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1.
Emerg Infect Dis ; 25(3): 473-481, 2019 03.
Artículo en Inglés | MEDLINE | ID: mdl-30789130

RESUMEN

Attention to environmental sources of Mycobacterium avium complex (MAC) infection is a vital component of disease prevention and control. We investigated MAC colonization of household plumbing in suburban Philadelphia, Pennsylvania, USA. We used variable-number tandem-repeat genotyping and whole-genome sequencing with core genome single-nucleotide variant analysis to compare M. avium from household plumbing biofilms with M. avium isolates from patient respiratory specimens. M. avium was recovered from 30 (81.1%) of 37 households, including 19 (90.5%) of 21 M. avium patient households. For 11 (52.4%) of 21 patients with M. avium disease, isolates recovered from their respiratory and household samples were of the same genotype. Within the same community, 18 (85.7%) of 21 M. avium respiratory isolates genotypically matched household plumbing isolates. Six predominant genotypes were recovered across multiple households and respiratory specimens. M. avium colonizing municipal water and household plumbing may be a substantial source of MAC pulmonary infection.


Asunto(s)
Microbiología Ambiental , Infección por Mycobacterium avium-intracellulare/epidemiología , Infección por Mycobacterium avium-intracellulare/microbiología , Mycobacterium avium/clasificación , Microbiología del Agua , Adulto , Anciano , Anciano de 80 o más Años , Femenino , Genotipo , Historia del Siglo XXI , Humanos , Masculino , Persona de Mediana Edad , Repeticiones de Minisatélite , Tipificación de Secuencias Multilocus , Mycobacterium avium/genética , Mycobacterium avium/aislamiento & purificación , Complejo Mycobacterium avium/clasificación , Complejo Mycobacterium avium/genética , Complejo Mycobacterium avium/aislamiento & purificación , Infección por Mycobacterium avium-intracellulare/historia , Philadelphia/epidemiología , Filogenia , Vigilancia en Salud Pública , Secuenciación Completa del Genoma
2.
J Clin Microbiol ; 56(8)2018 08.
Artículo en Inglés | MEDLINE | ID: mdl-29875193

RESUMEN

The accuracy and robustness of the Vitek MS v3.0 matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) system was evaluated by identifying mycobacteria from automated liquid-medium systems using patient samples. This is the first report to demonstrate that proteins within the liquid medium, its supplements, and decontamination reagents for nonsterile patient samples do not generate misidentification or false-positive results by use of the Vitek MS v3.0 system. Prior to testing with patient samples, a seeded-culture study was conducted to challenge the accuracy of the Vitek MS system at identifying mycobacteria from liquid medium by mimicking a clinical workflow. Seventy-seven Mycobacterium strains representing 21 species, seeded in simulated sputum, were decontaminated, inoculated into BacT/Alert MP liquid culture medium, incubated until positivity, and identified using the Vitek MS system. A total of 383 liquid cultures were tested, of which 379 (99%) were identified correctly to the species/complex/group level, 4 (1%) gave a "no-identification" result, and no misidentifications were observed. Following the simulated-sputum study, a total of 73 smear-positive liquid-medium cultures detected using BD BBL MGIT and VersaTREK Myco liquid media were identified by the Vitek MS system. Sixty-four cultures (87.7%) were correctly identified to the species/complex/group level; 7 (9.6%) resulted in no identification; and 2 (2.7%) were misidentified at the species level. These results indicate that the Vitek MS v3.0 system is an accurate tool for routine diagnostics of Mycobacterium species isolated from liquid cultures.


Asunto(s)
Técnicas Bacteriológicas/métodos , Infecciones por Mycobacterium no Tuberculosas/diagnóstico , Mycobacterium/clasificación , Mycobacterium/aislamiento & purificación , Espectrometría de Masa por Láser de Matriz Asistida de Ionización Desorción , Técnicas Bacteriológicas/instrumentación , Medios de Cultivo , Pruebas Diagnósticas de Rutina , Humanos , Mycobacterium/química , Esputo/microbiología
3.
J Clin Microbiol ; 56(6)2018 06.
Artículo en Inglés | MEDLINE | ID: mdl-29643203

RESUMEN

This multicenter study was designed to assess the accuracy and reproducibility of the Vitek MS v3.0 matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry system for identification of Mycobacterium and Nocardia species compared to DNA sequencing. A total of 963 clinical isolates representing 51 taxa were evaluated. In all, 663 isolates were correctly identified to the species level (69%), with another 231 (24%) correctly identified to the complex or group level. Fifty-five isolates (6%) could not be identified despite repeat testing. All of the tuberculous mycobacteria (45/45; 100%) and most of the nontuberculous mycobacteria (569/606; 94%) were correctly identified at least to the group or complex level. However, not all species or subspecies within the M. tuberculosis, M. abscessus, and M. avium complexes and within the M. fortuitum and M. mucogenicum groups could be differentiated. Among the 312 Nocardia isolates tested, 236 (76%) were correctly identified to the species level, with an additional 44 (14%) correctly identified to the complex level. Species within the N. nova and N. transvalensis complexes could not always be differentiated. Eleven percent of the isolates (103/963) underwent repeat testing in order to get a final result. Identification of a representative set of Mycobacterium and Nocardia species was highly reproducible, with 297 of 300 (99%) replicates correctly identified using multiple kit lots, instruments, analysts, and sites. These findings demonstrate that the system is robust and has utility for the routine identification of mycobacteria and Nocardia in clinical practice.


Asunto(s)
Mycobacterium tuberculosis/aislamiento & purificación , Nocardia/aislamiento & purificación , Micobacterias no Tuberculosas/aislamiento & purificación , Espectrometría de Masa por Láser de Matriz Asistida de Ionización Desorción/instrumentación , Espectrometría de Masa por Láser de Matriz Asistida de Ionización Desorción/métodos , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Mycobacterium tuberculosis/genética , Nocardia/genética , Nocardiosis/diagnóstico , Nocardiosis/microbiología , ARN Ribosómico 16S/genética , Juego de Reactivos para Diagnóstico , Reproducibilidad de los Resultados , Tuberculosis/diagnóstico , Tuberculosis/microbiología
4.
J Clin Microbiol ; 54(4): 891-901, 2016 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-26739155

RESUMEN

"Mycobacterium aviumsubsp.hominissuis" is an important cause of pulmonary disease. It is acquired from environmental sources, but there is no methodology for large population studies. We evaluated the potential of variable-number tandem-repeat (VNTR) analysis. Clinical and household biofilmM. aviumisolates underwent molecular identification. Testing for IS901was done to separateM. aviumsubsp.aviumfromM. aviumsubsp.hominissuis VNTR types were defined using VNTR loci, and subtyping was performed using 3'hsp65and internal transcribed spacer (ITS) sequencing. Forty-nine VNTR types and eight subtypes ofM. aviumsubsp.hominissuis(IS901negative) were identified among 416 isolates ofM. aviumfrom 121 patients and 80 biofilm sites. Of those types, 67% were found only among patient isolates, 11% only among household water isolates, and 23% among both. Of 13 VNTR types that included ≥4 patients, the majority (61.5%) represented geographic clustering (same city). Most VNTR types with multiple patients belonged to the same 3'hsp65sequence code (sequevar). A total of 44 isolates belonging to fourM. aviumsubsp.hominissuisVNTR types (8%), including three with the rare Mav-F ITS sequence and 0/8 subspecies, produced amplicons with IS901PCR primers. By sequencing, all 44 amplicons were not IS901but ISMav6, which was recently observed in Japan but had not been previously described among U.S. isolates. VNTR analysis ofM. aviumsubsp.hominissuisisolates is easier and faster than pulsed-field gel electrophoresis. Seven VNTR loci separated 417 isolates into 49 types. No isolates ofM. aviumsubsp.aviumwere identified. The distributions of the VNTR copy numbers, the allelic diversity, and the low prevalence of ISMav6 differed from the findings for respiratory isolates reported from Japan.


Asunto(s)
Biopelículas , Repeticiones de Minisatélite , Tipificación Molecular/métodos , Mycobacterium avium/clasificación , Mycobacterium avium/aislamiento & purificación , Tuberculosis/microbiología , Microbiología del Agua , Proteínas Bacterianas/genética , Chaperonina 60/genética , Análisis por Conglomerados , Elementos Transponibles de ADN , ADN Espaciador Ribosómico/genética , Composición Familiar , Genotipo , Humanos , Japón , Epidemiología Molecular/métodos , Mycobacterium avium/genética , Filogeografía , Reacción en Cadena de la Polimerasa/métodos
5.
J Clin Microbiol ; 53(4): 1211-5, 2015 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-25653399

RESUMEN

The erm(41) gene confers inducible macrolide resistance in Mycobacterium abscessus subsp. abscessus, calling into question the usefulness of macrolides for treating M. abscessus subsp. abscessus infections. With an extended incubation (14 days), isolates with MICs of ≥8 µg/ml are considered macrolide resistant by current CLSI guidelines. Our goals were to determine the incidence of macrolide susceptibility in U.S. isolates, the validity of currently accepted MIC breakpoints, and the erm(41) sequences associated with susceptibility. Of 349 isolates (excluding those with 23S rRNA gene mutations), 85 (24%) had clarithromycin MICs of ≤8 µg/ml. Sequencing of the erm(41) genes from these isolates, as well as from isolates with MICs of ≥16 µg/ml, including ATCC 19977T, revealed 10 sequevars. The sequence in ATCC 19977T was designated sequevar (type) 1; most macrolide-resistant isolates were of this type. Seven sequevars contained isolates with MICs of >16 µg/ml. The T28C substitution in erm(41), previously associated with macrolide susceptibility, was identified in 62 isolates (18%) comprising three sequevars, with MICs of ≤2 (80%), 4 (10%), and 8 (10%) µg/ml. No other nucleotide substitution was associated with macrolide susceptibility. We recommend that clarithromycin susceptibility breakpoints for M. abscessus subsp. abscessus be changed from ≤2 to ≤4 µg/ml and that isolates with an MIC of 8 µg/ml have repeat MIC testing or erm sequencing performed. Our studies suggest that macrolides are useful for treating approximately 20% of U.S. isolates of M. abscessus subsp. abscessus. Sequencing of the erm gene of M. abscessus subsp. abscessus will predict inducible macrolide susceptibility.


Asunto(s)
Antibacterianos/farmacología , Claritromicina/farmacología , Farmacorresistencia Bacteriana , Metiltransferasas/genética , Mycobacterium/efectos de los fármacos , Mycobacterium/enzimología , Genotipo , Humanos , Macrólidos/farmacología , Pruebas de Sensibilidad Microbiana , Datos de Secuencia Molecular , Proteínas Mutantes/genética , Mycobacterium/genética , Análisis de Secuencia de ADN , Estados Unidos
6.
J Clin Microbiol ; 53(3): 875-8, 2015 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-25568437

RESUMEN

Macrolide resistance has been linked to the presence of a functional erythromycin ribosomal methylase (erm) gene in most species of pathogenic rapidly growing mycobacteria (RGM). For these Mycobacterium isolates, extended incubation in clarithromycin is necessary to determine macrolide susceptibility. In contrast, the absence of a detectable erm gene in isolates of M. chelonae, M. senegalense, and M. peregrinum and a nonfunctional erm gene in M. abscessus subsp. massiliense and 15% to 20% of M. abscessus subsp. abscessus isolates renders these species intrinsically macrolide susceptible. Not all RGM species have been screened for the presence of an erm gene, including the Mycobacterium mucogenicum group (M. mucogenicum, M. phocaicum, and M. aubagnense) and Mycobacterium immunogenum. A total of 356 isolates of these two pathogenic RGM taxa from two reference laboratories (A.R.U.P. Reference Laboratories and the Mycobacteria/Nocardia Laboratory at the University of Texas Health Science Center at Tyler) underwent clarithromycin susceptibility testing with readings at 3 to 5 days and 14 days. Only 13 of the 356 isolates had resistant clarithromycin MICs at initial extended MIC readings, and repeat values on all available isolates were ≤2 µg/ml. These studies suggest that these two additional RGM groups do not harbor functional erm genes and, like M. chelonae, do not require extended clarithromycin susceptibility testing. We propose to the Clinical Laboratory and Standards Institute that isolates belonging to these above-mentioned six rapidly growing mycobacterial groups based on molecular identification with no known functional erm genes undergo only 3 to 5 days of susceptibility testing (to exclude mutational resistance).


Asunto(s)
Antibacterianos/farmacología , Claritromicina/farmacología , Metiltransferasas/genética , Micobacterias no Tuberculosas/efectos de los fármacos , Micobacterias no Tuberculosas/genética , Humanos , Macrólidos/farmacología , Pruebas de Sensibilidad Microbiana , Infecciones por Mycobacterium/microbiología , Micobacterias no Tuberculosas/aislamiento & purificación , Estudios Retrospectivos , Factores de Tiempo
7.
J Biol Chem ; 287(48): 40641-51, 2012 Nov 23.
Artículo en Inglés | MEDLINE | ID: mdl-23048028

RESUMEN

BACKGROUND: Histone methylation is believed to recruit specific histone-binding proteins. RESULTS: We identified SRP68/72 heterodimers as major nuclear proteins whose binding of histone H4 tail is inhibited by H4R3 methylation. CONCLUSION: SRP68/72 are novel histone H4-binding proteins. SIGNIFICANCE: Uncovers a novel chromatin regulatory function for SRP68/72 and suggests that histone arginine methylation may function mainly in inhibiting rather than recruiting effector proteins. Arginine methylation broadly occurs in the tails of core histones. However, the mechanisms by which histone arginine methylation regulates transcription remain poorly understood. In this study we attempted to identify nuclear proteins that specifically recognize methylated arginine 3 in the histone H4 (H4R3) tail using an unbiased proteomic approach. No major nuclear protein was observed to specifically bind to methylated H4R3 peptides. However, H4R3 methylation markedly inhibited the binding of two proteins to H4 tail peptide. These proteins were identified as the SRP68 and SRP72 heterodimers (SRP68/72), the components of the signal recognition particle (SRP). Only SRP68/72, but not the SRP complex, bound the H4 tail peptide. SRP68 and SRP72 bound the H4 tail in vitro and associated with chromatin in vivo. The chromatin association of SRP68 and SRP72 was regulated by PRMT5 and PRMT1. Both SRP68 and SRP72 activated transcription when tethered to a reporter via a heterologous DNA binding domain. Analysis of the genome-wide occupancy of SRP68 identified target genes regulated by SRP68. Taken together, these results demonstrate a role of H4R3 methylation in blocking the binding of effectors to chromatin and reveal a novel role for the SRP68/SRP72 heterodimer in the binding of chromatin and transcriptional regulation.


Asunto(s)
Arginina/metabolismo , Histonas/metabolismo , Partícula de Reconocimiento de Señal/metabolismo , Transcripción Genética , Secuencias de Aminoácidos , Arginina/genética , Sitios de Unión , Dimerización , Células HeLa , Histonas/química , Histonas/genética , Humanos , Metilación , Unión Proteica , Partícula de Reconocimiento de Señal/química , Partícula de Reconocimiento de Señal/genética
8.
J Clin Microbiol ; 51(10): 3389-94, 2013 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-23946523

RESUMEN

Amikacin is a major drug used for the treatment of Mycobacterium avium complex (MAC) disease, but standard laboratory guidelines for susceptibility testing are not available. This study presents in vitro amikacin MICs for 462 consecutive clinical isolates of the MAC using a broth microdilution assay. Approximately 50% of isolates had amikacin MICs of 8 µg/ml, and 86% had MICs of ≤16 µg/ml. Of the eight isolates (1.7%) with MICs of 64 µg/ml, five had an MIC of 32 µg/ml on repeat testing. Ten isolates (2.1%) had an initial amikacin MIC of >64 µg/ml, of which seven (1.5%) had MICs of >64 µg/ml on repeat testing. These seven isolates had a 16S rRNA gene A1408G mutation and included M. avium, Mycobacterium intracellulare, and Mycobacterium chimaera. Clinical data were available for five of these seven isolates, all of which had received prolonged (>6 months) prior therapy, with four that were known to be treated with amikacin. The 16S mutation was not detected in isolates with MICs of ≤64 µg/ml. We recommend primary testing of amikacin against isolates of the MAC and propose MIC guidelines for breakpoints that are identical to the CLSI guidelines for Mycobacterium abscessus: ≤16 µg/ml for susceptible, 32 µg/ml for intermediate, and ≥64 µg/ml for resistant. If considered and approved by the CLSI, this will be only the second drug recommended for primary susceptibility testing against the MAC and should facilitate its use for both intravenous and inhaled drug therapies.


Asunto(s)
Amicacina/farmacología , Antibacterianos/farmacología , Farmacorresistencia Bacteriana , Complejo Mycobacterium avium/efectos de los fármacos , Complejo Mycobacterium avium/genética , Mutación Puntual , ARN Ribosómico 16S/genética , Amicacina/uso terapéutico , Antibacterianos/uso terapéutico , Femenino , Humanos , Pruebas de Sensibilidad Microbiana , Persona de Mediana Edad , Complejo Mycobacterium avium/aislamiento & purificación , Infección por Mycobacterium avium-intracellulare/tratamiento farmacológico , Infección por Mycobacterium avium-intracellulare/microbiología
9.
J Clin Microbiol ; 51(2): 409-16, 2013 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-23175249

RESUMEN

Strain comparison is important to population genetics and to evaluate relapses in patients with Mycobacterium avium complex (MAC) lung disease, but the "gold standard" of pulsed-field gel electrophoresis (PFGE) is time-consuming and complex. We used variable-number tandem repeats (VNTR) for fingerprinting of respiratory isolates of M. intracellulare from patients with underlying bronchiectasis, to establish a nonsequence-based database for population analysis. Different genotypes identified by PFGE underwent species identification using a 16S rRNA gene multiplex PCR. Genotypes of M. intracellulare were confirmed by internal transcribed spacer 1 (ITS1) sequencing and characterized using seven VNTR primers. The pattern of VNTR amplicon sizes and repeat number defined each specific VNTR type. Forty-two VNTR types were identified among 84 genotypes. PFGE revealed most isolates with the same VNTR type to be clonal or exhibit similar grouping of bands. Repetitive sequence-based PCR (rep-PCR) showed minimal pattern diversity between VNTR types compared to PFGE. Fingerprinting of relapse isolates from 31 treated patients using VNTR combined with 16S multiplex PCR unambiguously and reliably distinguished different genotypes from the same patient, with results comparable to those of PFGE. VNTR for strain comparison is easier and faster than PFGE, is as accurate as PFGE, and does not require sequencing. Starting with a collection of 167 M. intracellulare isolates, VNTR distinguished M. intracellulare into 42 clonal groups. Comparison of isolates from different geographic areas, habitats, and clinical settings is now possible.


Asunto(s)
Genotipo , Repeticiones de Minisatélite , Complejo Mycobacterium avium/clasificación , Complejo Mycobacterium avium/genética , Infección por Mycobacterium avium-intracellulare/diagnóstico , Alelos , Técnicas de Tipificación Bacteriana , Bases de Datos de Ácidos Nucleicos , Humanos , Datos de Secuencia Molecular , Tipificación de Secuencias Multilocus , ARN Ribosómico 16S
10.
J Clin Microbiol ; 51(6): 1747-52, 2013 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-23536397

RESUMEN

Recent studies have shown that respiratory isolates from pulmonary disease patients and household water/biofilm isolates of Mycobacterium avium could be matched by DNA fingerprinting. To determine if this is true for Mycobacterium intracellulare, household water sources for 36 patients with Mycobacterium avium complex (MAC) lung disease were evaluated. MAC household water isolates from three published studies that included 37 additional MAC respiratory disease patients were also evaluated. Species identification was done initially using nonsequencing methods with confirmation by internal transcribed spacer (ITS) and/or partial 16S rRNA gene sequencing. M. intracellulare was identified by nonsequencing methods in 54 respiratory cultures and 41 household water/biofilm samples. By ITS sequencing, 49 (90.7%) respiratory isolates were M. intracellulare and 4 (7.4%) were Mycobacterium chimaera. In contrast, 30 (73%) household water samples were M. chimaera, 8 (20%) were other MAC X species (i.e., isolates positive with a MAC probe but negative with species-specific M. avium and M. intracellulare probes), and 3 (7%) were M. avium; none were M. intracellulare. In comparison, M. avium was recovered from 141 water/biofilm samples. These results indicate that M. intracellulare lung disease in the United States is acquired from environmental sources other than household water. Nonsequencing methods for identification of nontuberculous mycobacteria (including those of the MAC) might fail to distinguish closely related species (such as M. intracellulare and M. chimaera). This is the first report of M. chimaera recovery from household water. The study underscores the importance of taxonomy and distinguishing the many species and subspecies of the MAC.


Asunto(s)
Complejo Mycobacterium avium/clasificación , Complejo Mycobacterium avium/aislamiento & purificación , Tuberculosis Pulmonar/microbiología , Microbiología del Agua , Biopelículas , ADN Bacteriano/química , ADN Bacteriano/genética , ADN Ribosómico/química , ADN Ribosómico/genética , ADN Espaciador Ribosómico/química , ADN Espaciador Ribosómico/genética , Composición Familiar , Humanos , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN
12.
BMC Mol Biol ; 11: 83, 2010 Nov 13.
Artículo en Inglés | MEDLINE | ID: mdl-21073748

RESUMEN

BACKGROUND: Human cells depend critically on the signal recognition particle (SRP) for the sorting and delivery of their proteins. The SRP is a ribonucleoprotein complex which binds to signal sequences of secretory polypeptides as they emerge from the ribosome. Among the six proteins of the eukaryotic SRP, the largest protein, SRP72, is essential for protein targeting and possesses a poorly characterized RNA binding domain. RESULTS: We delineated the minimal region of SRP72 capable of forming a stable complex with an SRP RNA fragment. The region encompassed residues 545 to 585 of the full-length human SRP72 and contained a lysine-rich cluster (KKKKKKKKGK) at postions 552 to 561 as well as a conserved Pfam motif with the sequence PDPXRWLPXXER at positions 572 to 583. We demonstrated by site-directed mutagenesis that both regions participated in the formation of a complex with the RNA. In agreement with biochemical data and results from chymotryptic digestion experiments, molecular modeling of SRP72 implied that the invariant W577 was located inside the predicted structure of an RNA binding domain. The 11-nucleotide 5e motif contained within the SRP RNA fragment was shown by comparative electrophoresis on native polyacrylamide gels to conform to an RNA kink-turn. The model of the complex suggested that the conserved A240 of the K-turn, previously identified as being essential for the binding to SRP72, could protrude into a groove of the SRP72 RNA binding domain, similar but not identical to how other K-turn recognizing proteins interact with RNA. CONCLUSIONS: The results from the presented experiments provided insights into the molecular details of a functionally important and structurally interesting RNA-protein interaction. A model for how a ligand binding pocket of SRP72 can accommodate a new RNA K-turn in the 5e region of the eukaryotic SRP RNA is proposed.


Asunto(s)
Secuencias de Aminoácidos , ARN/metabolismo , Partícula de Reconocimiento de Señal/metabolismo , Secuencia de Aminoácidos , Sitios de Unión , Humanos , Lisina/genética , Modelos Moleculares , Datos de Secuencia Molecular , Mutagénesis Sitio-Dirigida , Conformación de Ácido Nucleico , Partícula de Reconocimiento de Señal/química , Partícula de Reconocimiento de Señal/genética
13.
RNA ; 14(6): 1143-53, 2008 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-18441046

RESUMEN

The signal recognition particle (SRP) plays a pivotal role in transporting proteins to cell membranes. In higher eukaryotes, SRP consists of an RNA molecule and six proteins. The largest of the SRP proteins, SRP72, was found previously to bind to the SRP RNA. A fragment of human SRP72 (72c') bound effectively to human SRP RNA but only weakly to the similar SRP RNA of the archaeon Methanococcus jannaschii. Chimeras between the human and M. jannaschii SRP RNAs were constructed and used as substrates for 72c'. SRP RNA helical section 5e contained the 72c' binding site. Systematic alteration within 5e revealed that the A240G and A240C changes dramatically reduced the binding of 72c'. Human SRP RNA with a single A240G change was unable to form a complex with full-length human SRP72. Two small RNA fragments, one composed of helical section 5ef, the other of section 5e, competed equally well for the binding of 72c', demonstrating that no other regions of the SRPR RNA were required. The biochemical data completely agreed with the nucleotide conservation pattern observed across the phylogenetic spectrum. Thus, most eukaryotic SRP RNAs are likely to require for function an adenosine within their 5e motifs. The human 5ef RNA was remarkably resistant to ribonucleolytic attack suggesting that the 240-AUC-242 "loop" and its surrounding nucleotides form a peculiar compact structure recognized only by SRP72.


Asunto(s)
Adenosina/química , Conformación de Ácido Nucleico , ARN Citoplasmático Pequeño/química , Partícula de Reconocimiento de Señal/química , Adenosina/metabolismo , Secuencia de Bases , Sitios de Unión , Humanos , Methanococcus/genética , Methanococcus/metabolismo , ARN Citoplasmático Pequeño/genética , ARN Citoplasmático Pequeño/metabolismo , Proteínas Recombinantes de Fusión/química , Proteínas Recombinantes de Fusión/genética , Proteínas Recombinantes de Fusión/metabolismo , Partícula de Reconocimiento de Señal/genética , Partícula de Reconocimiento de Señal/metabolismo , Especificidad por Sustrato
15.
Am J Clin Pathol ; 152(4): 527-536, 2019 09 09.
Artículo en Inglés | MEDLINE | ID: mdl-31314059

RESUMEN

OBJECTIVES: This multicenter study's aim was to assess the performance of two commercially available matrix-assisted laser desorption/ionization time of flight mass spectrometry systems in identifying a challenge collection of clinically relevant nontuberculous mycobacteria (NTM). METHODS: NTM clinical isolates (n = 244) belonging to 23 species/subspecies were identified by gene sequencing and analyzed using Bruker Biotyper with Mycobacterial Library v5.0.0 and bioMérieux VITEK MS with v3.0 database. RESULTS: Using the Bruker or bioMérieux systems, 92% and 95% of NTM strains, respectively, were identified at least to the complex/group level; 62% and 57%, respectively, were identified to the highest taxonomic level. Differentiation between members of Mycobacterium abscessus, M fortuitum, M mucogenicum, M avium, and M terrae complexes/groups was problematic for both systems, as was identification of M chelonae for the Bruker system. CONCLUSIONS: Both systems identified most NTM isolates to the group/complex level, and many to the highest taxonomic level. Performance was comparable.


Asunto(s)
Micobacterias no Tuberculosas/aislamiento & purificación , Espectrometría de Masa por Láser de Matriz Asistida de Ionización Desorción/métodos , Pruebas Diagnósticas de Rutina , Humanos
16.
RNA Biol ; 4(3): 154-9, 2007 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-18347438

RESUMEN

Within the large domain of the human signal recognition particle (SRP), 18 mutant SRP RNAs were constructed to disrupt Watson-Crick and G-U basepairs in helices 5, 6 and 8. Using a double-filter assay, the competitive binding of the mutant RNAs to purified human SRP68/72 or to a 7.4 kDa RNA-binding fragment of SRP72 (72frg) was measured. Binding of SRP68/72 was impaired by several mutations in the large domain with the most pronounced effects caused by changes in helix 5 (residues 222-231) and helix 8 (residues 176-191 and 202-214). Binding of the 72frg was diminished prominently by altering helix 5, in particular residues 120-128, and was unaffected by deleting helices 6 and 8. Deleting helix 8 diminished binding of SRP68/72 to a greater extent than deleting helix 6. The data suggest that nucleotide residues throughout most of the large SRP domain are directly and/or indirectly engaged in the binding of SRP68. In contrast, SRP72 binds only to a portion of the 5ef region.


Asunto(s)
Mutagénesis Sitio-Dirigida , Subunidades de Proteína/metabolismo , ARN/genética , ARN/metabolismo , Partícula de Reconocimiento de Señal/metabolismo , Sitios de Unión/genética , Humanos , Unión Proteica/genética , Subunidades de Proteína/genética , Partícula de Reconocimiento de Señal/genética
17.
Protein Sci ; 15(6): 1290-302, 2006 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-16672232

RESUMEN

The signal recognition particle (SRP) plays an important role in the delivery of secretory proteins to cellular membranes. Mammalian SRP is composed of six polypeptides among which SRP68 and SRP72 form a heterodimer that has been notoriously difficult to investigate. Human SRP68 was purified from overexpressing Escherichia coli cells and was found to bind to recombinant SRP72 as well as in vitro-transcribed human SRP RNA. Polypeptide fragments covering essentially the entire SRP68 molecule were generated recombinantly or by proteolytic digestion. The RNA binding domain of SRP68 included residues from positions 52 to 252. Ninety-four amino acids near the C terminus of SRP68 mediated the binding to SRP72. The SRP68-SRP72 interaction remained stable at elevated salt concentrations and engaged approximately 150 amino acids from the N-terminal region of SRP72. This portion of SRP72 was located within a predicted tandem array of four tetratricopeptide (TPR)-like motifs suggested to form a superhelical structure with a groove to accommodate the C-terminal region of SRP68.


Asunto(s)
ARN/metabolismo , Partícula de Reconocimiento de Señal/metabolismo , Secuencia de Bases , Sitios de Unión , Clonación Molecular , Humanos , Datos de Secuencia Molecular , Filogenia , Conformación Proteica , Estructura Terciaria de Proteína , Proteínas Recombinantes/genética , Proteínas Recombinantes/aislamiento & purificación , Proteínas Recombinantes/metabolismo , Partícula de Reconocimiento de Señal/genética , Partícula de Reconocimiento de Señal/aislamiento & purificación
18.
J Mol Biol ; 345(4): 659-66, 2005 Jan 28.
Artículo en Inglés | MEDLINE | ID: mdl-15588816

RESUMEN

The signal recognition particle (SRP) is a ribonucleoprotein complex that plays a crucial role during the delivery of secretory proteins from the ribosome to the cell membrane. Among the six proteins of the eukaryotic SRP, the 72 kDa protein (SRP72) is the largest and least characterized. Polypeptides corresponding to various regions of the entire human SRP72 sequence were expressed in Escherichia coli, purified, and partially proteolyzed. Human SRP RNA bound with high affinity to a 63 amino acid residue region near the C terminus of SRP72. Mild treatment of the fragment with chymotrypsin abolished its RNA-binding activity. A conserved sequence with the consensus PDPXRWLPXXER was identified within a 56 amino acid residue RNA-binding domain. Sucrose gradient centrifugation and filter-binding analysis using mutant SRP RNAs showed that SRP72 bound to the moderately conserved portion of SRP RNA helix 5. Nine tetratricopeptide-like repeats (TPRs) poised to interact with other SRP or ribosomal proteins were predicted in the NH2-terminal region. These identifications assign two important functions to a large portion of SRP72 and demonstrate the RNA-binding capacity of the protein.


Asunto(s)
ARN/metabolismo , Partícula de Reconocimiento de Señal/química , Partícula de Reconocimiento de Señal/metabolismo , Secuencias de Aminoácidos , Secuencia de Aminoácidos , Emparejamiento Base , Secuencia de Bases , Sitios de Unión , Expresión Génica , Humanos , Datos de Secuencia Molecular , Fragmentos de Péptidos/genética , Fragmentos de Péptidos/aislamiento & purificación , Fragmentos de Péptidos/metabolismo , ARN/química , ARN/genética , Partícula de Reconocimiento de Señal/genética , Partícula de Reconocimiento de Señal/aislamiento & purificación
19.
PLoS Negl Trop Dis ; 10(10): e0005068, 2016 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-27780201

RESUMEN

Lung disease caused by nontuberculous mycobacteria (NTM) is an emerging infectious disease of global significance. Epidemiologic studies have shown the Hawaiian Islands have the highest prevalence of NTM lung infections in the United States. However, potential environmental reservoirs and species diversity have not been characterized. In this cross-sectional study, we describe molecular and phylogenetic comparisons of NTM isolated from 172 household plumbing biofilms and soil samples from 62 non-patient households and 15 respiratory specimens. Although non-uniform geographic sampling and availability of patient information were limitations, Mycobacterium chimaera was found to be the dominant species in both environmental and respiratory specimens. In contrast to previous studies from the continental U.S., no Mycobacterium avium was identified. Mycobacterium intracellulare was found only in respiratory specimens and a soil sample. We conclude that Hawai'i's household water sources contain a unique composition of Mycobacterium avium complex (MAC), increasing our appreciation of NTM organisms of pulmonary importance in tropical environments.


Asunto(s)
Infecciones por Mycobacterium no Tuberculosas/microbiología , Micobacterias no Tuberculosas/aislamiento & purificación , Microbiología del Suelo , Biopelículas , Estudios Transversales , Hawaii , Vivienda , Humanos , Micobacterias no Tuberculosas/clasificación , Micobacterias no Tuberculosas/genética , Micobacterias no Tuberculosas/fisiología , Filogenia
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