Structure, interactions and evolutionary implications of a domain-swapped lectin dimer from Mycobacterium smegmatis

Crystal structure determination of the lectin domain of MSMEG_3662 from Mycobacterium smegmatis and its complexes with mannose and methyl-alpha-mannose, the first effort of its kind on a mycobacterial lectin, reveals a structure very similar to beta-prism II fold lectins from plant sources, but with extensive unprecedented domain swapping in dimer formation. The two subunits in a dimer often show small differences in structure, but the two domains, not always related by 2-fold symmetry, have the same structure. Each domain carries three sugar-binding sites, similar to those in plant lectins, one on each Greek key motif. The occurrence of beta-prism II fold lectins in bacteria, with characteristics similar to those from plants, indicates that this family of lectins is of ancient origin and had evolved into a mature system before bacteria and plants diverged. In plants, the number of binding sites per domain varies between one and three, whereas the number is two in the recently reported lectin domains from Pseudomonas putida and Pseudomonas aeruginosa. An analysis of the sequences of the lectins and the lectin domains shows that the level of sequence similarity among the three Greek keys in each domain has a correlation with the number of binding sites in it. Furthermore, sequence conservation among the lectins from different species is the highest for that Greek key which carries a binding site in all of them. Thus, it would appear that carbohydrate binding influences the course of the evolution of the lectin.

Characterization of a dual-active enzyme, DcpA, involved in cyclic diguanosine monophosphate turnover in Mycobacterium smegmatis

We have reported previously that the long-term survival of Mycobacterium smegmatis is facilitated by a dual-active enzyme MSDGC-1 (renamed DcpA), which controls the cellular turnover of cyclic diguanosine monophosphate (c-di-GMP). Most mycobacterial species possess at least a single copy of a DcpA orthologue that is highly conserved in terms of sequence similarity and domain architecture. Here, we show that DcpA exists in monomeric and dimeric forms. The dimerization of DcpA is due to non-covalent interactions between two protomers that are arranged in a parallel orientation. The dimer shows both synthesis and hydrolysis activities, whereas the monomer shows only hydrolysis activity. In addition, we have shown that DcpA is associated with the cytoplasmic membrane and exhibits heterogeneous cellular localization with a predominance at the cell poles. Finally, we have also shown that DcpA is involved in the change in cell length and colony morphology of M. smegmatis. Taken together, our study provides additional evidence about the role of the bifunctional protein involved in c-di-GMP signalling in M. smegmatis.

Paralogous cAMP Receptor Proteins in Mycobacterium smegmatis Show Biochemical and Functional Divergence

The cyclic AMP receptor protein (CRP) family of transcription factors consists of global regulators of bacterial gene expression. Here, we identify two paralogous CRPs in the genome of Mycobacterium smegmatis that have 78% identical sequences and characterize them biochemically and functionally. The two proteins (MSMEG_0539 and MSMEG_6189) show differences in cAMP binding affinity, trypsin sensitivity, and binding to a CRP site that we have identified upstream of the msmeg_3781 gene. MSMEG_6189 binds to the CRP site readily in the absence of cAMP, while MSMEG_0539 binds in the presence of cAMP, albeit weakly. msmeg_6189 appears to be an essential gene, while the ?msmeg_0539 strain was readily obtained. Using promoter-reporter constructs, we show that msmeg_3781 is regulated by CRP binding, and its transcription is repressed by MSMEG_6189. Our results are the first to characterize two paralogous and functional CRPs in a single bacterial genome. This gene duplication event has subsequently led to the evolution of two proteins whose biochemical differences translate to differential gene regulation, thus catering to the specific needs of the organism.

Combined inhalation and oral supplementation of Vitamin A and Vitamin D: A possible prevention and therapy for tuberculosis

Tuberculosis is continuing as a problem of mankind. With evolution, MDR and XDR forms of tuberculosis have emerged from drug sensitive strain. MDR and XDR strains are resistant to most of the antibiotics, making the management more difficult. BCG vaccine is not providing complete protection against tuberculosis. Therefore new infections are spreading at a tremendous rate. At the present moment there is experimental evidence to believe that Vitamin A and Vitamin D has anti-mycobacterial property. It is in this context, we have hypothesized a host based approach using the above vitamins that can cause possible prevention and cure of tuberculosis with minimal chance of resistance or toxicity. (C) 2015 Elsevier Ltd. All rights reserved.

Novel Functions of (p)ppGpp and Cyclic di-GMP in Mycobacterial Physiology Revealed by Phenotype Microarray Analysis of Wild-Type and Isogenic Strains of Mycobacterium smegmatis

The bacterial second messengers (p)ppGpp and bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) regulate important functions, such as transcription, virulence, biofilm formation, and quorum sensing. In mycobacteria, they regulate long-term survival during starvation, pathogenicity, and dormancy. Recently, a Pseudomonas aeruginosa strain lacking (p) ppGpp was shown to be sensitive to multiple classes of antibiotics and defective in biofilm formation. We were interested to find out whether Mycobacterium smegmatis strains lacking the gene for either (p)ppGpp synthesis (Delta rel(Msm)) or c-di-GMP synthesis (Delta dcpA) would display similar phenotypes. We used phenotype microarray technology to compare the growth of the wild-type and the knockout strains in the presence of several antibiotics. Surprisingly, the Delta rel(Msm) and Delta dcpA strains showed enhanced survival in the presence of many antibiotics, but they were defective in biofilm formation. These strains also displayed altered surface properties, like impaired sliding motility, rough colony morphology, and increased aggregation in liquid cultures. Biofilm formation and surface properties are associated with the presence of glycopeptidolipids (GPLs) in the cell walls of M. smegmatis. Thin-layer chromatography analysis of various cell wall fractions revealed that the levels of GPLs and polar lipids were reduced in the knockout strains. As a result, the cell walls of the knockout strains were significantly more hydrophobic than those of the wild type and the complemented strains. We hypothesize that reduced levels of GPLs and polar lipids may contribute to the antibiotic resistance shown by the knockout strains. Altogether, our data suggest that (p)ppGpp and c-di-GMP may be involved in the metabolism of glycopeptidolipids and polar lipids in M. smegmatis.

Structural characterization of a mitochondrial 3-ketoacyl-CoA (T1)-like thiolase from Mycobacterium smegmatis

Thiolases catalyze the degradation and synthesis of 3-ketoacyl-CoA molecules. Here, the crystal structures of a T1-like thiolase (MSM-13 thiolase) from Mycobacterium smegmatis in apo and liganded forms are described. Systematic comparisons of six crystallographically independent unliganded MSM-13 thiolase tetramers (dimers of tight dimers) from three different crystal forms revealed that the two tight dimers are connected to a rigid tetramerization domain via flexible hinge regions, generating an asymmetric tetramer. In the liganded structure, CoA is bound to those subunits that are rotated towards the tip of the tetramerization loop of the opposing dimer, suggesting that this loop is important for substrate binding. The hinge regions responsible for this rotation occur near Val123 and Arg149. The L alpha 1-covering loop-L alpha 2 region, together with the N beta 2-N alpha 2 loop of the adjacent subunit, defines a specificity pocket that is larger and more polar than those of other tetrameric thiolases, suggesting that MSM-13 thiolase has a distinct substrate specificity. Consistent with this finding, only residual activity was detected with acetoacetyl-CoA as the substrate in the degradative direction. No activity was observed with acetyl-CoA in the synthetic direction. Structural comparisons with other well characterized thiolases suggest that MSM-13 thiolase is probably a degradative thiolase that is specific for 3-ketoacyl-CoA molecules with polar, bulky acyl chains.

Negative Cooperativity and High Affinity in Chitooligosaccharide Binding by a Mycobacterium smegmatis Protein Containing LysM and Lectin Domains

LysM domains have been recognized in bacteria and eukaryotes as carbohydrate-binding protein modules, but the mechanism of their binding to chitooligosaccharides has been underexplored. Binding of a Mycobacterium smegmatis protein containing a lectin (MSL) and one LysM domain to chitooligosaccharides has been studied using isothermal titration calorimetry and fluorescence titration that demonstrate the presence of two binding sites of nonidentical affinities per dimeric MSL-LysM molecule. The affinity of the molecule for chitooligosaccharides correlates with the length of the carbohydrate chain. Its binding to chitooligosaccharides is characterized by negative cooperativity in the interactions of the two domains. Apparently, the flexibility of the long linker that connects the LysM and MSL domains plays a facilitating role in this recognition. The LysM domain in the MSL-LysM molecule, like other bacterial domains but unlike plant LysM domains, recognizes equally well peptidoglycan fragments as well as chitin polymers. Interestingly, in the case presented here, two LysM domains are enough for binding to peptidoglycan in contrast to the three reportedly required by the LysM domains of Bacillus subtilis and Lactococcus lactis. Also, the affinity of the MSL-LysM molecule for chitooligosaccharides is higher than that of LysM-chitooligosaccharide interactions reported so far.

First-in-Class Inhibitors of Sulfur Metabolism with Bactericidal Activity against Non-Replicating M-tuberculosis

Development of effective therapies to eradicate persistent, slowly replicating M. tuberculosis (Mtb) represents a significant challenge to controlling the global TB epidemic. To develop such therapies, it is imperative to translate information from metabolome and proteome adaptations of persistent Mtb into the drug discovery screening platforms. To this end, reductive sulfur metabolism is genetically and pharmacologically implicated in survival, pathogenesis, and redox homeostasis of persistent Mtb. Therefore, inhibitors of this pathway are expected to serve as powerful tools in its preclinical and clinical validation as a therapeutic target for eradicating persisters. Here, we establish a first functional HTS platform for identification of APS reductase (APSR) inhibitors, a critical enzyme in the assimilation of sulfate for the biosynthesis of cysteine and other essential sulfur-containing molecules. Our HTS campaign involving 38?350 compounds led to the discovery of three distinct structural classes of APSR inhibitors. A class of bioactive compounds with known pharmacology displayed potent bactericidal activity in wild-type Mtb as well as MDR and XDR clinical isolates. Top compounds showed markedly diminished potency in a conditional Delta APSR mutant, which could be restored by complementation with Mtb APSR. Furthermore, ITC studies on representative compounds provided evidence for direct engagement of the APSR target. Finally, potent APSR inhibitors significantly decreased the cellular levels of key reduced sulfur-containing metabolites and also induced an oxidative shift in mycothiol redox potential of live Mtb, thus providing functional validation of our screening data. In summary, we have identified first-in-class inhibitors of APSR that can serve as molecular probes in unraveling the links between Mtb persistence, antibiotic tolerance, and sulfate assimilation, in addition to their potential therapeutic value.

Molecular Mechanism Underlying ATP-Induced Conformational Changes in the Nucleoprotein Filament of Mycobacterium smegmatis RecA

RecA plays a central role in bacterial DNA repair, homologous recombination, and restoration of stalled replication forks by virtue of its active extended nucleoprotein filament. Binding of ATP and its subsequent recognition by the carboxamide group of a highly conserved glutamine (GIn196 in MsRecA) have been implicated in the formation of active RecA nucleoprotein filaments. Although the mechanism of ATP-dependent structural transitions in RecA has been proposed on the basis of low-resolution electron microscopic reconstructions, the precise sequence of events that constitute these transitions is poorly understood. On the basis of biochemical and crystallographic analyses of MsRecA variants carrying mutations in highly conserved Gln196 and Arg198 residues, we propose that the disposition of the interprotomer interface is the structural basis of allosteric activation of RecA. Furthermore, this study accounts, for the contributions of several conserved amino acids to ATP hydrolysis and to the transition from collapsed to extended filament forms in Mycobacterium smegmatis RecA (MsRecA). In addition to their role in the inactive compressed state, the study reveals a role for GIn196 and Arg198 along with Phe219 in ATP hydrolysis in the active extended nucleoprotein filament. Finally, our data suggest that the primary, but not secondary, nucleotide binding site in MsRecA isomerizes into the ATP binding site present in the extended nucleoprotein filament.

Regulation of Growth, Cell Shape, Cell Division, and Gene Expression by Second Messengers (p)ppGpp and Cyclic Di-GMP in Mycobacterium smegmatis

The alarmone (p)ppGpp regulates transcription, translation, replication, virulence, lipid synthesis, antibiotic sensitivity, biofilm formation, and other functions in bacteria. Signaling nucleotide cyclic di-GMP (c-di-GMP) regulates biofilm formation, motility, virulence, the cell cycle, and other functions. In Mycobacterium smegmatis, both (p) ppGpp and c-di-GMP are synthesized and degraded by bifunctional proteins Rel(Msm) and DcpA, encoded by rel(Msm) and dcpA genes, respectively. We have previously shown that the Delta rel(Msm) and Delta dcpA knockout strains are antibiotic resistant and defective in biofilm formation, show altered cell surface properties, and have reduced levels of glycopeptidolipids and polar lipids in their cell wall (K. R. Gupta, S. Kasetty, and D. Chatterji, Appl Environ Microbiol 81:2571-2578, 2015, http://dx.doi.org/10.1128/AEM.03999-14). In this work, we have explored the phenotypes that are affected by both (p) ppGpp and c-di-GMP in mycobacteria. We have shown that both (p) ppGpp and c-di-GMP are needed to maintain the proper growth rate under stress conditions such as carbon deprivation and cold shock. Scanning electron microscopy showed that low levels of these second messengers result in elongated cells, while high levels reduce the cell length and embed the cells in a biofilm-like matrix. Fluorescence microscopy revealed that the elongated Delta rel(Msm) and Delta dcpA cells are multinucleate, while transmission electron microscopy showed that the elongated cells are multiseptate. Gene expression analysis also showed that genes belonging to functional categories such as virulence, detoxification, lipid metabolism, and cell-wall-related processes were differentially expressed. Our results suggests that both (p) ppGpp and c-di-GMP affect some common phenotypes in M. smegmatis, thus raising a possibility of cross talk between these two second messengers in mycobacteria. IMPORTANCE Our work has expanded the horizon of (p) ppGpp and c-di-GMP signaling in Gram-positive bacteria. We have come across a novel observation that M. smegmatis needs (p) ppGpp and c-di-GMP for cold tolerance. We had previously shown that the Delta rel(Msm) and Delta dcpA strains are defective in biofilm formation. In this work, the overproduction of (p) ppGpp and c-di-GMP encased M. smegmatis in a biofilm-like matrix, which shows that both (p) ppGpp and c-di-GMP are needed for biofilm formation. The regulation of cell length and cell division by (p) ppGpp was known in mycobacteria, but our work shows that c-di-GMP also affects the cell size and cell division in mycobacteria. This is perhaps the first report of c-di-GMP regulating cell division in mycobacteria.

Estudio epidemiológico de la prevalencia de tuberculosis bovina, en el municipio de San Pedro de Lóvago, departamento de Chontales

El estudio se realizó en el municipio de San Pedro de Lóvago , departamento de Chontales , el cual comprende 18 Comarcas. La zona presenta coordenadas a 12° 07’ latitud norte y 85° 07’ latitud oeste y a una altura de 340 m.s.n.m , con una temperatura promedio de 26°, el clima del municipio es semi húmedo conocido como de sabana tropical, su precipitación varía entre 1200 y 1400mm, se encuentra a 193 Km. de la capital, con una extensión territorial de 604 kms cuadrados y una población aproximada de 700 habitantes. El trabajo se realizó en 5322 bovinos de ambos sexos pertenecientes a las 18 comarcas del municipio de San Pedro de Lóvago, de los cuales 142 eran machos y 5180 hembras, la edad mínima de los animales fue de seis meses. Con el objeto de determinar la Prevalencia de tuberculosis en el municipio de San Pedro de Lóvago, se realizaron pruebas diagnosticas individuales utilizando para esto la prueba alérgica de tuberculina PPD. Se aplicó una dosis de 0.1 ml de PPD bovino en el pliegue anocaudal, según el Reglamento del Programa Nacional de Vigilancia epidemiológica(PROVESA,2005. RESULTADOS x Encontrándose 18 animales reactores a la prueba de tuberculina (18/5322), representando el 0.34 % (Tabla No. 1). DISCUSIÓN Estos resultados son menores a los valores reportados por estudios realizados en los municipios del Almendro que obtuvo 24 animales reactores, el coral 20 animales, pero son superiores a los obtenido en el Municipio de Nueva Guinea con 12 animales y Muelle de los Bueyes con 1 animal rector (PROVESA, 2005). La Prevalencia encontrada en el estudio pudo ser influenciada por el tipo de explotación, la introducción de animales en los hatos, el manejo y el medio ambiente. La Comarca Llanos de los Pedros obtuvo la mayor frecuencia de animales reactores a la tuberculina. Aquí los animales permanecen la mayor parte del tiempo en corrales, o semiestabulado, aunque salen a pastar en potreros reducidos. Finalmente es necesario recordar que a estos animales reactores se le realizó la prueba comparativa a los 60 días después de haber realizado la primera prueba diagnóstica y dió como resultado un 0% de animales positivos a la tuberculina. Esto puede deberse a que los animales reaccionaron como falsos positivos, es decir que estábamos en presencia de un Mycrobacterium atípicos.

Factores de riesgo que permiten la prevalencia de brucelosis y tuberculosis en el hato ovino de la finca Santa Rosa en Octubre 2012

El presente estudio se realizó con el objetivo de analizar los factores de riesgo que permiten la prevalencia de Brucelosis y Tuberculosis en el hato ovino, estableciendo medidas de prevención y control que deben implementarse en la unidad de producción ovina de la Finca Sta. Rosa, Facultad de Ciencia Animal (FACA), de la Universidad Nacional Agraria, siendo de interés realizar un monitoreo para estar certificada por El Ministerio Agropecuario y Forestal (MAGFOR) como hato ovino libre de brucelosis y tuberculosis. El análisis estadístico midió la prevalencia muestreando 60 hembras en edades reproductivas, 36 de la población total del hato, a través de pruebas diagnósticas: aplicación de tuberculina PPD(Derivado Proteico Purificado) anocaudal (Tuberculosis) y muestra sanguínea para la realización de Rosa de bengala (Brucelosis), emitiendo dichas muestras a la red nacional de laboratorios de diagnóstico veterinario (RNLDV) del MAGFOR, se midieron los factores de exposición agrupados en tres subgrupos: primero: factores de infraestructura, segundo: factores de manejo y tercero: factores varios; a partir de la realización de encuestas cerradas determinando el cumplimiento de las medidas de bioseguridad, con una escala de calificación de cero a cinco donde cero es nulo y cinco es excelente, realizando el análisis estadístico T estudent, donde los factores de exposición y la calificación reportadas es significativa (P<0.005), es decir la frecuencia de calificación no aceptables además de ser mayores fueron significantes para el buen desempeño de la actividad y producción ovina. Obteniendo una prevalencia del 0% de Brucelosis y Tuberculosis. En la determinación de cumplimiento se encontró, para el primer subgrupo: Cero = nulo, a 2 factores: rotulación de la granja y área para oficina y comedor; Uno = malo, a 2 factores: rodiluvios, y pediluvios; Tres = bueno, a un factor: zona de parqueo para vehículos; Cuatro = muy bueno, a un factor: cerca perimetral. Para el segundo subgrupo: Cero = nulo, a un factor: registro de entrada y salida de la granja; Uno = malo, a 2 factores: baños en la entrada; Dos = regular, a un factor: calidad del agua; Cuatro (muy bueno) a un factor: control de plagas. Tercer subgrupo: Cero = nulo, a dos factores: intercambio de utensilios e ingreso de animales domésticos. Existe gran falta de cumplimiento de las medidas de bioseguridad en la unidad de producción ovina. Se debe realizar seguimiento epidemiológico para obtener la certificación de hato libre de estas zoonosis, y corrección o implementación de las medidas de bioseguridad en el hato ovino.

Diagnóstico epidemiológico de la prevalencia de brucelosis y tuberculosis a traves de las pruebas de campo Rosa de Bengala y Tuberculinica (Ano-caudal) respectivamente en bovinos del municipio de San José de los Remates, Boaco

La presente investigación se realizó con la finalidad de determinar la prevalencia de Brucelosis y Tuberculosis en condiciones tradicionales en hatos de doble propósito en diferentes comarcas del municipio de San José de los Remates. El municipio de San José de los Remates, se encuentra ubicado entre las coordenadas 12º35° de latitud norte y 85º45' longitud oeste, al noroeste del departamento de Boaco, asentado sobre la cordillera de Amerrisque, San José de los Remates se encuentra a 96 km de la capital Managua y a 44 km de la cabecera departamental. Boaco. Se llevó a cabo un estudio preliminar en 72 tincas, con un total 3,992 bovinos muestreados de los cuales se tomaron todas las muestras correspondientes a la zona del municipio antes mencionado siendo analizadas en el laboratorio regional de Juigalpa. Para la detección de anticuerpos contra Brucella abortus se utilizó la prueba de Rosa de Bengala y la prueb a tubercu linica ano-caud al para diagnosticar Tubercul osis. La in formación fue facilitada por los productores acerca de sus explotaciones pecuarias y los resultados en el caso de Rosa de Bengala fueron suministrados por el Departamento de Serología de la Red Nacional de Laboratorio de diagnóstico veterinario Región V. mientras que el de Tuberculosis fue dado por los encargados de la aplicación de tuberculina . Los resultad os manifiestan una prevalencia global de Brucelosis y Tuberculosis Bovina del 0.0% de las comarcas situadas en el municipio.