects of a pain management program that were perceived as valuable and impactful, areas that "missed the mark", and hypotheses to guide the implementation of service delivery and program redesign.


Asunto(s)
Dolor Crónico/terapia , Terapia por Ejercicio , Conocimientos, Actitudes y Práctica en Salud , Ejercicios de Estiramiento Muscular , Manejo del Dolor/métodos , Educación del Paciente como Asunto , Terapia por Relajación , Adulto , Anciano , Actitud Frente a la Salud , Australia , Duración de la Terapia , Femenino , Objetivos , Humanos , Masculino , Persona de Mediana Edad , Satisfacción del Paciente , Percepción , Solución de Problemas , Investigación Cualitativa
19.
J Bacteriol ; 2020 Dec 23.
Artículo en Inglés | MEDLINE | ID: mdl-33361196

RESUMEN

The ability of bacteria to synthesise complex polysaccharide chains at a controlled number of repeating units has wide implications for a range of biological activities that include: symbiosis, biofilm formation and immune system avoidance. Complex polysaccharide chains such as the O antigen (Oag) component of lipopolysaccharide and the enterobacterial common antigen (ECA) are synthesised by the most common polysaccharide synthesis pathway used in bacteria, known as the Wzy-dependent pathway. The Oag and ECA are polymerized into chains via the inner membrane proteins WzyB and WzyE, respectively, while the respective co-polymerases WzzB and WzzE modulate the number of repeat units in the chains or "the modal length" of the polysaccharide via a hypothesised interaction. Our data shows for the first time "cross-talk" between Oag and ECA synthesis in that WzzE is able to partially regulate Oag modal length via a potential interaction with WzyB. To investigate this, one or both of the transmembrane regions (TM1 and TM2) of WzzE and WzzB were swapped creating six chimera proteins. Several chimeric proteins showed significant increases Oag modal length control, while others reduced control. Additionally, co-purification experiments show an interaction between WzyB and WzzB for the first time without the use of a chemical cross-linker, and a novel interaction between WzyB and WzzE. These results suggest the TM2 region of Wzz proteins plays a critical role in Oag and ECA modal length control, presumably via the interaction with respective Wzy proteins, thus providing insight into the complex mechanism underlying the control of polysaccharide biosynthesis.ImportanceBacteria synthesise complex polysaccharide chains at a controlled number of repeating units, this has wide implications for a range of bacterial activities involved in virulence. Examples of complex polysaccharide chains include, the O antigen (Oag) component of lipopolysaccharide and the enterobacterial common antigen (ECA), both of these examples are predominantly synthesised by their own independent Wzy-dependent pathway. Our data show for the first time "cross-talk" between Oag and ECA synthesis and identifies novel physical protein-protein interactions between proteins in these systems. These findings further the understanding of how the system functions to control polysaccharide chain length which has great implications for novel biotechnologies and/or the combat of bacterial diseases.

20.
Am J Physiol Heart Circ Physiol ; 319(3): H547-H556, 2020 09 01.
Artículo en Inglés | MEDLINE | ID: mdl-32734819

RESUMEN

Tobacco cigarette (TC) smoking has never been lower in the United States, but electronic cigarette (EC) vaping has reached epidemic proportions among our youth. Endothelial dysfunction, as measured by flow-mediated vasodilation (FMD) is a predictor of future atherosclerosis and adverse cardiovascular events and is impaired in young TC smokers, but whether FMD is also reduced in young EC vapers is uncertain. The aim of this study in otherwise healthy young people was to compare the effects of acute and chronic tobacco cigarette (TC) smoking and electronic cigarette (EC) vaping on FMD. FMD was compared in 47 nonsmokers (NS), 49 chronic EC vapers, and 40 chronic TC smokers at baseline and then after EC vapers (n = 31) and nonsmokers (n = 47) acutely used an EC with nicotine (ECN), EC without nicotine (EC0), and nicotine inhaler (NI) at ~4-wk intervals and after TC smokers (n = 33) acutely smoked a TC, compared with sham control. Mean age (NS, 26.3 ± 5.2 vs. EC, 27.4 ± 5.45 vs. TC, 27.1 ± 5.51 yr, P = 0.53) was similar among the groups, but there were more female nonsmokers. Baseline FMD was not different among the groups (NS, 7.7 ± 4.5 vs. EC:6.6 ± 3.6 vs. TC, 7.9 ± 3.7%∆, P = 0.35), even when compared by group and sex. Acute TC smoking versus control impaired FMD (FMD pre-/postsmoking, -2.52 ± 0.92 vs. 0.65 ± 0.93%∆, P = 0.02). Although the increase in plasma nicotine was similar after EC vapers used the ECN versus TC smokers smoked the TC (5.75 ± 0.74 vs. 5.88 ± 0.69 ng/mL, P = 0.47), acute EC vaping did not impair FMD. In otherwise healthy young people who regularly smoke TCs or ECs, impaired FMD compared with that in nonsmokers was not present at baseline. However, FMD was significantly impaired after smoking one TC, but not after vaping an equivalent "dose" (estimated by change in plasma nicotine) of an EC, consistent with the notion that non-nicotine constituents in TC smoke mediate the impairment. Although it is reassuring that acute EC vaping did not acutely impair FMD, it would be dangerous and premature to conclude that ECs do not lead to atherosclerosis.NEW & NOTEWORTHY In our study of otherwise healthy young people, baseline flow-mediated dilation (FMD), a predictor of atherosclerosis and increased cardiovascular risk, was not different among tobacco cigarette (TC) smokers or electronic cigarette (EC) vapers who had refrained from smoking, compared with nonsmokers. However, acutely smoking one TC impaired FMD in smokers, whereas vaping a similar EC "dose" (as estimated by change in plasma nicotine levels) did not. Finally, although it is reassuring that acute EC vaping did not acutely impair FMD, it would be premature and dangerous to conclude that ECs do not lead to atherosclerosis or increase cardiovascular risk.


Asunto(s)
Arteria Braquial/fisiopatología , Fumar Cigarrillos/efectos adversos , Cigarrillo Electrónico a Vapor/efectos adversos , Sistemas Electrónicos de Liberación de Nicotina , Endotelio Vascular/fisiopatología , Vapeo/efectos adversos , Vasodilatación , Adulto , Aterosclerosis/etiología , Aterosclerosis/fisiopatología , Fumar Cigarrillos/fisiopatología , Seguridad de Productos para el Consumidor , Estudios Cruzados , Femenino , Voluntarios Sanos , Humanos , Masculino , Persona de Mediana Edad , Distribución Aleatoria , Medición de Riesgo , Factores de Riesgo , Adulto Joven
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